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| /* PDAP:PDTREE package for Mesquite copyright 2001-20089 P. Midford & W. MaddisonPDAP: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.FelsContrWithChar;/*~~ */import mesquite.lib.*;import mesquite.lib.characters.*;import mesquite.cont.lib.*;import mesquite.pdap.lib.*;/** ======================================================================== */public class FelsContrWithChar extends ContrastForChar { private int currentItem=0; private ContinuousDistribution observedStates; //private ContinuousDistribution observedStates2; //private MesquiteMenuItemSpec itemItem; private String itemName=null; private Tree lastUsedTree = null; private UnivariateContrastCalculator calculator = null; private long lastTreeVersion=-1; private int componentShown =0; //contrast option constants moved to ContrastForChar to avoid duplication and ensure everyone's on same page /*.................................................................................................................*/ public boolean startJob(String arguments, Object condition, boolean hiredByName) { return true; } /*.................................................................................................................*/ //Peter: I compacted these /** returns current parameters, for logging etc..*/ public String getBriefParameters() { String addendum = ""; if (itemName!=null) addendum = " (" + itemName + ")"; switch (componentShown) { case CONTRAST: return "Standardized contrast" + addendum; case ABSCONTRAST: return "Absolute value of contrast" + addendum; case RAWCONTRAST: return "Raw contrast" + addendum; case SD: return "Square root of branch length sum"; case VPRIME: return "v Prime"; case NODEVALUE: return "Estimated node value" + addendum; case CORRECTEDHEIGHT: return "Corrected Height"; case TIPS: return "Raw tip value" + addendum; case RESIDUAL: return "Residual" + addendum; case ABSRESIDUAL: return "Absolute value of residual" + addendum; case RAWHEIGHT: return "Uncorrected node height" ; } return "Error: unknown contrast request"; } /*.................................................................................................................*/ /** returns current parameters, for logging etc..*/ public String getParameters() { String addendum = ""; if (itemName!=null) addendum = " (" + itemName + ")"; switch (componentShown) { case CONTRAST: return "Standardized contrast" + addendum; case ABSCONTRAST: return "Absolute value of standardized contrast" + addendum; case RAWCONTRAST: return "Raw (uncorrected) contrast" + addendum; case SD: return "Square root of sum of corrected branch lengths"; case VPRIME: return "v Prime"; case NODEVALUE: return "Estimated value of base node" + addendum; case CORRECTEDHEIGHT: return "Corrected height of base node"; case TIPS: return "Observed states of terminal taxa" + addendum; case RESIDUAL: return "Residual" + addendum; case ABSRESIDUAL: return "Absolute value of residual" + addendum; case RAWHEIGHT: return "Uncorrected height of base node"; } return "Error: unknown contrast request"; } /** This is necessary for axis titles on screen 9 to show character names */ public String getItemName(){ if (itemName != null) return itemName; else return ""; } /*.................................................................................................................*/ public Snapshot getSnapshot(MesquiteFile file) { //TODO: allow change in assignTask, etc. Snapshot temp = new Snapshot(); temp.addLine("setItem " + (currentItem)); return temp; } /*.................................................................................................................*/ public Object doCommand(String commandName, String arguments, CommandChecker checker) { if (checker.compare(this.getClass(), "Sets which item (from a multi-item continuous matrix) is used", "[number of item]", commandName, "setItem")) { int ic = MesquiteInteger.fromString(arguments); if (!MesquiteInteger.isCombinable(ic) && observedStates!=null){ int numItems =observedStates.getNumItems(); String[] items = new String[numItems]; for (int i=0; i<items.length; i++){ if (StringUtil.blank(observedStates.getItemName(i))) items[i] = "(unnamed)"; else items[i]= observedStates.getItemName(i); } ic = ListDialog.queryList(containerOfModule(), "Item for contrasts", "Calculate contrasts for item:", MesquiteString.helpString, items, 0); } if (!MesquiteInteger.isCombinable(ic)) return null; if (observedStates !