From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 2 Nov 2015 15:00:13 +0000 (+0000)
Subject: JAL-1934 new preference to disable gap character normalisation when a new alignment... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d6810f1440c5b8c04d70445b53995231be56d57b;hp=41808a1d23eee33a6f16d62fac65ec096f57b332;p=jalview.git

JAL-1934 new preference to disable gap character normalisation when a new alignment view is constructed.
---

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 92c6355..a4b9a36 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -274,9 +274,11 @@ public class AlignViewport extends AlignmentViewport implements
 
     setFont(new Font(fontName, style, Integer.parseInt(fontSize)), true);
 
-    alignment
-            .setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(0));
-
+    if (Cache.getDefault("NORMALISE_GAPS", true))
+    {
+      alignment.setGapCharacter(Cache.getDefault("GAP_SYMBOL", "-").charAt(
+              0));
+    }
     // We must set conservation and consensus before setting colour,
     // as Blosum and Clustal require this to be done
     if (hconsensus == null && !isDataset)
@@ -482,6 +484,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getGapCharacter()
   {
     return getAlignment().getGapCharacter();
@@ -506,6 +509,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return colSel;
@@ -617,6 +621,7 @@ public class AlignViewport extends AlignmentViewport implements
   /**
    * Send the current selection to be broadcast to any selection listeners.
    */
+  @Override
   public void sendSelection()
   {
     jalview.structure.StructureSelectionManager
@@ -736,6 +741,7 @@ public class AlignViewport extends AlignmentViewport implements
     return seqvectors.toArray(new SequenceI[seqvectors.size()][]);
   }
 
+  @Override
   public boolean isNormaliseSequenceLogo()
   {
     return normaliseSequenceLogo;
@@ -750,6 +756,7 @@ public class AlignViewport extends AlignmentViewport implements
    * 
    * @return true if alignment characters should be displayed
    */
+  @Override
   public boolean isValidCharWidth()
   {
     return validCharWidth;