formatting

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index cbb3f95..ce5c7b0 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -73,10 +73,10 @@ public class AppVarna extends JInternalFrame implements
 
   AlignmentPanel ap;
 
-  public AppVarna(SequenceI seq, String strucseq, String struc,
-          String name, AlignmentPanel ap)
+  public AppVarna(String sname, SequenceI seq, String strucseq,
+          String struc, String name, AlignmentPanel ap)
   {
-    this.ap=ap;
+    this.ap = ap;
     ArrayList<RNA> rnaList = new ArrayList<RNA>();
     RNA rna1 = new RNA(name);
     try
@@ -89,12 +89,12 @@ public class AppVarna extends JInternalFrame implements
     {
       e3.printStackTrace();
     }
-    RNA trim = trimRNA(rna1);
+    RNA trim = trimRNA(rna1, "trimmed " + sname);
     rnaList.add(trim);
     rnaList.add(rna1);
     rnas.put(seq, rna1);
     rnas.put(seq, trim);
-    rna1.setName("consensus_" + rna1.getName());
+    rna1.setName(sname + " (with gaps)");
 
     {
       seqs.put(trim, seq);
@@ -110,7 +110,7 @@ public class AppVarna extends JInternalFrame implements
     vab = new AppVarnaBinding(rnaList);
     // vab = new AppVarnaBinding(seq,struc);
     // System.out.println("Hallo: "+name);
-    this.name = name;
+    this.name = sname + " trimmed to " + name;
     initVarna();
     ssm = ap.getStructureSelectionManager();
     ssm.addStructureViewerListener(this);
@@ -145,10 +145,10 @@ public class AppVarna extends JInternalFrame implements
     return newStr;
   }
 
-  public RNA trimRNA(RNA rna)
+  public RNA trimRNA(RNA rna, String name)
   {
     ShiftList offset = new ShiftList();
-    RNA rnaTrim = new RNA("trim_" + rna.getName());
+    RNA rnaTrim = new RNA(name);
     try
     {
       rnaTrim.setRNA(rna.getSeq(), replaceOddGaps(rna.getStructDBN()));
@@ -304,12 +304,13 @@ public class AppVarna extends JInternalFrame implements
       if (_lastRNAhighlighted != null)
       {
         _lastRNAhighlighted.removeHighlightRegion(_lastHighlight);
-        if (vab!=null) {
+        if (vab != null)
+        {
           vab.updateSelectedRNA(_lastRNAhighlighted);
         }
         _lastRNAhighlighted = null;
         _lastHighlight = null;
-        
+
       }
     }
   }
@@ -332,9 +333,9 @@ public class AppVarna extends JInternalFrame implements
       ShiftList shift = offsets.get(rna);
       if (shift != null)
       {
-   //      System.err.print("Orig pos:"+index);
-         index = shift.shift(index);
-   //      System.err.println("\nFinal pos:"+index);
+        // System.err.print("Orig pos:"+index);
+        index = shift.shift(index);
+        // System.err.println("\nFinal pos:"+index);
       }
       mouseOverHighlighter.highlightRegion(rna, index, index);
       vab.updateSelectedRNA(rna);
@@ -391,7 +392,7 @@ public class AppVarna extends JInternalFrame implements
       if (shift != null)
       {
         int i = shift.shift(arg1.getIndex());
- //       System.err.println("shifted "+(arg1.getIndex())+" to "+i);
+        // System.err.println("shifted "+(arg1.getIndex())+" to "+i);
         ssm.mouseOverVamsasSequence(seq, i, this);
       }
       else
@@ -404,8 +405,9 @@ public class AppVarna extends JInternalFrame implements
   @Override
   public void onSelectionChanged(BaseList arg0, BaseList arg1, BaseList arg2)
   {
-    // TODO translate selected regions in VARNA to a selection on the alignpanel.
-    
+    // TODO translate selected regions in VARNA to a selection on the
+    // alignpanel.
+
   }
 
 }