/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.beans.*;
-import java.io.*;
-import java.util.*;
-import javax.imageio.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.image.*;
-import javax.swing.*;
-
-import org.jibble.epsgraphics.*;
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
-import jalview.jbgui.*;
+import jalview.analysis.AlignmentSorter;
+import jalview.analysis.NJTree;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.bin.Cache;
+import jalview.commands.CommandI;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.NodeTransformI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceNode;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.io.NewickFile;
+import jalview.jbgui.GTreePanel;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MessageManager;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.image.BufferedImage;
+import java.beans.PropertyChangeEvent;
+import java.io.FileOutputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+import javax.swing.ButtonGroup;
+import javax.swing.JMenuItem;
+import javax.swing.JRadioButtonMenuItem;
+
+import org.jibble.epsgraphics.EpsGraphics2D;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class TreePanel
- extends GTreePanel
+public class TreePanel extends GTreePanel
{
String type;
+
String pwtype;
+
TreeCanvas treeCanvas;
+
NJTree tree;
+
AlignViewport av;
/**
* Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
- * @param s DOCUMENT ME!
- * @param e DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
+ * @param s
+ * DOCUMENT ME!
+ * @param e
+ * DOCUMENT ME!
*/
public TreePanel(AlignmentPanel ap, String type, String pwtype)
{
super();
initTreePanel(ap, type, pwtype, null, null);
- // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default
+ // We know this tree has distances. JBPNote TODO: prolly should add this as
+ // a userdefined default
// showDistances(true);
}
/**
* Creates a new TreePanel object.
- *
- * @param av DOCUMENT ME!
- * @param seqVector DOCUMENT ME!
- * @param newtree DOCUMENT ME!
- * @param type DOCUMENT ME!
- * @param pwtype DOCUMENT ME!
+ *
+ * @param av
+ * DOCUMENT ME!
+ * @param seqVector
+ * DOCUMENT ME!
+ * @param newtree
+ * DOCUMENT ME!
+ * @param type
+ * DOCUMENT ME!
+ * @param pwtype
+ * DOCUMENT ME!
*/
- public TreePanel(AlignmentPanel ap,
- String type,
- String pwtype,
- NewickFile newtree)
+ public TreePanel(AlignmentPanel ap, String type, String pwtype,
+ NewickFile newtree)
{
super();
initTreePanel(ap, type, pwtype, newtree, null);
}
- public TreePanel(AlignmentPanel av,
- String type,
- String pwtype,
- NewickFile newtree, AlignmentView inputData)
+ public TreePanel(AlignmentPanel av, String type, String pwtype,
+ NewickFile newtree, AlignmentView inputData)
{
super();
initTreePanel(av, type, pwtype, newtree, inputData);
return treeCanvas.av.getAlignment();
}
- public AlignViewport getViewPort()
+ public AlignmentViewport getViewPort()
{
return treeCanvas.av;
}
void initTreePanel(AlignmentPanel ap, String type, String pwtype,
- NewickFile newTree, AlignmentView inputData)
+ NewickFile newTree, AlignmentView inputData)
{
av = ap.av;
if (tree == null)
{
System.out.println("tree is null");
+ // TODO: deal with case when a change event is received whilst a
+ // tree is still being calculated - should save reference for
+ // processing message later.
+ return;
}
if (evt.getNewValue() == null)
{
- System.out.println("new alignment sequences vector value is null");
+ System.out
+ .println("new alignment sequences vector value is null");
}
- tree.UpdatePlaceHolders( (Vector) evt.getNewValue());
- treeCanvas.nameHash.clear(); // reset the mapping between canvas rectangles and leafnodes
+ tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
+ treeCanvas.nameHash.clear(); // reset the mapping between canvas
+ // rectangles and leafnodes
repaint();
}
}
void buildAssociatedViewMenu()
{
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av.
