package jalview.gui;
import jalview.analysis.AlignmentSorter;
+import jalview.analysis.AverageDistanceTree;
import jalview.analysis.NJTree;
+import jalview.analysis.TreeBuilder;
+import jalview.analysis.TreeModel;
import jalview.analysis.scoremodels.ScoreModels;
-import jalview.analysis.scoremodels.SimilarityParams;
import jalview.api.analysis.ScoreModelI;
-import jalview.api.analysis.ViewBasedAnalysisI;
+import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
-import jalview.datamodel.ColumnSelection;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.NodeTransformI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
*/
public class TreePanel extends GTreePanel
{
- String type;
+ String treeType;
- String pwtype;
+ String scoreModelName; // if tree computed
+
+ String treeTitle; // if tree loaded
+
+ SimilarityParamsI similarityParams;
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignViewport av;
/**
* Creates a new TreePanel object.
*
- * @param av
- * DOCUMENT ME!
- * @param seqVector
- * DOCUMENT ME!
+ * @param ap
* @param type
- * DOCUMENT ME!
- * @param pwtype
- * DOCUMENT ME!
- * @param s
- * DOCUMENT ME!
- * @param e
- * DOCUMENT ME!
+ * @param modelName
+ * @param options
*/
- public TreePanel(AlignmentPanel ap, String type, String pwtype)
+ public TreePanel(AlignmentPanel ap, String type, String modelName,
+ SimilarityParamsI options)
{
super();
- initTreePanel(ap, type, pwtype, null, null);
+ this.similarityParams = options;
+ initTreePanel(ap, type, modelName, null, null);
// We know this tree has distances. JBPNote TODO: prolly should add this as
// a userdefined default
// showDistances(true);
}
- public TreePanel(AlignmentPanel av, String type, String pwtype,
- NewickFile newtree, AlignmentView inputData)
+ public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
+ String theTitle, AlignmentView inputData)
{
super();
- initTreePanel(av, type, pwtype, newtree, inputData);
+ this.treeTitle = theTitle;
+ initTreePanel(alignPanel, null, null, newtree, inputData);
}
public AlignmentI getAlignment()
return treeCanvas.av;
}
- void initTreePanel(AlignmentPanel ap, String type, String pwtype,
+ void initTreePanel(AlignmentPanel ap, String type, String modelName,
NewickFile newTree, AlignmentView inputData)
{
av = ap.av;
- this.type = type;
- this.pwtype = pwtype;
+ this.treeType = type;
+ this.scoreModelName = modelName;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
}
});
- TreeLoader tl = new TreeLoader(newTree);
- if (inputData != null)
- {
- tl.odata = inputData;
- }
+ TreeLoader tl = new TreeLoader(newTree, inputData);
tl.start();
}
class TreeLoader extends Thread
{
- NewickFile newtree;
+ private NewickFile newtree;
- jalview.datamodel.AlignmentView odata = null;
+ private AlignmentView odata = null;
- public TreeLoader(NewickFile newtree)
+ public TreeLoader(NewickFile newickFile, AlignmentView inputData)
{
- this.newtree = newtree;
- if (newtree != null)
+ this.newtree = newickFile;
+ this.odata = inputData;
+
+ if (newickFile != null)
{
// Must be outside run(), as Jalview2XML tries to
// update distance/bootstrap visibility at the same time
- showBootstrap(newtree.HasBootstrap());
- showDistances(newtree.HasDistances());
+ showBootstrap(newickFile.HasBootstrap());
+ showDistances(newickFile.HasDistances());
}
}
if (newtree != null)
{
- if (odata == null)
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
- }
- else
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
- }
- if (!tree.hasOriginalSequenceData())
+ tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ newtree);
+ if (tree.getOriginalData() == null)
{
- allowOriginalSeqData(false);
+ originalSeqData.setVisible(false);
}
}
else
{
- int start, end;
- SequenceI[] seqs;
- boolean selview = av.getSelectionGroup() != null
- && av.getSelectionGroup().getSize() > 1;
- AlignmentView seqStrings = av.getAlignmentView(selview);
- if (!selview)
- {
- start = 0;
- end = av.getAlignment().getWidth();
- seqs = av.getAlignment().getSequencesArray();
- }
- else
- {
