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TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage
disequilibrium.
/*
* TASSEL - Trait Analysis by a aSSociation Evolution & Linkage
* Copyright (C) 2003 Ed Buckler
*
* This software evaluates linkage disequilibrium nucletide diversity and
* associations. For more information visit http://www.maizegenetics.net
*
* This software is distributed under GNU general public license and without
* any warranty ot technical support.
*
* You can redistribute and/or modify it under the terms of GNU General
* public license.
*
*/
package net.maizegenetics.tassel;
import net.maizegenetics.analysis.association.EqtlAssociationPlugin;
import net.maizegenetics.analysis.association.FixedEffectLMPlugin;
import net.maizegenetics.analysis.association.MLMPlugin;
import net.maizegenetics.analysis.data.GenotypeSummaryPlugin;
import net.maizegenetics.analysis.popgen.LinkageDisequilibriumPlugin;
import net.maizegenetics.analysis.popgen.SequenceDiversityPlugin;
import net.maizegenetics.dna.map.Chromosome;
import net.maizegenetics.dna.map.PositionList;
import net.maizegenetics.dna.map.TOPMInterface;
import net.maizegenetics.dna.snp.FilterList;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.dna.snp.NucleotideAlignmentConstants;
import net.maizegenetics.gui.GenotypeTableMask;
import net.maizegenetics.phenotype.Phenotype;
import net.maizegenetics.plugindef.DataSet;
import net.maizegenetics.plugindef.Datum;
import net.maizegenetics.plugindef.Plugin;
import net.maizegenetics.plugindef.PluginEvent;
import net.maizegenetics.plugindef.PluginListener;
import net.maizegenetics.taxa.IdentifierSynonymizer;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.distance.DistanceMatrix;
import net.maizegenetics.taxa.tree.SimpleTree;
import net.maizegenetics.taxa.tree.Tree;
import net.maizegenetics.util.GeneralAnnotation;
import net.maizegenetics.util.HDF5TableReport;
import net.maizegenetics.util.TableReport;
import org.apache.log4j.Logger;
import javax.swing.*;
import javax.swing.event.TreeModelEvent;
import javax.swing.event.TreeSelectionEvent;
import javax.swing.event.TreeSelectionListener;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeCellRenderer;
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.MutableTreeNode;
import javax.swing.tree.TreeNode;
import javax.swing.tree.TreePath;
import javax.swing.tree.TreeSelectionModel;
import java.awt.*;
import java.awt.event.KeyAdapter;
import java.awt.event.KeyEvent;
import java.io.Serializable;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
public class DataTreePanel extends JPanel implements PluginListener {
private static final Logger myLogger = Logger.getLogger(DataTreePanel.class);
public static final String NODE_TYPE_DATA = "Data";
public static final String NODE_TYPE_RESULT = "Result";
public static final String NODE_TYPE_SEQUENCE = "Sequence";
public static final String NODE_TYPE_POLYMORPHISMS = "Polymorphisms";
public static final String NODE_TYPE_NUMERICAL = "Numerical";
public static final String NODE_TYPE_HDF5_SCHEMA = "HDF5 Schema";
public static final String NODE_TYPE_MATRIX = "Matrix";
public static final String NODE_TYPE_TREE = "Tree";
public static final String NODE_TYPE_LISTS = "Lists";
public static final String NODE_TYPE_FILTERS = "Filters";
public static final String NODE_TYPE_FUSIONS = "Fusions";
public static final String NODE_TYPE_SYNONYMS = "Synonyms";
public static final String NODE_TYPE_DIVERSITY = "Diversity";
public static final String NODE_TYPE_SNP_ASSAYS = "SNP Assays";
public static final String NODE_TYPE_LD = "LD";
public static final String NODE_TYPE_ASSOCIATIONS = "Association";
public static final String NODE_TYPE_VARIANCES = "Variances";
public static final String NODE_TYPE_SYNONYMIZER = "Synonymizer";
public static final String NODE_TYPE_STEPWISE = "Stepwise";
public static final String NODE_TYPE_TOPM = "TOPM";
public static final String NODE_TYPE_GENO_SUMMARY = "Genotype Summary";
public static final String NODE_TYPE_DEFAULT = NODE_TYPE_DATA;
private static final List NODE_TYPE_DATA_CHILDREN = new ArrayList<>();
static {
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_SEQUENCE);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_POLYMORPHISMS);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_NUMERICAL);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_HDF5_SCHEMA);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_MATRIX);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_TREE);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_FUSIONS);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_TOPM);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_LISTS);
NODE_TYPE_DATA_CHILDREN.add(NODE_TYPE_FILTERS);
}
//Possible line styles...
