diff --git a/src/mesquite/pdap/PDAPDiagnosticChart/PDAPDiagnosticChart.java b/src/mesquite/pdap/PDAPDiagnosticChart/PDAPDiagnosticChart.java
index 66187eb..e72f92e 100755
--- a/src/mesquite/pdap/PDAPDiagnosticChart/PDAPDiagnosticChart.java
+++ b/src/mesquite/pdap/PDAPDiagnosticChart/PDAPDiagnosticChart.java
@@ -1 +1 @@
-/* PDAP:PDTREE package for Mesquite  copyright 2001-2009 P. Midford & W. Maddison
PDAP:PDTREE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
The web site for PDAP:PDTREE is http://mesquiteproject.org/pdap_mesquite/

This source code and its compiled class files are free and modifiable under the terms of 
GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
 */
package mesquite.pdap.PDAPDiagnosticChart;
/*~~  */

import java.awt.*;
import mesquite.lib.*;
import mesquite.lib.characters.*;
import mesquite.lib.duties.*;
import mesquite.pdap.lib.*;
import mesquite.cont.lib.*;

/* ======================================================================== */
/**=== Class PDAPDiagnosticChart.  ===
 * 
 * This is the main container for PDAP displays (not the transforms, exporter, etc.)
 * 
 * @author Peter E. Midford
 * created 2001
 * 
 * */

public class PDAPDiagnosticChart extends PDAPTreeWinAsstC implements ChartListener  {
    
    public void getEmployeeNeeds(){  //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed
        EmployeeNeed e = registerEmployeeNeed(DrawChart.class, getName() + "  needs a method to draw a chart.",
        "The method to draw a chart is selected initially");
        EmployeeNeed e2 = registerEmployeeNeed(CharSourceCoordObed.class, getName() + "  needs a method to supply characters.",
        "The method to supply characters is selected initially");
        EmployeeNeed e3 = registerEmployeeNeed(ContrastForChar.class, getName() + "  needs a method to calculate contrasts.",
        "The method to calculate contrasts is selected initially");
        EmployeeNeed e4 = registerEmployeeNeed(ResidualsCalculator.class, getName() + "  needs a method to calculate residuals.",
        "The method to calculate residuals is selected initially");
    }

    
    final static int SCREEN_COUNT = 14;
    
    ContrastForChar contrastsStatsTask;
    CharSourceCoordObed characterSourceTask;
    ResidualsCalculator residualsTask;
    public DrawChart charterTask;
    private Tree tree;
    int currentX = 0;
    int currentY = 1;
    NodeLabeller nsLabeller;
    boolean separateAxes = true;
    TreeDisplay treeDisplay;
    MesquiteCommand setXCommand, setYCommand;
    Taxa currentTaxa;
    private PDAPChartWindow window;

    int screen = 1;     // This is the first screen shown when the diagnostic chart is shown
    MesquiteCommand  cstC;
    MesquiteBoolean[] screenBoolean;
    PDAPScatterAsst diagnosticsTask;
    MesquiteBoolean showLegend;
    MesquiteBoolean verboseQueryMode;
    MesquiteBoolean showTreeLabels;
    MesquiteBoolean showSpotNames;
    MesquiteBoolean vhDefault;
    MesquiteDouble vh;
    private int dfReduction;
    private boolean vhQueryDone = false;
    private boolean dfQueryDone = false;
    private boolean ignoreRootTritomies = false;
    private boolean widthQueryDone;
    private double width1 = 0.95;
    private double width2 = 0.9;
    private boolean quiet;
    
    /*.................................................................................................................*/
    /**
     * @param arguments
     * @param condition
     * @param hiredByName
     * @return true unless an employee couldn't be hired
     */
    public boolean startJob(String arguments, Object condition, boolean hiredByName) {
        charterTask = (DrawChart)hireNamedEmployee(DrawChart.class, "#Scattergram");
        if (charterTask == null)
            return sorry(getName() + " couldn't start because no charting module obtained.");
        characterSourceTask = (CharSourceCoordObed)hireCompatibleEmployee(CharSourceCoordObed.class, ContinuousState.class, "Source of characters (for PDAP chart)");
        if (characterSourceTask == null) {
            return sorry(getName() + " couldn't start because no source of characters obtained");
        }
        contrastsStatsTask = (ContrastForChar)hireNamedEmployee(ContrastForChar.class, "#FelsContrWithChar");
        if (contrastsStatsTask == null)
            return sorry(getName() + " couldn't start because no calculating module obtained.");
        residualsTask = (ResidualsCalculator)hireNamedEmployee(ResidualsCalculator.class, "#ContrastResiduals");
        if (residualsTask == null)
            return sorry(getName() + " couldn't start because no calculating module for residuals obtained.");
        quiet = MesquiteThread.isScripting();
        cstC =  makeCommand("setCharacterSource",  (Commandable)this);
        characterSourceTask.setHiringCommand(cstC);
        screenBoolean = new MesquiteBoolean[SCREEN_COUNT];
        for (int i=0; i<SCREEN_COUNT; i++)
            screenBoolean[i] = new MesquiteBoolean(false);
        screenBoolean[screen].setValue(true);
        showLegend = new MesquiteBoolean(true);
        showSpotNames = new MesquiteBoolean(true);
       verboseQueryMode = new MesquiteBoolean(false);
        showTreeLabels = new MesquiteBoolean(false);
        loadPreferences();

        dfReduction = 0;
        vh = new MesquiteDouble(MesquiteDouble.unassigned);
        setXCommand = makeCommand("setX", (Commandable)this);
        setYCommand = makeCommand("setY", (Commandable)this);
        //ntxC =makeCommand("setScreen",  (Commandable)this);
        setScreen(screen);

        window =  new PDAPChartWindow(this);
        setModuleWindow(window);
        window.setWindowSize(400,400);
        addCheckMenuItem(null, "Abs. Contrast vs. Standard Deviation (1,2)", makeCommand("setScreen", this).setDefaultArguments("1"), screenBoolean[1]); //one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Abs. Contrast vs. Est. Node Value (3,4)", makeCommand("setScreen", this).setDefaultArguments("3"), screenBoolean[3]);//one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Abs. Contrast vs. Node Height (5,6)", makeCommand("setScreen", this).setDefaultArguments("5"), screenBoolean[5]);//one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Est. Node Value vs. Node Height (7,8)", makeCommand("setScreen", this).setDefaultArguments("7"), screenBoolean[7]);//one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Y Contrasts vs. X Contrasts (positivized) (9)", makeCommand("setScreen", this).setDefaultArguments("9"), screenBoolean[9]);//two char scroll; ScatterOriDiagnostics
        addCheckMenuItem(null, "Root Node Reconstructions (9A)", makeCommand("setScreen",this).setDefaultArguments("12"), screenBoolean[12]);//two char scroll; RootReconstruction with error bars
        addCheckMenuItem(null, "Conf. & Pred. Intervals (9B)",makeCommand("setScreen",this).setDefaultArguments("13"), screenBoolean[13]); //two char scroll; Regression with CI and PI intervals
        addCheckMenuItem(null, "Residual vs. Contrast (10)", makeCommand("setScreen", this).setDefaultArguments("10"), screenBoolean[10]);//two char scroll; ScatterResXDiagnost
        addCheckMenuItem(null, "Abs. Residual vs. Node Height (11)", makeCommand("setScreen", this).setDefaultArguments("11"), screenBoolean[11]);//two vert char scroll; ScatterRegDiagnostics
        addMenuItem("-", null);
        addCheckMenuItem(null, "Show Legend", makeCommand("toggleShowLegend",  (Commandable)this), showLegend);
        addCheckMenuItem(null, "Show Spot Names", makeCommand("toggleSpotNames",  (Commandable)this), showSpotNames);
       if (!MesquiteThread.isScripting()) 
            window.setVisible(true);
        //The following was turned off because it needs too much work
//        if (getEmployer() instanceof TreeWindowMaker) {
//            addMenuItem( "Tree labels", makeCommand("toggleTreeLabels",  (Commandable)this));
//            treeDisplay = ((TreeWindowMaker)getEmployer()).getTreeDisplay();
//            nsLabeller = new NodeLabeller(this, treeDisplay, (PDAPChartWindow)window);
//            nsLabeller.setShowLabels(showTreeLabels.getValue());
//
//            treeDisplay.addExtra(nsLabeller);
//        }
        makeMenu("PDAP.Chart");
        resetContainingMenuBar();
        resetAllWindowsMenus();
        return true;
    }

    public void employeeQuit(MesquiteModule m){
        iQuit();
    }
    /*.................................................................................................................*/
    /*.................................................................................................................*/
    public void windowGoAway(MesquiteWindow whichWindow) {
        whichWindow.hide();
        whichWindow.dispose();
        if (nsLabeller != null)
            nsLabeller.turnOff();
        iQuit();
    }
    /*...................................................................................................................*/
    public void pointMouseDown(MesquiteChart chart, int whichPoint, MesquiteNumber valueX, MesquiteNumber valueY, int x, int y, int modifiers, String message){
        if (nsLabeller==null) {
            if (message == null)
                message = "";
            else
                message += "\n";
            int i = whichPoint;
            if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) {
                message  += "Node " + i;
                if (tree instanceof MesquiteTree && ((MesquiteTree)tree).getNodeLabel(i)!=null)
                    message += " (" +  ((MesquiteTree)tree).getNodeLabel(i) + ")";
                String[] results = window.getStrings(i);
                if (results !=null)
                    for (int j = 0; j<results.length; j++)
                        message += "\n" + results[j];  
                chart.showQuickMessage(whichPoint, x, y, message);
                return;
            }

        }
        window.pointTouched(tree, whichPoint);
    }
    /*...................................................................................................................*/
    public void pointMouseUp(MesquiteChart chart, int whichPoint, int x, int y, int modifiers, String message){
        chart.hideQuickMessage();
        window.pointReleased(tree, whichPoint);
    }
    /*.................................................................................................................*/
    public long toExternal(long i){
        return(CharacterStates.toExternal((int)i));
    }
    /*.................................................................................................................*/
    public long toInternal(long i){
        return(CharacterStates.toInternal((int)i));
    }
    /*.................................................................................................................*/
    public long getMin(){
        return 0;
    }
    /*.................................................................................................................*/
    /** returns the maximum index for a character on this chart */
    public long getMax(){
        if (characterSourceTask==null || currentTaxa==null)
            return 0;
        return characterSourceTask.getNumberOfCharacters(currentTaxa)-1;
    }

    /*-----------------------------------------*/
    public void processPreferencesFromFile (String[] prefs) {
        if (prefs!=null && prefs.length>0)
            verboseQueryMode.setValue("v".equals(prefs[0]));
    }
    /*-----------------------------------------*/
    public String[] preparePreferencesForFile () {
        String[] prefs= new String[1];
        if (verboseQueryMode.getValue())
            prefs[0] = "v";
        else
            prefs[0] = "n";
        return prefs;
    }

    /*.................................................................................................................*/
    /** 
     * This saves the state of the chart to a Snapshot 
     * @param file
     * @return the new snapshot object
     */
    public Snapshot getSnapshot(MesquiteFile file) { 
        if (window ==null)
            return null;
        Snapshot result = new Snapshot();
        result.addLine("quiet");
        result.addLine( "getCharacterSource " , characterSourceTask);

        result.addLine("toggleShowLegend " + showLegend.toOffOnString());
       result.addLine("toggleTreeLabels " + showTreeLabels.toOffOnString()); 
        result.addLine("toggleDFQueryDone " + MesquiteBoolean.toOffOnString(dfQueryDone));
        result.addLine("toggleVhQueryDone " + MesquiteBoolean.toOffOnString(vhQueryDone));
        result.addLine("toggleIgnoreRootTritomies " + MesquiteBoolean.toOffOnString(ignoreRootTritomies));
        result.addLine("setDFReduction " + dfReduction); 
        if (!vh.isUnassigned())
            result.addLine("setVh " + vh.toString());
        result.addLine("setWidth1 " + MesquiteDouble.toString(width1));
        result.addLine("setWidth2 " + MesquiteDouble.toString(width2));
        result.addLine("setScreen " + screen); // don't do a bunch of bogus calculations on screen 9+; set things first

