import jalview.analysis.AlignmentSorter;
import jalview.analysis.NJTree;
+import jalview.analysis.scoremodels.ScoreModels;
+import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
import jalview.api.analysis.ViewBasedAnalysisI;
import jalview.bin.Cache;
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)
{
.println("new alignment sequences vector value is null");
}
- tree.UpdatePlaceHolders((List<SequenceI>) evt.getNewValue());
+ tree.updatePlaceHolders((List<SequenceI>) evt.getNewValue());
treeCanvas.nameHash.clear(); // reset the mapping between canvas
// rectangles and leafnodes
repaint();
seqs = av.getSelectionGroup().getSequencesInOrder(
av.getAlignment());
}
- ScoreModelI sm = ResidueProperties.getScoreModel(pwtype);
- 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());
- }
- tree = new NJTree(seqs, seqStrings, type, pwtype, sm, start, end);
- }
- else
- {
- tree = new NJTree(seqs, seqStrings, type, pwtype, null, start,
- end);
- }
+ ScoreModelI sm = configureScoreModel(pwtype);
+ tree = new NJTree(av, type, sm, SimilarityParams.Jalview);
showDistances(true);
}
{
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 ");
- }
-
- if (pwtype.equals("BL"))
- {
- buffer.append("BLOSUM62");
- }
- else
- {
- buffer.append("PID");
- }
+ String newTitle = getPanelTitle(type, pwtype);
- 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);
+ cap.setText(fout.print(tree.hasBootstrap(), tree.hasDistances(),
+ tree.hasRootDistance()));
+ Desktop.addInternalFrame(cap, newTitle, 500, 100);
} catch (OutOfMemoryError oom)
{
new OOMWarning("generating newick tree file", oom);
{
jalview.io.NewickFile fout = new jalview.io.NewickFile(
tree.getTopNode());
- String output = fout.print(tree.isHasBootstrap(),
- tree.isHasDistances(), tree.isHasRootDistance());
+ String output = fout.print(tree.hasBootstrap(),
+ tree.hasDistances(), tree.hasRootDistance());
java.io.PrintWriter out = new java.io.PrintWriter(
new java.io.FileWriter(choice));
out.println(output);
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);
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
}
});
}
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff