only recalc group conservation after last sequence operated on in a bulk add/remove...

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 7be007a..da6c6e5 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -73,7 +73,7 @@ public class AppVarna extends JInternalFrame implements
 
   AlignmentPanel ap;
 
-  public AppVarna(SequenceI seq, String strucseq, String struc,
+  public AppVarna(String sname, SequenceI seq, String strucseq, String struc,
           String name, AlignmentPanel ap)
   {
     this.ap = ap;
@@ -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()));