- getSequenceSetId());
+ AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId());
if (aps.length == 1 && treeCanvas.ap == aps[0])
{
associateLeavesMenu.setVisible(false);
associateLeavesMenu.setVisible(true);
- if ( (viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
+ if ((viewMenu.getItem(viewMenu.getItemCount() - 2) instanceof JMenuItem))
{
viewMenu.insertSeparator(viewMenu.getItemCount() - 1);
}
associateLeavesMenu.add(item);
}
- final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem("All Views");
+ final JRadioButtonMenuItem itemf = new JRadioButtonMenuItem(
+ MessageManager.getString("label.all_views"));
buttonGroup.add(itemf);
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
}
- class TreeLoader
- extends Thread
+ class TreeLoader extends Thread
{
NewickFile newtree;
+
jalview.datamodel.AlignmentView odata = null;
+
public TreeLoader(NewickFile newtree)
{
this.newtree = newtree;
{
if (odata == null)
{
- tree = new NJTree(av.alignment.getSequencesArray(),
- newtree);
+ tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
}
else
{
- tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);
+ tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
+ newtree);
}
if (!tree.hasOriginalSequenceData())
{
{
int start, end;
SequenceI[] seqs;
- AlignmentView seqStrings = av.getAlignmentView(av.getSelectionGroup() != null);
- if (av.getSelectionGroup() == null)
+ boolean selview = av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSize() > 1;
+ AlignmentView seqStrings = av.getAlignmentView(selview);
+ if (!selview)
{
start = 0;
- end = av.alignment.getWidth();
- seqs = av.alignment.getSequencesArray();
+ end = av.getAlignment().getWidth();
+ seqs = av.getAlignment().getSequencesArray();
}
else
{
start = av.getSelectionGroup().getStartRes();
end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+ seqs = av.getSelectionGroup().getSequencesInOrder(
+ av.getAlignment());
+ }
+ ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ if (sm instanceof ViewBasedAnalysisI)
+ {
+ try
+ {
+ sm = sm.getClass().newInstance();
+ ((ViewBasedAnalysisI) sm)
+ .configureFromAlignmentView(treeCanvas.ap);
+ } catch (Exception q)
+ {
+ Cache.log.error("Couldn't create a scoremodel instance for "
+ + sm.getName());
+ }
+ tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
+ }
+ else
+ {
+ tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
+ end);
}
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
showDistances(true);
}
treeCanvas.setTree(tree);
treeCanvas.repaint();
av.setCurrentTree(tree);
-
+ if (av.getSortByTree())
+ {
+ sortByTree_actionPerformed();
+ }
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public NJTree getTree()
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void textbox_actionPerformed(ActionEvent e)
{
buffer.append("PID");
}
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
+ try
+ {
+ cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
+ tree.isHasRootDistance()));
+ Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ } catch (OutOfMemoryError oom)
+ {
+ new OOMWarning("generating newick tree file", oom);
+ cap.dispose();
+ }
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
- cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
- tree.isHasRootDistance()));
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void saveAsNewick_actionPerformed(ActionEvent e)
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
- getProperty(
- "LAST_DIRECTORY"));
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save tree as newick file");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.save_tree_as_newick"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(null);
if (value == JalviewFileChooser.APPROVE_OPTION)
{
String choice = chooser.getSelectedFile().getPath();
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
try
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());
- String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
- tree.isHasRootDistance());
- java.io.PrintWriter out = new java.io.PrintWriter(new java.io.
- FileWriter(
- choice));
+ jalview.io.NewickFile fout = new jalview.io.NewickFile(
+ tree.getTopNode());
+ String output = fout.print(tree.isHasBootstrap(),
+ tree.isHasDistances(), tree.isHasRootDistance());
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter(choice));
out.println(output);
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void printMenu_actionPerformed(ActionEvent e)
{
- //Putting in a thread avoids Swing painting problems
+ // Putting in a thread avoids Swing painting problems
treeCanvas.startPrinting();
}
{
if (!tree.hasOriginalSequenceData())
{
- jalview.bin.Cache.log.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
+ jalview.bin.Cache.log
+ .info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
return;
}
- // decide if av alignment is sufficiently different to original data to warrant a new window to be created
- // create new alignmnt window with hidden regions (unhiding hidden regions yields unaligned seqs)
+ // decide if av alignment is sufficiently different to original data to
+ // warrant a new window to be created
+ // create new alignmnt window with hidden regions (unhiding hidden regions
+ // yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
- getGapCharacter());
+ char gc = '-';
+ try
+ {
+ // we try to get the associated view's gap character
+ // but this may fail if the view was closed...
+ gc = av.getGapCharacter();
+
+ } catch (Exception ex)
+ {
+ }
+ ;
+ Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- Alignment al = new Alignment( (SequenceI[]) alAndColsel[0]);
- Alignment dataset = av.getAlignment().getDataset();
+ Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
+ Alignment dataset = (av != null && av.getAlignment() != null) ? av
+ .getAlignment().getDataset() : null;
if (dataset != null)
{
al.setDataset(dataset);
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al, (ColumnSelection) alAndColsel[1],
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT
- );
+ AlignFrame af = new AlignFrame(al,
+ (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
- //>>>This is a fix for the moment, until a better solution is found!!<<<
+ // >>>This is a fix for the moment, until a better solution is
+ // found!!<<<
// af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
+ // af.addSortByOrderMenuItem(ServiceName + " Ordering",
+ // msaorder);
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ Desktop.addInternalFrame(af, MessageManager.formatMessage(
+ "label.original_data_for_params",
+ new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
}
}
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void fitToWindow_actionPerformed(ActionEvent e)
{
}
/**
+ * sort the associated alignment view by the current tree.
