/*.................................................................................................................*/ public String getStringForTree(int ic) { if (treesBlock == null) return ""; Tree tree = treesBlock.getTree(ic); if (tree == null) return ""; if (tree.hasPolytomies(tree.getRoot())) return "Yes"; else return "No"; }
/*..........................................ContinuousHistory................*/ private void fillDistribution(Tree tree, int node, ContinuousAdjustable dist) { if (tree.nodeIsTerminal(node)) { int t = tree.taxonNumberOfNode(node); for (int i = 0; i < getNumItems(); i++) dist.setState(t, i, getState(node, i)); } else for (int d = tree.firstDaughterOfNode(node); tree.nodeExists(d); d = tree.nextSisterOfNode(d)) fillDistribution(tree, d, dist); }
/*..........................................ContinuousHistory................*/ public void calcMinMaxStates(Tree tree, int node) { for (int i = 0; i < getNumItems(); i++) { double s = getState(node, i); maxState = MesquiteDouble.maximum(maxState, s); minState = MesquiteDouble.minimum(minState, s); } for (int d = tree.firstDaughterOfNode(node); tree.nodeExists(d); d = tree.nextSisterOfNode(d)) calcMinMaxStates(tree, d); }
/** * Returns a new object indicating the states at the tips (used whether or not History is * reconstruction) */ public CharacterDistribution getStatesAtTips(Tree tree) { if (observedStates != null) return (CharacterDistribution) observedStates.getAdjustableClone(); else { ContinuousAdjustable d = new ContinuousAdjustable(tree.getTaxa(), tree.getTaxa().getNumTaxa()); d.setItemsAs(this); fillDistribution(tree, tree.getRoot(), d); return d; } }
/** * This readjust procedure can be called to readjust the size of storage of states of a character * for nodes. */ public CharacterHistory adjustSize(Tree tree) { if (tree.getNumNodeSpaces() == this.getNumNodes()) return this; else { ContinuousHistory soc = new ContinuousHistory( tree.getTaxa(), tree.getNumNodeSpaces(), (ContinuousData) getParentData()); soc.setItemsAs(this); soc.setParentData(getParentData()); soc.setParentCharacter(getParentCharacter()); ((CharacterStates) soc).setExplanation(getExplanation()); return soc; } }
/*.................................................................................................................*/ public void modifyTree(Tree tree, MesquiteTree modified, RandomBetween rng) { if (tree == null || modified == null) return; if (tree.getTaxa().anySelected()) { // error fixed in 1. 12 int[] terminals = tree.getTerminalTaxa(tree.getRoot()); if (terminals == null) return; int numTerminals = 0; for (int i = 0; i < terminals.length; i++) if (tree.getTaxa().getSelected(terminals[i])) numTerminals++; if (numTerminals > numExcluded) { int[] selTerminals = new int[numTerminals]; int icount = 0; for (int i = 0; i < terminals.length; i++) if (tree.getTaxa().getSelected(terminals[i])) { selTerminals[icount] = terminals[i]; icount++; } terminals = selTerminals; for (int it = 0; it < numExcluded; it++) { int taxon = -1; int count = 0; int ntries = 100000; while (terminals[taxon = rng.randomIntBetween(0, numTerminals - 1)] < 0 && count < ntries) { count++; } if (count >= ntries) discreetAlert( "ERROR: Rarefy tree failed to find taxon to delete in " + ntries + " tries."); else { int nT = modified.nodeOfTaxonNumber(terminals[taxon]); modified.deleteClade(nT, false); terminals[taxon] = -1; } } } else MesquiteMessage.warnUser( "Sorry, the tree could not be rarefied because more taxa are to be excluded than those available"); } else { int numTerminals = tree.numberOfTerminalsInClade(tree.getRoot()); if (numTerminals > numExcluded) { for (int it = 0; it < numExcluded; it++) { int taxon = rng.randomIntBetween(0, numTerminals - it - 1); int nT = modified.getTerminalNode(modified.getRoot(), taxon); modified.deleteClade(nT, false); } } else MesquiteMessage.warnUser( "Sorry, the tree could not be rarefied because more taxa are to be excluded than those available"); } }