        result.addLine("setX " + toExternal(currentX)); 
        result.addLine("setY " + toExternal(currentY)); 
        Snapshot fromWindow = window.getSnapshot(file);
        result.addLine("getWindow");
        result.addLine("tell It");
        result.incorporate(fromWindow, true);
        result.addLine("endTell");
        result.addLine("toggleSpotNames " + showSpotNames.toOffOnString());
       result.addLine("showWindow");
        result.addLine("resume");
        return result;
    }
    /*.................................................................................................................*/
    /** fireAssistantIfNeeded is a helper method for hireIfNeeded.  The ordering of the tests in the conditional
	    were reversed to take advantage of "short-circuiting" && by putting the cheaper test first */
    private void fireAssistantIfNeeded(String name, String toBeHired){
        if (!name.equalsIgnoreCase(toBeHired) && charterTask.findEmployeeWithName(name)!=null)
            charterTask.doCommand("fireEmployee", name,CommandChecker.defaultChecker);
    }
    /** hireIfNeeded makes sure the appropriate calculation assistant is hired, after firing any that are
	  inappropriate.  */
    private Object hireIfNeeded(String name){
        fireAssistantIfNeeded("#ScatterRegDiagnostics", name);
        fireAssistantIfNeeded("#ScatterResXDiagnostics", name);
        fireAssistantIfNeeded("#ScatterOriDiagnostics", name);
        fireAssistantIfNeeded("#ScatterRootCIPI", name);
        fireAssistantIfNeeded("#ScatterRootRegCIPI",name);
        if (charterTask.findEmployeeWithName(name)==null) {
            Object obj = charterTask.doCommand("newAssistant", name,CommandChecker.defaultChecker);
            if (obj !=null && obj instanceof ScatterRegisterableAsst) {
                ((ScatterRegisterableAsst)obj).setChartModule(this);
            }
            return obj;
        }
        else {
            return charterTask.findEmployeeWithName(name);
        }
    }
    /*.................................................................................................................*/
    /** This method sets the screen, updates the boolean array that handles check marks in the menu
	and hires the appropriate diagnostics employee */
    private Object setScreen(int ic){
        screenBoolean[screen].setValue(false);
        screen = ic;
        screenBoolean[screen].setValue(true);
        Object hired = null;
        switch (ic){
        case 1:
        case 3:
        case 5:
        case 7:
        case 11: {
            hired = hireIfNeeded("#ScatterRegDiagnostics");
            break;
        }
        case 9: {	
            hired = hireIfNeeded("#ScatterOriDiagnostics");
            break;
        }
        case 10: {
            hired = hireIfNeeded("#ScatterResXDiagnostics");
            break;
        }
        case 12: {   //screen 9A
            hired = hireIfNeeded("#ScatterRootCIPI");
            break;
        }
        case 13: {	//screen 9B
            hired = hireIfNeeded("#ScatterRootRegCIPI");
            break;
        }
        }
        diagnosticsTask = (PDAPScatterAsst)hired;
        return hired;
    }
    MesquiteInteger pos = new MesquiteInteger();
    /*.................................................................................................................*/
    public Object doCommand(String commandName, String arguments, CommandChecker checker) {
        final Class thisClass = this.getClass();
        if (checker.compare(thisClass, "Sets module supplying characters", "[name of module]", commandName, "setCharacterSource")) {//temporary
            return characterSourceTask.doCommand(commandName, arguments, checker);
        }
        else if (checker.compare(thisClass, "Sets whether or not the legend is shown", "[on = show; off]", commandName, "toggleShowLegend")) {
            showLegend.toggleValue(parser.getFirstToken(arguments));
            window.setLegendVisible(showLegend.getValue());
        }
        else if (checker.compare(thisClass, "Sets whether or not the spot names are shown", "[on = show; off]", commandName, "toggleSpotNames")) {
            showSpotNames.toggleValue(parser.getFirstToken(arguments));
    		if (window != null){
    			window.charter.setShowNames(showSpotNames.getValue());
    			window.contentsChanged();
    		}
       }
       else if (checker.compare(thisClass, "Quiets notices", null, commandName, "quiet")) {
            quiet = true;
            return null;
        }
        else if (checker.compare(thisClass, "Returns module supplying characters", null, commandName, "resume")) {
            quiet = false;
            return null;
        }
        else if (checker.compare(thisClass, "Returns module supplying characters", null, commandName, "getCharacterSource")) {
            return characterSourceTask;
        }
        else if (checker.compare(thisClass, "Sets the screen shown", "[screen number, one of 1,3,5,7,9-13]", commandName, "setScreen")) {
            int ic = MesquiteInteger.fromString(arguments);
            if (validScreen(ic)) {               
                incrementMenuResetSuppression();
                Object o = setScreen(ic);
                doCounts();
                getModuleWindow().contentsChanged();
                decrementMenuResetSuppression();
                return o;
            }
        }
        else if (checker.compare(thisClass, "Sets which item is shown on the x axis (appropriate where the calculator can supply a series of items, e.g. characters)", "[item number]", commandName, "setX")) {
            int ic = (int)(MesquiteInteger.fromString(arguments));
            if (!MesquiteInteger.isCombinable(ic))
                ic = MesquiteInteger.queryInteger(containerOfModule(), "Choose ", "choose:", 1); //TODO have something more intelligent here
            if (!MesquiteInteger.isCombinable(ic))
                return null;
            int icInternal = ic-1;
            if ((icInternal>=0) && (icInternal<=getMax())) {  //no need to check for combinability, ic was just checked.
                currentX=icInternal;
                if (!MesquiteThread.isScripting()){
                    doCounts();
                }
            }
        }
        else if (checker.compare(thisClass, "Sets which item is shown on the y axis (appropriate where the calculator can supply a series of items, e.g. characters)", "[item number]", commandName, "setY")) {
            int ic = (MesquiteInteger.fromString(arguments));
            if (!MesquiteInteger.isCombinable(ic))
                ic = MesquiteInteger.queryInteger(containerOfModule(), "Choose an ", "choose:", 1); //TODO have something more intelligent here
            if (!MesquiteInteger.isCombinable(ic))
                return null;
            int icInternal = ic-1;
            if ((icInternal>=0) && (icInternal<=getMax())) {  //no need to check for combinability, ic was just checked.
                currentY=icInternal;
                if (!MesquiteThread.isScripting()){
                    doCounts();
                }
            }
        }
        else if (checker.compare(thisClass, "Sets whether or not the tree labels are shown", "[on or off]", commandName, "toggleTreeLabels")) {
            //TODO: use MesquiteBoolean checkmark
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleShowTreeLabels invoked without parameter");
            else
                showTreeLabels.toggleValue(parser.getFirstToken(arguments));
            if (nsLabeller!=null)
                nsLabeller.setShowLabels(showTreeLabels.getValue());
            if (treeDisplay !=null)
                treeDisplay.pleaseUpdate(false);
        } 
        else if (checker.compare(thisClass,"Sets the degrees of freedom adjustment", "[integer]",commandName, "setDFReduction")) {
            int dfr = (int)(MesquiteInteger.fromString(arguments));
            if (!MesquiteInteger.isCombinable(dfr))  //not a menu command..
                MesquiteMessage.warnProgrammer("setDFReduction invoked without parameter");
            else
                dfReduction = dfr;
        }  
        else if (checker.compare(thisClass,"Sets the length of the added branch for predication intervals", "[double]",commandName, "setVh")) {
            double vht = (double)(MesquiteDouble.fromString(arguments));
            if (!MesquiteDouble.isCombinable(vht))  //not a menu command..
                MesquiteMessage.warnProgrammer("setVh invoked without parameter");
            else
                vh.setValue(vht);
        }  
        else if (checker.compare(thisClass,"Sets the length of the added branch for predication intervals", "[double]",commandName, "setWidth1")) {
            double w1 = (double)(MesquiteDouble.fromString(arguments));
            if (!MesquiteDouble.isCombinable(w1))  //not a menu command..
                MesquiteMessage.warnProgrammer("setWidth1 invoked without parameter");
            else
                width1 = w1;
        }  
        else if (checker.compare(thisClass,"Sets the length of the added branch for predication intervals", "[double]",commandName, "setWidth2")) {
            double w2 = (double)(MesquiteDouble.fromString(arguments));
            if (!MesquiteDouble.isCombinable(w2))  //not a menu command..
                MesquiteMessage.warnProgrammer("setWidth2 invoked without parameter");
            else
                width2 = w2;
        }  
        else if (checker.compare(thisClass,"Sets state of Vh query done", "[on/off]",commandName, "toggleVhQueryDone")) {
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleVhQueryDone invoked without parameter");
            else{
                String s = parser.getFirstToken(arguments);
                if ("on".equalsIgnoreCase(s))
                    vhQueryDone = true;
                else if  ("off".equalsIgnoreCase(s))
                    vhQueryDone = false;
                else
                    vhQueryDone = !vhQueryDone;
            }   
        }
        else if (checker.compare(thisClass,"Sets state of df query done", "[on/off]",commandName, "toggleDFQueryDone")) {
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleDFQueryDone invoked without parameter");
            else{
                String s = parser.getFirstToken(arguments);
                if ("on".equalsIgnoreCase(s))
                    dfQueryDone = true;
                else if  ("off".equalsIgnoreCase(s))
                    dfQueryDone = false;
                else
                    dfQueryDone = !dfQueryDone;
            }
        }
        else if (checker.compare(thisClass,"Sets state of ignore root tritomies", "[on/off]",commandName, "toggleIgnoreRootTritomies")) {
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleIgnoreRootTritomies invoked without parameter");
            else{
                String s = parser.getFirstToken(arguments);
                if ("on".equalsIgnoreCase(s))
                    ignoreRootTritomies = true;
                else if  ("off".equalsIgnoreCase(s))
                    ignoreRootTritomies = false;
                else
                    ignoreRootTritomies = !ignoreRootTritomies;
            }
        }
        else
            return  super.doCommand(commandName, arguments, checker);
        return null;
    }

    /* This checks whether the screenNumber specifies a valid screen; if new screens are added, this needs to be updated */
    final private boolean validScreens[] = {false, true, false, true, false, true, false, true, false, true, true, true, true, true};
    private boolean validScreen(int screenNumber) {
        if (screenNumber < 0 || screenNumber > 13)
            return false;
        else return validScreens[screenNumber];
    }



    long oldTreeID = -1;
    long oldTreeVersion = 0;
    /*.................................................................................................................*/
    public void setTree(Tree tree) {
        if (tree==null)
            return;
        if (!((MesquiteTree)tree).allLengthsAssigned(false) && !(MesquiteThread.isScripting()  && quiet)) {
            alert("The tree you want to analyze contains one or more branches with unassigned branch lengths. " +
            "You should go back to the tree window and specify branch lengths (e.g set to 1, Pagel's method, etc.).");
            //iQuit();
            //window.dispose();
            //return;
        }
        if (this.tree !=null && this.tree instanceof NoPolyTree && this.tree !=tree) { // about to set new tree
            ((NoPolyTree)this.tree).disconnect();
        }
        if (tree instanceof NoPolyTree)
            this.tree=tree;
        else 
            this.tree = new NoPolyTree((MesquiteTree)tree);
        if (oldTreeID==-1 || tree.getID() != oldTreeID || tree.getVersionNumber() != oldTreeVersion){
            setDFQueryDone(false);  // make sure these are reset before any redraws
            setVhQueryDone(false);
            vh.setToUnassigned();
        }
        if (this.tree instanceof Selectionable)
            charterTask.pointsAreSelectable(true, (Selectionable)this.tree, false);
        currentTaxa = this.tree.getTaxa();
        if (oldTreeID==-1) {
            if (contrastsStatsTask==null || residualsTask == null)
                return;
            //setDFQueryDone(false);
            //setVhQueryDone(false);
            //vh.setToUnassigned();
            contrastsStatsTask.initialize(tree);
            residualsTask.initialize(tree);
            characterSourceTask.initialize(tree.getTaxa());
            doCounts();
        }
        else if (tree.getID() != oldTreeID || tree.getVersionNumber() != oldTreeVersion) {
            //setDFQueryDone(false);
            //setVhQueryDone(false);
            //vh.setToUnassigned();
            doCounts();
        }
        else {
            if (window!=null && window.getChart()!=null ) {
                window.getChart().getField().repaint(); //for selection Only
                window.getChart().repaint();
            }
        }
        oldTreeID = tree.getID();
        oldTreeVersion = tree.getVersionNumber();
    }

    /*.................................................................................................................*/
    public void employeeParametersChanged(MesquiteModule employee, MesquiteModule source, Notification notification) {
        if (contrastsStatsTask!=null && residualsTask!=null && characterSourceTask !=null) {
            doCounts();
        }
    }
    /*.................................................................................................................*/
    public CharacterDistribution getObserved1(){
        return window.observedStates;
    }
    /*.................................................................................................................*/
    public CharacterDistribution getObserved2(){
        return window.observedStates2;
    }
    /*.................................................................................................................*/
    public Tree getTree(){
        return tree;
    }

    /*.................................................................................................................*/
    public boolean getDFQueryDone(){
        return dfQueryDone;
    }

    /*.................................................................................................................*/
    public void setDFQueryDone(boolean value){
        dfQueryDone = value;
    }

    /*.................................................................................................................*/
    public int getDFReduction(){
        return dfReduction;
    }

    public void setDFReduction(int value){
        dfReduction = value;
    }

    public int queryDFReduce(PDAP2CTStatPak sp, boolean notifyIfZero){
        if(!MesquiteThread.isScripting()){  //if scripting use 0 (default) or value set by script
            sp.countInternalNodes(tree, tree.getRoot());
            int polytomies = ((NoPolyTree)tree).countZLBs(sp.getIgnoreRootTritomies());     // Zero-Length-Branches are what PDAP calls "polytomies", count to inform the user
            if ((polytomies >0)) {
                int tmp = MesquiteInteger.queryInteger(window,  
                        "DF Reduce ",
                        "This tree contains polytomies, indicated by the presence \n" +
                        "of " + polytomies + " zero-length branch(es).\n" +
                        "If some of these collapsed branches indicate\n" +
                        "soft polytomies, then you may want to reduce\n" +
                        "degrees of freedom (see Purvis and Garland, 1993,\n" +
                        "Syst. Biol. 42:569-575; Garland and Diaz-Uriarte, 1999,\n" +
                        "Syst. Biol. 48:547-558).\n\n " +
                        "Enter number of Degrees of Freedom to subtract for soft polytomies",
                        dfReduction,
                        0,
                        MesquiteInteger.infinite);

                if (MesquiteInteger.isCombinable(tmp)) {
                    dfReduction = tmp;
                }
            }
            else {
                if (notifyIfZero) {
                    int tmp = MesquiteInteger.queryInteger(window,  
                            "DF Reduce ",
                            "This tree is fully dichotomized and contains no polytomies.\n" +
                            "If, for whatever reason, you wish to decrease\n" +
                            "degrees of freedom (see Purvis and Garland, 1993,\n" +
                            "Syst. Biol. 42:569-575; Garland and Diaz-Uriarte, 1999,\n" +
                            "Syst. Biol. 48:547-558), you may do so here.\n\n" +
                            "Enter degrees of freedom to subtract",
                            dfReduction,
                            0,
                            MesquiteInteger.infinite);
                    //alert(null,"","The tree has no polytomies, hence there is no need to reduce degrees of freedom to compensate for polytomies.");
                    if (MesquiteInteger.isCombinable(tmp)) 
                        dfReduction = tmp;
                    else
                        dfReduction = 0;
                }
            }
        }
        return dfReduction;
    }

    /*-----------------------------------------*/
    /** 
     * This prompts the user and sets the CI/PI widths. The results are saved in the width1 and width2 fields.
     */
    public void queryWidths(){
        if (!MesquiteThread.isScripting()){ // if scripting, widths either default or set elsewhere
            MesquiteDouble tmp1 = new MesquiteDouble(width1);
            MesquiteDouble tmp2 = new MesquiteDouble(width2);
            MesquiteBoolean ans = new MesquiteBoolean();

            MesquiteDouble.queryTwoDoubles(window,
                    "Interval Widths",
                    "Enter the first (2-tailed) p-value width for CI/PI plots",
                    "Enter the second (2-tailed) p-value width for CI/PI plots",
                    ans,
                    tmp1,
                    tmp2);
            if (tmp1.isCombinable()) {
                double tp1 = tmp1.getValue();
                if ((tp1 <= 1.0) && (tp1 >= 0.0))
                    width1 = tp1;
            }
            if (tmp2.isCombinable()){
                double tp2 = tmp2.getValue();
                if ((tp2 <= 1.0) && (tp2 >= 0.0))
                    width2 = tp2;
            }
        }
    }


    public double getWidth1(){
        return width1;
    }
    public double getWidth2(){
        return width2;
    }
    public void setWidthQueryDone(boolean value){
        widthQueryDone = value;
    }
    public boolean getWidthQueryDone(){
        return widthQueryDone;
    }


    /*.................................................................................................................*/
    public boolean getVhQueryDone(){
        return vhQueryDone;
    }

    /*.................................................................................................................*/
    public void setVhQueryDone(boolean value){
        vhQueryDone = value;
    }

    public double getVh(){
        return vh.getValue();
    }

    /*.................................................................................................................*/

