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.api.analysis.ScoreModelI;
-import jalview.api.analysis.SimilarityParamsI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.OrderCommand;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
-import jalview.ext.archaeopteryx.Testo;
+import jalview.ext.archaeopteryx.ArchaeopteryxNewickInit;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.io.NewickFile;
import java.awt.event.ActionListener;
import java.awt.image.BufferedImage;
import java.beans.PropertyChangeEvent;
-import java.io.File;
import java.io.FileOutputStream;
-import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
*/
public class TreePanel extends GTreePanel
{
- String treeType;
+ String substitutionMatrix;
- String scoreModelName; // if tree computed
+ String treeType;
String treeTitle; // if tree loaded
- SimilarityParamsI similarityParams;
-
TreeCanvas treeCanvas;
TreeModel tree;
* Creates a new TreePanel object.
*
* @param ap
- * @param type
- * @param modelName
- * @param options
+ * @param tree
*/
- public TreePanel(AlignmentPanel ap, String type, String modelName,
- SimilarityParamsI options)
+ public TreePanel(AlignmentPanel ap, TreeModel tree, String treeType,
+ String substitutionMatrix)
{
super();
- this.similarityParams = options;
- initTreePanel(ap, type, modelName, null, null);
+ this.treeType = treeType;
+ this.substitutionMatrix = substitutionMatrix;
+ this.tree = tree;
+ initNewTreePanel(ap, tree);
// We know this tree has distances. JBPNote TODO: prolly should add this as
// a userdefined default
// showDistances(true);
}
+ /**
+ * Creates a new TreePanel object.
+ *
+ * @param alignPanel
+ * @param newtree
+ * @param theTitle
+ * @param inputData
+ * @param viewport
+ */
public TreePanel(AlignmentPanel alignPanel, NewickFile newtree,
String theTitle, AlignmentView inputData)
{
super();
this.treeTitle = theTitle;
- initTreePanel(alignPanel, null, null, newtree, inputData);
+ initLoadedTreePanel(alignPanel, newtree, inputData);
}
public AlignmentI getAlignment()
return treeCanvas.av;
}
- void initTreePanel(AlignmentPanel ap, String type, String modelName,
+ void initNewTreePanel(AlignmentPanel ap, TreeModel tree)
+ {
+ buildTreeCanvas(ap);
+
+ TreeLoader tl = new TreeLoader(null, null);
+ tl.start();
+
+ }
+ void initLoadedTreePanel(AlignmentPanel ap,
NewickFile newTree, AlignmentView inputData)
{
+ buildTreeCanvas(ap);
- av = ap.av;
- this.treeType = type;
- this.scoreModelName = modelName;
+ TreeLoader tl = new TreeLoader(newTree, inputData);
+ tl.start();
+ }
+
+public void buildTreeCanvas(AlignmentPanel ap) {
+ av = ap.av;
treeCanvas = new TreeCanvas(this, ap, scrollPane);
scrollPane.setViewportView(treeCanvas);
+
PaintRefresher.Register(this, ap.av.getSequenceSetId());
buildAssociatedViewMenu();
});
- TreeLoader tl = new TreeLoader(newTree, inputData);
- tl.start();
+
}
class TreeLoader extends Thread
{
- private NewickFile newtree;
+ private NewickFile newTree;
private AlignmentView odata = null;
public TreeLoader(NewickFile newickFile, AlignmentView inputData)
{
- this.newtree = newickFile;
+ this.newTree = newickFile;
this.odata = inputData;
- if (newickFile != null)
+ if (newTree != null)
{
// Must be outside run(), as Jalview2XML tries to
// update distance/bootstrap visibility at the same time
- showBootstrap(newickFile.hasBootstrap());
- showDistances(newickFile.hasDistances());
+ showBootstrap(newTree.hasBootstrap());
+ showDistances(newTree.hasDistances());
}
public void run()
{
- if (newtree != null)
+ if (newTree != null)
{
tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
- newtree);
+ newTree);
if (tree.getOriginalData() == null)
{
originalSeqData.setVisible(false);
}
+
+
+
}
- else
- {
- 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);
- }
+ showTree(tree);
+ }
+
+ public void showTree(TreeModel tree)
+ {
tree.reCount(tree.getTopNode());
tree.findHeight(tree.getTopNode());
treeCanvas.setTree(tree);
treeCanvas.repaint();
- Testo test = new Testo();
- NewickFile newickTree = test.treeToNewick(tree);
- File newickAsFile = test.newickToArchaeopteryx(newickTree);
- try
- {
- String[] archaeCommandlineArgs = {
- "-open", newickAsFile.getCanonicalPath() };
- test.startArchaeopteryx(archaeCommandlineArgs);
- } catch (IOException e)
- {
- e.printStackTrace();
- }
av.setCurrentTree(tree);
if (av.getSortByTree())
{
sortByTree_actionPerformed();
}
+
+ ArchaeopteryxNewickInit archae = new ArchaeopteryxNewickInit(tree);
+ archae.startArchaeopteryx();
}
}
*
* @return
*/
- public String getPanelTitle()
+ public String getPanelTitle() // to be moved/fixed
{
if (treeTitle != null)
{
return treeTitle;
}
-
- /*
- * i18n description of Neighbour Joining or Average Distance method
- */
- String treecalcnm = MessageManager
- .getString("label.tree_calc_" + treeType.toLowerCase());
-
- /*
- * short score model name (long description can be too long)
- */
- String smn = scoreModelName;
-
- /*
- * put them together as <method> Using <model>
- */
- final String ttl = MessageManager.formatMessage("label.treecalc_title",
- treecalcnm, smn);
- return ttl;
+ else
+ {
+ /*
+ * i18n description of Neighbour Joining or Average Distance method
+ */
+ String treecalcnm = MessageManager
+ .getString("label.tree_calc_" + treeType.toLowerCase());
+
+ /*
+ * short score model name (long description can be too long)
+ */
+ String smn = substitutionMatrix;
+
+ /*
+ * put them together as <method> Using <model>
+ */
+ final String ttl = MessageManager
+ .formatMessage("label.treecalc_title", treecalcnm, smn);
+ return ttl;
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff