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Mesquite_PDAP/src/mesquite/pdap/RootReconstructionCIs/RootReconstructionCIs.java
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/* 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.RootReconstructionCIs;
import mesquite.cont.lib.ContinuousDistribution;
import mesquite.cont.lib.ContinuousStateTest;
import mesquite.lib.CommandChecker;
import mesquite.lib.CompatibilityTest;
import mesquite.lib.EmployeeNeed;
import mesquite.lib.MesquiteDouble;
import mesquite.lib.MesquiteFile;
import mesquite.lib.MesquiteInteger;
import mesquite.lib.MesquiteMessage;
import mesquite.lib.MesquiteModule;
import mesquite.lib.MesquiteNumber;
import mesquite.lib.MesquiteString;
import mesquite.lib.MesquiteSubmenuSpec;
import mesquite.lib.MesquiteTree;
import mesquite.lib.NumberArray;
import mesquite.lib.Snapshot;
import mesquite.lib.StringArray;
import mesquite.lib.StringUtil;
import mesquite.lib.Tree;
import mesquite.lib.characters.CharacterDistribution;
import mesquite.lib.duties.NumberFor2CharAndTree;
import mesquite.pdap.SPRootReconstruction.SPRootReconstruction;
import mesquite.pdap.lib.ContrastForChar;
import mesquite.pdap.lib.NoPolyTree;
import mesquite.pdap.lib.PDAPRootReconStatPak;
public class RootReconstructionCIs extends NumberFor2CharAndTree {
public void getEmployeeNeeds(){ //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed
EmployeeNeed e = registerEmployeeNeed(ContrastForChar.class, getName() + " needs a method to calculate contrasts.",
"The method to write FIC reports is selected initially");
EmployeeNeed e1 = registerEmployeeNeed(SPRootReconstruction.class, getName() + " needs a method to calculate correlations.",
"The method to calculate correlations is selected initially");
}
static final int REPORT_upper_x = 0;
static final int REPORT_lower_x = 1;
static final int REPORT_upper_y = 2;
static final int REPORT_lower_y = 3;
private ContrastForChar contrastsTask;
private SPRootReconstruction statPakTask;
private NumberArray xArray, yArray;
private StringArray modes;
private MesquiteString modeName;
private int reportMode = REPORT_upper_x;
private double ciWidth = 0.95;
private int dfReduce = 0;
private boolean ignoreRootTritomies = false;
public boolean startJob(String arguments, Object condition, boolean hiredByName) {
contrastsTask = (ContrastForChar)hireNamedEmployee(ContrastForChar.class, "#FelsContrWithChar");
if (contrastsTask == null)
return sorry(getName() + " couldn't start because no calculator of Felsenstein's contrasts obtained.");
contrastsTask.setOption(ContrastForChar.CONTRAST);
statPakTask = (SPRootReconstruction)hireNamedEmployee(SPRootReconstruction.class, "#SPRootReconstruction");
if (statPakTask == null)
return sorry(getName() + " couldn't start because no calculator of correlations obtained.");
xArray = new NumberArray(3);
yArray = new NumberArray(3);
modes = new StringArray(4);
modes.setValue(REPORT_upper_x, "upper-CI-X"); //the strings passed will be the menu item labels
modes.setValue(REPORT_lower_x, "lower-CI-X");
modes.setValue(REPORT_upper_y, "upper-CI-Y");
modes.setValue(REPORT_lower_y, "lower-CI-Y");
modeName = new MesquiteString(modes.getValue(reportMode)); //this helps the menu keep track of checkmenuitems
final MesquiteSubmenuSpec mss = addSubmenu(null, "Select CI", makeCommand("setReportMode", this), modes);
mss.setSelected(modeName);
return true; //false if no appropriate employees!
}
public CompatibilityTest getCompatibilityTest(){
return new ContinuousStateTest();
}
public void employeeQuit(MesquiteModule m){
if (m==contrastsTask)
iQuit();
}
public Snapshot getSnapshot(MesquiteFile file) {
final Snapshot temp = new Snapshot();
temp.addLine("setReportMode " + StringUtil.tokenize(modes.getValue(reportMode)));
return temp;
}
public Object doCommand(String commandName, String arguments, CommandChecker checker) {
final Class thisClass = getClass();
if (checker.compare(thisClass, "Sets the report mode", "[One of 'upper-CI-X','lower-CI-X', 'upper-CI-Y', 'lower-CI-Y']", commandName, "setReportMode")) {
final String name = parser.getFirstToken(arguments); //get argument passed of option chosen
int newMode = modes.indexOf(name); //see if the option is recognized by its name
if (newMode >=0 && newMode!=reportMode){
reportMode = newMode; //change mode
modeName.setValue(modes.getValue(reportMode)); //so that menu item knows to become checked
parametersChanged(); //this tells employer module that things changed, and recalculation should be requested
}
}
else if (checker.compare(thisClass,"Sets the CI width", "[double]",commandName, "setWidth")) {
final double w1 = MesquiteDouble.fromString(arguments);
if (!MesquiteDouble.isCombinable(w1)) //not a menu command..
