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| /* PDAP:PDTREE package for Mesquite copyright 2001-2009 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.RootReconstructions;/* ~~ */import mesquite.lib.*;import mesquite.lib.characters.*;import mesquite.cont.lib.*;import mesquite.pdap.SPRootReconstruction.SPRootReconstruction;import mesquite.pdap.lib.*;/* ======================================================================== */public class RootReconstructions extends RootRegressionCalculator { public void getEmployeeNeeds(){ //This gets called on startup to harvest information; override this and inside, call registerEmployeeNeed EmployeeNeed e = registerEmployeeNeed(SPRootReconstruction.class, getName() + " needs a method to calculate correlations.", "The method to calculate correlations is selected initially"); } private TreeReference lastTreeReference; private SPRootReconstruction sps; private PDAPRootReconStatPak myStats = null; private MesquiteChart chart; private PDAPTreeWinAsstC chartModule = null; /* ................................................................................................................. */ public boolean startJob(String arguments, Object condition, boolean hiredByName) { loadPreferences(); // verboseQueryMode.setValue(false); lastTreeReference = null; addMenuItem("Root Calculation Query Mode...", makeCommand("setVerboseQueryMode", (Commandable) this)); addMenuItem("Set CI/PI width...", makeCommand("setwidth",(Commandable) this)); addMenuItem("Set Polytomy DF Reduction...", makeCommand("setDFReduction", (Commandable) this)); addMenuItem("Ignore Root Tritomies...", makeCommand("setIgnoreRootTritomies", (Commandable)this)); sps = (SPRootReconstruction) hireNamedEmployee(SPRootReconstruction.class, "#SPRootReconstruction"); if (sps == null) return sorry(getName() + " couldn't start because no calculator of correlation obtained."); return true; } /*-----------------------------------------*/ public Snapshot getSnapshot(MesquiteFile file) { final Snapshot temp = new Snapshot(); if (myStats == null || !MesquiteDouble.isCombinable(myStats.getWidth1())) temp.addLine("setwidth1 0.95"); else temp.addLine("setwidth1 " + myStats.getWidth1()); if (myStats == null || !MesquiteDouble.isCombinable(myStats.getWidth2())) temp.addLine("setwidth2 0.90"); else temp.addLine("setwidth2 " + myStats.getWidth2()); if (myStats == null || !MesquiteDouble.isCombinable(myStats.getDFReduction())) temp.addLine("setDFReduction 0"); else temp.addLine("setDFReduction " + myStats.getDFReduction()); return temp; } /*-----------------------------------------*/ final MesquiteInteger zeroPos = new MesquiteInteger(0); /** */ public Object doCommand(String commandName, String arguments, CommandChecker checker) { final Class thisClass = getClass(); if (checker.compare(thisClass,"Sets the first width for the confidence and prediction intervals","[a confidence width e.g., 0.95]", commandName,"setwidth1")) { if (myStats == null) myStats = (PDAPRootReconStatPak)sps.getStatPak(); double newWidth = MesquiteDouble.fromString(arguments, zeroPos); if (!MesquiteDouble.isCombinable(newWidth)){ chartModule.queryWidths(); newWidth = chartModule.getWidth1(); } myStats.setWidth1(newWidth); if (chartModule != null) chartModule.setWidthQueryDone(true); parametersChanged(); } else if (checker.compare(thisClass,"Sets the second width for the confidence and prediction intervals","[a confidence width e.g., 0.90]", commandName,"setwidth2")) { if (myStats == null) myStats = (PDAPRootReconStatPak)sps.getStatPak(); double newWidth = MesquiteDouble.fromString(arguments, zeroPos); if (!MesquiteDouble.isCombinable(newWidth)){ chartModule.queryWidths(); newWidth = chartModule.getWidth2(); } myStats.setWidth2(newWidth); if (chartModule != null) chartModule.setWidthQueryDone(true); parametersChanged(); } else if (checker.compare(thisClass,"Sets both widths for the confidence and prediction intervals","[two confidence widths e.g., 0.95 0.90]", commandName,"setwidth")) { if (myStats == null) myStats = (PDAPRootReconStatPak)sps.getStatPak(); double newWidth1 = MesquiteDouble.fromString(arguments, zeroPos); MesquiteInteger pos2 = null; double newWidth2 = MesquiteDouble.unassigned; if (MesquiteDouble.isCombinable(newWidth1)) { pos2 = new MesquiteInteger(arguments.indexOf(' ', 0)); if (pos2.getValue() > 0) newWidth2 = MesquiteDouble.fromString(arguments, pos2); } if (!MesquiteDouble.isCombinable(newWidth1) || !MesquiteDouble.isCombinable(newWidth2)){ chartModule.queryWidths(); newWidth1 = chartModule.getWidth1(); newWidth2 = chartModule.getWidth2(); } myStats.setWidth1(newWidth1); myStats.setWidth2(newWidth2); if (chartModule != null) chartModule.setWidthQueryDone(true); parametersChanged(); } else if (checker.compare(thisClass,"Sets the number of DF's reduced because of polytomies","[number of dof]", commandName, "setDFReduction")) { if (myStats == null) myStats = (PDAPRootReconStatPak)sps.getStatPak(); int dfReduction = MesquiteInteger.fromFirstToken(arguments, zeroPos); if (chartModule != null){ if (!MesquiteInteger.isCombinable(dfReduction)) chartModule.queryDFReduce(myStats, true); else chartModule.setDFReduction(dfReduction); chartModule.setDFQueryDone(true); myStats.setDFReduction(chartModule.getDFReduction()); } else if (MesquiteInteger.isCombinable(dfReduction)) myStats.setDFReduction(dfReduction); parametersChanged(); } else if (checker.compare(thisClass,"Sets the query mode to verbose or not", "[on/off]",commandName, "setVerboseQueryMode")) { if (chartModule != null) if (StringUtil.blank(arguments)) chartModule.queryVerboseQueryMode(); else chartModule.toggleVerboseQueryMode(parser.getFirstToken(arguments)); } else if (checker.compare(thisClass,"Sets whether to ignore a tritomy at the root ", "[boolean]",commandName, "setIgnoreRootTritomies")){ if (StringUtil.blank(arguments)) chartModule.queryIgnoreRootTritomies(); else{ chartModule.setIgnoreRootTritomies("on".equalsIgnoreCase(parser.getFirstToken(arguments))); } myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); } else return super.doCommand(commandName, arguments, checker); return null; } /*-----------------------------------------*/ public void setChartModule(PDAPTreeWinAsstC module) { chartModule = module; myStats = (PDAPRootReconStatPak)sps.getStatPak(); updateStats(); } /** * Simply returns the statPak so the charter can access the slope and other * interesting results. */ public PDAPRootStatPak getStatPak() { if (chartModule == null){ MesquiteMessage.warnProgrammer("No chartModule set for "+this); return null; } if (myStats == null){ myStats = (PDAPRootReconStatPak)sps.getStatPak(); updateStats(); } return myStats; } private void updateStats(){ myStats.setDFReduction(chartModule.getDFReduction()); myStats.setWidth1(chartModule.getWidth1()); myStats.setWidth2(chartModule.getWidth2()); myStats.setIgnoreRootTritomies(chartModule.getIgnoreRootTritomies()); } /*-----------------------------------------*/ public void setChart(MesquiteChart chart) { this.chart = chart; } /* ................................................................................................................. */ /** * */ public void calculateNumbers(Tree tree, CharacterDistribution charDistribution1, CharacterDistribution charDistribution2, NumberArray result, MesquiteString resultString) { ContinuousDistribution observedStates1 = null; ContinuousDistribution observedStates2 = null; if (result == null || tree == null) return; if (!(charDistribution1 instanceof ContinuousDistribution) || !(charDistribution2 instanceof ContinuousDistribution)) return; clearResultAndLastResult(result); result.zeroArray(); int root = tree.getRoot(); observedStates1 = (ContinuousDistribution) charDistribution1; observedStates2 = (ContinuousDistribution) charDistribution2; // Peter: tighter restrictions; any change will provoke query or reset if ((lastTreeReference == null) || (tree instanceof MesquiteTree && !((MesquiteTree) tree).sameTreeVersions(lastTreeReference, true, true))) { // first create and initialize the new rootStatPak if (myStats == null){ myStats = (PDAPRootReconStatPak)sps.getStatPak(); if (!MesquiteThread.isScripting()){ updateStats(); chartModule.setDFQueryDone(true); } else{ MesquiteMessage.warnUser("Setting df and confidence intervals to defaults"); } } else if (!MesquiteThread.isScripting()){ updateStats(); chartModule.setDFQueryDone(true); } // otherwise myStats exists and the widths and df corrections should already have been set // now set the tree so doCalculations will do the right thing... myStats.setTree(tree); myStats.countInternalNodes(tree, root); // count the internal nodes, // to set number int zlb = ((NoPolyTree)tree).countZLBs(myStats.getIgnoreRootTritomies()); // Zero-Length-Branches are what // PDAP calls "polytomies"; count to // inform the user // now ask the user to set df Reductions if (!MesquiteThread.isScripting()){ if (!chartModule.getDFQueryDone() && (zlb > 0 || chartModule.getVerboseQueryMode())){ chartModule.queryDFReduce(myStats, true); myStats.setDFReduction(chartModule.getDFReduction()); chartModule.setDFQueryDone(true); } if (chartModule.getVerboseQueryMode() && !chartModule.getWidthQueryDone()){ chartModule.queryWidths(); myStats.setWidth1(chartModule.getWidth1()); myStats.setWidth2(chartModule.getWidth2()); chartModule.setWidthQueryDone(true); } } } lastTreeReference = ((MesquiteTree) tree).getTreeReference(lastTreeReference); if ((observedStates1 != null) || (observedStates2 != null)) { NumberArray xArray = new NumberArray(); NumberArray yArray = new NumberArray(); myStats.setObserved1(observedStates1); myStats.setObserved2(observedStates2); boolean munch = myStats.doCalculations(xArray, yArray, chart); if (resultString == null) MesquiteMessage.warnProgrammer("RootReconstructions should NOT be called with an empty result string - uncontrolled recursion may occur"); else { if (munch) resultString.setValue("Needs remunching"); else resultString.setValue("Reconstructed Root Values"); } } saveLastResult(result); saveLastResultString(resultString); } /* ................................................................................................................. */ /*.................................................................................................................*/ public Class getCharacterClass() { return ContinuousState.class; } /*.................................................................................................................*/ public CompatibilityTest getCompatibilityTest() { return new ContinuousStateTest(); } /** returns current parameters, for logging etc..*/ /*.................................................................................................................*/ public String getParameters() { return "Reconstructed root stats"; } /*.................................................................................................................*/ public String getAuthors() { return "Peter E. Midford, Ted Garland Jr., and Wayne P. Maddison"; } /*.................................................................................................................*/ public String getVersion() { return "1.15"; } /*.................................................................................................................*/ public boolean isPrerelease() { return false; } /*.................................................................................................................*/ public String getName() { return "Reconstructed Root Value"; } /*.................................................................................................................*/ public String getExplanation() { return "Calculates statistics related to a reconstruction of the character at the root."; }} |