From 8af8289df86798d5e283e1d0aa275b8f98e563dc Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 17 Dec 2004 14:18:13 +0000
Subject: [PATCH] Use the isGap method in utils

---
 src/jalview/datamodel/Alignment.java  |   12 +++++++-----
 src/jalview/gui/AlignFrame.java       |    2 +-
 src/jalview/gui/ScorePanel.java       |    2 +-
 src/jalview/gui/SequenceRenderer.java |    2 +-
 4 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3fa1379..f480f0f 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -112,7 +112,7 @@ public class Alignment implements AlignmentI
         if (current.getLength() > i)
         {
 	    /* MC Should move this to a method somewhere */
-          if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')
+          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))
             delete = false;
 
         }
@@ -385,12 +385,14 @@ public class Alignment implements AlignmentI
   }
 
   /**    */
-  public int findIndex(SequenceI s) {
+  public int findIndex(SequenceI s)
+  {
     int i=0;
-    while (i < sequences.size()) {
-      if (s == getSequenceAt(i)) {
+    while (i < sequences.size())
+    {
+      if (s == getSequenceAt(i))
         return i;
-      }
+
       i++;
     }
     return -1;
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7feadb9..c0216aa 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -280,7 +280,7 @@ public class AlignFrame extends GAlignFrame
       current = viewport.getAlignment().getSequenceAt(i);
       jSize = current.getLength();
       for (int j=0; j < jSize; j++)
-        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')
+        if(jalview.util.Comparison.isGap(current.getCharAt(i)))
         {
           current.deleteCharAt(j);
           j--;
diff --git a/src/jalview/gui/ScorePanel.java b/src/jalview/gui/ScorePanel.java
index b4bb3c9..e6ba4b3 100755
--- a/src/jalview/gui/ScorePanel.java
+++ b/src/jalview/gui/ScorePanel.java
@@ -92,7 +92,7 @@ public class ScorePanel extends JPanel
      value = (int) ( (float) value /
                     Float.parseFloat(hash.get("size").toString()) * 55);
 
-     if (character != ' ' && character != '.' && character != '-')
+     if ( !jalview.util.Comparison.isGap(character))
        g.fillRect( (int) (i * av.charWidth),
                   60 - value,
                   (int) av.charWidth,
diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 82124ce..5022050 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -101,7 +101,7 @@ try{
         else
           s = ' ';
 
-        if(!renderGaps && (s=='-' || s=='.' || s==' '))
+        if(!renderGaps && jalview.util.Comparison.isGap(s))
           continue;
 
         g.setColor(Color.black);
-- 
1.7.10.2