Modified for hidden region/group calculation

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index d1b2da9..2b53d76 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1624,21 +1624,9 @@ public void itemStateChanged(ItemEvent evt)
 \r
     }\r
 \r
-    final TreePanel tp;\r
-    if (viewport.getSelectionGroup() != null &&\r
-        viewport.getSelectionGroup().getSize(false) > 3)\r
-    {\r
-      tp = new TreePanel(viewport,\r
-                         viewport.getSelectionGroup().getSequences(false),\r
+    final TreePanel tp = new TreePanel(viewport,\r
                          type,\r
-                         pwType,\r
-                         0, viewport.alignment.getWidth());\r
-    }\r
-    else\r
-    {\r
-      tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
-                         type, pwType, 0, viewport.alignment.getWidth());\r
-    }\r
+                         pwType);\r
 \r
     addTreeMenuItem(tp, title);\r
 \r
@@ -1658,8 +1646,9 @@ public void itemStateChanged(ItemEvent evt)
   public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
   {\r
     TreePanel tp = new TreePanel(viewport,\r
-                      viewport.getAlignment().getSequences(),\r
-                      tree, "From File - ", treeFile);\r
+                                 treeFile,\r
+                                 "From File - ",\r
+                                 tree);\r
     jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
     addTreeMenuItem(tp, treeFile);\r
   }\r

diff --git a/src/jalview/appletgui/PCAPanel.java b/src/jalview/appletgui/PCAPanel.java
index 849a0a9..6465ee8 100755 (executable)
--- a/src/jalview/appletgui/PCAPanel.java
+++ b/src/jalview/appletgui/PCAPanel.java
@@ -90,7 +90,7 @@ public class PCAPanel
    */\r
   public void run()\r
   {\r
-              pca = new PCA(seqs);\r
+              pca = null;//new PCA(seqs);\r
               pca.run();\r
 \r
               // Now find the component coordinates\r

diff --git a/src/jalview/appletgui/RedundancyPanel.java b/src/jalview/appletgui/RedundancyPanel.java
index c71fe29..7608cb9 100755 (executable)
--- 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;\r
 \r
   Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
-  Vector originalSequences;\r
-  Hashtable originalColours;\r
-  SequenceI[] oldAlignment;\r
   float [] redundancy;\r
+  SequenceI [] originalSequences;\r
+  Hashtable originalColours;\r
   Frame frame;\r
 \r
   public RedundancyPanel(AlignmentPanel ap)\r
@@ -95,65 +94,69 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 \r
       validate();\r
 \r
-      Vector sel = new Vector();\r
+      String[] omitHidden = null;\r
+\r
       SequenceGroup sg = ap.av.getSelectionGroup();\r
       int height;\r
-      originalSequences = new Vector();\r
+\r
       originalColours = new Hashtable();\r
+      int start, end;\r
 \r
       if ( (sg != null) && (sg.getSize(false) >= 1))\r
       {\r
-         height = sg.getSize(false);\r
-        for (int i = 0; i < sg.getSize(false); i++)\r
-        {\r
-          sel.addElement(sg.getSequenceAt(i));\r
-        }\r
+         originalSequences = sg.getSequencesInOrder(ap.av.alignment);\r
+         start = sg.getStartRes();\r
+         end = sg.getEndRes();\r
       }\r
       else\r
       {\r
-        height = ap.av.alignment.getHeight();\r
-        for (int i = 0; i < ap.av.alignment.getHeight(); i++)\r
-        {\r
-          sel.addElement(ap.av.alignment.getSequenceAt(i));\r
-        }\r
+        originalSequences = ap.av.alignment.getSequencesArray();\r
+        start = 0;\r
+        end = ap.av.alignment.getWidth();\r
       }\r
 \r
+      height = originalSequences.length;\r
+\r
       redundancy = new float[height];\r
       for (int i = 0; i < height; i++)\r
       {\r
         redundancy[i] = 0f;\r
       }\r
 \r
+    //  if (ap.av.hasHiddenColumns)\r
+      {\r
+     //   omitHidden = ap.av.getSelectionAsString();\r
+      }\r
+\r
 \r
      // long start = System.currentTimeMillis();\r
 \r
       float pid;\r
-      SequenceI seqi, seqj;\r
-      for (int i = 0; i < sel.size(); i++)\r
+      String seqi, seqj;\r
+      for (int i = 0; i < height; i++)\r
       {\r
-          originalSequences.addElement(sel.elementAt(i));\r
-          originalColours.put(sel.elementAt(i),\r
-                             ((SequenceI) sel.elementAt(i)).getColor());\r
+          originalColours.put(originalSequences[i],\r
+                             originalSequences[i].getColor());\r
 \r
           for (int j = 0; j < i; j++)\r
           {\r
             if(i==j)\r
               continue;\r
 \r
-            seqi = (SequenceI) sel.elementAt(i);\r
-            seqj = (SequenceI) sel.elementAt(j);\r
-\r
-            if (sg != null)\r
+            if(omitHidden==null)\r
             {\r
-              pid = jalview.util.Comparison.PID(seqi,\r
-                                                seqj,\r
-                                                sg.getStartRes(), sg.getEndRes());\r
+              seqi = originalSequences[i].getSequence(start, end);\r
+              seqj = originalSequences[j].getSequence(start, end);\r
             }\r
             else\r
-              pid = jalview.util.Comparison.PID( seqi,  seqj );\r
+            {\r
+              seqi = omitHidden[i];\r
+              seqj = omitHidden[j];\r
+            }\r
 \r
+            pid = jalview.util.Comparison.PID( seqi,  seqj );\r
 \r
-            if(seqj.getLength() < seqi.getLength())\r
+            if(seqj.length() < seqi.length())\r
               redundancy[j] = Math.max(pid, redundancy[j]);\r
             else\r
               redundancy[i] = Math.max(pid, redundancy[i]);\r
@@ -181,9 +184,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
     for(int i=0; i<redundancy.length; i++)\r
     {\r
       if (value > redundancy[i])\r
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.white);\r
+         originalSequences[i].setColor(java.awt.Color.white);\r
       else\r
-         ((SequenceI)originalSequences.elementAt(i)).setColor(java.awt.Color.red);\r
+         originalSequences[i].setColor(java.awt.Color.red);\r
     }\r
 \r
     PaintRefresher.Refresh(null,ap.av.alignment);\r
@@ -212,7 +215,7 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
             {\r
               if (value <= redundancy[i])\r
               {\r
-                SequenceI seq = (SequenceI) originalSequences.elementAt(i);\r
+                SequenceI seq = originalSequences[i];\r
                 ap.av.alignment.deleteSequence(seq);\r
                 del.addElement(seq);\r
                 if (sg != null)\r
@@ -270,9 +273,9 @@ public class RedundancyPanel extends SliderPanel implements Runnable, WindowList
 \r
   public void windowClosing(WindowEvent evt)\r
   {\r
-    for(int i=0; i<originalSequences.size(); i++)\r
+    for(int i=0; i<originalSequences.length; i++)\r
     {\r
-      SequenceI seq = (SequenceI)originalSequences.elementAt(i);\r
+      SequenceI seq = originalSequences[i];\r
       seq.setColor( (java.awt.Color)originalColours.get(seq));\r
     }\r
 \r

