From 0c0f58648af5512096275b634158c37c87989eaa Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Tue, 18 Jul 2006 15:50:18 +0000
Subject: [PATCH] Modified for hidden region/group calculation

---
 src/jalview/appletgui/AlignFrame.java      |   21 ++------
 src/jalview/appletgui/PCAPanel.java        |    2 +-
 src/jalview/appletgui/RedundancyPanel.java |   71 +++++++++++++++-------------
 src/jalview/appletgui/TreePanel.java       |   59 +++++++++++++++--------
 4 files changed, 83 insertions(+), 70 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d1b2da9..2b53d76 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1624,21 +1624,9 @@ public void itemStateChanged(ItemEvent evt)
 
     }
 
-    final TreePanel tp;
-    if (viewport.getSelectionGroup() != null &&
-        viewport.getSelectionGroup().getSize(false) > 3)
-    {
-      tp = new TreePanel(viewport,
-                         viewport.getSelectionGroup().getSequences(false),
+    final TreePanel tp = new TreePanel(viewport,
                          type,
-                         pwType,
-                         0, viewport.alignment.getWidth());
-    }
-    else
-    {
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),
-                         type, pwType, 0, viewport.alignment.getWidth());
-    }
+                         pwType);
 
     addTreeMenuItem(tp, title);
 
@@ -1658,8 +1646,9 @@ public void itemStateChanged(ItemEvent evt)
   public void loadTree(jalview.io.NewickFile tree, String treeFile)
   {
     TreePanel tp = new TreePanel(viewport,
-                      viewport.getAlignment().getSequences(),
-                      tree, "From File - ", treeFile);
+                                 treeFile,
+                                 "From File - ",
+                                 tree);
     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
     addTreeMenuItem(tp, treeFile);
   }
diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 849a0a9..6465ee8 100755
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -90,7 +90,7 @@ public class PCAPanel
    */
   public void run()
   {
-              pca = new PCA(seqs);
+              pca = null;//new PCA(seqs);
               pca.run();
 
               // Now find the component coordinates
diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index c71fe29..7608cb9 100755
--- a/src/jalview/appletgui/RedundancyPanel.java
+++ b/src/jalview/appletgui/RedundancyPanel.java
@@ -33,10 +33,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
   AlignmentPanel ap;
 
   Stack historyList = new Stack(); // simpler than synching with alignFrame.
-  Vector originalSequences;
-  Hashtable originalColours;
-  SequenceI[] oldAlignment;
   float [] redundancy;
+  SequenceI [] originalSequences;
+  Hashtable originalColours;
   Frame frame;
 
   public RedundancyPanel(AlignmentPanel ap)
@@ -95,65 +94,69 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
       validate();
 
-      Vector sel = new Vector();
+      String[] omitHidden = null;
+
       SequenceGroup sg = ap.av.getSelectionGroup();
       int height;
-      originalSequences = new Vector();
+
       originalColours = new Hashtable();
+      int start, end;
 
       if ( (sg != null) && (sg.getSize(false) >= 1))
       {
-         height = sg.getSize(false);
-        for (int i = 0; i < sg.getSize(false); i++)
-        {
-          sel.addElement(sg.getSequenceAt(i));
-        }
+         originalSequences = sg.getSequencesInOrder(ap.av.alignment);
+         start = sg.getStartRes();
+         end = sg.getEndRes();
       }
       else
       {
-        height = ap.av.alignment.getHeight();
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)
-        {
-          sel.addElement(ap.av.alignment.getSequenceAt(i));
-        }
+        originalSequences = ap.av.alignment.getSequencesArray();
+        start = 0;
+        end = ap.av.alignment.getWidth();
       }
 
+      height = originalSequences.length;
+
       redundancy = new float[height];
       for (int i = 0; i < height; i++)
       {
         redundancy[i] = 0f;
       }
 
+    //  if (ap.av.hasHiddenColumns)
+      {
+     //   omitHidden = ap.av.getSelectionAsString();
+      }
+
 
      // long start = System.currentTimeMillis();
 
       float pid;
-      SequenceI seqi, seqj;
-      for (int i = 0; i < sel.size(); i++)
+      String seqi, seqj;
+      for (int i = 0; i < height; i++)
       {
-          originalSequences.addElement(sel.elementAt(i));
-          originalColours.put(sel.elementAt(i),
-                             ((SequenceI) sel.elementAt(i)).getColor());
+          originalColours.put(originalSequences[i],
+                             originalSequences[i].getColor());
 
           for (int j = 0; j < i; j++)
           {
             if(i==j)
               continue;
 
