RefreshPanels after a colour change

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 3fa1379..dd02bc1 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
@@ -318,6 +318,24 @@ public class Alignment implements AlignmentI
 \r
     }\r
     return null;\r
+  }\r
+\r
+  public SequenceGroup [] findAllGroups(SequenceI s)\r
+  {\r
+\r
+    ArrayList temp = new ArrayList();\r
+\r
+    for (int i = 0; i < this.groups.size();i++)\r
+    {\r
+      SequenceGroup sg = (SequenceGroup)groups.elementAt(i);\r
+      if (sg.sequences.contains(s))\r
+       temp.add(sg);\r
+    }\r
+\r
+    SequenceGroup [] ret = new SequenceGroup[temp.size()];\r
+    temp.toArray( ret );\r
+\r
+    return ret;\r
 \r
   }\r
   /**    */\r
@@ -385,12 +403,14 @@ 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