- start = av.getSelectionGroup().getStartRes();
- end = av.getSelectionGroup().getEndRes() + 1;
- seqs = av.getSelectionGroup().getSequencesInOrder(
- av.getAlignment());
- }
- ScoreModelI sm = configureScoreModel(pwtype);
- tree = new NJTree(av, type, sm, SimilarityParams.Jalview);
+ ScoreModelI sm = ScoreModels.getInstance().getScoreModel(
+ scoreModelName, treeCanvas.ap);
+ TreeBuilder njtree = treeType.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+ av, sm, similarityParams) : new AverageDistanceTree(av, sm,
+ similarityParams);
+ tree = new TreeModel(njtree);
showDistances(true);
}
treeCanvas.setMarkPlaceholders(b);
}
- private void allowOriginalSeqData(boolean b)
- {
- originalSeqData.setVisible(b);
- }
-
/**
* DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}
{
CutAndPasteTransfer cap = new CutAndPasteTransfer();
- String newTitle = getPanelTitle(type, pwtype);
+ String newTitle = getPanelTitle();
NewickFile fout = new NewickFile(tree.getTopNode());
try
@Override
public void originalSeqData_actionPerformed(ActionEvent e)
{
- if (!tree.hasOriginalSequenceData())
+ AlignmentView originalData = tree.getOriginalData();
+ if (originalData == null)
{
jalview.bin.Cache.log
.info("Unexpected call to originalSeqData_actionPerformed - should have hidden this menu action.");
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = tree.seqData.getAlignmentAndColumnSelection(gc);
+
+ Object[] alAndColsel = originalData.getAlignmentAndHiddenColumns(gc);
if (alAndColsel != null && alAndColsel[0] != null)
{
if (true)
{
// make a new frame!
- AlignFrame af = new AlignFrame(al,
- (ColumnSelection) alAndColsel[1], AlignFrame.DEFAULT_WIDTH,
+ AlignFrame af = new AlignFrame(al, (HiddenColumns) alAndColsel[1],
+ AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
// >>>This is a fix for the moment, until a better solution is
public CommandI sortAlignmentIn(AlignmentPanel ap)
{
- AlignmentViewport av = ap.av;
- SequenceI[] oldOrder = av.getAlignment().getSequencesArray();
- AlignmentSorter.sortByTree(av.getAlignment(), tree);
+ AlignmentViewport viewport = ap.av;
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
+ AlignmentSorter.sortByTree(viewport.getAlignment(), tree);
CommandI undo;
- undo = new OrderCommand("Tree Sort", oldOrder, av.getAlignment());
+ undo = new OrderCommand("Tree Sort", oldOrder, viewport.getAlignment());
ap.paintAlignment(true);
return undo;
return treeCanvas.font;
}
- public void setTreeFont(Font font)
+ public void setTreeFont(Font f)
{
if (treeCanvas != null)
{
- treeCanvas.setFont(font);
+ treeCanvas.setFont(f);
}
}
}
if (newname == null)
{
- SequenceFeature sf[] = sq.getSequenceFeatures();
- for (int i = 0; sf != null && i < sf.length; i++)
+ List<SequenceFeature> features = sq.getFeatures()
+ .getPositionalFeatures(labelClass);
+ for (SequenceFeature feature : features)
{
- if (sf[i].getType().equals(labelClass))
+ if (newname == null)
{
- if (newname == null)
- {
- newname = new String(sf[i].getDescription());
- }
- else
- {
- newname = newname + "; " + sf[i].getDescription();
- }
+ newname = feature.getDescription();
+ }
+ else
+ {
+ newname = newname + "; " + feature.getDescription();
}
}
}
}
if (newname != null)
{
- String oldname = ((SequenceNode) node).getName();
- // TODO : save in the undo object for this modification.
+ // String oldname = ((SequenceNode) node).getName();
+ // TODO : save oldname in the undo object for this modification.
((SequenceNode) node).setName(newname);
}
}
* 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)
+ public String getPanelTitle()
{
- if (NJTree.FROM_FILE.equals(treeType))
+ if (treeTitle != null)
{
- return modelOrFileName;
+ return treeTitle;
}
/*
+ treeType.toLowerCase());
/*
- * i18n description (if any) of score model used
+ * short score model name (long description can be too long)
*/
- String smn = MessageManager.getStringOrReturn("label.score_model_",
- modelOrFileName);
+ String smn = scoreModelName;
/*
* put them together as <method> Using <model>
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