-            seqi = (SequenceI) sel.elementAt(i);
-            seqj = (SequenceI) sel.elementAt(j);
-
-            if (sg != null)
+            if(omitHidden==null)
             {
-              pid = jalview.util.Comparison.PID(seqi,
-                                                seqj,
-                                                sg.getStartRes(), sg.getEndRes());
+              seqi = originalSequences[i].getSequence(start, end);
+              seqj = originalSequences[j].getSequence(start, end);
             }
             else
-              pid = jalview.util.Comparison.PID( seqi,  seqj );
+            {
+              seqi = omitHidden[i];
+              seqj = omitHidden[j];
+            }
 
+            pid = jalview.util.Comparison.PID( seqi,  seqj );
 
-            if(seqj.getLength() < seqi.getLength())
+            if(seqj.length() < seqi.length())
               redundancy[j] = Math.max(pid, redundancy[j]);
             else
               redundancy[i] = Math.max(pid, redundancy[i]);
@@ -181,9 +184,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     for(int i=0; i<redundancy.length; i++)
     {
       if (value > redundancy[i])
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);
+         originalSequences[i].setColor(java.awt.Color.white);
       else
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);
+         originalSequences[i].setColor(java.awt.Color.red);
     }
 
     PaintRefresher.Refresh(null,ap.av.alignment);
@@ -212,7 +215,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
             {
               if (value <= redundancy[i])
               {
-                SequenceI seq = (SequenceI) originalSequences.elementAt(i);
+                SequenceI seq = originalSequences[i];
                 ap.av.alignment.deleteSequence(seq);
                 del.addElement(seq);
                 if (sg != null)
@@ -270,9 +273,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 
   public void windowClosing(WindowEvent evt)
   {
-    for(int i=0; i<originalSequences.size(); i++)
+    for(int i=0; i<originalSequences.length; i++)
     {
-      SequenceI seq = (SequenceI)originalSequences.elementAt(i);
+      SequenceI seq = originalSequences[i];
       seq.setColor( (java.awt.Color)originalColours.get(seq));
     }
 
diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 6d17918..e770a16 100755
--- a/src/jalview/appletgui/TreePanel.java
+++ b/src/jalview/appletgui/TreePanel.java
@@ -54,8 +54,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param s DOCUMENT ME!
    * @param e DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, Vector seqVector, String type,
-                   String pwtype, int s, int e)
+  public TreePanel(AlignViewport av, String type, String pwtype)
   {
     try
     {
@@ -67,7 +66,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       ex.printStackTrace();
     }
 
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);
+    initTreePanel(av, type, pwtype, null);
   }
 
   /**
@@ -79,8 +78,10 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param type DOCUMENT ME!
    * @param pwtype DOCUMENT ME!
    */
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,
-                   String type, String pwtype)
+  public TreePanel(AlignViewport av,
+                   String type,
+                   String pwtype,
+                   NewickFile newtree)
   {
     try
     {
@@ -92,26 +93,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       e.printStackTrace();
     }
 
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);
+    initTreePanel(av, type, pwtype, newtree);
   }
 
 
-  void initTreePanel(AlignViewport av, Vector seqVector, String type,
-                     String pwtype, int s, int e, NewickFile newTree)
+  void initTreePanel(AlignViewport av,
+                     String type,
+                     String pwtype,
+                     NewickFile newTree)
   {
 
     this.av = av;
     this.type = type;
     this.pwtype = pwtype;
 
-    start = s;
-    end = e;
-
-    seq = new Sequence[seqVector.size()];
-    for(int i=0; i<seqVector.size(); i++)
-      seq[i] = (SequenceI)seqVector.elementAt(i);
-
-
     treeCanvas = new TreeCanvas(av, scrollPane);
     scrollPane.add(treeCanvas);
 
@@ -132,10 +127,34 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 
     public void run()
     {
-      if(newtree!=null)
-        tree = new NJTree(seq, newtree);
+      if (newtree != null)
+        tree = new NJTree(av.alignment.getSequencesArray(),
+                          newtree);
       else
-        tree = new NJTree(seq, type, pwtype, start, end);
+        {
+          int start, end;
+          SequenceI [] seqs;
+          String [] seqStrings = null;
+       //   if (av.hasHiddenColumns)
+          {
+        //    seqStrings = av.getSelectionAsString();
+          }
+
+          if(av.getSelectionGroup()==null)
+          {
+            start = 0;
+            end = av.alignment.getWidth();
+            seqs = av.alignment.getSequencesArray();
+          }
+          else
+          {
+            start = av.getSelectionGroup().getStartRes();
+            end = av.getSelectionGroup().getEndRes()+1;
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);
+          }
+
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);
+        }
 
       tree.reCount(tree.getTopNode());
       tree.findHeight(tree.getTopNode());
@@ -213,6 +232,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   }
 
 
+
+
   BorderLayout borderLayout1 = new BorderLayout();
   protected ScrollPane scrollPane = new ScrollPane();
   MenuBar jMenuBar1 = new MenuBar();
-- 
1.7.10.2