    /** This prompts the user and sets Vh */    
    public double queryVh(PDAP2CTStatPak sp){
        double tmp = sp.getMeanHeight(tree);
        if (!MesquiteThread.isScripting()){
            String contempString;

            if (sp.getContempTips())
                contempString = "All tips are contemporaneous in the uncorrected tree.";
            else
                contempString = "The tips are not contemporaneous in the uncorrected tree.";
            tmp = MesquiteDouble.queryDouble(window,
                    "Vh",
                    "The calculations for prediction intervals effectively assume " +
                    "that the species to be predicted is attached at the root " +
                    "(basal node) of the phylogenetic tree (see Garland and Ives, " +
                    "2000, Am. Nat. 155:346-364).  By default, the branch length (Vh) " +
                    "leading to the predicted species is assumed to equal the average" +
                    "length of the (uncorrected) branches from root to tips. \n\n" +
                    contempString + "\n\n Enter a value for Vh\n",       
                    tmp,
                    0,
                    MesquiteDouble.infinite);
            if (MesquiteDouble.isCombinable(tmp)){
                vh.setValue(tmp);
                vhQueryDone = true;
            }

            else{ 
                AlertDialog.notice(window, "Vh undefined",
                        "Vh could not be estimated and is not meaningful because one or more " +
                        "branches in the tree have undefined branch lengths.  Either assign lengths " +
                        "or use a constant transform to set all branches equal to one.  No confidence or " +
                "prediction intervals will be displayed.");
                vh.setToUnassigned();
            }
        }
        else vh.setValue(tmp);

        return vh.getValue(); 
    }


    public void queryVerboseQueryMode(){
        MesquiteBoolean ok = MesquiteBoolean.queryCheckBox(window,
                "Set Verbose Query Preference","In verbose mode you will be asked for settings for PDAP root reconstruction frequently; otherwise you change the settings using menu items","Use Verbose Mode", verboseQueryMode.getValue());
        if (!ok.isUnassigned()) {
            verboseQueryMode.setValue(ok.getValue());
            storePreferences();
        }
    }

    public void toggleVerboseQueryMode(String arg){
        verboseQueryMode.toggleValue(arg);
        storePreferences();
    }

    public boolean getVerboseQueryMode(){
        return verboseQueryMode.getValue();
    }

    /*................................................................*/

    public void queryIgnoreRootTritomies(){
        MesquiteBoolean ok = MesquiteBoolean.queryCheckBox(window,
                "Set Ignore Basal Tritomies",
                "Some tree inference programs return trees that PDAP sees as having tritomies at the root; checking the box will ignore any tritomies at the root in counting or detecting polytomies for degrees of freedom adjustment",
                "Ignore Root Tritomies",
                ignoreRootTritomies);
        if (!ok.isUnassigned()){
            ignoreRootTritomies = ok.getValue();
        }
    }

    public boolean getIgnoreRootTritomies(){
        return ignoreRootTritomies;
    }

    public void setIgnoreRootTritomies(boolean value){
        ignoreRootTritomies = value;
    }


    /*................................................................*/    
    public String nameForWritableResults(){
        return "PDAP Diagnostics from StatPak";
    }
    public boolean suppliesWritableResults(){
        return diagnosticsTask.suppliesWritableResults();
    }
    public Object getWritableResults(){
        return diagnosticsTask.getWritableResults();
    }
    public Object getResultsHeading(){
        return diagnosticsTask.getResultsHeading();
    }


    /*.................................................................................................................*/
    private void doCounts() {
        window.blankChart();
        window.setTree(tree);
        window.recalcChart();
        window.contentsChanged();
    }
    /*.................................................................................................................*/
    public String getName() {
        return "PDAP Diagnostic Chart";
    }
    /*.................................................................................................................*/
    public String getAuthors() {
        return "Peter E. Midford, Ted Garland Jr., and Wayne P. Maddison" ;
    }
    /*.................................................................................................................*/
    public String getVersion() {
        return "1.15";
    }
    /*.................................................................................................................*/
    //Peter: add this method returning true for all citable modules, e.g. main calculations
    public boolean showCitation(){
        return true;
    }
    /*.................................................................................................................*/
    public boolean isPrerelease() {
        return false;
    }
    /*.................................................................................................................*/
    public boolean requestPrimaryChoice() {
        return true;
    }

    /*.................................................................................................................*/
    /** returns an explanation of what the module does.*/
    public String getExplanation() {
        return "Shows independent constrasts and related values for nodes of tree via a scattergram." ;
    }
    /*.................................................................................................................*/
    public void endJob() {
        if (treeDisplay !=null && nsLabeller !=null)
            treeDisplay.removeExtra(nsLabeller);
        super.endJob();
    }
}

/* ======================================================================== */
/**=== Local Class BannerPanel.  ===*/

class BannerPanel extends MesquitePanel{
    public void paint(Graphics g){
        g.setColor(Color.cyan);
        g.drawString("PDAP: PDTREE module", 16, getBounds().height-4);
    }
}
/*========================================================*/
class NodeLabeller extends TreeDisplayExtra {
    LabelsAtNodes labelsAtNodes;
    PDAPChartWindow chartWindow;
    final static Color brightGreen = new Color((float)0.4, (float)1.0, (float)0.4);
    final static Color brightbrightGreen = new Color((float)0.6, (float)1.0, (float)0.6);
    boolean showLabels = true;
    int labelDrawn = -1;
    

    public NodeLabeller (MesquiteModule ownerModule, TreeDisplay treeDisplay, PDAPChartWindow chartWindow) {
        super(ownerModule, treeDisplay);
        this.chartWindow =chartWindow;
    }
    /*.................................................................................................................*/
    void drawOneLabel(int N, Tree tree, Graphics g) {
        makeSureLabelsReady(tree);
        int nodeX = treeDisplay.getTreeDrawing().x[N];
        int nodeY = treeDisplay.getTreeDrawing().y[N];
        MesquiteLabel c = (MesquiteLabel)labelsAtNodes.getPanel(N);

        c.setColor(brightbrightGreen); 
        c.setText("Node " + N);  
        String[] results = chartWindow.getStrings(N);
        for (int i = 0; i<results.length; i++)
            c.addLine(results[i]);  

        c.setVisible(true);
        c.repaint();
        int w = c.getWidth(g);
        if (w+nodeX+16>treeDisplay.getBounds().width)
            c.setLocation(treeDisplay.getBounds().width- w, nodeY + 18);
        else
            c.setLocation(nodeX + 16, nodeY + 18);
        g.setColor(brightGreen);
        g.setXORMode(Color.white);
        g.drawLine(nodeX, nodeY, c.getBounds().x, c.getBounds().y);
        g.drawLine(nodeX, nodeY+1, c.getBounds().x, c.getBounds().y + 1);
        g.drawLine(nodeX, nodeY+2, c.getBounds().x, c.getBounds().y + 2);
        g.drawLine(nodeX, nodeY+3, c.getBounds().x, c.getBounds().y + 3);
        g.setPaintMode();
        g.setColor(Color.black);
        labelDrawn = N;
    }
    /*.................................................................................................................*/
    void hideOneLabel(int N, Graphics g) {
        MesquiteLabel c = (MesquiteLabel)labelsAtNodes.getPanel(N);
        if (c==null || g==null)
            return;
        c.setVisible(false);
        final int nodeX = treeDisplay.getTreeDrawing().x[N];
        final int nodeY = treeDisplay.getTreeDrawing().y[N];
        g.setColor(brightGreen);
        g.setXORMode(Color.white);
        g.drawLine(nodeX, nodeY, c.getBounds().x, c.getBounds().y);
        g.drawLine(nodeX, nodeY+1, c.getBounds().x, c.getBounds().y + 1);
        g.drawLine(nodeX, nodeY+2, c.getBounds().x, c.getBounds().y + 2);
        g.drawLine(nodeX, nodeY+3, c.getBounds().x, c.getBounds().y + 3);
        g.setPaintMode();
        labelDrawn = -1;
    }
    /*.................................................................................................................*/
    private void drawLabels(int N, Tree tree, Graphics g) {
        for (int d = tree.firstDaughterOfNode(N); tree.nodeExists(d); d = tree.nextSisterOfNode(d))
            drawLabels(d, tree, g);
        drawOneLabel(N, tree, g);
    }
    /*.................................................................................................................*/
    void hideLabels() {
        if (labelsAtNodes==null)
            return;
        Graphics g = treeDisplay.getGraphics();
        for (int N = 0; N<labelsAtNodes.getNumNodes(); N++) {
            if (N== labelDrawn)
                hideOneLabel(N, g);
            else
                labelsAtNodes.getPanel(N).setVisible(false);
        }
        if (g!=null)
            g.dispose();
    }
    /*.................................................................................................................*/
    void setShowLabels(boolean show) {
        showLabels = show;
        if (labelsAtNodes!=null && !showLabels)
            hideLabels();

    }
    /*.................................................................................................................*/
    private void makeSureLabelsReady(Tree tree){
        if (labelsAtNodes==null) {
            labelsAtNodes = new LabelsAtNodes(ownerModule, tree.getNumNodeSpaces(), treeDisplay);
        }
        else if (labelsAtNodes.getNumNodes()!=tree.getNumNodeSpaces() ) {
            labelsAtNodes.resetNumNodes(tree.getNumNodeSpaces());
        }
    }
    /*.................................................................................................................*/
    public void drawOnTree(Tree tree, int drawnRoot, Graphics g) {
        if (showLabels && g != null) {
            makeSureLabelsReady(tree);
            drawLabels(drawnRoot, tree, g);
            g.setColor(Color.black);
        }
    }
    /*.................................................................................................................*/
    public void printOnTree(Tree tree, int drawnRoot, Graphics g) {
        drawOnTree(tree, drawnRoot, g);
    }
    /*.................................................................................................................*/
    public void setTree(Tree tree) {
    }
    /*.................................................................................................................*/
    public void turnOff() {
        super.turnOff();
        if (labelsAtNodes!=null)
            labelsAtNodes.dispose();
    }
}

/*========================================================*/
class PDAPChartWindow extends ChartWindow {
    final static String scrollBoxTitle = "character";
    
    // Legend messages
    final private static String SCREEN1LEGEND = "Plot of absolute value of contrast vs. standard deviation";
    final private static String SCREEN3LEGEND = "Plot of absolute value of contrast vs. estimated value of associated node";
    final private static String SCREEN5LEGEND = "Plot of absolute value of contrast vs. height of associated node";
    final private static String SCREEN7LEGEND = "Plot of estimated value of associated node vs. its height";
    final private static String SCREEN9LEGEND = "Plot of contrasts vs. positivized contrasts";
    final private static String SCREEN10LEGEND = "Plot of residuals from screen 9 vs. contrast values";
    final private static String SCREEN11LEGEND = "Plot of absolute value of residual vs. height of associated node";
    final private static String SCREEN12LEGEND = "Plot of tip values and confidence intervals for reconstructed root values";
    final private static String SCREEN13LEGEND = "Plot of phylogenetically correct (OLS) regression and " +  
            "associated CI's (red-95%, orange-90%) and PI (green-95%, cyan-90%), "+
            "mapped onto the original tip data space. (see Garland and Ives 2000, Am. Nat. 155:346-364).";

    // Polytomy warning for legends
    final private static String POLYTOMYWARNING = "/n Warning: arbitrary resolution of zero-length branches due to polytomies";
    
    BannerPanel banner;
    int bannerHeight = 24;
    private int windowWidth=0;
    private int windowHeight=0;
    private PDAPDiagnosticChart ownerModule;
    private NumberArray xArray, yArray; //, zArray;
    private boolean weightedBranches = true;
    String nameA, nameB;
    Charter charter;
    PDAPLegend legend;
    Tree tree;
    DoubleMiniScroll scrollBox;
    MesquiteChart chart;
    ContinuousDistribution observedStates, observedStates2;
    private MesquiteNumber resultX = new MesquiteNumber();
    private MesquiteNumber resultY = new MesquiteNumber();

    public PDAPChartWindow (PDAPDiagnosticChart ownerModule) {
        super(ownerModule, true); //infobar
        this.ownerModule = ownerModule;
        charter = ownerModule.charterTask.createCharter(ownerModule);
        charter.setShowNames(true);
        chart=new MesquiteChart(ownerModule, 100, 0, charter);
        setChart(chart);
        xArray = new NumberArray(3);
        yArray = new NumberArray(3);
        //zArray = new NumberArray(3);
        chart.deassignChart();
        addToWindow(chart);
        chart.setVisible(true);
        chart.setBackground(getBackground());
        scrollBox = new DoubleMiniScroll(ownerModule.setXCommand, ownerModule.setYCommand, 0,0,0,0,0,0);
        chart.add(scrollBox);
        scrollBox.setYTitle("Y");
        scrollBox.setXTitle("X");
        //scrollBox.setLocation(10, getHeight()-10);
        scrollBox.setLocation(2, getHeight()-24- scrollBox.getBounds().height);
        banner = new BannerPanel();
        addToWindow(banner);
        banner.setLocation(0, 0);
        banner.setFontSize(18);
        banner.setVisible(true);
        banner.setBackground(Color.blue);
        legend = new PDAPLegend();
        chart.getField().add(legend);
        legend.setVisible(true);
        resetTitle();
    }

