Implemented CIGAR representation of an Alignment view for passing to

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

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index f636257..a0de682 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -71,7 +71,7 @@ public class TreePanel extends GTreePanel
       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
+      // showDistances(true);\r
     }\r
 \r
     /**\r
@@ -137,7 +137,7 @@ public class TreePanel extends GTreePanel
     class TreeLoader extends Thread\r
     {\r
       NewickFile newtree;\r
-\r
+      jalview.datamodel.CigarArray odata=null;\r
       public TreeLoader(NewickFile newtree)\r
       {\r
         this.newtree = newtree;\r
@@ -153,19 +153,22 @@ public class TreePanel extends GTreePanel
       public void run()\r
       {\r
 \r
-        if(newtree!=null)\r
-          tree = new NJTree(av.alignment.getSequencesArray(),\r
-                            newtree);\r
+        if(newtree!=null) {\r
+\r
+          if (odata==null) {\r
+            tree = new NJTree(av.alignment.getSequencesArray(),\r
+                              newtree);\r
+          } else {\r
+            tree = new NJTree(av.alignment.getSequencesArray(), odata, newtree);\r
+          }\r
+          if (!tree.hasOriginalSequenceData())\r
+            allowOriginalSeqData(false);\r
+        }\r
         else\r
         {\r
           int start, end;\r
           SequenceI [] seqs;\r
-          String [] seqStrings = null;\r
-          if (av.hasHiddenColumns)\r
-          {\r
-            seqStrings = av.getViewAsString(true);\r
-          }\r
-\r
+          CigarArray seqStrings = av.getViewAsCigars(av.getSelectionGroup()!=null);\r
           if(av.getSelectionGroup()==null)\r
           {\r
             start = 0;\r
@@ -180,15 +183,14 @@ public class TreePanel extends GTreePanel
           }\r
 \r
           tree = new NJTree(seqs, seqStrings, type, pwtype, start, end);\r
+          showDistances(true);\r
         }\r
 \r
 \r
         tree.reCount(tree.getTopNode());\r
         tree.findHeight(tree.getTopNode());\r
         treeCanvas.setTree(tree);\r
-\r
         treeCanvas.repaint();\r
-\r
         av.setCurrentTree(tree);\r
 \r
       }\r
@@ -211,7 +213,9 @@ public class TreePanel extends GTreePanel
       placeholdersMenu.setState(b);\r
       treeCanvas.setMarkPlaceholders(b);\r
     }\r
-\r
+    private void allowOriginalSeqData(boolean b) {\r
+      originalSeqData.setVisible(b);\r
+    }\r
 \r
 \r
 \r
@@ -312,10 +316,16 @@ public class TreePanel extends GTreePanel
 \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
+      String originalData = tree.printOriginalSequenceData();\r
+      if (originalData!=null) {\r
+        CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+        cap.setText(originalData);\r
+        Desktop.addInternalFrame(cap, "Original Data",\r
+                                 400, 400);\r
+      } else {\r
+        System.err.println("IMPLEMENTATION BUG! originalSeqData is not available.");\r
+      }\r
+\r
     }\r
 \r
 \r