();
+ 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)
{
- buffer.append("Neighbour joining tree using ");
+ for (CommandI tsort : commands)
+ {
+ tsort.undoCommand(views);
+ }
}
- if (pwtype.equals("BL"))
+ @Override
+ public int getSize()
{
- buffer.append("BLOSUM62");
+ return commands.size();
}
- else
+
+ @Override
+ public String getDescription()
{
- buffer.append("PID");
+ return "Tree Sort (many views)";
}
- Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);
-
- 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!
- */
- public void saveAsNewick_actionPerformed(ActionEvent e)
- {
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
- "LAST_DIRECTORY"));
- chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Save tree as newick file");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(null);
-
- if (value == JalviewFileChooser.APPROVE_OPTION)
+ @Override
+ public void doCommand(AlignmentI[] views)
{
- String choice = chooser.getSelectedFile().getPath();
- 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));
- out.println(output);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ 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();
+ }
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void printMenu_actionPerformed(ActionEvent e)
+ else
{
- //Putting in a thread avoids Swing painting problems
- treeCanvas.startPrinting();
+ treeCanvas.ap.alignFrame
+ .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
}
-
- public void originalSeqData_actionPerformed(ActionEvent e)
+ }
+
+ public CommandI sortAlignmentIn(AlignmentPanel ap)
+ {
+ AlignmentViewport viewport = ap.av;
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
+ CommandI undo;
+ undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
+
+ ap.paintAlignment(true);
+ return undo;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void font_actionPerformed(ActionEvent e)
+ {
+ if (treeCanvas == null)
{
- if (!tree.hasOriginalSequenceData())
- {
- 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)
- // or create a selection box around columns in alignment view
- // test Alignment(SeqCigar[])
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(av.
- getGapCharacter());
-
-
- if (alAndColsel != null && alAndColsel[0]!=null)
- {
- // AlignmentOrder origorder = new AlignmentOrder(alAndColsel[0]);
-
- Alignment al = new Alignment((SequenceI[]) alAndColsel[0]);
- Alignment dataset = av.getAlignment().getDataset();
- 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
-);
-
- //>>>This is a fix for the moment, until a better solution is found!!<<<
- // af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
-
- // af.addSortByOrderMenuItem(ServiceName + " Ordering",
- // msaorder);
-
- Desktop.addInternalFrame(af, "Original Data for " + this.title,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- }
- }
+ return;
}
+ new FontChooser(this);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void fitToWindow_actionPerformed(ActionEvent e)
- {
- treeCanvas.fitToWindow = fitToWindow.isSelected();
- repaint();
- }
+ public Font getTreeFont()
+ {
+ return treeCanvas.font;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void font_actionPerformed(ActionEvent e)
+ public void setTreeFont(Font f)
+ {
+ if (treeCanvas != null)
{
- if (treeCanvas == null)
- {
- return;
- }
-
- new FontChooser(this);
+ treeCanvas.setFont(f);
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void distanceMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowDistances(distanceMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void bootstrapMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void placeholdersMenu_actionPerformed(ActionEvent e)
+ {
+ treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void epsTree_actionPerformed(ActionEvent e)
+ {
+ boolean accurateText = true;
+
+ String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
+ "Prompt each time");
- public Font getTreeFont()
+ // 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")))
{
- return treeCanvas.font;
- }
+ EPSOptions eps = new EPSOptions();
+ renderStyle = eps.getValue();
- public void setTreeFont(Font font)
- {
- if(treeCanvas!=null)
- treeCanvas.setFont(font);
- }
+ if (renderStyle == null || eps.cancelled)
+ {
+ return;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void distanceMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setShowDistances(distanceMenu.isSelected());
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void bootstrapMenu_actionPerformed(ActionEvent e)
+ if (renderStyle.equalsIgnoreCase("text"))
