X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreePanel.java;h=905a54ad815c372e84c1847a37aaa207b2be79cb;hb=933794f42ed55d57850424e3459a54cd2d92c933;hp=65f3d9156a22cf76fb34df2f4fa5eb0b48648c92;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 65f3d91..905a54a 100644
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -1,28 +1,51 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.io.*;
+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.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceI;
+import jalview.io.NewickFile;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.CheckboxMenuItem;
+import java.awt.Color;
+import java.awt.Menu;
+import java.awt.MenuBar;
+import java.awt.MenuItem;
+import java.awt.ScrollPane;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.ItemEvent;
+import java.awt.event.ItemListener;
public class TreePanel extends EmbmenuFrame implements ActionListener,
ItemListener
@@ -39,17 +62,18 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
TreeCanvas treeCanvas;
- NJTree tree;
+ TreeModel tree;
AlignmentPanel ap;
AlignViewport av;
- public NJTree getTree()
+ public TreeModel getTree()
{
return tree;
}
+ @Override
public void finalize() throws Throwable
{
ap = null;
@@ -140,7 +164,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
// yields unaligned seqs)
// or create a selection box around columns in alignment view
// test Alignment(SeqCigar[])
- if (tree.seqData != null)
+ if (tree.getOriginalData() != null)
{
char gc = '-';
try
@@ -151,8 +175,8 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
} catch (Exception ex)
{
}
- ;
- Object[] alAndColsel = tree.seqData
+
+ Object[] alAndColsel = tree.getOriginalData()
.getAlignmentAndColumnSelection(gc);
if (alAndColsel != null && alAndColsel[0] != null)
@@ -181,43 +205,21 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
this.newtree = newtree;
}
+ @Override
public void run()
{
if (newtree != null)
{
- if (odata == null)
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), newtree);
- }
- else
- {
- tree = new NJTree(av.getAlignment().getSequencesArray(), odata,
- newtree);
- }
-
+ tree = new TreeModel(av.getAlignment().getSequencesArray(), odata,
+ newtree);
}
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());
- }
-
- tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+ ScoreModelI sm = configureScoreModel(pwtype);
+ TreeBuilder njtree = type.equals(TreeBuilder.NEIGHBOUR_JOINING) ? new NJTree(
+ av, sm, SimilarityParams.Jalview)
+ : new AverageDistanceTree(av, sm, SimilarityParams.Jalview);
+ tree = new TreeModel(njtree);
}
tree.reCount(tree.getTopNode());
@@ -248,6 +250,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
}
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == newickOutput)
@@ -264,6 +267,7 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
}
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == fitToWindow)
@@ -351,22 +355,24 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
setLayout(borderLayout1);
this.setBackground(Color.white);
this.setFont(new java.awt.Font("Verdana", 0, 12));
- jMenu2.setLabel("View");
- fontSize.setLabel("Font...");
+ jMenu2.setLabel(MessageManager.getString("action.view"));
+ fontSize.setLabel(MessageManager.getString("action.font"));
fontSize.addActionListener(this);
- bootstrapMenu.setLabel("Show Bootstrap Values");
+ bootstrapMenu.setLabel(MessageManager
+ .getString("label.show_bootstrap_values"));
bootstrapMenu.addItemListener(this);
- distanceMenu.setLabel("Show Distances");
+ distanceMenu.setLabel(MessageManager.getString("label.show_distances"));
distanceMenu.addItemListener(this);
- placeholdersMenu.setLabel("Mark Unassociated Leaves");
+ placeholdersMenu.setLabel(MessageManager
+ .getString("label.mark_unassociated_leaves"));
placeholdersMenu.addItemListener(this);
fitToWindow.setState(true);
- fitToWindow.setLabel("Fit To Window");
+ fitToWindow.setLabel(MessageManager.getString("label.fit_to_window"));
fitToWindow.addItemListener(this);
- fileMenu.setLabel("File");
- newickOutput.setLabel("Newick Format");
+ fileMenu.setLabel(MessageManager.getString("action.file"));
+ newickOutput.setLabel(MessageManager.getString("label.newick_format"));
newickOutput.addActionListener(this);
- inputData.setLabel("Input Data...");
+ inputData.setLabel(MessageManager.getString("label.input_data"));
add(scrollPane, BorderLayout.CENTER);
jMenuBar1.add(fileMenu);
@@ -381,4 +387,29 @@ public class TreePanel extends EmbmenuFrame implements ActionListener,
inputData.addActionListener(this);
}
+ /**
+ * 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;
+ }
+
}