/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.analysis.AlignmentSorter;
import jalview.analysis.NJTree;
-import jalview.api.analysis.ScoreModelI;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.api.analysis.DistanceModelI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.io.JalviewFileView;
import jalview.io.NewickFile;
import jalview.jbgui.GTreePanel;
-import jalview.schemes.ResidueProperties;
+import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
// 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!
- */
- 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)
{
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
}
+ @Override
public void viewMenu_menuSelected()
{
buildAssociatedViewMenu();
buttonGroup.add(item);
item.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = false;
itemf.setSelected(treeCanvas.applyToAllViews);
itemf.addActionListener(new ActionListener()
{
+ @Override
public void actionPerformed(ActionEvent evt)
{
treeCanvas.applyToAllViews = itemf.isSelected();
}
}
+ @Override
public void run()
{
seqs = av.getSelectionGroup().getSequencesInOrder(
av.getAlignment());
}
- ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
+ DistanceModelI sm = ScoreModels.getInstance().forName(pwtype);
if (sm instanceof ViewBasedAnalysisI)
{
try
* @param e
* DOCUMENT ME!
*/
+ @Override
public void textbox_actionPerformed(ActionEvent e)
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- StringBuffer buffer = new StringBuffer();
-
- if (type.equals("AV"))
- {
- buffer.append("Average distance tree using ");
- }
- else
- {
- buffer.append("Neighbour joining tree using ");
- }
+ String newTitle = getPanelTitle(type, pwtype);
- if (pwtype.equals("BL"))
- {
- buffer.append("BLOSUM62");
- }
- else
- {
- buffer.append("PID");
- }
-
- jalview.io.NewickFile fout = new jalview.io.NewickFile(
- tree.getTopNode());
+ NewickFile fout = new NewickFile(tree.getTopNode());
try
{
cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(),
tree.isHasRootDistance()));
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
+ Desktop.addInternalFrame(cap, newTitle, 500, 100);
} catch (OutOfMemoryError oom)
{
new OOMWarning("generating newick tree file", oom);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void saveAsNewick_actionPerformed(ActionEvent e)
{
JalviewFileChooser chooser = new JalviewFileChooser(
* @param e
* DOCUMENT ME!
*/
+ @Override
public void printMenu_actionPerformed(ActionEvent e)
{
// Putting in a thread avoids Swing painting problems
treeCanvas.startPrinting();
}
+ @Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
if (!tree.hasOriginalSequenceData())
{
// AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- Alignment dataset = (av != null && av.getAlignment() != null) ? av
+ AlignmentI al = new Alignment((SequenceI[]) alAndColsel[0]);
+ AlignmentI dataset = (av != null && av.getAlignment() != null) ? av
.getAlignment().getDataset() : null;
if (dataset != null)
{
* @param e
* DOCUMENT ME!
*/
+ @Override
public void fitToWindow_actionPerformed(ActionEvent e)
{
treeCanvas.fitToWindow = fitToWindow.isSelected();
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
* @param e
* DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
* @param e
* DOCUMENT ME!
*/
+ @Override
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
try
{
- jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
- jalview.bin.Cache.getProperty("LAST_DIRECTORY"), new String[]
- { "eps" }, new String[] { "Encapsulated Postscript" },
- "Encapsulated Postscript");
- chooser.setFileView(new jalview.io.JalviewFileView());
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ ImageMaker.EPS_EXTENSION, ImageMaker.EPS_EXTENSION);
+ chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager
.getString("label.create_eps_from_tree"));
chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
return;
}
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser
- .getSelectedFile().getParent());
+ Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile()
+ .getParent());
FileOutputStream out = new FileOutputStream(chooser.getSelectedFile());
EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
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");
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
chooser.setFileView(new jalview.io.JalviewFileView());
chooser.setDialogTitle(MessageManager
tree.applyToNodes(new NodeTransformI()
{
+ @Override
public void transform(BinaryNode node)
{
if (node instanceof SequenceNode
{
// search dbrefs, features and annotation
DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
- sq.getDBRef(),
+ sq.getDBRefs(),
new String[] { labelClass.toUpperCase() });
if (refs != null)
{
}
});
}
+
+ /**
+ * Formats a localised title for the tree panel, like
+ * <p>
+ * Neighbour Joining Using BLOSUM62
+ * <p>
+ * For a tree loaded from file, just uses the file name
+ *
+ * @param treeType
+ * NJ or AV or FromFile
+ * @param modelOrFileName
+ * @return
+ */
+ public static String getPanelTitle(String treeType, String modelOrFileName)
+ {
+ if (NJTree.FROM_FILE.equals(treeType))
+ {
+ return modelOrFileName;
+ }
+
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager.getString("label.tree_calc_"
+ + treeType.toLowerCase());
+
+ /*
+ * i18n description (if any) of score model used
+ */
+ String smn = MessageManager.getStringOrReturn("label.score_model_",
+ modelOrFileName);
+
+ /*
+ * put them together as <method> Using <model>
+ */
+ final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ treecalcnm, smn);
+ return ttl;
+ }
}
git://source.jalview.org / jalview.git / blobdiff