public Object getValueAt(int row, int col) { // PartitionData partition = options.getPartitionDataNoSpecies().get(row); PartitionData partition = options.getNonTraitsDataList().get(row); switch (col) { case 0: return partition.getName(); case 1: return partition.getFileName(); case 2: return "" + partition.getTaxaCount(); case 3: return "" + partition.getSiteCount(); // sequence length case 4: return partition.getDataType(); case 5: // return partition.getPloidyType(); // case 6: return partition.getPartitionSubstitutionModel().getName(); case 6: return partition.getPartitionClockModel().getName(); case 7: return partition.getPartitionTreeModel().getName(); default: throw new IllegalArgumentException("unknown column, " + col); } }
public void unlinkTrees() { // reuse previous PartitionTreePrior int[] selRows = dataTable.getSelectedRows(); for (int row : selRows) { PartitionData partition = options.dataPartitions.get(row); PartitionTreeModel model = partition.getPartitionTreeModel(); if (!model.getName().equals(partition.getName()) && partition.getTraitType() == null) { // not a trait PartitionTreeModel newTree = new PartitionTreeModel(options, partition); // this prevents partition not broken, and used for unsharing tree prior only, // because sharing uses shareSameTreePrior, unsharing uses getPartitionTreePrior // newTree.setPartitionTreePrior(newPrior); // important partition.setPartitionTreeModel(newTree); } } options.linkTreePriors(frame.getCurrentPartitionTreePrior()); modelsChanged(); fireDataChanged(); options.taxonSets.clear(); options.taxonSetsMono.clear(); repaint(); }
public void unlinkModels() { int[] selRows = dataTable.getSelectedRows(); for (int row : selRows) { PartitionData partition = options.dataPartitions.get(row); PartitionSubstitutionModel model = partition.getPartitionSubstitutionModel(); if (!model.getName().equals(partition.getName())) { PartitionSubstitutionModel newModel = new PartitionSubstitutionModel(options, partition); partition.setPartitionSubstitutionModel(newModel); } } modelsChanged(); fireDataChanged(); repaint(); }
public void unlinkClocks() { // reuse previous PartitionTreePrior int[] selRows = dataTable.getSelectedRows(); for (int row : selRows) { PartitionData partition = options.dataPartitions.get(row); PartitionClockModel model = partition.getPartitionClockModel(); if (!model.getName().equals(partition.getName())) { PartitionClockModel newModel = new PartitionClockModel(options, partition); partition.setPartitionClockModel(newModel); } } modelsChanged(); fireDataChanged(); repaint(); }
/** * write tree log to file * * @param writer XMLWriter */ public void writeTreeLogToFile(XMLWriter writer) { writer.writeComment("write tree log to file"); if (options.useStarBEAST) { // species // species tree log writer.writeOpenTag( TreeLoggerParser.LOG_TREE, new Attribute[] { new Attribute.Default<String>( XMLParser.ID, TraitData.TRAIT_SPECIES + "." + TREE_FILE_LOG), // speciesTreeFileLog new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, options.logEvery + ""), new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, "true"), new Attribute.Default<String>( TreeLoggerParser.FILE_NAME, options.fileNameStem + "." + options.starBEASTOptions.SPECIES_TREE_FILE_NAME), new Attribute.Default<String>(TreeLoggerParser.SORT_TRANSLATION_TABLE, "true") }); writer.writeIDref(SpeciesTreeModelParser.SPECIES_TREE, SP_TREE); if (options.hasData()) { // we have data... writer.writeIDref("posterior", "posterior"); } writer.writeCloseTag(TreeLoggerParser.LOG_TREE); } // gene tree log // TODO make code consistent to MCMCPanel for (PartitionTreeModel tree : options.getPartitionTreeModels()) { String treeFileName; if (options.substTreeLog) { treeFileName = options.fileNameStem + "." + tree.getPrefix() + "(time)." + STARBEASTOptions.TREE_FILE_NAME; } else { treeFileName = options.fileNameStem + "." + tree.getPrefix() + STARBEASTOptions.TREE_FILE_NAME; // stem.partitionName.tree } if (options.treeFileName.get(0).endsWith(".txt")) { treeFileName += ".txt"; } List<Attribute> attributes = new ArrayList<Attribute>(); attributes.add( new Attribute.Default<String>( XMLParser.ID, tree.getPrefix() + TREE_FILE_LOG)); // partionName.treeFileLog attributes.add( new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, options.logEvery + "")); attributes.add(new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, "true")); attributes.add(new Attribute.Default<String>(TreeLoggerParser.FILE_NAME, treeFileName)); attributes.add( new Attribute.Default<String>(TreeLoggerParser.SORT_TRANSLATION_TABLE, "true")); // if (options.clockModelOptions.getRateOptionClockModel() == FixRateType.RElATIVE_TO && // tree.containsUncorrelatedRelaxClock()) { //TODO: Sibon's discretized branch length stuff // double aveFixedRate = // options.clockModelOptions.getSelectedRate(options.getPartitionClockModels()); // attributes.add(new Attribute.Default<String>(TreeLoggerParser.NORMALISE_MEAN_RATE_TO, // Double.toString(aveFixedRate))); // } // generate <logTree> writer.writeOpenTag(TreeLoggerParser.LOG_TREE, attributes); // writer.writeOpenTag(TreeLoggerParser.LOG_TREE, // new Attribute[]{ // new Attribute.Default<String>(XMLParser.ID, tree.getPrefix() + // TREE_FILE_LOG), // partionName.treeFileLog // new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, // options.logEvery + ""), // new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, // "true"), // new Attribute.Default<String>(TreeLoggerParser.FILE_NAME, // treeFileName), // new // Attribute.Default<String>(TreeLoggerParser.SORT_TRANSLATION_TABLE, "true") // }); writer.writeIDref(TreeModel.TREE_MODEL, tree.getPrefix() + TreeModel.TREE_MODEL); for (PartitionClockModel model : options.getPartitionClockModels(options.getAllPartitionData(tree))) { if (options.getAllPartitionData(model).get(0).getTraitType() == null) { switch (model.getClockType()) { case STRICT_CLOCK: writer.writeIDref( StrictClockBranchRatesParser.STRICT_CLOCK_BRANCH_RATES, model.getPrefix() + BranchRateModel.BRANCH_RATES); break; case UNCORRELATED_EXPONENTIAL: case UNCORRELATED_LOGNORMAL: writer.writeIDref( DiscretizedBranchRatesParser.DISCRETIZED_BRANCH_RATES, options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix()) + BranchRateModel.BRANCH_RATES); break; case RANDOM_LOCAL_CLOCK: writer.writeIDref( RandomLocalClockModelParser.LOCAL_BRANCH_RATES, model.getPrefix() + BranchRateModel.BRANCH_RATES); break; case AUTOCORRELATED_LOGNORMAL: writer.writeIDref( ACLikelihoodParser.AC_LIKELIHOOD, options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix()) + BranchRateModel.BRANCH_RATES); break; default: throw new IllegalArgumentException("Unknown clock model"); } } } if (options.hasData()) { // we have data... writer.writeIDref("posterior", "posterior"); } if (options.hasDiscreteIntegerTraitsExcludeSpecies()) { for (PartitionData partitionData : options.getAllPartitionData( tree)) { // Each TD except Species has one AncestralTreeLikelihood if (partitionData.getTraitType() != null && (!partitionData.getName().equalsIgnoreCase(TraitData.TRAIT_SPECIES.toString()))) writer.writeIDref( AncestralStateTreeLikelihoodParser.RECONSTRUCTING_TREE_LIKELIHOOD, partitionData.getPrefix() + TreeLikelihoodParser.TREE_LIKELIHOOD); } } writer.writeCloseTag(TreeLoggerParser.LOG_TREE); } // end For loop generateInsertionPoint(ComponentGenerator.InsertionPoint.IN_TREES_LOG, writer); if (options.substTreeLog) { if (options.useStarBEAST) { // species // TODO: species sub tree } // gene tree for (PartitionTreeModel tree : options.getPartitionTreeModels()) { // write tree log to file writer.writeOpenTag( TreeLoggerParser.LOG_TREE, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, tree.getPrefix() + SUB_TREE_FILE_LOG), new Attribute.Default<String>(TreeLoggerParser.LOG_EVERY, options.logEvery + ""), new Attribute.Default<String>(TreeLoggerParser.NEXUS_FORMAT, "true"), new Attribute.Default<String>( TreeLoggerParser.FILE_NAME, options.fileNameStem + "." + tree.getPrefix() + "(subst)." + STARBEASTOptions.TREE_FILE_NAME), new Attribute.Default<String>( TreeLoggerParser.BRANCH_LENGTHS, TreeLoggerParser.SUBSTITUTIONS) }); writer.writeIDref(TreeModel.TREE_MODEL, tree.getPrefix() + TreeModel.TREE_MODEL); for (PartitionClockModel model : options.getPartitionClockModels(options.getAllPartitionData(tree))) { if (options.getAllPartitionData(model).get(0).getTraitType() == null) { switch (model.getClockType()) { case STRICT_CLOCK: writer.writeIDref( StrictClockBranchRatesParser.STRICT_CLOCK_BRANCH_RATES, model.getPrefix() + BranchRateModel.BRANCH_RATES); break; case UNCORRELATED_EXPONENTIAL: case UNCORRELATED_LOGNORMAL: writer.writeIDref( DiscretizedBranchRatesParser.DISCRETIZED_BRANCH_RATES, options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix()) + BranchRateModel.BRANCH_RATES); break; case RANDOM_LOCAL_CLOCK: writer.writeIDref( RandomLocalClockModelParser.LOCAL_BRANCH_RATES, model.getPrefix() + BranchRateModel.BRANCH_RATES); break; case AUTOCORRELATED_LOGNORMAL: writer.writeIDref( ACLikelihoodParser.AC_LIKELIHOOD, options.noDuplicatedPrefix(model.getPrefix(), tree.getPrefix()) + BranchRateModel.BRANCH_RATES); break; default: throw new IllegalArgumentException("Unknown clock model"); } } } writer.writeCloseTag(TreeLoggerParser.LOG_TREE); } } generateInsertionPoint(ComponentGenerator.InsertionPoint.AFTER_TREES_LOG, writer); }