X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FTreePanel.java;h=25f4c1be3835a0e5d97e75f877e3ec9a7c08e365;hb=517dab88dfe59707fe225eac761d3c46719a72eb;hp=6ce68b3383874aed94b20e7158f434055e76cc80;hpb=7b39c1ea0410b4cc8410b69b2d008ed0af3b6cb5;p=jalview.git diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 6ce68b3..25f4c1b 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 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. * @@ -42,7 +42,9 @@ 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; import java.awt.Font; import java.awt.Graphics; @@ -138,7 +140,7 @@ public class TreePanel extends GTreePanel return treeCanvas.av.getAlignment(); } - public AlignViewport getViewPort() + public AlignmentViewport getViewPort() { return treeCanvas.av; } @@ -160,6 +162,7 @@ public class TreePanel extends GTreePanel av.addPropertyChangeListener(new java.beans.PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -195,6 +198,7 @@ public class TreePanel extends GTreePanel } + @Override public void viewMenu_menuSelected() { buildAssociatedViewMenu(); @@ -230,6 +234,7 @@ public class TreePanel extends GTreePanel buttonGroup.add(item); item.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = false; @@ -242,11 +247,13 @@ public class TreePanel extends GTreePanel 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() { + @Override public void actionPerformed(ActionEvent evt) { treeCanvas.applyToAllViews = itemf.isSelected(); @@ -274,6 +281,7 @@ public class TreePanel extends GTreePanel } } + @Override public void run() { @@ -343,7 +351,7 @@ public class TreePanel extends GTreePanel av.setCurrentTree(tree); if (av.getSortByTree()) { - sortByTree_actionPerformed(null); + sortByTree_actionPerformed(); } } } @@ -387,6 +395,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void textbox_actionPerformed(ActionEvent e) { CutAndPasteTransfer cap = new CutAndPasteTransfer(); @@ -432,12 +441,14 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void saveAsNewick_actionPerformed(ActionEvent e) { JalviewFileChooser chooser = new JalviewFileChooser( jalview.bin.Cache.getProperty("LAST_DIRECTORY")); chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_tree_as_newick")); + chooser.setDialogTitle(MessageManager + .getString("label.save_tree_as_newick")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(null); @@ -471,12 +482,14 @@ public class TreePanel extends GTreePanel * @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()) @@ -508,8 +521,8 @@ public class TreePanel extends GTreePanel { // 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) { @@ -531,8 +544,8 @@ public class TreePanel extends GTreePanel // msaorder); Desktop.addInternalFrame(af, MessageManager.formatMessage( - "label.original_data_for_params", new String[] - { this.title }), AlignFrame.DEFAULT_WIDTH, + "label.original_data_for_params", + new Object[] { this.title }), AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); } } @@ -544,6 +557,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void fitToWindow_actionPerformed(ActionEvent e) { treeCanvas.fitToWindow = fitToWindow.isSelected(); @@ -555,7 +569,8 @@ public class TreePanel extends GTreePanel * * @param e */ - public void sortByTree_actionPerformed(ActionEvent e) + @Override + public void sortByTree_actionPerformed() { if (treeCanvas.applyToAllViews) @@ -617,7 +632,7 @@ public class TreePanel extends GTreePanel public CommandI sortAlignmentIn(AlignmentPanel ap) { - AlignViewport av = ap.av; + AlignmentViewport av = ap.av; SequenceI[] oldOrder = av.getAlignment().getSequencesArray(); AlignmentSorter.sortByTree(av.getAlignment(), tree); CommandI undo; @@ -633,6 +648,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void font_actionPerformed(ActionEvent e) { if (treeCanvas == null) @@ -662,6 +678,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void distanceMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowDistances(distanceMenu.isSelected()); @@ -673,6 +690,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void bootstrapMenu_actionPerformed(ActionEvent e) { treeCanvas.setShowBootstrap(bootstrapMenu.isSelected()); @@ -684,6 +702,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void placeholdersMenu_actionPerformed(ActionEvent e) { treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected()); @@ -695,6 +714,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void epsTree_actionPerformed(ActionEvent e) { boolean accurateText = true; @@ -728,23 +748,22 @@ public class TreePanel extends GTreePanel 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()); - chooser.setDialogTitle(MessageManager.getString("label.create_eps_from_tree")); + 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); @@ -767,6 +786,7 @@ public class TreePanel extends GTreePanel * @param e * DOCUMENT ME! */ + @Override public void pngTree_actionPerformed(ActionEvent e) { int width = treeCanvas.getWidth(); @@ -774,13 +794,12 @@ public class TreePanel extends GTreePanel 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.getString("label.create_png_from_tree")); + chooser.setDialogTitle(MessageManager + .getString("label.create_png_from_tree")); chooser.setToolTipText(MessageManager.getString("action.save")); int value = chooser.showSaveDialog(this); @@ -822,6 +841,7 @@ public class TreePanel extends GTreePanel tree.applyToNodes(new NodeTransformI() { + @Override public void transform(BinaryNode node) { if (node instanceof SequenceNode @@ -834,8 +854,8 @@ public class TreePanel extends GTreePanel { // search dbrefs, features and annotation DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs( - sq.getDBRef(), new String[] - { labelClass.toUpperCase() }); + sq.getDBRefs(), + new String[] { labelClass.toUpperCase() }); if (refs != null) { for (int i = 0; i < refs.length; i++)