//"Angled", "Horizontal", and "None" (the default).
private String myLineStyle = "Angled";
private JTree myTree;
private DefaultTreeModel myTreeModel;
private TASSELMainFrame myTASSELMainFrame;
private HashMap myNodeHash = new HashMap<>();
private LinkedHashMap myDataSetList = new LinkedHashMap();
private Datum myLastBookSelected;
private DefaultMutableTreeNode myTopNode;
private DefaultMutableTreeNode myDataNode;
private DefaultMutableTreeNode myResultNode;
private DefaultMutableTreeNode myLastNode = null;
private TreeSelectionListener myTreeSelectionListener = null;
public DataTreePanel(TASSELMainFrame theQAF) {
super();
myTASSELMainFrame = theQAF;
myTopNode = new DefaultMutableTreeNode("top");
createNodes();
myTreeModel = new DefaultTreeModel(myTopNode);
myTree = new JTree(myTreeModel);
myTree.setRootVisible(false);
myTree.setEditable(true);
myTreeModel.addTreeModelListener(new MyTreeModelListener(this));
myTree.getSelectionModel().setSelectionMode(TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION);
myTree.setLargeModel(true);
//Listen for when the selection changes.
initSelectionListener();
initKeyStrokeListener();
myTree.putClientProperty("JTree.lineStyle", myLineStyle);
myTree.setCellRenderer(new DefaultTreeCellRenderer() {
public Component getTreeCellRendererComponent(JTree pTree,
Object pValue, boolean pIsSelected, boolean pIsExpanded,
boolean pIsLeaf, int pRow, boolean pHasFocus) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode) pValue;
Datum nodeInfo = (Datum) node.getUserObject();
Component result = super.getTreeCellRendererComponent(pTree, pValue, pIsSelected,
pIsExpanded, pIsLeaf, pRow, pHasFocus);
Object data = nodeInfo.getData();
if (data instanceof GenotypeTableMask) {
result.setForeground(((GenotypeTableMask) nodeInfo.getData()).getColor());
}
return result;
}
});
try {
jbInit();
} catch (Exception e) {
e.printStackTrace();
}
}
public DataTreePanel getThis() {
return this;
}
private void processMyKeyStroke(KeyEvent e) {
// only respond if the KeyEvent is a key released event.
if (e.getID() == KeyEvent.KEY_RELEASED) {
if (KeyEvent.VK_DELETE == e.getKeyCode()) {
TreePath[] currentSelection = myTree.getSelectionPaths();
String pluralQuestion = "Are you sure you want to delete these " + currentSelection.length + " nodes?";
String question = "Are you sure you want to delete this node?";
if (currentSelection.length > 1) {
question = pluralQuestion;
}
int userResponse = JOptionPane.showOptionDialog(myTASSELMainFrame, question, "Node Deletion",
JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, null, null, null);
if (userResponse == JOptionPane.YES_OPTION) {
deleteSelectedNodes();
}
}
}
}
private void initKeyStrokeListener() {
myTree.addKeyListener(new KeyAdapter() {
/**
* Invoked when a key has been released.
