From: jprocter <Jim Procter>
Date: Thu, 10 May 2007 08:41:07 +0000 (+0000)
Subject: documentation
X-Git-Tag: Release_2_3~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c8a5e53fe8b07e36f805fd7e21568064c20922f0;p=jalview.git

documentation
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 70752be..c7887da 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1619,19 +1619,17 @@ public class AlignFrame
            AlignmentAnnotation sann[] = sequences[i].getAnnotation();
            if (sann == null)
              continue;
-           for (int avnum = 0; avnum < alview.length; avnum++)
+           for (int avnum=0;avnum<alview.length; avnum++)
            {
-
-             if (alview[avnum] != alignment)
+             if (alview[avnum]!=alignment)
              {
                // duplicate in a view other than the one with input focus
-               int avwidth = alview[avnum].getWidth() + 1;
-
-               // this relies on sann being preserved after we modify the sequence's annotation array
+               int avwidth = alview[avnum].getWidth()+1;
+               // this relies on sann being preserved after we 
+               // modify the sequence's annotation array for each duplication
                for (int a=0; a<sann.length; a++)
                {
                  AlignmentAnnotation newann = new AlignmentAnnotation(sann[a]);
-
                  sequences[i].addAlignmentAnnotation(newann);
                  newann.padAnnotation(avwidth);
                  alview[avnum].addAnnotation(newann); // annotation was duplicated earlier