=null && observedStates instanceof ContinuousDistribution) { if ((ic>=0) && (ic<=observedStates.getNumItems()-1)) { currentItem = ic; parametersChanged(); } } } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Felsenstein's Contrasts", null, commandName, "showContrast")) { setOptionWithChangeParameters(CONTRAST); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Absolute Value of Felsenstein's Contrasts", null, commandName, "showAbsContrast")) { setOptionWithChangeParameters(ABSCONTRAST); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Raw Contrasts", null, commandName, "showRawContrast")) { setOptionWithChangeParameters(RAWCONTRAST); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Standard Deviation", null, commandName, "showSD")) { setOptionWithChangeParameters(SD); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to V Prime", null, commandName, "showVPrime")) { setOptionWithChangeParameters(VPRIME); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Estimated Node Values", null, commandName, "showNodeValue")) { setOptionWithChangeParameters(NODEVALUE); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Corrected Height", null, commandName, "showCorrectedHeight")) { setOptionWithChangeParameters(CORRECTEDHEIGHT); } else if (checker.compare(this.getClass(), "Sets the component to be calculated to Raw Height", null, commandName, "showRawHeight")) { setOptionWithChangeParameters(RAWHEIGHT); } else return super.doCommand(commandName, arguments, checker); return null; } /* Peter: Other calls would need to be aware that parametersChanged might be called and hence do other parameter settings first before parametersChanged is called. Wayne: I tried this, but it causes a hang in PDAPDiagnosticChart (try changing the call on line 709 to setOptionWithChangeParameters). Not sure how to proceed.*/ public void setOption(int option){ componentShown = option; //parametersChanged(); } /** @param int specifies the component (contrast related calculation) to be displayed @param CommandRec passed on to parametersChanged */ public void setOptionWithChangeParameters(int option){ componentShown = option; parametersChanged(); } /** stub? */ public void setXCharForReport(int xChar) { } public void setYCharForReport(int yChar) { } /*Wayne: The following is my best guess as to how to protect take control against multiple calls. It seems to fix the problem with duplicate items on the submenu - which was one of the problems Ted noticed - but extra analysis is still being dumped on the text pane. /*Peter: this should be protected against being called more than once -- i.e., menu items should be added only if not yet exist, and should be deleted if !take */ private MesquiteMenuItemSpec showContrastItem = null; private MesquiteMenuItemSpec showAbsContrastItem = null; private MesquiteMenuItemSpec showRawContrastItem = null; private MesquiteMenuItemSpec showSDItem = null; private MesquiteMenuItemSpec showVPrimeItem = null; private MesquiteMenuItemSpec showNodeValueItem = null; private MesquiteMenuItemSpec showCorrectedHeightItem = null; MesquiteSubmenuSpec mss = null; public void takeControl(boolean take){ if (take){ MesquiteCommand itemChoiceCommand = MesquiteModule.makeCommand("setItem", (Commandable)this); if (mss == null) mss = addSubmenu(null, "Contrast Component", null); if (showContrastItem == null) { showContrastItem = addItemToSubmenu(null, mss, "Felsenstein's Contrast", makeCommand("showContrast", this)); showAbsContrastItem = addItemToSubmenu(null, mss, "Absolute Value of Felsenstein's Contrast", makeCommand("showAbsContrast", this)); showRawContrastItem = addItemToSubmenu(null, mss, "Raw (uncorrected) Contrast", makeCommand("showRawContrast", this)); showSDItem = addItemToSubmenu(null, mss, "Standard Deviation", makeCommand("showSD", this)); showVPrimeItem = addItemToSubmenu(null, mss, "Vprime", makeCommand("showVPrime", this)); showNodeValueItem = addItemToSubmenu(null, mss, "Estimated Node Value", makeCommand("showNodeValue", this)); showCorrectedHeightItem = addItemToSubmenu(null, mss, "Corrected Height", makeCommand("showCorrectedHeight", this)); } } else if ((mss != null) && (showContrastItem != null)) { if (showContrastItem != null) { deleteMenuItem(showContrastItem); showContrastItem = null; deleteMenuItem(showAbsContrastItem); showAbsContrastItem = null; deleteMenuItem(showRawContrastItem); showRawContrastItem = null; deleteMenuItem(showSDItem); showSDItem = null; deleteMenuItem(showVPrimeItem); showVPrimeItem = null; deleteMenuItem(showNodeValueItem); showNodeValueItem = null; deleteMenuItem(showCorrectedHeightItem); showCorrectedHeightItem = null; } } } /*.................................................................................................................