();
- for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+ 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)
+ 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)
+ for (CommandI tsort : commands)
{
tsort.doCommand(views);
- }
+ }
}
});
- for (AlignmentPanel ap: PaintRefresher.getAssociatedPanels(av
+ 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));
+ }
+ else
+ {
+ treeCanvas.ap.alignFrame
+ .addHistoryItem(sortAlignmentIn(treeCanvas.ap));
}
}
+
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;
- undo=new OrderCommand("Tree Sort", oldOrder,
- av.alignment);
+ undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
- ap.paintAlignment(true);
+ ap.paintAlignment(true);
return undo;
}
+
/**
* DOCUMENT ME!
*
* @param e
* DOCUMENT ME!
*/
+ @Override
public void font_actionPerformed(ActionEvent e)
{
if (treeCanvas == null)
@@ -610,6 +621,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void distanceMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowDistances(distanceMenu.isSelected());
@@ -621,6 +633,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void bootstrapMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setShowBootstrap(bootstrapMenu.isSelected());
@@ -632,6 +645,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void placeholdersMenu_actionPerformed(ActionEvent e)
{
treeCanvas.setMarkPlaceholders(placeholdersMenu.isSelected());
@@ -643,6 +657,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void epsTree_actionPerformed(ActionEvent e)
{
boolean accurateText = true;
@@ -676,23 +691,22 @@ 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("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);
@@ -715,6 +729,7 @@ public class TreePanel extends GTreePanel
* @param e
* DOCUMENT ME!
*/
+ @Override
public void pngTree_actionPerformed(ActionEvent e)
{
int width = treeCanvas.getWidth();
@@ -722,14 +737,13 @@ 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("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);
@@ -770,6 +784,7 @@ public class TreePanel extends GTreePanel
tree.applyToNodes(new NodeTransformI()
{
+ @Override
public void transform(BinaryNode node)
{
if (node instanceof SequenceNode
@@ -782,8 +797,8 @@ 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++)
@@ -827,4 +842,68 @@ public class TreePanel extends GTreePanel
}
});
}
+
+ /**
+ * 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;
+ }
}