Highlight hidden columns after revealing

[jalview.git] / src / jalview / gui / TreePanel.java

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 1d197c3..190f15c 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -49,13 +49,11 @@ import java.beans.PropertyChangeEvent;
  */\r
 public class TreePanel extends GTreePanel\r
 {\r
-    SequenceI[] seq;\r
     String type;\r
     String pwtype;\r
-    int start;\r
-    int end;\r
     TreeCanvas treeCanvas;\r
     NJTree tree;\r
+    AlignViewport av;\r
 \r
     /**\r
      * Creates a new TreePanel object.\r
@@ -67,11 +65,10 @@ public class TreePanel extends GTreePanel
      * @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
       super();\r
-      initTreePanel(av, seqVector, type, pwtype, s, e, null);\r
+      initTreePanel(av, type, pwtype, null);\r
 \r
       // We know this tree has distances. JBPNote TODO: prolly should add this as a userdefined default\r
       showDistances(true);\r
@@ -86,28 +83,28 @@ public class TreePanel extends GTreePanel
      * @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
       super();\r
-      initTreePanel(av, seqVector, type, pwtype, 0, seqVector.size(), newtree);\r
+      initTreePanel(av, type, pwtype, newtree);\r
     }\r
 \r
+    public AlignmentI getAlignment()\r
+    {\r
+      return treeCanvas.av.getAlignment();\r
+    }\r
 \r
-    void initTreePanel(AlignViewport av, Vector seqVector, String type,\r
-                       String pwtype, int s, int e, NewickFile newTree)\r
+\r
+    void initTreePanel(AlignViewport av, String type,  String pwtype,\r
+                       NewickFile newTree)\r
     {\r
 \r
       this.type = type;\r
       this.pwtype = pwtype;\r
 \r
-      start = s;\r
-      end = e;\r
-\r
-      seq = new Sequence[seqVector.size()];\r
-      seqVector.toArray(seq);\r
-\r
-\r
       treeCanvas = new TreeCanvas(av, scrollPane);\r
       scrollPane.setViewportView(treeCanvas);\r
 \r
@@ -129,6 +126,8 @@ public class TreePanel extends GTreePanel
         }\r
       });\r
 \r
+      this.av = av;\r
+\r
 \r
       TreeLoader tl = new TreeLoader(newTree);\r
       tl.start();\r
@@ -153,10 +152,36 @@ public class TreePanel extends GTreePanel
 \r
       public void run()\r
       {\r
+\r
         if(newtree!=null)\r
-          tree = new NJTree(seq, newtree);\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
 \r
         tree.reCount(tree.getTopNode());\r
         tree.findHeight(tree.getTopNode());\r
@@ -164,6 +189,8 @@ public class TreePanel extends GTreePanel
 \r
         treeCanvas.repaint();\r
 \r
+        av.setCurrentTree(tree);\r
+\r
       }\r
     }\r
 \r
@@ -231,7 +258,7 @@ public class TreePanel extends GTreePanel
         Desktop.addInternalFrame(cap, buffer.toString(), 500, 100);\r
 \r
         jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
-        cap.setText(fout.print(false, true));\r
+        cap.setText(fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance()));\r
     }\r
 \r
     /**\r
@@ -258,7 +285,7 @@ public class TreePanel extends GTreePanel
             try\r
             {\r
                 jalview.io.NewickFile fout = new jalview.io.NewickFile(tree.getTopNode());\r
-                String output = fout.print(false, true); // distances only\r
+                String output = fout.print(tree.isHasBootstrap(), tree.isHasDistances(), tree.isHasRootDistance());\r
                 java.io.PrintWriter out = new java.io.PrintWriter(new java.io.FileWriter(\r
                             choice));\r
                 out.println(output);\r
@@ -282,6 +309,16 @@ public class TreePanel extends GTreePanel
         treeCanvas.startPrinting();\r
     }\r
 \r
+\r
+    public void originalSeqData_actionPerformed(ActionEvent e)\r
+    {\r
+      CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+      cap.setText(tree.printOriginalSequenceData());\r
+      Desktop.addInternalFrame(cap, "Original Data",\r
+          400, 400);\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r