*/
public void keyReleased(KeyEvent e) {
super.keyReleased(e);
processMyKeyStroke(e);
}
});
}
private void initSelectionListener() {
myTreeSelectionListener = (new TreeSelectionListener() {
@Override
public void valueChanged(TreeSelectionEvent e) {
try {
DefaultMutableTreeNode node = null;
if ((e != null) && (e.getSource() instanceof DefaultMutableTreeNode)) {
node = (DefaultMutableTreeNode) e.getSource();
} else {
node = (DefaultMutableTreeNode) myTree.getLastSelectedPathComponent();
}
if (node == null) {
return;
}
if (myLastNode == node) {
return;
}
myLastNode = node;
Object nodeInfo = node.getUserObject();
myLastBookSelected = (Datum) nodeInfo;
Datum book = (Datum) nodeInfo;
myLogger.info("initSelectionListener: node type: " + book.getDataType());
StringBuilder builder = new StringBuilder();
if (book.getData() instanceof GenotypeTable) {
GenotypeTable a = (GenotypeTable) book.getData();
builder.append("Number of taxa: ");
builder.append(a.numberOfTaxa());
builder.append("\n");
builder.append("Number of sites: ");
builder.append(a.numberOfSites());
builder.append("\n");
Chromosome[] loci = a.chromosomes();
PositionList positions = null;
boolean first = true;
int numLoci = 0;
if (loci != null) {
numLoci = loci.length;
positions = a.positions();
}
for (int i = 0; i < numLoci; i++) {
String name = loci[i].getName();
if ((name == null) || (name.length() == 0)) {
continue;
}
if (first) {
builder.append("\nChromosomes...\n\n");
first = false;
}
builder.append(name);
int[] firstLast = a.firstLastSiteOfChromosome(loci[i]);
builder.append(": ");
builder.append(firstLast[1] - firstLast[0] + 1);
builder.append(" sites:\n");
builder.append(firstLast[0]);
builder.append(" (");
builder.append(positions.get(firstLast[0]).getPosition());
builder.append(") - ");
builder.append(firstLast[1]);
builder.append(" (");
builder.append(positions.get(firstLast[1]).getPosition());
builder.append(")");
builder.append("\n\n");
}
}
if (book.getData() instanceof GenotypeTable) {
try {
GenotypeTable a = (GenotypeTable) book.getData();
if ((a.hasGenotype()) && (NucleotideAlignmentConstants.isNucleotideEncodings(a.alleleDefinitions()))) {
builder.append("\n");
builder.append("Nucleotide Codes\n(Derived from IUPAC)...\n");
builder.append("A A:A\n");
builder.append("C C:C\n");
builder.append("G G:G\n");
builder.append("T T:T\n");
builder.append("R A:G\n");
builder.append("Y C:T\n");
builder.append("S C:G\n");
builder.append("W A:T\n");
builder.append("K G:T\n");
builder.append("M A:C\n");
builder.append("+ +:+ (insertion)\n");
builder.append("0 +:-\n");
builder.append("- -:- (deletion)\n");
builder.append("N Unknown\n\n");
}
} catch (Exception ex) {
myLogger.debug(ex.getMessage(), ex);
}
}
if (book.getData() instanceof TableReport) {
TableReport tr = (TableReport) book.getData();
long numColumns = tr.getColumnCount();
long numRows = tr.getRowCount();
builder.append("Table Title: ");
builder.append(tr.getTableTitle());
builder.append("\n");
builder.append("Number of columns: ");
builder.append(numColumns);
builder.append("\n");
builder.append("Number of rows: ");
builder.append(numRows);
builder.append("\n");
builder.append("Matrix size (excludes row headers): ");
builder.append((numColumns - 1) * numRows);
builder.append("\n");
}
if (book.getData() instanceof TOPMInterface) {
TOPMInterface topm = (TOPMInterface) book.getData();
builder.append("Number of Tags: ");
builder.append(topm.getSize());
builder.append("\n");
}
