Use the isGap method in utils

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3fa1379..f480f0f 100755 (executable)
--- 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)\r
         {\r
            /* MC Should move this to a method somewhere */\r
-          if (current.getCharAt(i)!='-' && current.getCharAt(i)!='.' && current.getCharAt(i)!=' ')\r
+          if ( !jalview.util.Comparison.isGap(current.getCharAt(i)))\r
             delete = false;\r
 \r
         }\r
@@ -385,12 +385,14 @@ public class Alignment implements AlignmentI
   }\r
 \r
   /**    */\r
-  public int findIndex(SequenceI s) {\r
+  public int findIndex(SequenceI s)\r
+  {\r
     int i=0;\r
-    while (i < sequences.size()) {\r
-      if (s == getSequenceAt(i)) {\r
+    while (i < sequences.size())\r
+    {\r
+      if (s == getSequenceAt(i))\r
         return i;\r
-      }\r
+\r
       i++;\r
     }\r
     return -1;\r

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7feadb9..c0216aa 100755 (executable)
--- 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);\r
       jSize = current.getLength();\r
       for (int j=0; j < jSize; j++)\r
-        if (current.getCharAt(j)=='-' || current.getCharAt(j)=='.' || current.getCharAt(j)==' ')\r
+        if(jalview.util.Comparison.isGap(current.getCharAt(i)))\r
         {\r
           current.deleteCharAt(j);\r
           j--;\r

diff --git a/src/jalview/gui/ScorePanel.java b/src/jalview/gui/ScorePanel.java
index b4bb3c9..e6ba4b3 100755 (executable)
--- 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 /\r
                     Float.parseFloat(hash.get("size").toString()) * 55);\r
 \r
-     if (character != ' ' && character != '.' && character != '-')\r
+     if ( !jalview.util.Comparison.isGap(character))\r
        g.fillRect( (int) (i * av.charWidth),\r
                   60 - value,\r
                   (int) av.charWidth,\r

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 82124ce..5022050 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -101,7 +101,7 @@ try{
         else\r
           s = ' ';\r
 \r
-        if(!renderGaps && (s=='-' || s=='.' || s==' '))\r
+        if(!renderGaps && jalview.util.Comparison.isGap(s))\r
           continue;\r
 \r
         g.setColor(Color.black);\r