    /*.................................................................................................................*/
    /** When called the window will determine its own title.  MesquiteWindows need
	to be self-titling so that when things change (names of files, blocks, etc.)
	they can reset their titles properly*/
    public void resetTitle(){
        setTitle("PDAP Diagnostic Chart");
    }

    void setLegendVisible(boolean vis){
        if (legend!=null)
            legend.setVisible(vis);
    }
    /*.................................................................................................................*/
    public Snapshot getSnapshot(MesquiteFile file) { 
        Snapshot temp = super.getSnapshot(file);
        temp.addLine( "getLegend");
        temp.addLine("tell It");

        temp.incorporate(legend.getSnapshot(file), true);
        temp.addLine("endTell");
        return temp;
    }
    /*.................................................................................................................*/
    public Object doCommand(String commandName, String arguments, CommandChecker checker) { 
        if (checker.compare(this.getClass(), "Returns the legend", null, commandName, "getLegend")) {
            return legend;
        }
        else 
            return  super.doCommand(commandName, arguments, checker);
    }
    /*.................................................................................................................*/
    private void resetScrolls(){
        final int min = (int)ownerModule.toExternal(ownerModule.getMin());
        final int max = (int)ownerModule.toExternal(ownerModule.getMax());
        final int curX = (int)ownerModule.toExternal(ownerModule.currentX);
        final int curY = (int)ownerModule.toExternal(ownerModule.currentY);
        final int screen = ownerModule.screen;
        scrollBox.setYTitle(scrollBoxTitle);
        // one character scroll //is this really correct for screen 11?
        if (screen == 1 || screen == 3 || screen == 5 ||screen == 7 || screen == 11) {
            scrollBox.setYValues(min, curY, max);
            scrollBox.setYVisible(true);
            scrollBox.setXVisible(false);
        }
        // two character scroll, one for X and one for Y
        else if (screen == 9 || screen == 10) {
            scrollBox.setXTitle(scrollBoxTitle);
            scrollBox.setXValues(min, curX, max);
            scrollBox.setXVisible(true);
            scrollBox.setYValues(min, curY, max);
            scrollBox.setYVisible(true);
        }
        // two character scroll, both for Y
        else {
            scrollBox.setXTitle(scrollBoxTitle);
            scrollBox.setXValues(min, curX, max);
            scrollBox.setXVisible(true);
            scrollBox.setYValues(min, curY, max);
            scrollBox.setYVisible(true);
        }
    }
    /*.................................................................................................................*/
    public void setVisible(boolean vis){
        windowResized();
        super.setVisible(vis);
    }
 	/*.................................................................................................................*/
    void setCharter(Charter charter) {
        charter.setShowNames(true);
        chart.setCharter(charter);
    }
    /*.................................................................................................................*/
    String[] getStrings(int index) {
        return new String[] {"X (" + ownerModule.contrastsStatsTask.getParameters() +
                "): " + xArray.toString(index), 
                "Y (" + ownerModule.contrastsStatsTask.getParameters() + 
                "): " + yArray.toString(index)};
    }
    /*.................................................................................................................*/
    void setTree(Tree tree) {
        if (this.tree !=null && this.tree instanceof NoPolyTree && this.tree !=tree) { // about to set new tree
            ((NoPolyTree)this.tree).disconnect();
        }
        if (tree instanceof NoPolyTree){
            this.tree=tree;
        }
        else {
            this.tree = new NoPolyTree((MesquiteTree)tree);
        }
        if (this.tree instanceof Selectionable)
            ownerModule.charterTask.pointsAreSelectable(true, (Selectionable)this.tree, false);
    }
    /*.................................................................................................................*/
    String axisName(String template, ContinuousDistribution obsStates, int screen, boolean xAxis){
        if (obsStates == null)
            return template;
        // X axis of screens 1 2 5 6 7 8 11 don't use characters
        if (xAxis && (screen == 1 || screen == 2 || screen == 5 || screen == 6 || screen == 7 || screen == 8 || screen == 11))
            return template;
        String chName = obsStates.getName();
        if (chName == null)
            return template;
        if (chName.length()>20)
            chName = chName.substring(0, 17) + "...";
        return chName + " (" + template + ")";
    }
    /*.................................................................................................................*/
    public void recalcChart() {
        chart.deassignChart();
        if (ownerModule.contrastsStatsTask != null && ownerModule.residualsTask != null) {
            resetScrolls();
            final int numNodes = tree.getNumNodeSpaces();
            xArray.resetSize(numNodes);
            yArray.resetSize(numNodes);
            //zArray.resetSize(numNodes);
            //if (ownerModule.contrastsStatsTask instanceof Incrementable)
            //	((Incrementable)ownerModule.contrastsStatsTask).setCurrent(ownerModule.currentX); 
            // check for polytomies, set warning
            boolean hasPolytomies;
            if (tree instanceof NoPolyTree)
                hasPolytomies = ((NoPolyTree)tree).hasZLBs();
            else
                hasPolytomies = tree.hasPolytomies(tree.getRoot());
            //x values
            int iChar = ownerModule.currentX;  // actually this is *only* true for bivariate plots (screens 9&10).
            switch (ownerModule.screen){
            case 1:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.SD);
                iChar = ownerModule.currentY;    //currentY is the character specified in the single scroll - both axes are functions of this.
                //Plot of absolute value of contrast vs. standard deviation
                if (hasPolytomies)
                    legend.setMessage(SCREEN1LEGEND + POLYTOMYWARNING);
                else
                    legend.setMessage(SCREEN1LEGEND);                    
                break;
            }
            case 3:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.NODEVALUE);
                iChar = ownerModule.currentY; 
                //Plot of absolute value of contrast vs. estimated value of associated node
                if (hasPolytomies)
                    legend.setMessage(SCREEN3LEGEND + POLYTOMYWARNING);
                else
                    legend.setMessage(SCREEN3LEGEND);
                break;
            }
            case 5:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CORRECTEDHEIGHT);
                iChar = ownerModule.currentY; 
                //Plot of absolute value of contrast vs. height of associated node
                if (hasPolytomies)
                    legend.setMessage(SCREEN5LEGEND + POLYTOMYWARNING);
                else
                    legend.setMessage(SCREEN5LEGEND);
                break;
            }
            case 7:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CORRECTEDHEIGHT);
                iChar = ownerModule.currentY; 
                //Plot of estimated value of associated node vs. its height
                legend.setMessage(SCREEN7LEGEND);
                break;
            }
            case 9:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CONTRAST);
                iChar = ownerModule.currentX;   // character specified in the horizontal scroll 
                //Plot of contrasts vs. positivized contrasts
                legend.setMessage(SCREEN9LEGEND);
                break;
            }
            case 10:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.ABSCONTRAST);
                iChar = ownerModule.currentX;  // character specified in the horizontal scroll
                //Plot of residuals from screen 9 vs. contrast values
                legend.setMessage(SCREEN10LEGEND);
                break;
            }
            case 11:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CORRECTEDHEIGHT);
                iChar = ownerModule.currentX; 
                //Plot of absolute value of residual vs. height of associated node
                legend.setMessage(SCREEN11LEGEND);
                break;
            }
            case 12:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.TIPS);
                iChar = ownerModule.currentX; 
                //Plot of tip values and confidence intervals for reconstructed root values
                legend.setMessage(SCREEN12LEGEND);//Peter: what of this depends on diagnostics being active?
                break;
            }
            case 13:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.TIPS);
                iChar = ownerModule.currentX;  //?
                //"Plot of phylogenetically correct (OLS) regression and associated CI's"   //Peter: what of this depends on diagnostics being active?
                legend.setMessage(SCREEN13LEGEND);  //Peter: what of this depends on diagnostics being active?
            }
            }

            if (true ) { 
                //if one character calculation, don't get character unless needed
                observedStates = (ContinuousDistribution)ownerModule.characterSourceTask.getCharacter(tree, iChar);
            }
            ownerModule.contrastsStatsTask.calculateNumbers(tree, observedStates, xArray, null);  // This does the work for the x-axis
            chart.setXAxisName(axisName(ownerModule.contrastsStatsTask.getParameters(), observedStates, ownerModule.screen, true));   //set to correct name
            String xItem = ownerModule.contrastsStatsTask.getItemName();
            if (ownerModule.contrastsStatsTask instanceof Incrementable)
                ((Incrementable)ownerModule.contrastsStatsTask).setCurrent(ownerModule.currentY);
            //y values
            switch (ownerModule.screen){
            case 1:
            case 3:
            case 5: {
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.ABSCONTRAST);
                break;
            }
            case 7:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.NODEVALUE);
                break;
            }
            case 9:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CONTRAST);
                break;
            }
            case 10:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.RESIDUAL);
                ownerModule.residualsTask.setOption(0);//raw
                break;
            }
            case 11:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.ABSRESIDUAL);
                ownerModule.residualsTask.setOption(1);//absolute
                break;
            }
            case 12:
            case 13:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.TIPS);
                break;
            }
            }
            if (true ) { 
                //if one character calculation, don't get character unless needed  TODO: make this work
                observedStates2 = (ContinuousDistribution)ownerModule.characterSourceTask.getCharacter(tree, ownerModule.currentY);
            }
            switch (ownerModule.screen) {
            case 1:
            case 3:
            case 5:
            case 7:
            case 9: {
                //ownerModule.contrastsStatsTask.setXCharForReport(ownerModule.currentX); 
                //ownerModule.contrastsStatsTask.setYCharForReport(ownerModule.currentY); 
                ownerModule.contrastsStatsTask.calculateNumbers(tree, observedStates2, yArray, null);  // This does the work for the y-axis
                break;
            }
            case 10:
            case 11: {

                ownerModule.residualsTask.calculateNumbers(tree, observedStates, observedStates2, yArray, null);
                break;
            }
            case 12:
            case 13: {
                ownerModule.contrastsStatsTask.setXCharForReport(ownerModule.currentX); 
                ownerModule.contrastsStatsTask.setYCharForReport(ownerModule.currentY); 
                ownerModule.contrastsStatsTask.calculateNumbers(tree, observedStates2, yArray, null);
                break;
            }
            }
            // maybe call it here??

            chart.setYAxisName(axisName(ownerModule.contrastsStatsTask.getParameters(), observedStates2, ownerModule.screen, false));  //TODO: this should use string passed back from calculateNumbers ???
            boolean showTips = false;
            if ((ownerModule.screen == 12) || (ownerModule.screen == 13)) 
                showTips = true;
            else if (ownerModule.screen == 9){
                chart.setXAxisName(axisName("Positivized Contrasts - CAUTION if any values are zero", observedStates, ownerModule.screen, true));   //force to correct name
                chart.setYAxisName(axisName("Contrasts Positivized on the X variable (Garland et al. 1992)", observedStates2, ownerModule.screen, false));
            }
            for (int i=0; i<numNodes; i++) {
                if (tree.nodeInTree(i) && (showTips || tree.nodeIsInternal(i))) { //todo: have toggle for internal only
                    xArray.placeValue(i, resultX);
                    yArray.placeValue(i, resultY);
                    if (ownerModule.screen == 9){ //positivizing for screen 9
                        if (resultX.isNegative()) {
                            resultY.changeSign();
                            resultX.abs();
                        }
                    }
                    //zArray.placeValue(i, resultZ);

                    int point = chart.addPoint(resultX, resultY);
                    //int point = chart.addPoint(resultX, resultY, resultZ);
                    String label = tree.getNodeLabel(i);
                    if (label == null)
                        chart.setName(point, Integer.toString(i));
                    else
                        chart.setName(point, label);
                    //chart.setCategory(point, nodeJustInternal(tree, i));
                }
                else { //these are here to ensure number of points is in parallel with numbering of nodes, for selection and other purposes
                    resultX.setToUnassigned();
                    chart.addPoint(resultX, resultY);
                }
            }
            contentsChanged();
            chart.munch();
            if (ownerModule.diagnosticsTask != null) {
                String s = ownerModule.diagnosticsTask.getLegendText();
                if (!StringUtil.blank(s))
                    legend.appendToMessage("\n\n" + s);
            }
        }
        if (ownerModule.treeDisplay!=null)
            ownerModule.treeDisplay.pleaseUpdate(false);
    }
    /*.................................................................................................................*/
    void pointTouched(Tree tree, int which) {
        if (ownerModule.nsLabeller==null) {
            return;
        }
        //the following looks wrong; which should be the node number directly; no need to search
        int count = 0;
        final Graphics g = ownerModule.treeDisplay.getGraphics();
        if (g!=null) {
            for (int i=0; i<tree.getNumNodeSpaces(); i++) {
                if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) {
                    if (count == which) {
                        ownerModule.nsLabeller.drawOneLabel(i, tree, g);
                    }
                    count++;
                }
            }
            g.dispose();
        }
    }
    /*.................................................................................................................*/
    void pointReleased(Tree tree, int which) {
        if (ownerModule.nsLabeller==null)
            return;
        if (ownerModule.nsLabeller.showLabels)
            return;
        int count = 0;
        final Graphics g = ownerModule.treeDisplay.getGraphics();
        if (g!=null) {
            for (int i=0; i<tree.getNumNodeSpaces(); i++) {
                if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) {
                    if (count == which) {
                        ownerModule.nsLabeller.hideOneLabel(i, g);
                    }
                    count++;
                }
            }
            g.dispose();
        }
        ownerModule.nsLabeller.hideLabels();
    }

    /*............................................................................................................*/
    public void windowResized() {
        if (MesquiteWindow.checkDoomed(this))
            return;
        if (chart!=null && (windowWidth!=getWidth() || windowHeight!=getHeight())) {
            windowWidth=getWidth();
            windowHeight=getHeight();
            if (chart!=null){
                chart.setLocation(0, bannerHeight+20);
                chart.setChartSize(windowWidth-20, windowHeight-20 - bannerHeight);
            }
            if (scrollBox !=null)
                scrollBox.setLocation(2, getHeight()-24- bannerHeight- scrollBox.getBounds().height);
            if (banner !=null)
                banner.setSize(windowWidth-20, bannerHeight);
        }
        MesquiteWindow.uncheckDoomed(this);
    }

    public void dispose(){
        if (tree !=null && tree instanceof NoPolyTree)
            ((NoPolyTree)tree).disconnect();
        super.dispose();
    }
}

/** This defines the legend box for the plot
 */
class PDAPLegend extends ResizableLegend {
    TextArea specsBox;
    private static final int grabHeight = 6;
    private static final int bottomHeight = 4;
    private static final int defaultSpecsHeight = (12 + MesquiteModule.textEdgeCompensationHeight) * 3;
    private static final int defaultLegendWidth=142;
    private static final int defaultLegendHeight=grabHeight + defaultSpecsHeight + 2 + bottomHeight;
    private int specsHeight = defaultSpecsHeight;
    
    public PDAPLegend() {
        super(defaultLegendWidth, defaultLegendHeight);
        setVisible(false);
        setOffsetX(0);
        setOffsetY(0);

        setBackground(Color.white);
        setLayout(null);
        specsBox = new TextArea(" ", 2, 2, TextArea.SCROLLBARS_VERTICAL_ONLY);
        specsBox.setEditable(false);
        add(specsBox);


        setSize(legendWidth,legendHeight);
        specsBox.setVisible(true);
    }

    public void paint(Graphics g) {
        if (MesquiteWindow.checkDoomed(this))
            return;
        g.setColor(Color.cyan);
        g.drawRect(0, 0, legendWidth-1, legendHeight-1);
        g.fillRect(0, 0, legendWidth-1, grabHeight);
        g.fillRect(legendWidth-grabHeight, legendHeight-grabHeight, grabHeight, grabHeight);
        g.setColor(Color.black);

        MesquiteWindow.uncheckDoomed(this);
    }

    void sizeChanged(int w, int h){
        specsHeight  = h - (grabHeight + 2 + bottomHeight);
        specsBox.setBounds(1,grabHeight,w-2, specsHeight);
        legendHeight = h;
        legendWidth = w;

    }

    public void setSize(int w, int h){
        sizeChanged(w, h);
        super.setSize(w, h);
    }
    public void setBounds(int x, int y, int w, int h){
        sizeChanged(w, h);
        super.setBounds(x, y, w, h);
    }
    void setMessage(String s) {
        specsBox.setText(s);
    }
    void appendToMessage(String s) {
        specsBox.setText(specsBox.getText() + s);
    }
}
\ No newline at end of file
+/* PDAP:PDTREE package for Mesquite  copyright 2001-2009 P. Midford & W. Maddison
PDAP:PDTREE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY.
The web site for PDAP:PDTREE is http://mesquiteproject.org/pdap_mesquite/