*/ public void employeeParametersChanged(MesquiteModule employee, MesquiteModule source, Notification notification) { observedStates = null;//to force recalculation super.employeeParametersChanged(module, source, notification); } /** 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){ } // Holds and caches a NoPolyTree expansion of the tree. NoPolyTree localTree; private boolean[] localDeleted; //holds corresponding deletion array /*.................................................................................................................*/ public double[] calculateStandardDeviations(Tree tree) { if (tree == null) return null; if (tree == lastUsedTree && lastTreeVersion == tree.getVersionNumber() && calculator != null) return calculator.getStdDev(); calculator = new UnivariateContrastCalculator(localTree,observedStates); return calculator.stdDevCalculation(); } /*.................................................................................................................*/ public void calculateNumbers(Tree tree, CharacterDistribution charDistribution, NumberArray result, MesquiteString resultString) { observedStates = null; if (result==null || tree == null) return; clearResultAndLastResult(result); if (!(charDistribution instanceof ContinuousDistribution)) return; if (tree instanceof NoPolyTree){ localTree = (NoPolyTree) tree; } else { localTree = new NoPolyTree((MesquiteTree)tree); } observedStates = (ContinuousDistribution)charDistribution; itemName=charDistribution.getName(); lastUsedTree = tree; lastTreeVersion = tree.getVersionNumber(); int root = localTree.getRoot(localDeleted); if (observedStates != null) { calculator = new UnivariateContrastCalculator(localTree,observedStates); if (componentShown == TIPS){ // no need to calculate contrasts, just copy values from x double [] x = calculator.fillTips(root); for (int i=0; i<x.length; i++) { result.setValue(i, x[i]); } } else { switch (componentShown) { case SD: { double [] stdDev = calculator.stdDevCalculation(); for (int i=0; i<stdDev.length; i++) result.setValue(i, stdDev[i]); break; } case CONTRAST: { double [] contrasts = calculator.contrastCalculation(); for (int i=0; i<contrasts.length; i++) result.setValue(i, contrasts[i]); break; } case ABSCONTRAST: { double [] contrasts = calculator.contrastCalculation(); for (int i=0; i<contrasts.length; i++) { if (contrasts[i] < 0) result.setValue(i, -1*contrasts[i]); else result.setValue(i, contrasts[i]); } break; } case RAWCONTRAST: { double [] raw = calculator.rawContrastCalculation(); for (int i=0; i<raw.length; i++) result.setValue(i, raw[i]); break; } case VPRIME: { double [] vPrime = calculator.vPrimeCalculation(); for (int i=0; i<vPrime.length; i++) result.setValue(i, vPrime[i]); break; } case CORRECTEDHEIGHT: case RAWHEIGHT: { double [] height = calculator.heightCalculation(componentShown); // If a node has a reconstructed value, but no contrast, // its value is really a pass through and should not be // used in calculations... for (int i=0; i<height.length; i++) result.setValue(i, height[i]); break; } case NODEVALUE: { double [] x = calculator.nodeValueCalculation(); // If a node has a reconstructed value, but no contrast, // its value is really a pass through and should not be // used in calculations... for (int i=0; i<x.length; i++) { if (localTree.nodeIsInternal(i)) { if (MesquiteDouble.isCombinable(x[i])) { // a value was set, so i specifies a node int left = tree.firstDaughterOfNode(i); int right = tree.lastDaughterOfNode(i); if (MesquiteDouble.isCombinable(x[left]) && MesquiteDouble.isCombinable(x[right])) result.setValue(i, x[i]); } } else result.setValue(i,x[i]); // it's a tip so either it does or it doesn't have a value. } break; } } } } saveLastResult(result); saveLastResultString(resultString); } /*.................................................................................................................