/*.................................................................................................................*/ public void calculateNumber( Tree tree1, Tree tree2, MesquiteNumber result, MesquiteString resultString) { if (result == null) return; clearResultAndLastResult(result); if (tree1 == null) return; if (tree2 == null) return; int numTaxa = tree1.getTaxa().getNumTaxa(); double[][] patristic1 = null; patristic1 = p1.calculatePatristic( tree1, numTaxa, patristic1); // for this tree calculate patristic distances (number of nodes separating // terminals; no branch lengths) double[][] patristic2 = null; patristic2 = p2.calculatePatristic( tree2, numTaxa, patristic2); // for this tree calculate patristic distances (number of nodes separating // terminals; no branch lengths) double correl = offDiagonalPMCorrelationFILTERED(patristic1, patristic2); if (isDistance && (MesquiteDouble.isCombinable(correl))) correl = -correl + 1.0; // shifting 1 to -1 to be 0 to 2 to act as distance result.setValue(correl); if (resultString != null) { if (isDistance) resultString.setValue( "Patristic correlation (converted to distance): " + result.toString()); else resultString.setValue("Patristic correlation: " + result.toString()); } saveLastResult(result); saveLastResultString(resultString); }
/*.................................................................................................................*/ public Object doCommand(String commandName, String arguments, CommandChecker checker) { Tree trt = treeDisplay.getTree(); MesquiteTree t = null; if (trt instanceof MesquiteTree) t = (MesquiteTree) trt; if (checker.compare( this.getClass(), "Adjust tool has touched branch", "[branch number][x coordinate touched][y coordinate touched][modifiers]", commandName, "touchedPositionAdjust")) { if (t == null) return null; MesquiteInteger io = new MesquiteInteger(0); int node = MesquiteInteger.fromString(arguments, io); int x = MesquiteInteger.fromString(arguments, io); int y = MesquiteInteger.fromString(arguments, io); String mod = ParseUtil.getRemaining(arguments, io); Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y); originalX = newOnLine.x; originalY = newOnLine.y; // lastX= newOnLine.x; // lastY = newOnLine.y; Graphics g = null; if (GraphicsUtil.useXORMode(null, false)) { g = treeDisplay.getGraphics(); g.setXORMode(Color.white); g.setColor(Color.red); } // double bX = treeDisplay.getTreeDrawing().lineBaseX[node]; // double bY = treeDisplay.getTreeDrawing().lineBaseY[node]; // Math.sqrt((originalY-bY)*(originalY-bY) + (originalX-bX)*(originalX-bX)); lastBL = tree.getBranchLength(node); double shortestAbove = MesquiteDouble.unassigned; for (int daughter = t.firstDaughterOfNode(node); t.nodeExists(daughter); daughter = t.nextSisterOfNode(daughter)) shortestAbove = MesquiteDouble.minimum(shortestAbove, tree.getBranchLength(daughter)); if (shortestAbove == MesquiteDouble.unassigned) upperLimit = MesquiteDouble.infinite; else if (MesquiteDouble.isCombinable(lastBL)) upperLimit = shortestAbove + lastBL; else upperLimit = shortestAbove + 1.0; int ibX = treeDisplay.getTreeDrawing().lineBaseX[node]; int ibY = treeDisplay.getTreeDrawing().lineBaseY[node]; lastX = treeDisplay.getTreeDrawing().lineTipX[node]; lastY = treeDisplay.getTreeDrawing().lineTipY[node]; if (GraphicsUtil.useXORMode(null, false)) { drawThickLine(g, ibX, ibY, lastX, lastY); for (int daughter = t.firstDaughterOfNode(node); t.nodeExists(daughter); daughter = t.nextSisterOfNode(daughter)) drawThickLine( g, treeDisplay.getTreeDrawing().lineTipX[daughter], treeDisplay.getTreeDrawing().lineTipY[daughter], lastX, lastY); g.fillOval( lastX - ovalRadius, lastY - ovalRadius, ovalRadius + ovalRadius, ovalRadius + ovalRadius); try { g.drawString(MesquiteDouble.toString(lastBL), lastX + 10, lastY); } catch (InternalError e) { // workaround for bug on windows java 1.7. } catch (Throwable e) { } lineOn = true; g.dispose(); } } else if (checker.compare( this.getClass(), "Adjust tool has been dropped", "[branch number][x coordinate dropped][y coordinate dropped]", commandName, "droppedPositionAdjust")) { if (t == null) return null; if (editorOn) return null; MesquiteInteger io = new MesquiteInteger(0); int node = MesquiteInteger.fromString(arguments, io); int x = MesquiteInteger.fromString(arguments, io); int y = MesquiteInteger.fromString(arguments, io); if (lineOn) { Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y); double bX = treeDisplay.getTreeDrawing().lineBaseX[node]; double bY = treeDisplay.getTreeDrawing().lineBaseY[node]; double tX = treeDisplay.getTreeDrawing().lineTipX[node]; double tY = treeDisplay.getTreeDrawing().lineTipY[node]; double lengthLine = Math.sqrt((originalY - bY) * (originalY - bY) + (originalX - bX) * (originalX - bX)); double bL; if (lengthLine != 0) { double extension = Math.sqrt( (newOnLine.y - bY) * (newOnLine.y - bY) + (newOnLine.x - bX) * (newOnLine.x - bX)) / lengthLine; if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) bL = extension; else bL = t.getBranchLength(node) * extension; } else bL = 1; if (bL > upperLimit) bL = upperLimit; else if (bL < lowerLimit) bL = lowerLimit; double oldBL = t.getBranchLength(node); if (!MesquiteDouble.isCombinable(oldBL)) oldBL = 