/*.................................................................................................................*/ public void processSingleXMLPreference(String tag, String content) { if ("bootStrapReps".equalsIgnoreCase(tag)) bootstrapreps = MesquiteInteger.fromString(content); if ("mxram".equalsIgnoreCase(tag)) mxram = MesquiteInteger.fromString(content); if ("convertGapsToMissing".equalsIgnoreCase(tag)) convertGapsToMissing = MesquiteBoolean.fromTrueFalseString(content); if ("resamplingAllConsensusTrees".equalsIgnoreCase(tag)) resamplingAllConsensusTrees = MesquiteBoolean.fromTrueFalseString(content); if ("harvestOnlyStrictConsensus".equalsIgnoreCase(tag)) harvestOnlyStrictConsensus = MesquiteBoolean.fromTrueFalseString(content); if ("searchStyle".equalsIgnoreCase(tag)) searchStyle = MesquiteInteger.fromString(content); if ("searchArguments".equalsIgnoreCase(tag)) searchArguments = StringUtil.cleanXMLEscapeCharacters(content); if ("bootstrapSearchArguments".equalsIgnoreCase(tag)) bootstrapSearchArguments = StringUtil.cleanXMLEscapeCharacters(content); if ("otherOptions".equalsIgnoreCase(tag)) otherOptions = StringUtil.cleanXMLEscapeCharacters(content); // parallel, etc. preferencesSet = true; }
/*.................................................................................................................*/ public Tree retrieveTreeBlock(TreeVector treeList, MesquiteDouble finalScore) { logln("Preparing to receive TNT trees."); boolean success = false; taxa = treeList.getTaxa(); // TODO finalScore.setValue(finalValue); suppressProjectPanelReset(); CommandRecord oldCR = MesquiteThread.getCurrentCommandRecord(); CommandRecord scr = new CommandRecord(true); MesquiteThread.setCurrentCommandRecord(scr); // define file paths and set tree files as needed. setFileNames(); String[] outputFilePaths = externalProcRunner.getOutputFilePaths(); String treeFilePath = outputFilePaths[OUT_TREEFILE]; taxonNumberTranslation = getTaxonNumberTranslation(taxa); namer.setNumberTranslationTable(taxonNumberTranslation); runFilesAvailable(); // read in the tree files success = false; Tree t = null; MesquiteBoolean readSuccess = new MesquiteBoolean(false); // TreeVector tv = new TreeVector(taxa); if (bootstrapOrJackknife()) { if (resamplingAllConsensusTrees) t = ZephyrUtil.readTNTTreeFile( this, treeList, taxa, treeFilePath, "TNT " + getResamplingKindName() + " Rep", 0, readSuccess, false, false, null, namer); // set first tree number as 0 as will remove the first one later. else t = ZephyrUtil.readTNTTreeFile( this, treeList, taxa, treeFilePath, "TNT " + getResamplingKindName() + " Majority Rule Tree", 1, readSuccess, false, false, freqRef, namer); } else t = ZephyrUtil.readTNTTreeFile( this, treeList, taxa, treeFilePath, "TNTTree", 1, readSuccess, false, harvestOnlyStrictConsensus, null, namer); success = t != null; if (success && bootstrapOrJackknife() && resamplingAllConsensusTrees) { t = t.cloneTree(); treeList.removeElementAt(0, false); // get rid of first one as this is the bootstrap tree } MesquiteThread.setCurrentCommandRecord(oldCR); success = readSuccess.getValue(); if (!success) { logln("Execution of TNT unsuccessful [2]"); if (!beanWritten) postBean("unsuccessful [2]", false); beanWritten = true; } else { if (!beanWritten) postBean("successful", false); beanWritten = true; } desuppressProjectPanelReset(); if (data != null) data.decrementEditInhibition(); // manager.deleteElement(tv); // get rid of temporary tree block externalProcRunner.finalCleanup(); if (success) return t; return null; }