*/ public void calculateBiVariateNumbers(Tree tree, ContinuousDistribution charDistribution, ContinuousDistribution charDistribution2, NumberArray result, MesquiteString resultString) { observedStates = null; //observedStates2 = null; if (result==null || tree == null) return; result.deassignArray(); if (!(charDistribution instanceof ContinuousDistribution) || !(charDistribution2 instanceof ContinuousDistribution)) return; if (tree instanceof NoPolyTree) localTree = (NoPolyTree) tree; else localTree = new NoPolyTree((MesquiteTree)tree); observedStates = (ContinuousDistribution)charDistribution; //observedStates2 = (ContinuousDistribution)charDistribution2; itemName=null; lastUsedTree = tree; lastTreeVersion = tree.getVersionNumber(); final int root = localTree.getRoot(); if (observedStates != null) { calculator = new UnivariateContrastCalculator(localTree,observedStates); if (componentShown == TIPS){ // no need to calculate contrasts, just copy values from x final double [] x = calculator.fillTips(root); for (int i=0; i<x.length; i++) { result.setValue(i, x[i]); } } else { switch (componentShown) { case SD: { final double [] stdDev = calculator.stdDevCalculation(); for (int i=0; i<stdDev.length; i++) result.setValue(i, stdDev[i]); break; } case CONTRAST: { final double [] contrasts = calculator.contrastCalculation(); for (int i=0; i<contrasts.length; i++) result.setValue(i, contrasts[i]); break; } case ABSCONTRAST: { final double [] contrasts = calculator.contrastCalculation(); for (int i=0; i<contrasts.length; i++) { if (contrasts[i] < 0) result.setValue(i, -1*contrasts[i]); else result.setValue(i, contrasts[i]); } break; } case RAWCONTRAST: { final double [] raw = calculator.rawContrastCalculation(); for (int i=0; i<raw.length; i++) result.setValue(i, raw[i]); break; } case VPRIME: { final double [] vPrime = calculator.vPrimeCalculation(); for (int i=0; i<vPrime.length; i++) result.setValue(i, vPrime[i]); break; } case CORRECTEDHEIGHT: case RAWHEIGHT: { final double [] height = calculator.heightCalculation(componentShown); // If a node has a reconstructed value, but no contrast, // its value is really a pass through and should not be // used in calculations... for (int i=0; i<height.length; i++) result.setValue(i, height[i]); break; } case NODEVALUE: { final double [] x = calculator.nodeValueCalculation(); // If a node has a reconstructed value, but no contrast, // its value is really a pass through and should not be // used in calculations... for (int i=0; i<x.length; i++) { if (localTree.nodeIsInternal(i)) { if (MesquiteDouble.isCombinable(x[i])) { // a value was set, so i specifies a node int left = tree.firstDaughterOfNode(i); int right = tree.lastDaughterOfNode(i); if (MesquiteDouble.isCombinable(x[left]) && MesquiteDouble.isCombinable(x[right])) result.setValue(i, x[i]); } } else result.setValue(i,x[i]); // it's a tip so either it does or it doesn't have a value. } break; } } } } } /*.................................................................................................................*/ public String getName() { return "PDAP contrast calculations"; } /*.................................................................................................................*/ public String getVersion() { return "1.15"; } /*.................................................................................................................*/ public boolean isPrerelease() { return false; } /** * This module is substantive only because the univariate calculator it uses is a simple java object, not a MesquiteModule, * so the calculator can't be substantive (and be subject to blame), so the blame goes here. * */ public boolean isSubstantive(){ return true; //TODO make the univariatecalculator a module so this can return false } /** returns an explanation of what the module does.*/ public String getExplanation() { return "Calculates Felsenstein's contrasts and other related statistics for continuous-valued characters on a tree."; } /*.................................................................................................................*/ public String getAuthors() { return "Peter E. Midford, Ted Garland Jr., and Wayne P. Maddison"; }} |