();
+ 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!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
@@ -486,9 +617,11 @@ public class TreePanel
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
@@ -496,9 +629,11 @@ public class TreePanel
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
@@ -506,9 +641,11 @@ public class TreePanel
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
@@ -516,22 +653,23 @@ public class TreePanel
/**
* DOCUMENT ME!
- *
- * @param e 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");
+ "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();
@@ -553,30 +691,25 @@ public class TreePanel
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");
+ 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);
+ EpsGraphics2D pg = new EpsGraphics2D("Tree", out, 0, 0, width, height);
pg.setAccurateTextMode(accurateText);
@@ -584,8 +717,7 @@ public class TreePanel
pg.flush();
pg.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
@@ -593,9 +725,11 @@ public class TreePanel
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
@@ -603,17 +737,13 @@ public class TreePanel
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("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);
@@ -622,23 +752,158 @@ public class TreePanel
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()
+ {
+
+ @Override
+ 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.getDBRefs(),
+ 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);
+ }
+ }
+ }
+ });
+ }
+
+ /**
+ * Formats a localised title for the tree panel, like
+ *
+ * Neighbour Joining Using BLOSUM62
+ *
+ * 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 Using
+ */
+ final String ttl = MessageManager.formatMessage("label.treecalc_title",
+ treecalcnm, smn);
+ return ttl;
+ }
+
+ /**
+ * Gets the score model for the given name. If the score model is one that
+ * requires to get state data from the current view, allow it to do so
+ *
+ * @param sm
+ * @return
+ */
+ protected ScoreModelI configureScoreModel(String modelName)
+ {
+ ScoreModelI sm = ScoreModels.getInstance().forName(modelName);
+ 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());
+ }
+ }
+ return sm;
+ }
}