+ *
+ * @param e
+ */
+ @Override
+ public void sortByTree_actionPerformed()
+ {
+
+ if (treeCanvas.applyToAllViews)
+ {
+ final ArrayList<CommandI> commands = new ArrayList<CommandI>();
+ for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId()))
+ {
+ commands.add(sortAlignmentIn(ap.av.getAlignPanel()));
+ }
+ av.getAlignPanel().alignFrame.addHistoryItem(new CommandI()
+ {
+
+ @Override
+ public void undoCommand(AlignmentI[] views)
+ {
+ for (CommandI tsort : commands)
+ {
+ tsort.undoCommand(views);
+ }
+ }
+
+ @Override
+ public int getSize()
+ {
+ return commands.size();
+ }
+
+ @Override
+ public String getDescription()
+ {
+ return "Tree Sort (many views)";
+ }
+
+ @Override
+ public void doCommand(AlignmentI[] views)
+ {
+
+ for (CommandI tsort : commands)
+ {
+ tsort.doCommand(views);
+ }
+ }
+ });
+ for (AlignmentPanel ap : PaintRefresher.getAssociatedPanels(av
+ .getSequenceSetId()))
+ {
+ // ensure all the alignFrames refresh their GI after adding an undo item
+ ap.alignFrame.updateEditMenuBar();
+ }
+ }
+ else
+ {
+ treeCanvas.ap.alignFrame
+ .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
+ }
+
+ }
+
+ public CommandI sortAlignmentIn(AlignmentPanel ap)
+ {
+ AlignmentViewport av = ap.av;
+ SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(av.getAlignment(), tree);
+ CommandI undo;
+ undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
+
+ ap.paintAlignment(true);
+ return undo;
+ }
+
+ /**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void font_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void distanceMenu_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
+ "Prompt each time");
// If we need to prompt, and if the GUI is visible then
// Prompt for EPS rendering style
if (renderStyle.equalsIgnoreCase("Prompt each time")
- && !
- (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true")))
+ && !(System.getProperty("java.awt.headless") != null && System
+ .getProperty("java.awt.headless").equals("true")))
{
EPSOptions eps = new EPSOptions();
renderStyle = eps.getValue();
try
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[]
- {"eps"},
- new String[]
- {"Encapsulated Postscript"},
- "Encapsulated Postscript");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "eps" }, new String[] { "Encapsulated Postscript" },
+ "Encapsulated Postscript");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create EPS file from tree");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_eps_from_tree"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
- EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
- height);
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
pg.setAccurateTextMode(accurateText);
pg.flush();
pg.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
public void pngTree_actionPerformed(ActionEvent e)
{
try
{
jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"), new String[]
- {"png"},
- new String[]
- {"Portable network graphics"},
- "Portable network graphics");
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
+ { "png" }, new String[] { "Portable network graphics" },
+ "Portable network graphics");
chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create PNG image from tree");
- chooser.setToolTipText("Save");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.create_png_from_tree"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY",
- chooser.getSelectedFile().getParent());
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
+ .getSelectedFile().getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
BufferedImage bi = new BufferedImage(width, height,
- BufferedImage.TYPE_INT_RGB);
+ BufferedImage.TYPE_INT_RGB);
Graphics png = bi.getGraphics();
treeCanvas.draw(png, width, height);
ImageIO.write(bi, "png", out);
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
}
+
+ /**
+ * change node labels to the annotation referred to by labelClass TODO:
+ * promote to a datamodel modification that can be undone TODO: make argument
+ * one case of a generic transformation function ie { undoStep = apply(Tree,
+ * TransformFunction)};
+ *
+ * @param labelClass
+ */
+ public void changeNames(final String labelClass)
+ {
+ tree.applyToNodes(new NodeTransformI()
+ {
+
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode
+ && !((SequenceNode) node).isPlaceholder()
+ && !((SequenceNode) node).isDummy())
+ {
+ String newname = null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq != null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
+ sq.getDBRef(),
+ new String[] { labelClass.toUpperCase() });
+ if (refs != null)
+ {
+ for (int i = 0; i < refs.length; i++)
+ {
+ if (newname == null)
+ {
+ newname = new String(refs[i].getAccessionId());
+ }
+ else
+ {
+ newname = newname + "; " + refs[i].getAccessionId();
+ }
+ }
+ }
+ if (newname == null)
+ {
+ SequenceFeature sf[] = sq.getSequenceFeatures();
+ for (int i = 0; sf != null && i < sf.length; i++)
+ {
+ if (sf[i].getType().equals(labelClass))
+ {
+ if (newname == null)
+ {
+ newname = new String(sf[i].getDescription());
+ }
+ else
+ {
+ newname = newname + "; " + sf[i].getDescription();
+ }
+ }
+ }
+ }
+ }
+ if (newname != null)
+ {
+ String oldname = ((SequenceNode) node).getName();
+ // TODO : save in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
}
git://source.jalview.org / jalview.git / blobdiff