if (book.getData() instanceof DistanceMatrix) {
DistanceMatrix matrix = (DistanceMatrix) book.getData();
GeneralAnnotation annotations = matrix.annotations();
if ((annotations != null) && (annotations.numAnnotations() != 0)) {
builder.append("\nAnnotations...\n");
for (Map.Entry entry : annotations.getAllAnnotationEntries()) {
builder.append(entry.getKey());
builder.append(": ");
builder.append(entry.getValue());
builder.append("\n");
}
builder.append("\n");
}
}
if (book.getData() instanceof TaxaList) {
TaxaList taxa = (TaxaList) book.getData();
builder.append("Number of Taxa: ");
builder.append(taxa.numberOfTaxa());
builder.append("\n\n");
}
String comment = book.getComment();
if ((comment != null) && (comment.length() != 0)) {
builder.append(comment);
}
myTASSELMainFrame.setNoteText(builder.toString());
if (book.getData() != null) {
myTASSELMainFrame.mainDisplayPanel.removeAll();
if (book.getData() instanceof TableReport) {
long size = ((TableReport) book.getData()).getElementCount();
myLogger.info("initSelectionListener: Table Report Size: " + size);
if (size == 0) {
JPanel blankPanel = new JPanel();
blankPanel.setLayout(new BorderLayout());
blankPanel.add(new JLabel(" Nothing to Display"), BorderLayout.CENTER);
myTASSELMainFrame.mainDisplayPanel.add(blankPanel, BorderLayout.CENTER);
} else {
TableReportPanel theATP = TableReportPanel.getInstance((TableReport) book.getData());
myTASSELMainFrame.mainDisplayPanel.add(theATP, BorderLayout.CENTER);
}
} else if (book.getData() instanceof FilterList) {
TableReportPanel theATP = TableReportPanel.getInstance((FilterList) book.getData());
myTASSELMainFrame.mainDisplayPanel.add(theATP, BorderLayout.CENTER);
} else if (book.getData() instanceof TOPMInterface) {
int size = ((TOPMInterface) book.getData()).getTagCount();
myLogger.info("initSelectionListener: TOPM Tag Count: " + size);
if (size == 0) {
JPanel blankPanel = new JPanel();
blankPanel.setLayout(new BorderLayout());
blankPanel.add(new JLabel(" No Tags"), BorderLayout.CENTER);
myTASSELMainFrame.mainDisplayPanel.add(blankPanel, BorderLayout.CENTER);
} else {
String name = book.getName();
if (name.endsWith("(Graphical)")) {
SeqViewerPanel seqViewer = SeqViewerPanel.getInstance((TOPMInterface) book.getData(), getThis());
myTASSELMainFrame.mainDisplayPanel.add(seqViewer, BorderLayout.CENTER);
} else {
TableReportPanel theATP = TableReportPanel.getInstance((TOPMInterface) book.getData());
myTASSELMainFrame.mainDisplayPanel.add(theATP, BorderLayout.CENTER);
}
}
} else if (book.getData() instanceof TaxaList) {
int size = ((TaxaList) book.getData()).numberOfTaxa();
myLogger.info("initSelectionListener: Number of Taxa: " + size);
if (size == 0) {
JPanel blankPanel = new JPanel();
blankPanel.setLayout(new BorderLayout());
blankPanel.add(new JLabel(" No Taxa"), BorderLayout.CENTER);
myTASSELMainFrame.mainDisplayPanel.add(blankPanel, BorderLayout.CENTER);
} else {
TableReportPanel theATP = TableReportPanel.getInstance((TaxaList) book.getData());
myTASSELMainFrame.mainDisplayPanel.add(theATP, BorderLayout.CENTER);
}
} else if (book.getData() instanceof PositionList) {
int size = ((PositionList) book.getData()).numberOfSites();
myLogger.info("initSelectionListener: Number of Positions: " + size);
if (size == 0) {
JPanel blankPanel = new JPanel();
blankPanel.setLayout(new BorderLayout());
blankPanel.add(new JLabel(" No Positions"), BorderLayout.CENTER);
myTASSELMainFrame.mainDisplayPanel.add(blankPanel, BorderLayout.CENTER);
} else {