diff --git a/src/jalview/appletgui/TreePanel.java b/src/jalview/appletgui/TreePanel.java
index 6d17918..e770a16 100755 (executable)
--- 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!\r
    * @param e DOCUMENT ME!\r
    */\r
-  public TreePanel(AlignViewport av, Vector seqVector, String type,\r
-                   String pwtype, int s, int e)\r
+  public TreePanel(AlignViewport av, String type, String pwtype)\r
   {\r
     try\r
     {\r
@@ -67,7 +66,7 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       ex.printStackTrace();\r
     }\r
 \r
-    initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+    initTreePanel(av, type, pwtype, null);\r
   }\r
 \r
   /**\r
@@ -79,8 +78,10 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
    * @param type DOCUMENT ME!\r
    * @param pwtype DOCUMENT ME!\r
    */\r
-  public TreePanel(AlignViewport av, Vector seqVector, NewickFile newtree,\r
-                   String type, String pwtype)\r
+  public TreePanel(AlignViewport av,\r
+                   String type,\r
+                   String pwtype,\r
+                   NewickFile newtree)\r
   {\r
     try\r
     {\r
@@ -92,26 +93,20 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
       e.printStackTrace();\r
     }\r
 \r
-    initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+    initTreePanel(av, type, pwtype, newtree);\r
   }\r
 \r
 \r
-  void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
-                     String pwtype, int s, int e, NewickFile newTree)\r
+  void initTreePanel(AlignViewport av,\r
+                     String type,\r
+                     String pwtype,\r
+                     NewickFile newTree)\r
   {\r
 \r
     this.av = av;\r
     this.type = type;\r
     this.pwtype = pwtype;\r
 \r
-    start = s;\r
-    end = e;\r
-\r
-    seq = new Sequence[seqVector.size()];\r
-    for(int i=0; i<seqVector.size(); i++)\r
-      seq[i] = (SequenceI)seqVector.elementAt(i);\r
-\r
-\r
     treeCanvas = new TreeCanvas(av, scrollPane);\r
     scrollPane.add(treeCanvas);\r
 \r
@@ -132,10 +127,34 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
 \r
     public void run()\r
     {\r
-      if(newtree!=null)\r
-        tree = new NJTree(seq, newtree);\r
+      if (newtree != null)\r
+        tree = new NJTree(av.alignment.getSequencesArray(),\r
+                          newtree);\r
       else\r
-        tree = new NJTree(seq, type, pwtype, start, end);\r
+        {\r
+          int start, end;\r
+          SequenceI [] seqs;\r
+          String [] seqStrings = null;\r
+       //   if (av.hasHiddenColumns)\r
+          {\r
+        //    seqStrings = av.getSelectionAsString();\r
+          }\r
+\r
+          if(av.getSelectionGroup()==null)\r
+          {\r
+            start = 0;\r
+            end = av.alignment.getWidth();\r
+            seqs = av.alignment.getSequencesArray();\r
+          }\r
+          else\r
+          {\r
+            start = av.getSelectionGroup().getStartRes();\r
+            end = av.getSelectionGroup().getEndRes()+1;\r
+            seqs = av.getSelectionGroup().getSequencesInOrder(av.alignment);\r
+          }\r
+\r
+          tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+        }\r
 \r
       tree.reCount(tree.getTopNode());\r
       tree.findHeight(tree.getTopNode());\r
@@ -213,6 +232,8 @@ public class TreePanel extends Frame implements ActionListener, ItemListener
   }\r
 \r
 \r
+\r
+\r
   BorderLayout borderLayout1 = new BorderLayout();\r
   protected ScrollPane scrollPane = new ScrollPane();\r
   MenuBar jMenuBar1 = new MenuBar();\r