This source code and its compiled class files are free and modifiable under the terms of 
GNU Lesser General Public License.  (http://www.gnu.org/copyleft/lesser.html)
 */
package mesquite.pdap.PDAPDiagnosticChart;
/*~~  */

import java.awt.*;
import mesquite.lib.*;
import mesquite.lib.characters.*;
import mesquite.lib.duties.*;
import mesquite.pdap.lib.*;
import mesquite.cont.lib.*;

/* ======================================================================== */
/**=== Class PDAPDiagnosticChart.  ===
 * 
 * This is the main container for PDAP displays (not the transforms, exporter, etc.)
 * 
 * @author Peter E. Midford
 * created 2001
 * 
 * */

public class PDAPDiagnosticChart extends PDAPTreeWinAsstC implements ChartListener  {
    
    public void getEmployeeNeeds(){  //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed
        EmployeeNeed e = registerEmployeeNeed(DrawChart.class, getName() + "  needs a method to draw a chart.",
        "The method to draw a chart is selected initially");
        EmployeeNeed e2 = registerEmployeeNeed(CharSourceCoordObed.class, getName() + "  needs a method to supply characters.",
        "The method to supply characters is selected initially");
        EmployeeNeed e3 = registerEmployeeNeed(ContrastForChar.class, getName() + "  needs a method to calculate contrasts.",
        "The method to calculate contrasts is selected initially");
        EmployeeNeed e4 = registerEmployeeNeed(ResidualsCalculator.class, getName() + "  needs a method to calculate residuals.",
        "The method to calculate residuals is selected initially");
    }

    
    final static int SCREEN_COUNT = 14;
    
    ContrastForChar contrastsStatsTask;
    CharSourceCoordObed characterSourceTask;
    ResidualsCalculator residualsTask;
    public DrawChart charterTask;
    private Tree tree;
    int currentX = 0;
    int currentY = 1;
    NodeLabeller nsLabeller;
    boolean separateAxes = true;
    TreeDisplay treeDisplay;
    MesquiteCommand setXCommand, setYCommand;
    Taxa currentTaxa;
    private PDAPChartWindow window;

    int screen = 1;     // This is the first screen shown when the diagnostic chart is shown
    MesquiteCommand  cstC;
    MesquiteBoolean[] screenBoolean;
    PDAPScatterAsst diagnosticsTask;
    MesquiteBoolean showLegend;
    MesquiteBoolean verboseQueryMode;
    MesquiteBoolean showTreeLabels;
    MesquiteBoolean showSpotNames;
    MesquiteBoolean vhDefault;
    MesquiteDouble vh;
    private int dfReduction;
    private boolean vhQueryDone = false;
    private boolean dfQueryDone = false;
    private boolean ignoreRootTritomies = false;
    private boolean widthQueryDone;
    private double width1 = 0.95;
    private double width2 = 0.9;
    private boolean quiet;
    
    /*.................................................................................................................*/
    /**
     * @param arguments
     * @param condition
     * @param hiredByName
     * @return true unless an employee couldn't be hired
     */
    public boolean startJob(String arguments, Object condition, boolean hiredByName) {
        charterTask = (DrawChart)hireNamedEmployee(DrawChart.class, "#Scattergram");
        if (charterTask == null)
            return sorry(getName() + " couldn't start because no charting module obtained.");
        characterSourceTask = (CharSourceCoordObed)hireCompatibleEmployee(CharSourceCoordObed.class, ContinuousState.class, "Source of characters (for PDAP chart)");
        if (characterSourceTask == null) {
            return sorry(getName() + " couldn't start because no source of characters obtained");
        }
        contrastsStatsTask = (ContrastForChar)hireNamedEmployee(ContrastForChar.class, "#FelsContrWithChar");
        if (contrastsStatsTask == null)
            return sorry(getName() + " couldn't start because no calculating module obtained.");
        residualsTask = (ResidualsCalculator)hireNamedEmployee(ResidualsCalculator.class, "#ContrastResiduals");
        if (residualsTask == null)
            return sorry(getName() + " couldn't start because no calculating module for residuals obtained.");
        quiet = MesquiteThread.isScripting();
        cstC =  makeCommand("setCharacterSource",  (Commandable)this);
        characterSourceTask.setHiringCommand(cstC);
        screenBoolean = new MesquiteBoolean[SCREEN_COUNT];
        for (int i=0; i<SCREEN_COUNT; i++)
            screenBoolean[i] = new MesquiteBoolean(false);
        screenBoolean[screen].setValue(true);
        showLegend = new MesquiteBoolean(true);
        showSpotNames = new MesquiteBoolean(true);
       verboseQueryMode = new MesquiteBoolean(false);
        showTreeLabels = new MesquiteBoolean(false);
        loadPreferences();

        dfReduction = 0;
        vh = new MesquiteDouble(MesquiteDouble.unassigned);
        setXCommand = makeCommand("setX", (Commandable)this);
        setYCommand = makeCommand("setY", (Commandable)this);
        //ntxC =makeCommand("setScreen",  (Commandable)this);
        setScreen(screen);

        window =  new PDAPChartWindow(this);
        setModuleWindow(window);
        window.setWindowSize(400,400);
        addCheckMenuItem(null, "Abs. Contrast vs. Standard Deviation (1,2)", makeCommand("setScreen", this).setDefaultArguments("1"), screenBoolean[1]); //one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Abs. Contrast vs. Est. Node Value (3,4)", makeCommand("setScreen", this).setDefaultArguments("3"), screenBoolean[3]);//one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Abs. Contrast vs. Node Height (5,6)", makeCommand("setScreen", this).setDefaultArguments("5"), screenBoolean[5]);//one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Est. Node Value vs. Node Height (7,8)", makeCommand("setScreen", this).setDefaultArguments("7"), screenBoolean[7]);//one char scroll; ScatterRegDiagnostics
        addCheckMenuItem(null, "Y Contrasts vs. X Contrasts (positivized) (9)", makeCommand("setScreen", this).setDefaultArguments("9"), screenBoolean[9]);//two char scroll; ScatterOriDiagnostics
        addCheckMenuItem(null, "Root Node Reconstructions (9A)", makeCommand("setScreen",this).setDefaultArguments("12"), screenBoolean[12]);//two char scroll; RootReconstruction with error bars
        addCheckMenuItem(null, "Conf. & Pred. Intervals (9B)",makeCommand("setScreen",this).setDefaultArguments("13"), screenBoolean[13]); //two char scroll; Regression with CI and PI intervals
        addCheckMenuItem(null, "Residual vs. Contrast (10)", makeCommand("setScreen", this).setDefaultArguments("10"), screenBoolean[10]);//two char scroll; ScatterResXDiagnost
        addCheckMenuItem(null, "Abs. Residual vs. Node Height (11)", makeCommand("setScreen", this).setDefaultArguments("11"), screenBoolean[11]);//two vert char scroll; ScatterRegDiagnostics
        addMenuItem("-", null);
        addCheckMenuItem(null, "Show Legend", makeCommand("toggleShowLegend",  (Commandable)this), showLegend);
        addCheckMenuItem(null, "Show Spot Names", makeCommand("toggleSpotNames",  (Commandable)this), showSpotNames);
       if (!MesquiteThread.isScripting()) 
            window.setVisible(true);
        //The following was turned off because it needs too much work
//        if (getEmployer() instanceof TreeWindowMaker) {
//            addMenuItem( "Tree labels", makeCommand("toggleTreeLabels",  (Commandable)this));
//            treeDisplay = ((TreeWindowMaker)getEmployer()).getTreeDisplay();
//            nsLabeller = new NodeLabeller(this, treeDisplay, (PDAPChartWindow)window);
//            nsLabeller.setShowLabels(showTreeLabels.getValue());
//
//            treeDisplay.addExtra(nsLabeller);
//        }
        makeMenu("PDAP.Chart");
        resetContainingMenuBar();
        resetAllWindowsMenus();
        return true;
    }

    public void employeeQuit(MesquiteModule m){
        iQuit();
    }
    /*.................................................................................................................*/
    /*.................................................................................................................*/
    public void windowGoAway(MesquiteWindow whichWindow) {
        whichWindow.hide();
        whichWindow.dispose();
        if (nsLabeller != null)
            nsLabeller.turnOff();
        iQuit();
    }
    /*...................................................................................................................*/
    public void pointMouseDown(MesquiteChart chart, int whichPoint, MesquiteNumber valueX, MesquiteNumber valueY, int x, int y, int modifiers, String message){
        if (nsLabeller==null) {
            if (message == null)
                message = "";
            else
                message += "\n";
            int i = whichPoint;
            if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) {
                message  += "Node " + i;
                if (tree instanceof MesquiteTree && ((MesquiteTree)tree).getNodeLabel(i)!=null)
                    message += " (" +  ((MesquiteTree)tree).getNodeLabel(i) + ")";
                String[] results = window.getStrings(i);
                if (results !=null)
                    for (int j = 0; j<results.length; j++)
                        message += "\n" + results[j];  
                chart.showQuickMessage(whichPoint, x, y, message);
                return;
            }

        }
        window.pointTouched(tree, whichPoint);
    }
    /*...................................................................................................................*/
    public void pointMouseUp(MesquiteChart chart, int whichPoint, int x, int y, int modifiers, String message){
        chart.hideQuickMessage();
        window.pointReleased(tree, whichPoint);
    }
    /*.................................................................................................................*/
    public long toExternal(long i){
        return(CharacterStates.toExternal((int)i));
    }
    /*.................................................................................................................*/
    public long toInternal(long i){
        return(CharacterStates.toInternal((int)i));
    }
    /*.................................................................................................................*/
    public long getMin(){
        return 0;
    }
    /*.................................................................................................................*/
    /** returns the maximum index for a character on this chart */
    public long getMax(){
        if (characterSourceTask==null || currentTaxa==null)
            return 0;
        return characterSourceTask.getNumberOfCharacters(currentTaxa)-1;
    }

    /*-----------------------------------------*/
    public void processPreferencesFromFile (String[] prefs) {
        if (prefs!=null && prefs.length>0)
            verboseQueryMode.setValue("v".equals(prefs[0]));
    }
    /*-----------------------------------------*/
    public String[] preparePreferencesForFile () {
        String[] prefs= new String[1];
        if (verboseQueryMode.getValue())
            prefs[0] = "v";
        else
            prefs[0] = "n";
        return prefs;
    }

    /*.................................................................................................................*/
    /** 
     * This saves the state of the chart to a Snapshot 
     * @param file
     * @return the new snapshot object
     */
    public Snapshot getSnapshot(MesquiteFile file) { 
        if (window ==null)
            return null;
        Snapshot result = new Snapshot();
        result.addLine("quiet");
        result.addLine( "getCharacterSource " , characterSourceTask);

        result.addLine("toggleShowLegend " + showLegend.toOffOnString());
       result.addLine("toggleTreeLabels " + showTreeLabels.toOffOnString()); 
        result.addLine("toggleDFQueryDone " + MesquiteBoolean.toOffOnString(dfQueryDone));
        result.addLine("toggleVhQueryDone " + MesquiteBoolean.toOffOnString(vhQueryDone));
        result.addLine("toggleIgnoreRootTritomies " + MesquiteBoolean.toOffOnString(ignoreRootTritomies));
        result.addLine("setDFReduction " + dfReduction); 
        if (!vh.isUnassigned())
            result.addLine("setVh " + vh.toString());
        result.addLine("setWidth1 " + MesquiteDouble.toString(width1));
        result.addLine("setWidth2 " + MesquiteDouble.toString(width2));
        result.addLine("setScreen " + screen); // don't do a bunch of bogus calculations on screen 9+; set things first