TableReportPanel theATP = TableReportPanel.getInstance((PositionList) book.getData());
myTASSELMainFrame.mainDisplayPanel.add(theATP, BorderLayout.CENTER);
}
} else if (book.getData() instanceof GenotypeTable) {
GenotypeTable align = (GenotypeTable) book.getData();
List masks = new ArrayList();
for (int i = 0, n = node.getChildCount(); i < n; i++) {
try {
DefaultMutableTreeNode currentNode = (DefaultMutableTreeNode) node.getChildAt(i);
Datum currentDatum = (Datum) currentNode.getUserObject();
Object currentMask = currentDatum.getData();
if ((currentMask != null) && (currentMask instanceof GenotypeTableMask)) {
masks.add(currentMask);
}
} catch (Exception ex) {
ex.printStackTrace();
}
}
SeqViewerPanel seqViewer = null;
if (masks.size() != 0) {
GenotypeTableMask[] masksArray = new GenotypeTableMask[masks.size()];
masks.toArray(masksArray);
seqViewer = SeqViewerPanel.getInstance(align, masksArray, getThis());
} else {
seqViewer = SeqViewerPanel.getInstance(align, getThis());
}
myTASSELMainFrame.mainDisplayPanel.add(seqViewer, BorderLayout.CENTER);
} else if (book.getData() instanceof GenotypeTableMask) {
GenotypeTableMask mask = (GenotypeTableMask) book.getData();
if (mask.getColor() != null) {
Color tempColor = JColorChooser.showDialog(myTASSELMainFrame, "Select Mask Color...", mask.getColor());
//myTree.setSelectionPath(new TreePath(parentNode.getPath()));
if (tempColor != null) {
mask.setColor(tempColor);
book.setName(mask.toString());
}
}
myLastNode = null;
DefaultMutableTreeNode parentNode = (DefaultMutableTreeNode) node.getParent();
TreeSelectionEvent event = new TreeSelectionEvent(parentNode, null, false, null, null);
myTreeSelectionListener.valueChanged(event);
} else if (book.getData() instanceof SimpleTree) {
myTASSELMainFrame.mainDisplayPanel.add(myTASSELMainFrame.mainPanelScrollPane, BorderLayout.CENTER);
SimpleTree tree = (SimpleTree) book.getData();
StringWriter writer = null;
try {
if (tree.getExternalNodeCount() < 300) {
writer = new StringWriter();
tree.report(writer);
myTASSELMainFrame.setMainText(writer.toString());
} else {
myTASSELMainFrame.setMainText(tree.toString());
}
} catch (Exception ex) {
myLogger.debug(ex.getMessage(), ex);
} finally {
try {
writer.close();
} catch (Exception ex) {
// do nothing
}
}
} else {
myTASSELMainFrame.mainDisplayPanel.add(myTASSELMainFrame.mainPanelScrollPane, BorderLayout.CENTER);
String s = book.getData().toString();
if (s.length() > 2000000) {
s = s.substring(1, 2000000) + "\n Truncated view. Too much to display. Save it to a file.";
}
myTASSELMainFrame.setMainText(s);
}
myTASSELMainFrame.sendMessage(book.getData().getClass().toString());
myTASSELMainFrame.mainDisplayPanel.revalidate();
myTASSELMainFrame.mainDisplayPanel.repaint();
}
} catch (Throwable e1) {
String userMessage = "TASSEL has experienced an error. ";
if (e1 instanceof java.lang.OutOfMemoryError) {
userMessage = "You have used up all of the memory allocated to the Java Virtual Machine. \n"
+ "It is recommneded that you adjust your heap settings and possibly add more memory to the computer\n"
+ "Additionally, some operations are not recommended on a full dataset, i.e., select SNPs *before* determining LD";
}
JOptionPane.showMessageDialog(myTASSELMainFrame, userMessage, "Fatal Error", JOptionPane.ERROR_MESSAGE);
e1.printStackTrace();
}
}
});
myTree.addTreeSelectionListener(myTreeSelectionListener);
}
private void createNodes() {
myDataNode = new DefaultMutableTreeNode(new Datum(NODE_TYPE_DATA, "Node on data tree", "Holds the basic data structures"));