{
- treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
+ accurateText = false;
}
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void placeholdersMenu_actionPerformed(ActionEvent e)
- {
- treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
- }
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void epsTree_actionPerformed(ActionEvent e)
+ try
{
- boolean accurateText = true;
+ 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"));
- String renderStyle = jalview.bin.Cache.getDefault("EPS_RENDERING",
- "Prompt each time");
+ int value = chooser.showSaveDialog(this);
- // 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")))
+ if (value != JalviewFileChooser.APPROVE_OPTION)
{
- EPSOptions eps = new EPSOptions();
- renderStyle = eps.getValue();
+ return;
+ }
- if (renderStyle==null || eps.cancelled)
- return;
+ Cache.setProperty("LAST_DIRECTORY",
+ chooser.getSelectedFile().getParent());
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width,
+ height);
- }
+ pg.setAccurateTextMode(accurateText);
- if (renderStyle.equalsIgnoreCase("text"))
- {
- accurateText = false;
- }
+ treeCanvas.draw(pg, width, height);
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
+ pg.flush();
+ pg.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void pngTree_actionPerformed(ActionEvent e)
+ {
+ int width = treeCanvas.getWidth();
+ int height = treeCanvas.getHeight();
+
+ try
+ {
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ ImageMaker.PNG_EXTENSION, ImageMaker.PNG_DESCRIPTION);
- 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("Create EPS file from tree");
- chooser.setToolTipText("Save");
+ chooser.setFileView(new jalview.io.JalviewFileView());
+ chooser.setDialogTitle(
+ MessageManager.getString("label.create_png_from_tree"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
- int value = chooser.showSaveDialog(this);
+ int value = chooser.showSaveDialog(this);
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
- {
- return;
- }
+ if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ {
+ 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);
+ FileOutputStream out = new FileOutputStream(
+ chooser.getSelectedFile());
- pg.setAccurateTextMode(accurateText);
+ BufferedImage bi = new BufferedImage(width, height,
+ BufferedImage.TYPE_INT_RGB);
+ Graphics png = bi.getGraphics();
- treeCanvas.draw(pg, width, height);
+ treeCanvas.draw(png, width, height);
- pg.flush();
- pg.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
+ ImageIO.write(bi, "png", out);
+ out.close();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void pngTree_actionPerformed(ActionEvent e)
+ }
+
+ /**
+ * 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()
{
- int width = treeCanvas.getWidth();
- int height = treeCanvas.getHeight();
- try
+ @Override
+ public void transform(BinaryNode node)
+ {
+ if (node instanceof SequenceNode
+ && !((SequenceNode) node).isPlaceholder()
+ && !((SequenceNode) node).isDummy())
{
- 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");
-
- chooser.setFileView(new jalview.io.JalviewFileView());
- chooser.setDialogTitle("Create PNG image from tree");
- chooser.setToolTipText("Save");
-
- int value = chooser.showSaveDialog(this);
-
- if (value != jalview.io.JalviewFileChooser.APPROVE_OPTION)
+ String newname = null;
+ SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+ if (sq != null)
+ {
+ // search dbrefs, features and annotation
+ DBRefEntry[] refs = jalview.util.DBRefUtils
+ .selectRefs(sq.getDBRefs(), new String[]
+ { labelClass.toUpperCase() });
+ if (refs != null)
{
- return;
+ 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 oldname in the undo object for this modification.
+ ((SequenceNode) node).setName(newname);
+ }
+ }
+ }
+ });
+ }
+
+ /**
+ * Formats a localised title for the tree panel, like
+ *
+ * Neighbour Joining Using BLOSUM62
+ *
+ * For a tree loaded from file, just uses the file name
+ *
+ * @return
+ */
+ public String getPanelTitle()
+ {
+ if (treeTitle != null)
+ {
+ return treeTitle;
+ }
- 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);
- Graphics png = bi.getGraphics();
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
- treeCanvas.draw(png, width, height);
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = scoreModelName;
- ImageIO.write(bi, "png", out);
- out.close();
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
+ /*
+ * put them together as Using
+ */
+ final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ treecalcnm, smn);
+ return ttl;
+ }
}