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 8e821a2..6988615 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -39,7 +39,7 @@ public class Sequence implements SequenceI
     int start;\r
     int end;\r
     Color color = Color.white;\r
-    String pdbId;\r
+    Vector pdbIds;\r
     String vamsasId;\r
     Vector dbrefs;\r
 \r
@@ -96,6 +96,7 @@ public class Sequence implements SequenceI
            {\r
              if (st.countTokens() == 2)\r
              {\r
+\r
                shortName = st.nextToken();\r
 \r
                limits = st.nextToken();\r
@@ -108,6 +109,10 @@ public class Sequence implements SequenceI
                  setEnd(Integer.valueOf(st.nextToken()).intValue());\r
                }\r
              }\r
+\r
+             // If we're still in this loop, parsing of start and end was ok\r
+             // Therefore remove it from the sequence name\r
+             name = name.substring(0, name.indexOf("/"));\r
            }\r
            catch (NumberFormatException ex)\r
            {\r
@@ -116,6 +121,7 @@ public class Sequence implements SequenceI
              shortName += "/" + limits;\r
            }\r
          }\r
+\r
     }\r
 \r
     void checkValidRange()\r
@@ -191,14 +197,22 @@ 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
      * @param id DOCUMENT ME!\r
      */\r
-    public void setPDBId(String id)\r
+    public void setPDBId(Vector id)\r
     {\r
-        pdbId = id;\r
+        pdbIds = id;\r
     }\r
 \r
     /**\r
@@ -206,9 +220,9 @@ public class Sequence implements SequenceI
      *\r
      * @return DOCUMENT ME!\r
      */\r
-    public String getPDBId()\r
+    public Vector getPDBId()\r
     {\r
-        return pdbId;\r
+        return pdbIds;\r
     }\r
 \r
     /**\r
@@ -408,9 +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
@@ -616,4 +628,9 @@ public class Sequence implements SequenceI
       return datasetSequence;\r
     }\r
 \r
+    public String getShortName()\r
+    {\r
+      return shortName;\r
+    }\r
+\r
 }\r