myTopNode.add(myDataNode);
myNodeHash.put(NODE_TYPE_DATA, myDataNode);
myResultNode = new DefaultMutableTreeNode(new Datum(NODE_TYPE_RESULT, "Node on data tree", "Holds the basic result structures"));
myTopNode.add(myResultNode);
myNodeHash.put(NODE_TYPE_RESULT, myResultNode);
}
private synchronized DefaultMutableTreeNode getTreeNode(String nodeString) {
DefaultMutableTreeNode result = myNodeHash.get(nodeString);
if (result == null) {
if (NODE_TYPE_DATA_CHILDREN.contains(nodeString)) {
result = new DefaultMutableTreeNode(new Datum(nodeString, nodeString, nodeString));
int childIndex = getInsertLocation(myDataNode, nodeString);
myTreeModel.insertNodeInto(result, myDataNode, childIndex);
myNodeHash.put(nodeString, result);
} else {
result = new DefaultMutableTreeNode(new Datum(nodeString, nodeString, nodeString));
int childIndex = getInsertLocation(myResultNode, nodeString);
myTreeModel.insertNodeInto(result, myResultNode, childIndex);
myNodeHash.put(nodeString, result);
}
}
return result;
}
private int getInsertLocation(DefaultMutableTreeNode node, String newNode) {
Enumeration children = node.children();
int result = 0;
while (children.hasMoreElements()) {
DefaultMutableTreeNode currentNode = (DefaultMutableTreeNode) children.nextElement();
Datum current = (Datum) currentNode.getUserObject();
if (current.getName().compareTo(newNode) > 0) {
break;
}
result++;
}
return result;
}
private void jbInit() throws Exception {
JScrollPane jScrollPane1 = new JScrollPane(myTree);
jScrollPane1.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
setLayout(new BorderLayout());
add(jScrollPane1, BorderLayout.CENTER);
}
private void deleteDatumFromList(Datum datum) {
Iterator itr = myDataSetList.keySet().iterator();
while (itr.hasNext()) {
Datum current = (Datum) itr.next();
if (current == datum) {
itr.remove();
break;
}
}
}
public void addDataSet(DataSet theDataSet, String defaultNode) {
Plugin theCreator = theDataSet.getCreator();
for (int i = 0; i < theDataSet.getSize(); i++) {
Datum d = theDataSet.getData(i);
if ((theCreator instanceof MLMPlugin)
|| (theCreator instanceof FixedEffectLMPlugin)
|| (theCreator instanceof EqtlAssociationPlugin)) {
addDatum(NODE_TYPE_ASSOCIATIONS, d);
continue;
}
if (theCreator instanceof GenotypeSummaryPlugin) {
addDatum(NODE_TYPE_GENO_SUMMARY, d);
continue;
}
if (theCreator instanceof SequenceDiversityPlugin) {
addDatum(NODE_TYPE_DIVERSITY, d);
continue;
}
if (theCreator instanceof LinkageDisequilibriumPlugin) {
addDatum(NODE_TYPE_LD, d);
continue;
}
if (d.getData() instanceof GenotypeTable) {
addDatum(NODE_TYPE_SEQUENCE, d);
continue;
}
if (d.getData() instanceof GenotypeTableMask) {
addDatum(d);
continue;
}
if (d.getData() instanceof IdentifierSynonymizer) {
addDatum(NODE_TYPE_SYNONYMIZER, d);
continue;
}
if (d.getData() instanceof Phenotype) {
addDatum(NODE_TYPE_NUMERICAL, d);
continue;
}
if (d.getData() instanceof DistanceMatrix) {
addDatum(NODE_TYPE_MATRIX, d);
continue;
}
if (d.getData() instanceof HDF5TableReport) {
addDatum(NODE_TYPE_HDF5_SCHEMA, d);
continue;
}
if (d.getData() instanceof TableReport) {
addDatum(NODE_TYPE_NUMERICAL, d);
continue;
}
if (d.getData() instanceof FilterList) {
addDatum(NODE_TYPE_FILTERS, d);
continue;
}
if (d.getData() instanceof Tree) {
addDatum(NODE_TYPE_TREE, d);
continue;
}
if (d.getData() instanceof TaxaList) {
addDatum(NODE_TYPE_LISTS, d);
continue;
}
if (d.getData() instanceof PositionList) {