        result.addLine("setX " + toExternal(currentX)); 
        result.addLine("setY " + toExternal(currentY)); 
        Snapshot fromWindow = window.getSnapshot(file);
        result.addLine("getWindow");
        result.addLine("tell It");
        result.incorporate(fromWindow, true);
        result.addLine("endTell");
        result.addLine("toggleSpotNames " + showSpotNames.toOffOnString());
       result.addLine("showWindow");
        result.addLine("resume");
        return result;
    }
    /*.................................................................................................................*/
    /** fireAssistantIfNeeded is a helper method for hireIfNeeded.  The ordering of the tests in the conditional
	    were reversed to take advantage of "short-circuiting" && by putting the cheaper test first */
    private void fireAssistantIfNeeded(String name, String toBeHired){
        if (!name.equalsIgnoreCase(toBeHired) && charterTask.findEmployeeWithName(name)!=null)
            charterTask.doCommand("fireEmployee", name,CommandChecker.defaultChecker);
    }
    /** hireIfNeeded makes sure the appropriate calculation assistant is hired, after firing any that are
	  inappropriate.  */
    private Object hireIfNeeded(String name){
        fireAssistantIfNeeded("#ScatterRegDiagnostics", name);
        fireAssistantIfNeeded("#ScatterResXDiagnostics", name);
        fireAssistantIfNeeded("#ScatterOriDiagnostics", name);
        fireAssistantIfNeeded("#ScatterRootCIPI", name);
        fireAssistantIfNeeded("#ScatterRootRegCIPI",name);
        if (charterTask.findEmployeeWithName(name)==null) {
            Object obj = charterTask.doCommand("newAssistant", name,CommandChecker.defaultChecker);
            if (obj !=null && obj instanceof ScatterRegisterableAsst) {
                ((ScatterRegisterableAsst)obj).setChartModule(this);
            }
            return obj;
        }
        else {
            return charterTask.findEmployeeWithName(name);
        }
    }
    /*.................................................................................................................*/
    /** This method sets the screen, updates the boolean array that handles check marks in the menu
	and hires the appropriate diagnostics employee */
    private Object setScreen(int ic){
        screenBoolean[screen].setValue(false);
        screen = ic;
        screenBoolean[screen].setValue(true);
        Object hired = null;
        switch (ic){
        case 1:
        case 3:
        case 5:
        case 7:
        case 11: {
            hired = hireIfNeeded("#ScatterRegDiagnostics");
            break;
        }
        case 9: {	
            hired = hireIfNeeded("#ScatterOriDiagnostics");
            break;
        }
        case 10: {
            hired = hireIfNeeded("#ScatterResXDiagnostics");
            break;
        }
        case 12: {   //screen 9A
            hired = hireIfNeeded("#ScatterRootCIPI");
            break;
        }
        case 13: {	//screen 9B
            hired = hireIfNeeded("#ScatterRootRegCIPI");
            break;
        }
        }
        diagnosticsTask = (PDAPScatterAsst)hired;
        return hired;
    }
    MesquiteInteger pos = new MesquiteInteger();
    /*.................................................................................................................*/
    public Object doCommand(String commandName, String arguments, CommandChecker checker) {
        final Class thisClass = this.getClass();
        if (checker.compare(thisClass, "Sets module supplying characters", "[name of module]", commandName, "setCharacterSource")) {//temporary
            return characterSourceTask.doCommand(commandName, arguments, checker);
        }
        else if (checker.compare(thisClass, "Sets whether or not the legend is shown", "[on = show; off]", commandName, "toggleShowLegend")) {
            showLegend.toggleValue(parser.getFirstToken(arguments));
            window.setLegendVisible(showLegend.getValue());
        }
        else if (checker.compare(thisClass, "Sets whether or not the spot names are shown", "[on = show; off]", commandName, "toggleSpotNames")) {
            showSpotNames.toggleValue(parser.getFirstToken(arguments));
    		if (window != null){
    			window.charter.setShowNames(showSpotNames.getValue());
    			window.contentsChanged();
    		}
       }
       else if (checker.compare(thisClass, "Quiets notices", null, commandName, "quiet")) {
            quiet = true;
            return null;
        }
        else if (checker.compare(thisClass, "Returns module supplying characters", null, commandName, "resume")) {
            quiet = false;
            return null;
        }
        else if (checker.compare(thisClass, "Returns module supplying characters", null, commandName, "getCharacterSource")) {
            return characterSourceTask;
        }
        else if (checker.compare(thisClass, "Sets the screen shown", "[screen number, one of 1,3,5,7,9-13]", commandName, "setScreen")) {
            int ic = MesquiteInteger.fromString(arguments);
            if (validScreen(ic)) {               
                incrementMenuResetSuppression();
                Object o = setScreen(ic);
                doCounts();
                getModuleWindow().contentsChanged();
                decrementMenuResetSuppression();
                return o;
            }
        }
        else if (checker.compare(thisClass, "Sets which item is shown on the x axis (appropriate where the calculator can supply a series of items, e.g. characters)", "[item number]", commandName, "setX")) {
            int ic = (int)(MesquiteInteger.fromString(arguments));
            if (!MesquiteInteger.isCombinable(ic))
                ic = MesquiteInteger.queryInteger(containerOfModule(), "Choose ", "choose:", 1); //TODO have something more intelligent here
            if (!MesquiteInteger.isCombinable(ic))
                return null;
            int icInternal = ic-1;
            if ((icInternal>=0) && (icInternal<=getMax())) {  //no need to check for combinability, ic was just checked.
                currentX=icInternal;
                if (!MesquiteThread.isScripting()){
                    doCounts();
                }
            }
        }
        else if (checker.compare(thisClass, "Sets which item is shown on the y axis (appropriate where the calculator can supply a series of items, e.g. characters)", "[item number]", commandName, "setY")) {
            int ic = (MesquiteInteger.fromString(arguments));
            if (!MesquiteInteger.isCombinable(ic))
                ic = MesquiteInteger.queryInteger(containerOfModule(), "Choose an ", "choose:", 1); //TODO have something more intelligent here
            if (!MesquiteInteger.isCombinable(ic))
                return null;
            int icInternal = ic-1;
            if ((icInternal>=0) && (icInternal<=getMax())) {  //no need to check for combinability, ic was just checked.
                currentY=icInternal;
                if (!MesquiteThread.isScripting()){
                    doCounts();
                }
            }
        }
        else if (checker.compare(thisClass, "Sets whether or not the tree labels are shown", "[on or off]", commandName, "toggleTreeLabels")) {
            //TODO: use MesquiteBoolean checkmark
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleShowTreeLabels invoked without parameter");
            else
                showTreeLabels.toggleValue(parser.getFirstToken(arguments));
            if (nsLabeller!=null)
                nsLabeller.setShowLabels(showTreeLabels.getValue());
            if (treeDisplay !=null)
                treeDisplay.pleaseUpdate(false);
        } 
        else if (checker.compare(thisClass,"Sets the degrees of freedom adjustment", "[integer]",commandName, "setDFReduction")) {
            int dfr = (int)(MesquiteInteger.fromString(arguments));
            if (!MesquiteInteger.isCombinable(dfr))  //not a menu command..
                MesquiteMessage.warnProgrammer("setDFReduction invoked without parameter");
            else
                dfReduction = dfr;
        }  
        else if (checker.compare(thisClass,"Sets the length of the added branch for predication intervals", "[double]",commandName, "setVh")) {
            double vht = (double)(MesquiteDouble.fromString(arguments));
            if (!MesquiteDouble.isCombinable(vht))  //not a menu command..
                MesquiteMessage.warnProgrammer("setVh invoked without parameter");
            else
                vh.setValue(vht);
        }  
        else if (checker.compare(thisClass,"Sets the length of the added branch for predication intervals", "[double]",commandName, "setWidth1")) {
            double w1 = (double)(MesquiteDouble.fromString(arguments));
            if (!MesquiteDouble.isCombinable(w1))  //not a menu command..
                MesquiteMessage.warnProgrammer("setWidth1 invoked without parameter");
            else
                width1 = w1;
        }  
        else if (checker.compare(thisClass,"Sets the length of the added branch for predication intervals", "[double]",commandName, "setWidth2")) {
            double w2 = (double)(MesquiteDouble.fromString(arguments));
            if (!MesquiteDouble.isCombinable(w2))  //not a menu command..
                MesquiteMessage.warnProgrammer("setWidth2 invoked without parameter");
            else
                width2 = w2;
        }  
        else if (checker.compare(thisClass,"Sets state of Vh query done", "[on/off]",commandName, "toggleVhQueryDone")) {
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleVhQueryDone invoked without parameter");
            else{
                String s = parser.getFirstToken(arguments);
                if ("on".equalsIgnoreCase(s))
                    vhQueryDone = true;
                else if  ("off".equalsIgnoreCase(s))
                    vhQueryDone = false;
                else
                    vhQueryDone = !vhQueryDone;
            }   
        }
        else if (checker.compare(thisClass,"Sets state of df query done", "[on/off]",commandName, "toggleDFQueryDone")) {
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleDFQueryDone invoked without parameter");
            else{
                String s = parser.getFirstToken(arguments);
                if ("on".equalsIgnoreCase(s))
                    dfQueryDone = true;
                else if  ("off".equalsIgnoreCase(s))
                    dfQueryDone = false;
                else
                    dfQueryDone = !dfQueryDone;
            }
        }
        else if (checker.compare(thisClass,"Sets state of ignore root tritomies", "[on/off]",commandName, "toggleIgnoreRootTritomies")) {
            if (StringUtil.blank(arguments)) //not a menu command..
                MesquiteMessage.warnProgrammer("toggleIgnoreRootTritomies invoked without parameter");
            else{
                String s = parser.getFirstToken(arguments);
                if ("on".equalsIgnoreCase(s))
                    ignoreRootTritomies = true;
                else if  ("off".equalsIgnoreCase(s))
                    ignoreRootTritomies = false;
                else
                    ignoreRootTritomies = !ignoreRootTritomies;
            }
        }
        else
            return  super.doCommand(commandName, arguments, checker);
        return null;
    }

    /* This checks whether the screenNumber specifies a valid screen; if new screens are added, this needs to be updated */
    final private boolean validScreens[] = {false, true, false, true, false, true, false, true, false, true, true, true, true, true};
    private boolean validScreen(int screenNumber) {
        if (screenNumber < 0 || screenNumber > 13)
            return false;
        else return validScreens[screenNumber];
    }



    long oldTreeID = -1;
    long oldTreeVersion = 0;
    /*.................................................................................................................*/
    public void setTree(Tree tree) {
        if (tree==null)
            return;
        if (!((MesquiteTree)tree).allLengthsAssigned(false) && !(MesquiteThread.isScripting()  && quiet)) {
            alert("The tree you want to analyze contains one or more branches with unassigned branch lengths. " +
            "You should go back to the tree window and specify branch lengths (e.g set to 1, Pagel's method, etc.).");
            //iQuit();
            //window.dispose();
            //return;
        }
        if (this.tree !=null && this.tree instanceof NoPolyTree && this.tree !=tree) { // about to set new tree
            ((NoPolyTree)this.tree).disconnect();
        }
        if (tree instanceof NoPolyTree)
            this.tree=tree;
        else 
            this.tree = new NoPolyTree((MesquiteTree)tree);
        if (oldTreeID==-1 || tree.getID() != oldTreeID || tree.getVersionNumber() != oldTreeVersion){
            setDFQueryDone(false);  // make sure these are reset before any redraws
            setVhQueryDone(false);
            vh.setToUnassigned();
        }
        if (this.tree instanceof Selectionable)
            charterTask.pointsAreSelectable(true, (Selectionable)this.tree, false);
        currentTaxa = this.tree.getTaxa();
        if (oldTreeID==-1) {
            if (contrastsStatsTask==null || residualsTask == null)
                return;
            //setDFQueryDone(false);
            //setVhQueryDone(false);
            //vh.setToUnassigned();
            contrastsStatsTask.initialize(tree);
            residualsTask.initialize(tree);
            characterSourceTask.initialize(tree.getTaxa());
            doCounts();
        }
        else if (tree.getID() != oldTreeID || tree.getVersionNumber() != oldTreeVersion) {
            //setDFQueryDone(false);
            //setVhQueryDone(false);
            //vh.setToUnassigned();
            doCounts();
        }
        else {
            if (window!=null && window.getChart()!=null ) {
                window.getChart().getField().repaint(); //for selection Only
                window.getChart().repaint();
            }
        }
        oldTreeID = tree.getID();
        oldTreeVersion = tree.getVersionNumber();
    }

    /*.................................................................................................................*/
    public void employeeParametersChanged(MesquiteModule employee, MesquiteModule source, Notification notification) {
        if (contrastsStatsTask!=null && residualsTask!=null && characterSourceTask !=null) {
            doCounts();
        }
    }
    /*.................................................................................................................*/
    public CharacterDistribution getObserved1(){
        return window.observedStates;
    }
    /*.................................................................................................................*/
    public CharacterDistribution getObserved2(){
        return window.observedStates2;
    }
    /*.................................................................................................................*/
    public Tree getTree(){
        return tree;
    }

    /*.................................................................................................................*/
    public boolean getDFQueryDone(){
        return dfQueryDone;
    }

    /*.................................................................................................................*/
    public void setDFQueryDone(boolean value){
        dfQueryDone = value;
    }

    /*.................................................................................................................*/
    public int getDFReduction(){
        return dfReduction;
    }

    public void setDFReduction(int value){
        dfReduction = value;
    }

    public int queryDFReduce(PDAP2CTStatPak sp, boolean notifyIfZero){
        if(!MesquiteThread.isScripting()){  //if scripting use 0 (default) or value set by script
            sp.countInternalNodes(tree, tree.getRoot());
            int polytomies = ((NoPolyTree)tree).countZLBs(sp.getIgnoreRootTritomies());     // Zero-Length-Branches are what PDAP calls "polytomies", count to inform the user
            if ((polytomies >0)) {
                int tmp = MesquiteInteger.queryInteger(window,  
                        "DF Reduce ",
                        "This tree contains polytomies, indicated by the presence \n" +
                        "of " + polytomies + " zero-length branch(es).\n" +
                        "If some of these collapsed branches indicate\n" +
                        "soft polytomies, then you may want to reduce\n" +
                        "degrees of freedom (see Purvis and Garland, 1993,\n" +
                        "Syst. Biol. 42:569-575; Garland and Diaz-Uriarte, 1999,\n" +
                        "Syst. Biol. 48:547-558).\n\n " +
                        "Enter number of Degrees of Freedom to subtract for soft polytomies",
                        dfReduction,
                        0,
                        MesquiteInteger.infinite);

                if (MesquiteInteger.isCombinable(tmp)) {
                    dfReduction = tmp;
                }
            }
            else {
                if (notifyIfZero) {
                    int tmp = MesquiteInteger.queryInteger(window,  
                            "DF Reduce ",
                            "This tree is fully dichotomized and contains no polytomies.\n" +
                            "If, for whatever reason, you wish to decrease\n" +
                            "degrees of freedom (see Purvis and Garland, 1993,\n" +
                            "Syst. Biol. 42:569-575; Garland and Diaz-Uriarte, 1999,\n" +
                            "Syst. Biol. 48:547-558), you may do so here.\n\n" +
                            "Enter degrees of freedom to subtract",
                            dfReduction,
                            0,
                            MesquiteInteger.infinite);
                    //alert(null,"","The tree has no polytomies, hence there is no need to reduce degrees of freedom to compensate for polytomies.");
                    if (MesquiteInteger.isCombinable(tmp)) 
                        dfReduction = tmp;
                    else
                        dfReduction = 0;
                }
            }
        }
        return dfReduction;
    }

    /*-----------------------------------------*/
    /** 
     * This prompts the user and sets the CI/PI widths. The results are saved in the width1 and width2 fields.
     */
    public void queryWidths(){
        if (!MesquiteThread.isScripting()){ // if scripting, widths either default or set elsewhere
            MesquiteDouble tmp1 = new MesquiteDouble(width1);
            MesquiteDouble tmp2 = new MesquiteDouble(width2);
            MesquiteBoolean ans = new MesquiteBoolean();

            MesquiteDouble.queryTwoDoubles(window,
                    "Interval Widths",
                    "Enter the first (2-tailed) p-value width for CI/PI plots",
                    "Enter the second (2-tailed) p-value width for CI/PI plots",
                    ans,
                    tmp1,
                    tmp2);
            if (tmp1.isCombinable()) {
                double tp1 = tmp1.getValue();
                if ((tp1 <= 1.0) && (tp1 >= 0.0))
                    width1 = tp1;
            }
            if (tmp2.isCombinable()){
                double tp2 = tmp2.getValue();
                if ((tp2 <= 1.0) && (tp2 >= 0.0))
                    width2 = tp2;
            }
        }
    }


    public double getWidth1(){
        return width1;
    }
    public double getWidth2(){
        return width2;
    }
    public void setWidthQueryDone(boolean value){
        widthQueryDone = value;
    }
    public boolean getWidthQueryDone(){
        return widthQueryDone;
    }


    /*.................................................................................................................*/
    public boolean getVhQueryDone(){
        return vhQueryDone;
    }

    /*.................................................................................................................*/
    public void setVhQueryDone(boolean value){
        vhQueryDone = value;
    }

    public double getVh(){
        return vh.getValue();
    }

    /*.................................................................................................................*/

