Don't initialise a char in findIndex

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d90c231..6988615 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -197,6 +197,14 @@ public class Sequence implements SequenceI
         return sequenceFeatures;\r
     }\r
 \r
+    public void addPDBId(PDBEntry entry)\r
+    {\r
+      if(pdbIds == null)\r
+        pdbIds = new Vector();\r
+\r
+      pdbIds.addElement(entry);\r
+    }\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -414,9 +422,7 @@ public class Sequence implements SequenceI
 \r
         while ((i < sequence.length()) && (j <= end) && (j <= pos))\r
         {\r
-            char c = sequence.charAt(i);\r
-\r
-            if (!jalview.util.Comparison.isGap((c)))\r
+            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))\r
             {\r
                 j++;\r
             }\r
@@ -622,4 +628,9 @@ public class Sequence implements SequenceI
       return datasetSequence;\r
     }\r
 \r
+    public String getShortName()\r
+    {\r
+      return shortName;\r
+    }\r
+\r
 }\r