addDatum(NODE_TYPE_LISTS, d);
continue;
}
if (d.getData() instanceof TOPMInterface) {
addDatum(NODE_TYPE_TOPM, new Datum(d.getName() + " (Text)", d.getData(), null));
addDatum(NODE_TYPE_TOPM, new Datum(d.getName() + " (Graphical)", d.getData(), null));
continue;
}
if (defaultNode == null) {
addDatum(NODE_TYPE_DEFAULT, d);
continue;
}
addDatum(defaultNode, d);
}
}
public synchronized void addDatum(String dataParent, Datum theDatum) {
if (theDatum.getData() instanceof GenotypeTableMask) {
addDatum(theDatum);
return;
}
DefaultMutableTreeNode temp = findOnTree(theDatum);
if (temp != null) {
myTree.scrollPathToVisible(new TreePath(temp.getPath()));
myTree.validate();
myTree.repaint();
return;
}
DefaultMutableTreeNode parentNode = getTreeNode(dataParent);
DefaultMutableTreeNode childNode = new DefaultMutableTreeNode(theDatum);
myNodeHash.put(theDatum.getName(), childNode);
myTreeModel.insertNodeInto(childNode, parentNode, parentNode.getChildCount());
myTree.scrollPathToVisible(new TreePath(childNode.getPath()));
if (theDatum instanceof Serializable) {
myDataSetList.put(theDatum, dataParent);
}
}
public synchronized void addDatum(Datum theDatum) {
GenotypeTableMask mask = null;
try {
mask = (GenotypeTableMask) theDatum.getData();
} catch (Exception e) {
throw new IllegalArgumentException("DataTreePanel: addDatum: input must be AlignmentMask.");
}
GenotypeTable align = mask.getAlignment();
Iterator itr = myNodeHash.values().iterator();
while (itr.hasNext()) {
DefaultMutableTreeNode parentNode = (DefaultMutableTreeNode) itr.next();
Object current = ((Datum) parentNode.getUserObject()).getData();
if ((current instanceof GenotypeTable) && (current == align)) {
DefaultMutableTreeNode childNode = new DefaultMutableTreeNode(theDatum);
myTreeModel.insertNodeInto(childNode, parentNode, parentNode.getChildCount());
myTree.scrollPathToVisible(new TreePath(childNode.getPath()));
myLastNode = null;
myTree.setSelectionPath(new TreePath(parentNode.getPath()));
myTree.scrollPathToVisible(new TreePath(parentNode.getPath()));
myTreeSelectionListener.valueChanged(null);
if (theDatum instanceof Serializable) {
myDataSetList.put(theDatum, "NA");
}
break;
}
}
}
public void setSelectionPath(Datum theDatum) {
DefaultMutableTreeNode temp = findOnTree(theDatum);
if (temp != null) {
myTree.scrollPathToVisible(new TreePath(temp.getPath()));
myTree.setSelectionPath(new TreePath(temp.getPath()));
myTree.validate();
myTree.repaint();
}
}
private DefaultMutableTreeNode findOnTree(Datum theDatum) {
if (theDatum == null) {
return null;
}
Iterator itr = myNodeHash.values().iterator();
while (itr.hasNext()) {
DefaultMutableTreeNode parentNode = (DefaultMutableTreeNode) itr.next();
Datum current = (Datum) parentNode.getUserObject();
if ((current != null) && (current.equals(theDatum))) {
return parentNode;
}
}
return null;
}
public DataSet getSelectedTasselDataSet() {
int n = myTree.getSelectionCount();
String parentNodeName = null;
ArrayList data = new ArrayList();
TreePath[] tp = myTree.getSelectionPaths();
for (int i = 0; i < n; i++) {
DefaultMutableTreeNode node = (DefaultMutableTreeNode) tp[i].getLastPathComponent();
if (node == null) {
return null;
}
//if the parents don't share the same name then leave blank
if (i == 0) {
parentNodeName = node.getParent().toString();
} else if (!node.getParent().toString().equals(parentNodeName)) {
parentNodeName = null;
}
data.add((Datum) node.getUserObject());
}
return new DataSet(data, null);
}