    /** This prompts the user and sets Vh */    
    public double queryVh(PDAP2CTStatPak sp){
        double tmp = sp.getMeanHeight(tree);
        if (!MesquiteThread.isScripting()){
            String contempString;

            if (sp.getContempTips())
                contempString = "All tips are contemporaneous in the uncorrected tree.";
            else
                contempString = "The tips are not contemporaneous in the uncorrected tree.";
            tmp = MesquiteDouble.queryDouble(window,
                    "Vh",
                    "The calculations for prediction intervals effectively assume " +
                    "that the species to be predicted is attached at the root " +
                    "(basal node) of the phylogenetic tree (see Garland and Ives, " +
                    "2000, Am. Nat. 155:346-364).  By default, the branch length (Vh) " +
                    "leading to the predicted species is assumed to equal the average" +
                    "length of the (uncorrected) branches from root to tips. \n\n" +
                    contempString + "\n\n Enter a value for Vh\n",       
                    tmp,
                    0,
                    MesquiteDouble.infinite);
            if (MesquiteDouble.isCombinable(tmp)){
                vh.setValue(tmp);
                vhQueryDone = true;
            }

            else{ 
                AlertDialog.notice(window, "Vh undefined",
                        "Vh could not be estimated and is not meaningful because one or more " +
                        "branches in the tree have undefined branch lengths.  Either assign lengths " +
                        "or use a constant transform to set all branches equal to one.  No confidence or " +
                "prediction intervals will be displayed.");
                vh.setToUnassigned();
            }
        }
        else vh.setValue(tmp);

        return vh.getValue(); 
    }


    public void queryVerboseQueryMode(){
        MesquiteBoolean ok = MesquiteBoolean.queryCheckBox(window,
                "Set Verbose Query Preference","In verbose mode you will be asked for settings for PDAP root reconstruction frequently; otherwise you change the settings using menu items","Use Verbose Mode", verboseQueryMode.getValue());
        if (!ok.isUnassigned()) {
            verboseQueryMode.setValue(ok.getValue());
            storePreferences();
        }
    }

    public void toggleVerboseQueryMode(String arg){
        verboseQueryMode.toggleValue(arg);
        storePreferences();
    }

    public boolean getVerboseQueryMode(){
        return verboseQueryMode.getValue();
    }

    /*................................................................*/

    public void queryIgnoreRootTritomies(){
        MesquiteBoolean ok = MesquiteBoolean.queryCheckBox(window,
                "Set Ignore Basal Tritomies",
                "Some tree inference programs return trees that PDAP sees as having tritomies at the root; checking the box will ignore any tritomies at the root in counting or detecting polytomies for degrees of freedom adjustment",
                "Ignore Root Tritomies",
                ignoreRootTritomies);
        if (!ok.isUnassigned()){
            ignoreRootTritomies = ok.getValue();
        }
    }

    public boolean getIgnoreRootTritomies(){
        return ignoreRootTritomies;
    }

    public void setIgnoreRootTritomies(boolean value){
        ignoreRootTritomies = value;
    }


    /*................................................................*/    
    public String nameForWritableResults(){
        return "PDAP Diagnostics from StatPak";
    }
    public boolean suppliesWritableResults(){
        return diagnosticsTask.suppliesWritableResults();
    }
    public Object getWritableResults(){
        return diagnosticsTask.getWritableResults();
    }
    public Object getResultsHeading(){
        return diagnosticsTask.getResultsHeading();
    }


    /*.................................................................................................................*/
    private void doCounts() {
        window.blankChart();
        window.setTree(tree);
        window.recalcChart();
        window.contentsChanged();
    }
    /*.................................................................................................................*/
    public String getName() {
        return "PDAP Diagnostic Chart";
    }
    /*.................................................................................................................*/
    public String getAuthors() {
        return "Peter E. Midford, Ted Garland Jr., and Wayne P. Maddison" ;
    }
    /*.................................................................................................................*/
    public String getVersion() {
        return "1.15";
    }
    /*.................................................................................................................*/
    //Peter: add this method returning true for all citable modules, e.g. main calculations
    public boolean showCitation(){
        return true;
    }
    /*.................................................................................................................*/
    public boolean isPrerelease() {
        return false;
    }
    /*.................................................................................................................*/
    public boolean requestPrimaryChoice() {
        return true;
    }

    /*.................................................................................................................*/
    /** returns an explanation of what the module does.*/
    public String getExplanation() {
        return "Shows independent constrasts and related values for nodes of tree via a scattergram." ;
    }
    /*.................................................................................................................*/
    public void endJob() {
        if (treeDisplay !=null && nsLabeller !=null)
            treeDisplay.removeExtra(nsLabeller);
        super.endJob();
    }
}

/* ======================================================================== */
/**=== Local Class BannerPanel.  ===*/

class BannerPanel extends MesquitePanel{
    public void paint(Graphics g){
        g.setColor(Color.cyan);
        g.drawString("PDAP: PDTREE module", 16, getBounds().height-4);
    }
}
/*========================================================*/
class NodeLabeller extends TreeDisplayExtra {
    LabelsAtNodes labelsAtNodes;
    PDAPChartWindow chartWindow;
    final static Color brightGreen = new Color((float)0.4, (float)1.0, (float)0.4);
    final static Color brightbrightGreen = new Color((float)0.6, (float)1.0, (float)0.6);
    boolean showLabels = true;
    int labelDrawn = -1;
    

    public NodeLabeller (MesquiteModule ownerModule, TreeDisplay treeDisplay, PDAPChartWindow chartWindow) {
        super(ownerModule, treeDisplay);
        this.chartWindow =chartWindow;
    }
    /*.................................................................................................................*/
    void drawOneLabel(int N, Tree tree, Graphics g) {
        makeSureLabelsReady(tree);
        int nodeX = (int)treeDisplay.getTreeDrawing().getX(N);
        int nodeY = (int)treeDisplay.getTreeDrawing().getY(N);
        MesquiteLabel c = (MesquiteLabel)labelsAtNodes.getPanel(N);

        c.setColor(brightbrightGreen); 
        c.setText("Node " + N);  
        String[] results = chartWindow.getStrings(N);
        for (int i = 0; i<results.length; i++)
            c.addLine(results[i]);  

        c.setVisible(true);
        c.repaint();
        int w = c.getWidth(g);
        if (w+nodeX+16>treeDisplay.getBounds().width)
            c.setLocation(treeDisplay.getBounds().width- w, nodeY + 18);
        else
            c.setLocation(nodeX + 16, nodeY + 18);
        g.setColor(brightGreen);
        g.setXORMode(Color.white);
        g.drawLine(nodeX, nodeY, c.getBounds().x, c.getBounds().y);
        g.drawLine(nodeX, nodeY+1, c.getBounds().x, c.getBounds().y + 1);
        g.drawLine(nodeX, nodeY+2, c.getBounds().x, c.getBounds().y + 2);
        g.drawLine(nodeX, nodeY+3, c.getBounds().x, c.getBounds().y + 3);
        g.setPaintMode();
        g.setColor(Color.black);
        labelDrawn = N;
    }
    /*.................................................................................................................*/
    void hideOneLabel(int N, Graphics g) {
        MesquiteLabel c = (MesquiteLabel)labelsAtNodes.getPanel(N);
        if (c==null || g==null)
            return;
        c.setVisible(false);
        final int nodeX = (int)treeDisplay.getTreeDrawing().getX(N);
        final int nodeY = (int)treeDisplay.getTreeDrawing().getY(N);
        g.setColor(brightGreen);
        g.setXORMode(Color.white);
        g.drawLine(nodeX, nodeY, c.getBounds().x, c.getBounds().y);
        g.drawLine(nodeX, nodeY+1, c.getBounds().x, c.getBounds().y + 1);
        g.drawLine(nodeX, nodeY+2, c.getBounds().x, c.getBounds().y + 2);
        g.drawLine(nodeX, nodeY+3, c.getBounds().x, c.getBounds().y + 3);
        g.setPaintMode();
        labelDrawn = -1;
    }
    /*.................................................................................................................*/
    private void drawLabels(int N, Tree tree, Graphics g) {
        for (int d = tree.firstDaughterOfNode(N); tree.nodeExists(d); d = tree.nextSisterOfNode(d))
            drawLabels(d, tree, g);
        drawOneLabel(N, tree, g);
    }
    /*.................................................................................................................*/
    void hideLabels() {
        if (labelsAtNodes==null)
            return;
        Graphics g = treeDisplay.getGraphics();
        for (int N = 0; N<labelsAtNodes.getNumNodes(); N++) {
            if (N== labelDrawn)
                hideOneLabel(N, g);
            else
                labelsAtNodes.getPanel(N).setVisible(false);
        }
        if (g!=null)
            g.dispose();
    }
    /*.................................................................................................................*/
    void setShowLabels(boolean show) {
        showLabels = show;
        if (labelsAtNodes!=null && !showLabels)
            hideLabels();

    }
    /*.................................................................................................................*/
    private void makeSureLabelsReady(Tree tree){
        if (labelsAtNodes==null) {
            labelsAtNodes = new LabelsAtNodes(ownerModule, tree.getNumNodeSpaces(), treeDisplay);
        }
        else if (labelsAtNodes.getNumNodes()!=tree.getNumNodeSpaces() ) {
            labelsAtNodes.resetNumNodes(tree.getNumNodeSpaces());
        }
    }
    /*.................................................................................................................*/
    public void drawOnTree(Tree tree, int drawnRoot, Graphics g) {
        if (showLabels && g != null) {
            makeSureLabelsReady(tree);
            drawLabels(drawnRoot, tree, g);
            g.setColor(Color.black);
        }
    }
    /*.................................................................................................................*/
    public void printOnTree(Tree tree, int drawnRoot, Graphics g) {
        drawOnTree(tree, drawnRoot, g);
    }
    /*.................................................................................................................*/
    public void setTree(Tree tree) {
    }
    /*.................................................................................................................*/
    public void turnOff() {
        super.turnOff();
        if (labelsAtNodes!=null)
            labelsAtNodes.dispose();
    }
}

/*========================================================*/
class PDAPChartWindow extends ChartWindow {
    final static String scrollBoxTitle = "character";
    
    // Legend messages
    final private static String SCREEN1LEGEND = "Plot of absolute value of contrast vs. standard deviation";
    final private static String SCREEN3LEGEND = "Plot of absolute value of contrast vs. estimated value of associated node";
    final private static String SCREEN5LEGEND = "Plot of absolute value of contrast vs. height of associated node";
    final private static String SCREEN7LEGEND = "Plot of estimated value of associated node vs. its height";
    final private static String SCREEN9LEGEND = "Plot of contrasts vs. positivized contrasts";
    final private static String SCREEN10LEGEND = "Plot of residuals from screen 9 vs. contrast values";
    final private static String SCREEN11LEGEND = "Plot of absolute value of residual vs. height of associated node";
    final private static String SCREEN12LEGEND = "Plot of tip values and confidence intervals for reconstructed root values";
    final private static String SCREEN13LEGEND = "Plot of phylogenetically correct (OLS) regression and " +  
            "associated CI's (red-95%, orange-90%) and PI (green-95%, cyan-90%), "+
            "mapped onto the original tip data space. (see Garland and Ives 2000, Am. Nat. 155:346-364).";

    // Polytomy warning for legends
    final private static String POLYTOMYWARNING = "/n Warning: arbitrary resolution of zero-length branches due to polytomies";
    
    BannerPanel banner;
    int bannerHeight = 24;
    private int windowWidth=0;
    private int windowHeight=0;
    private PDAPDiagnosticChart ownerModule;
    private NumberArray xArray, yArray; //, zArray;
    private boolean weightedBranches = true;
    String nameA, nameB;
    Charter charter;
    PDAPLegend legend;
    Tree tree;
    DoubleMiniScroll scrollBox;
    MesquiteChart chart;
    ContinuousDistribution observedStates, observedStates2;
    private MesquiteNumber resultX = new MesquiteNumber();
    private MesquiteNumber resultY = new MesquiteNumber();

    public PDAPChartWindow (PDAPDiagnosticChart ownerModule) {
        super(ownerModule, true); //infobar
        this.ownerModule = ownerModule;
        charter = ownerModule.charterTask.createCharter(ownerModule);
        charter.setShowNames(true);
        chart=new MesquiteChart(ownerModule, 100, 0, charter);
        setChart(chart);
        xArray = new NumberArray(3);
        yArray = new NumberArray(3);
        //zArray = new NumberArray(3);
        chart.deassignChart();
        addToWindow(chart);
        chart.setVisible(true);
        chart.setBackground(getBackground());
        scrollBox = new DoubleMiniScroll(ownerModule.setXCommand, ownerModule.setYCommand, 0,0,0,0,0,0);
        chart.add(scrollBox);
        scrollBox.setYTitle("Y");
        scrollBox.setXTitle("X");
        //scrollBox.setLocation(10, getHeight()-10);
        scrollBox.setLocation(2, getHeight()-24- scrollBox.getBounds().height);
        banner = new BannerPanel();
        addToWindow(banner);
        banner.setLocation(0, 0);
        banner.setFontSize(18);
        banner.setVisible(true);
        banner.setBackground(Color.blue);
        legend = new PDAPLegend();
        chart.getField().add(legend);
        legend.setVisible(true);
        resetTitle();
    }