MesquiteMessage.warnProgrammer("setWidth invoked without parameter");
else
ciWidth = w1;
}
else if (checker.compare(thisClass,"Sets the degrees of freedom adjustment", "[integer]",commandName, "setDFReduction")){
final int dfr = MesquiteInteger.fromString(arguments);
if (!MesquiteInteger.isCombinable(dfr))
MesquiteMessage.warnProgrammer("setDFReduction invoked without parameter");
else
dfReduce = dfr;
}
else if (checker.compare(thisClass,"Sets whether to ignore a tritomy at the root ", "[boolean]",commandName, "toggleIgnoreRootTritomies")){
if (StringUtil.blank(arguments)) //not a menu command..
MesquiteMessage.warnProgrammer("toggleIgnoreRootTritomies invoked without parameter");
else{
final 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;
}
/** Called to provoke any necessary initialization. This helps prevent the module's intialization queries to the user from
happening at inopportune times (e.g., while a long chart calculation is in mid-progress)*/
public void initialize(Tree tree, CharacterDistribution charStatesX, CharacterDistribution charStatesY){
}
public void calculateNumber(Tree tree, CharacterDistribution charStatesX, CharacterDistribution charStatesY, MesquiteNumber result, MesquiteString resultString) {
if (result==null)
return;
clearResultAndLastResult(result);
if (tree==null || charStatesX ==null || charStatesY ==null) {
if (resultString!=null)
resultString.setValue("Root reconstruction confidence interval can't be calculated because tree or characters not supplied");
}
else if (!(charStatesX instanceof ContinuousDistribution) || !(charStatesY instanceof ContinuousDistribution)) {
if (resultString!=null)
resultString.setValue("Root reconstruction confidence interval can't be calculated because characters supplied aren't continuous");
}
else {
final int numNodes = tree.getNumNodeSpaces();
xArray.resetSize(numNodes);
yArray.resetSize(numNodes);
MesquiteNumber resultX = new MesquiteNumber();
MesquiteNumber resultY = new MesquiteNumber();
contrastsTask.calculateNumbers(tree, charStatesX, xArray, null);
contrastsTask.calculateNumbers(tree, charStatesY, yArray, null);
for (int i=0; i<numNodes; i++) {
if (tree.nodeInTree(i) && tree.nodeIsInternal(i)) { //todo: have toggle for internal only
xArray.placeValue(i, resultX);
yArray.placeValue(i, resultY);
if (resultX.isNegative()) {
resultY.changeSign();
resultX.abs();
xArray.setValue(i, resultX);
yArray.setValue(i, resultY);
}
}
}
NoPolyTree localTree;
if (tree instanceof NoPolyTree){
localTree = (NoPolyTree) tree;
}
else {
localTree = new NoPolyTree((MesquiteTree)tree);
}
final PDAPRootReconStatPak myStats = (PDAPRootReconStatPak)statPakTask.getStatPak();
myStats.setDFReduction(dfReduce);
myStats.setTree(localTree);
myStats.setObserved1((ContinuousDistribution) charStatesX);
myStats.setObserved2((ContinuousDistribution) charStatesY);
myStats.setWidth1(ciWidth);
myStats.setIgnoreRootTritomies(ignoreRootTritomies);
myStats.doCalculations(xArray, yArray, null);
if (reportMode == REPORT_upper_x){
result.setValue((myStats.getMean(0)+myStats.getRootCI(0)));
resultString.setValue("Root reconstruction x upper CI: " + result);
}
else if (reportMode == REPORT_lower_x){
result.setValue((myStats.getMean(0)-myStats.getRootCI(0)));
resultString.setValue("Root reconstruction x upper CI: " + result);
}
else if (reportMode == REPORT_upper_y){
result.setValue((myStats.getMean(1)+myStats.getRootCI(1)));
resultString.setValue("Root reconstruction y upper CI: " + result);
}
else if (reportMode == REPORT_lower_y){
result.setValue((myStats.getMean(1)-myStats.getRootCI(1)));
resultString.setValue("Root reconstruction y upper CI: " + result);
}
}
saveLastResult(result);
saveLastResultString(resultString);
}
/*.................................................................................................................*/
public String getParameters(){
return "Root Reconstruction Confidence Interval, reporting " + modeName.getValue();
}
/*.................................................................................................................*/
public String getName() {
return "Root Reconstruction CI";
}
/*.................................................................................................................*/
/** Returns the name of the module in very short form. For use for column headings and other constrained places. Unless overridden returns getName()*/
public String getVeryShortName(){
return "Correlation";
}
/*.................................................................................................................*/
public String getVersion() {
return "1.15";
}
/*.................................................................................................................*/
public boolean isPrerelease() {
return false;
}
}