formatting

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

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index da6c6e5..ce5c7b0 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -73,8 +73,8 @@ public class AppVarna extends JInternalFrame implements
 
   AlignmentPanel ap;
 
-  public AppVarna(String sname, 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;
     ArrayList<RNA> rnaList = new ArrayList<RNA>();
@@ -89,12 +89,12 @@ public class AppVarna extends JInternalFrame implements
     {
       e3.printStackTrace();
     }
-    RNA trim = trimRNA(rna1, "trimmed "+sname);
+    RNA trim = trimRNA(rna1, "trimmed " + sname);
     rnaList.add(trim);
     rnaList.add(rna1);
     rnas.put(seq, rna1);
     rnas.put(seq, trim);
-    rna1.setName(sname+" (with gaps)");
+    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 = sname+" trimmed to "+name;
+    this.name = sname + " trimmed to " + name;
     initVarna();
     ssm = ap.getStructureSelectionManager();
     ssm.addStructureViewerListener(this);
@@ -333,9 +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);
@@ -392,7 +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