    /*.................................................................................................................*/
    /** When called the window will determine its own title.  MesquiteWindows need
	to be self-titling so that when things change (names of files, blocks, etc.)
	they can reset their titles properly*/
    public void resetTitle(){
        setTitle("PDAP Diagnostic Chart");
    }

    void setLegendVisible(boolean vis){
        if (legend!=null)
            legend.setVisible(vis);
    }
    /*.................................................................................................................*/
    public Snapshot getSnapshot(MesquiteFile file) { 
        Snapshot temp = super.getSnapshot(file);
        temp.addLine( "getLegend");
        temp.addLine("tell It");

        temp.incorporate(legend.getSnapshot(file), true);
        temp.addLine("endTell");
        return temp;
    }
    /*.................................................................................................................*/
    public Object doCommand(String commandName, String arguments, CommandChecker checker) { 
        if (checker.compare(this.getClass(), "Returns the legend", null, commandName, "getLegend")) {
            return legend;
        }
        else 
            return  super.doCommand(commandName, arguments, checker);
    }
    /*.................................................................................................................*/
    private void resetScrolls(){
        final int min = (int)ownerModule.toExternal(ownerModule.getMin());
        final int max = (int)ownerModule.toExternal(ownerModule.getMax());
        final int curX = (int)ownerModule.toExternal(ownerModule.currentX);
        final int curY = (int)ownerModule.toExternal(ownerModule.currentY);
        final int screen = ownerModule.screen;
        scrollBox.setYTitle(scrollBoxTitle);
        // one character scroll //is this really correct for screen 11?
        if (screen == 1 || screen == 3 || screen == 5 ||screen == 7 || screen == 11) {
            scrollBox.setYValues(min, curY, max);
            scrollBox.setYVisible(true);
            scrollBox.setXVisible(false);
        }
        // two character scroll, one for X and one for Y
        else if (screen == 9 || screen == 10) {
            scrollBox.setXTitle(scrollBoxTitle);
            scrollBox.setXValues(min, curX, max);
            scrollBox.setXVisible(true);
            scrollBox.setYValues(min, curY, max);
            scrollBox.setYVisible(true);
        }
        // two character scroll, both for Y
        else {
            scrollBox.setXTitle(scrollBoxTitle);
            scrollBox.setXValues(min, curX, max);
            scrollBox.setXVisible(true);
            scrollBox.setYValues(min, curY, max);
            scrollBox.setYVisible(true);
        }
    }
    /*.................................................................................................................*/
    public void setVisible(boolean vis){
        windowResized();
        super.setVisible(vis);
    }
 	/*.................................................................................................................*/
    void setCharter(Charter charter) {
        charter.setShowNames(true);
        chart.setCharter(charter);
    }
    /*.................................................................................................................*/
    String[] getStrings(int index) {
        return new String[] {"X (" + ownerModule.contrastsStatsTask.getParameters() +
                "): " + xArray.toString(index), 
                "Y (" + ownerModule.contrastsStatsTask.getParameters() + 
                "): " + yArray.toString(index)};
    }
    /*.................................................................................................................*/
    void setTree(Tree tree) {
        if (this.tree !=null && this.tree instanceof NoPolyTree && this.tree !=tree) { // about to set new tree
            ((NoPolyTree)this.tree).disconnect();
        }
        if (tree instanceof NoPolyTree){
            this.tree=tree;
        }
        else {
            this.tree = new NoPolyTree((MesquiteTree)tree);
        }
        if (this.tree instanceof Selectionable)
            ownerModule.charterTask.pointsAreSelectable(true, (Selectionable)this.tree, false);
    }
    /*.................................................................................................................*/
    String axisName(String template, ContinuousDistribution obsStates, int screen, boolean xAxis){
        if (obsStates == null)
            return template;
        // X axis of screens 1 2 5 6 7 8 11 don't use characters
        if (xAxis && (screen == 1 || screen == 2 || screen == 5 || screen == 6 || screen == 7 || screen == 8 || screen == 11))
            return template;
        String chName = obsStates.getName();
        if (chName == null)
            return template;
        if (chName.length()>20)
            chName = chName.substring(0, 17) + "...";
        return chName + " (" + template + ")";
    }
    /*.................................................................................................................*/
    public void recalcChart() {
        chart.deassignChart();
        if (ownerModule.contrastsStatsTask != null && ownerModule.residualsTask != null) {
            resetScrolls();
            final int numNodes = tree.getNumNodeSpaces();
            xArray.resetSize(numNodes);
            yArray.resetSize(numNodes);
            //zArray.resetSize(numNodes);
            //if (ownerModule.contrastsStatsTask instanceof Incrementable)
            //	((Incrementable)ownerModule.contrastsStatsTask).setCurrent(ownerModule.currentX); 
            // check for polytomies, set warning
            boolean hasPolytomies;
            if (tree instanceof NoPolyTree)
                hasPolytomies = ((NoPolyTree)tree).hasZLBs();
            else
                hasPolytomies = tree.hasPolytomies(tree.getRoot());
            //x values
            int iChar = ownerModule.currentX;  // actually this is *only* true for bivariate plots (screens 9&10).
            switch (ownerModule.screen){
            case 1:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.SD);
                iChar = ownerModule.currentY;    //currentY is the character specified in the single scroll - both axes are functions of this.
                //Plot of absolute value of contrast vs. standard deviation
                if (hasPolytomies)
                    legend.setMessage(SCREEN1LEGEND + POLYTOMYWARNING);
                else
                    legend.setMessage(SCREEN1LEGEND);                    
                break;
            }
            case 3:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.NODEVALUE);
                iChar = ownerModule.currentY; 
                //Plot of absolute value of contrast vs. estimated value of associated node
                if (hasPolytomies)
                    legend.setMessage(SCREEN3LEGEND + POLYTOMYWARNING);
                else
                    legend.setMessage(SCREEN3LEGEND);
                break;
            }
            case 5:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CORRECTEDHEIGHT);
                iChar = ownerModule.currentY; 
                //Plot of absolute value of contrast vs. height of associated node
                if (hasPolytomies)
                    legend.setMessage(SCREEN5LEGEND + POLYTOMYWARNING);
                else
                    legend.setMessage(SCREEN5LEGEND);
                break;
            }
            case 7:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CORRECTEDHEIGHT);
                iChar = ownerModule.currentY; 
                //Plot of estimated value of associated node vs. its height
                legend.setMessage(SCREEN7LEGEND);
                break;
            }
            case 9:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CONTRAST);
                iChar = ownerModule.currentX;   // character specified in the horizontal scroll 
                //Plot of contrasts vs. positivized contrasts
                legend.setMessage(SCREEN9LEGEND);
                break;
            }
            case 10:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.ABSCONTRAST);
                iChar = ownerModule.currentX;  // character specified in the horizontal scroll
                //Plot of residuals from screen 9 vs. contrast values
                legend.setMessage(SCREEN10LEGEND);
                break;
            }
            case 11:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CORRECTEDHEIGHT);
                iChar = ownerModule.currentX; 
                //Plot of absolute value of residual vs. height of associated node
                legend.setMessage(SCREEN11LEGEND);
                break;
            }
            case 12:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.TIPS);
                iChar = ownerModule.currentX; 
                //Plot of tip values and confidence intervals for reconstructed root values
                legend.setMessage(SCREEN12LEGEND);//Peter: what of this depends on diagnostics being active?
                break;
            }
            case 13:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.TIPS);
                iChar = ownerModule.currentX;  //?
                //"Plot of phylogenetically correct (OLS) regression and associated CI's"   //Peter: what of this depends on diagnostics being active?
                legend.setMessage(SCREEN13LEGEND);  //Peter: what of this depends on diagnostics being active?
            }
            }

            if (true ) { 
                //if one character calculation, don't get character unless needed
                observedStates = (ContinuousDistribution)ownerModule.characterSourceTask.getCharacter(tree, iChar);
            }
            ownerModule.contrastsStatsTask.calculateNumbers(tree, observedStates, xArray, null);  // This does the work for the x-axis
            chart.setXAxisName(axisName(ownerModule.contrastsStatsTask.getParameters(), observedStates, ownerModule.screen, true));   //set to correct name
            String xItem = ownerModule.contrastsStatsTask.getItemName();
            if (ownerModule.contrastsStatsTask instanceof Incrementable)
                ((Incrementable)ownerModule.contrastsStatsTask).setCurrent(ownerModule.currentY);
            //y values
            switch (ownerModule.screen){
            case 1:
            case 3:
            case 5: {
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.ABSCONTRAST);
                break;
            }
            case 7:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.NODEVALUE);
                break;
            }
            case 9:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.CONTRAST);
                break;
            }
            case 10:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.RESIDUAL);
                ownerModule.residualsTask.setOption(0);//raw
                break;
            }
            case 11:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.ABSRESIDUAL);
                ownerModule.residualsTask.setOption(1);//absolute
                break;
            }
            case 12:
            case 13:{
                ownerModule.contrastsStatsTask.setOption(ContrastForChar.TIPS);
                break;
            }
            }
            if (true ) { 
                //if one character calculation, don't get character unless needed  TODO: make this work
                observedStates2 = (ContinuousDistribution)ownerModule.characterSourceTask.getCharacter(tree, ownerModule.currentY);
            }
            switch (ownerModule.screen) {
            case 1:
            case 3:
            case 5:
            case 7:
            case 9: {
                //ownerModule.contrastsStatsTask.setXCharForReport(ownerModule.currentX); 
                //ownerModule.contrastsStatsTask.setYCharForReport(ownerModule.currentY); 
                ownerModule.contrastsStatsTask.calculateNumbers(tree, observedStates2, yArray, null);  // This does the work for the y-axis
                break;
            }
            case 10:
            case 11: {

                ownerModule.residualsTask.calculateNumbers(tree, observedStates, observedStates2, yArray, null);
                break;
            }
            case 12:
            case 13: {
                ownerModule.contrastsStatsTask.setXCharForReport(ownerModule.currentX); 
                ownerModule.contrastsStatsTask.setYCharForReport(ownerModule.currentY); 
                ownerModule.contrastsStatsTask.calculateNumbers(tree, observedStates2, yArray, null);
                break;
            }
            }
            // maybe call it here??

            chart.setYAxisName(axisName(ownerModule.contrastsStatsTask.getParameters(), observedStates2, ownerModule.screen, false));  //TODO: this should use string passed back from calculateNumbers ???
            boolean showTips = false;
            if ((ownerModule.screen == 12) || (ownerModule.screen == 13)) 
                showTips = true;
            else if (ownerModule.screen == 9){
                chart.setXAxisName(axisName("Positivized Contrasts - CAUTION if any values are zero", observedStates, ownerModule.screen, true));   //force to correct name
                chart.setYAxisName(axisName("Contrasts Positivized on the X variable (Garland et al. 1992)", observedStates2, ownerModule.screen, false));
            }
            for (int i=0; i<numNodes; i++) {
                if (tree.nodeInTree(i) && (showTips || tree.nodeIsInternal(i))) { //todo: have toggle for internal only
                    xArray.placeValue(i, resultX);
                    yArray.placeValue(i, resultY);
                    if (ownerModule.screen == 9){ //positivizing for screen 9
                        if (resultX.isNegative()) {
                            resultY.changeSign();
                            resultX.abs();
                        }
                    }
                    //zArray.placeValue(i, resultZ);

                    int point = chart.addPoint(resultX, resultY);
                    //int point = chart.addPoint(resultX, resultY, resultZ);
                    String label = tree.getNodeLabel(i);
                    if (label == null)
                        chart.setName(point, Integer.toString(i));
                    else
                        chart.setName(point, label);
                    //chart.setCategory(point, nodeJustInternal(tree, i));
                }
                else { //these are here to ensure number of points is in parallel with numbering of nodes, for selection and other purposes
                    resultX.setToUnassigned();
                    chart.addPoint(resultX, resultY);
                }
            }
            contentsChanged();
            chart.munch();
            if (ownerModule.diagnosticsTask != null) {
                String s = ownerModule.diagnosticsTask.getLegendText();
                if (!StringUtil.blank(s))
                    legend.appendToMessage("\n\n" + s);
            }
        }
        if (ownerModule.treeDisplay!=null)
            ownerModule.treeDisplay.pleaseUpdate(false);
    }
    /*.................................................................................................................*/
    void pointTouched(Tree tree, int which) {
        if (ownerModule.nsLabeller==null) {
            return;
        }
        //the following looks wrong; which should be the node number directly; no need to search
        int count = 0;
        final Graphics g = ownerModule.treeDisplay.getGraphics();
        if (g!=null) {
            for (int i=0; i<tree.getNumNodeSpaces(); i++) {
                if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) {
                    if (count == which) {
                        ownerModule.nsLabeller.drawOneLabel(i, tree, g);
                    }
                    count++;
                }
            }
            g.dispose();
        }
    }
    /*.................................................................................................................*/
    void pointReleased(Tree tree, int which) {
        if (ownerModule.nsLabeller==null)
            return;
        if (ownerModule.nsLabeller.showLabels)
            return;
        int count = 0;
        final Graphics g = ownerModule.treeDisplay.getGraphics();
        if (g!=null) {
            for (int i=0; i<tree.getNumNodeSpaces(); i++) {
                if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) {
                    if (count == which) {
                        ownerModule.nsLabeller.hideOneLabel(i, g);
                    }
                    count++;
                }
            }
            g.dispose();
        }
        ownerModule.nsLabeller.hideLabels();
    }

    /*............................................................................................................*/
    public void windowResized() {
        if (MesquiteWindow.checkDoomed(this))
            return;
        if (chart!=null && (windowWidth!=getWidth() || windowHeight!=getHeight())) {
            windowWidth=getWidth();
            windowHeight=getHeight();
            if (chart!=null){
                chart.setLocation(0, bannerHeight+20);
                chart.setChartSize(windowWidth-20, windowHeight-20 - bannerHeight);
            }
            if (scrollBox !=null)
                scrollBox.setLocation(2, getHeight()-24- bannerHeight- scrollBox.getBounds().height);
            if (banner !=null)
                banner.setSize(windowWidth-20, bannerHeight);
        }
        MesquiteWindow.uncheckDoomed(this);
    }

    public void dispose(){
        if (tree !=null && tree instanceof NoPolyTree)
            ((NoPolyTree)tree).disconnect();
        super.dispose();
    }
}

/** This defines the legend box for the plot
 */
class PDAPLegend extends ResizableLegend {
    TextArea specsBox;
    private static final int grabHeight = 6;
    private static final int bottomHeight = 4;
    private static final int defaultSpecsHeight = (12 + MesquiteModule.textEdgeCompensationHeight) * 3;
    private static final int defaultLegendWidth=142;
    private static final int defaultLegendHeight=grabHeight + defaultSpecsHeight + 2 + bottomHeight;
    private int specsHeight = defaultSpecsHeight;
    
    public PDAPLegend() {
        super(defaultLegendWidth, defaultLegendHeight);
        setVisible(false);
        setOffsetX(0);
        setOffsetY(0);

        setBackground(Color.white);
        setLayout(null);
        specsBox = new TextArea(" ", 2, 2, TextArea.SCROLLBARS_VERTICAL_ONLY);
        specsBox.setEditable(false);
        add(specsBox);


        setSize(legendWidth,legendHeight);
        specsBox.setVisible(true);
    }

    public void paint(Graphics g) {
        if (MesquiteWindow.checkDoomed(this))
            return;
        g.setColor(Color.cyan);
        g.drawRect(0, 0, legendWidth-1, legendHeight-1);
        g.fillRect(0, 0, legendWidth-1, grabHeight);
        g.fillRect(legendWidth-grabHeight, legendHeight-grabHeight, grabHeight, grabHeight);
        g.setColor(Color.black);

        MesquiteWindow.uncheckDoomed(this);
    }

    void sizeChanged(int w, int h){
        specsHeight  = h - (grabHeight + 2 + bottomHeight);
        specsBox.setBounds(1,grabHeight,w-2, specsHeight);
        legendHeight = h;
        legendWidth = w;

    }

    public void setSize(int w, int h){
        sizeChanged(w, h);
        super.setSize(w, h);
    }
    public void setBounds(int x, int y, int w, int h){
        sizeChanged(w, h);
        super.setBounds(x, y, w, h);
    }
    void setMessage(String s) {
        specsBox.setText(s);
    }
    void appendToMessage(String s) {
        specsBox.setText(specsBox.getText() + s);
    }
}
\ No newline at end of file