public void deleteSelectedNodes() {
TreePath[] currentSelection = myTree.getSelectionPaths();
if (currentSelection != null) {
for (int i = 0; i < currentSelection.length; i++) {
myLogger.info("Start Deleting at Selection: " + currentSelection[i]);
if (currentSelection[i] != null) {
DefaultMutableTreeNode currentNode = (DefaultMutableTreeNode) (currentSelection[i].getLastPathComponent());
myLogger.info("Deleting Node : " + currentNode);
deleteNode(currentNode);
}
}
}
}
private void deleteNode(DefaultMutableTreeNode currentNode) {
int size = currentNode.getChildCount();
for (int i = size - 1; i >= 0; i--) {
DefaultMutableTreeNode current = (DefaultMutableTreeNode) currentNode.getChildAt(i);
deleteNode(current);
}
if ((currentNode == myDataNode) || (currentNode == myResultNode)) {
return;
}
MutableTreeNode parent = (MutableTreeNode) (currentNode.getParent());
if ((parent != null) && (parent != myDataNode) && (parent != myResultNode)) {
myTreeModel.removeNodeFromParent(currentNode);
Iterator itr = myNodeHash.keySet().iterator();
while (itr.hasNext()) {
Object key = itr.next();
if (myNodeHash.get(key) == currentNode) {
itr.remove();
}
}
try {
Datum datum = (Datum) currentNode.getUserObject();
deleteDatumFromList(datum);
} catch (Exception ex) {
// do nothing
}
try {
if (((Datum) currentNode.getUserObject()).getData() instanceof GenotypeTableMask) {
myLastNode = null;
myTree.setSelectionPath(new TreePath(((DefaultMutableTreeNode) parent).getPath()));
myTree.scrollPathToVisible(new TreePath(((DefaultMutableTreeNode) parent).getPath()));
myTreeSelectionListener.valueChanged(null);
}
} catch (Exception e) {
// do nothing
}
try {
if (((Datum) currentNode.getUserObject()).getData() instanceof GenotypeTable) {
SeqViewerPanel.removeInstance((GenotypeTable) ((Datum) currentNode.getUserObject()).getData());
}
} catch (Exception e) {
// do nothing
}
}
}
public Map getDataList() {
return Collections.unmodifiableMap(myDataSetList);
}
public JTree getTree() {
return myTree;
}
/**
* Returns Tassel data set after complete.
*
* @param event event
*/
public void dataSetReturned(PluginEvent event) {
DataSet tds = (DataSet) event.getSource();
if (tds != null) {
addDataSet(tds, DataTreePanel.NODE_TYPE_DEFAULT);
setSelectionPath(tds.getData(0));
}
}
/**
* Returns progress of execution.
*
* @param event event
*/
public void progress(PluginEvent event) {
//do nothing
}
class MyTreeModelListener implements javax.swing.event.TreeModelListener {
DataTreePanel theDTP;
public MyTreeModelListener(DataTreePanel theDTP) {
this.theDTP = theDTP;
}
public void treeNodesChanged(TreeModelEvent e) {
DefaultMutableTreeNode node;
node = (DefaultMutableTreeNode) (e.getTreePath().getLastPathComponent());
/*
* If the event lists children, then the changed
* node is the child of the node we've already
* gotten. Otherwise, the changed node and the
* specified node are the same.
*/
try {
int index = e.getChildIndices()[0];
node = (DefaultMutableTreeNode) (node.getChildAt(index));
} catch (NullPointerException exc) {
}
String s = (String) node.getUserObject();
theDTP.myLastBookSelected.setName(s);
node.setUserObject(theDTP.myLastBookSelected);
System.out.println("The user has finished editing the node.");
System.out.println("New value: " + node.getUserObject());
}
public void treeNodesInserted(TreeModelEvent e) {
}
public void treeNodesRemoved(TreeModelEvent e) {
}
public void treeStructureChanged(TreeModelEvent e) {
}
}
}
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