1.0; t.setBranchLength(node, bL, false); double difference = oldBL - t.getBranchLength(node); for (int daughter = t.firstDaughterOfNode(node); t.nodeExists(daughter); daughter = t.nextSisterOfNode(daughter)) if (MesquiteDouble.isCombinable(t.getBranchLength(daughter))) t.setBranchLength(daughter, t.getBranchLength(daughter) + difference, false); t.notifyListeners(this, new Notification(MesquiteListener.BRANCHLENGTHS_CHANGED)); Graphics g = treeDisplay.getGraphics(); g.setPaintMode(); g.dispose(); treeDisplay.pleaseUpdate(true); lineOn = false; } } else if (checker.compare( this.getClass(), "Adjust tool is being dragged", "[branch number][x coordinate][y coordinate]", commandName, "draggedPositionAdjust")) { if (t == null) return null; if (editorOn) return null; MesquiteInteger io = new MesquiteInteger(0); int node = MesquiteInteger.fromString(arguments, io); int x = MesquiteInteger.fromString(arguments, io); int y = MesquiteInteger.fromString(arguments, io); if (lineOn) { Point newOnLine = treeDisplay.getTreeDrawing().projectionOnLine(node, x, y); // WARNING": This shouldn't result in length increase if simple click and release with no // drag; must subtract original X, Y Graphics g = null; if (GraphicsUtil.useXORMode(null, false)) { g = treeDisplay.getGraphics(); g.setXORMode(Color.white); g.setColor(Color.red); } // g.fillOval(lastX-ovalRadius, lastY-ovalRadius, ovalRadius + ovalRadius, ovalRadius + // ovalRadius); // g.fillOval(newOnLine.x-ovalRadius, newOnLine.y -ovalRadius, ovalRadius + ovalRadius, // ovalRadius + ovalRadius); // g.drawLine(originalX, originalY, lastX, lastY); // g.drawLine(originalX, originalY, newOnLine.x, newOnLine.y); // if decreasing, & unassigned involved: push unassigned down and assign values to // unassigned above; if increasing, push unassigne up int ibX = treeDisplay.getTreeDrawing().lineBaseX[node]; int ibY = treeDisplay.getTreeDrawing().lineBaseY[node]; int itX = treeDisplay.getTreeDrawing().lineTipX[node]; int itY = treeDisplay.getTreeDrawing().lineTipY[node]; double bX = ibX; double bY = ibY; double tX = itX; double tY = itY; double lengthLine = Math.sqrt((originalY - bY) * (originalY - bY) + (originalX - bX) * (originalX - bX)); if (lengthLine != 0) { if (GraphicsUtil.useXORMode(null, false)) { if (MesquiteTrunk.isMacOSX() && MesquiteTrunk.getJavaVersionAsDouble() >= 1.5 && MesquiteTrunk.getJavaVersionAsDouble() < 1.6) // due to a JVM bug g.fillRect(lastX, lastY - 20, 100, 20); g.drawString(MesquiteDouble.toString(lastBL), lastX + 10, lastY); if (MesquiteTrunk.isMacOSX() && MesquiteTrunk.getJavaVersionAsDouble() >= 1.5 && MesquiteTrunk.getJavaVersionAsDouble() < 1.6) // due to a JVM bug g.fillRect(lastX, lastY - 20, 100, 20); } double extension = Math.sqrt( (newOnLine.y - bY) * (newOnLine.y - bY) + (newOnLine.x - bX) * (newOnLine.x - bX)) / lengthLine; double bL; if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) bL = extension; else bL = t.getBranchLength(node) * extension; if (bL > upperLimit) { bL = upperLimit; if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) extension = upperLimit; else extension = upperLimit / t.getBranchLength(node); } else if (bL < lowerLimit) { bL = lowerLimit; if (t.getBranchLength(node) == 0 || t.branchLengthUnassigned(node)) extension = lowerLimit; else extension = lowerLimit / t.getBranchLength(node); } lastBL = bL; if (GraphicsUtil.useXORMode(null, false)) { drawThickLine(g, ibX, ibY, lastX, lastY); for (int daughter = t.firstDaughterOfNode(node); t.nodeExists(daughter); daughter = t.nextSisterOfNode(daughter)) drawThickLine( g, treeDisplay.getTreeDrawing().lineTipX[daughter], treeDisplay.getTreeDrawing().lineTipY[daughter], lastX, lastY); g.fillOval( lastX - ovalRadius, lastY - ovalRadius, ovalRadius + ovalRadius, ovalRadius + ovalRadius); } int newX = ibX + (int) (extension * (tX - bX)); int newY = ibY + (int) (extension * (tY - bY)); if (GraphicsUtil.useXORMode(null, false)) { g.drawString(MesquiteDouble.toString(bL), newX + 10, newY); drawThickLine(g, ibX, ibY, newX, newY); for (int daughter = t.firstDaughterOfNode(node); t.nodeExists(daughter); daughter = t.nextSisterOfNode(daughter)) drawThickLine( g, treeDisplay.getTreeDrawing().lineTipX[daughter], treeDisplay.getTreeDrawing().lineTipY[daughter], newX, newY); g.fillOval( newX - ovalRadius, newY - ovalRadius, ovalRadius + ovalRadius, ovalRadius + ovalRadius); } lastX = newX; lastY = newY; } // lastX= newOnLine.x; // lastY = newOnLine.y; } } return null; }
/*.................................................................................................................*/ 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; }