RefreshPanels after a colour change

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cc5d760..d35cbe8 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -144,19 +144,18 @@ public class Sequence implements SequenceI
 \r
     while (i< sequence.length() && j <= end && j <= pos) {\r
 \r
-      String s = sequence.substring(i,i+1);\r
+      char c = sequence.charAt(i);\r
 \r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         j++;\r
-      }\r
+\r
       i++;\r
     }\r
-    if (j == end && j < pos) {\r
+    if (j == end && j < pos)\r
       return end+1;\r
-    } else {\r
-\r
+    else\r
       return i;\r
-    }\r
+\r
   }\r
 \r
   public int findPosition(int i) {\r
@@ -164,12 +163,13 @@ public class Sequence implements SequenceI
     int j   = 0;\r
     int pos = start;\r
 \r
-    while (j < i) {\r
-      String s = sequence.substring(j,j+1);\r
+    while (j < i)\r
+    {\r
+      char c = sequence.charAt(j);\r
 \r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         pos++;\r
-      }\r
+\r
       j++;\r
     }\r
     return pos;\r