alignment from seqCigars will correctly mark deleted residues as

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 50b1e2b..562440f 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,14 +33,14 @@ public class Sequence implements SequenceI
 {\r
     SequenceI datasetSequence;\r
     String name;\r
-    String sequence;\r
+    private String sequence;\r
     String description;\r
     int start;\r
     int end;\r
     Color color = Color.white;\r
     Vector pdbIds;\r
     String vamsasId;\r
-    Vector dbrefs;\r
+    DBRefEntry [] dbrefs;\r
 \r
     /** This annotation is displayed below the alignment but the\r
      * positions are tied to the residues of this sequence */\r
@@ -445,7 +445,7 @@ public class Sequence implements SequenceI
     public int[] gapMap()\r
     {\r
         // Returns an int array giving the position of each residue in the sequence in the alignment\r
-        String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence);\r
+        String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.GapChars, sequence);\r
         int[] map = new int[seq.length()];\r
         int j = 0;\r
         int p = 0;\r
@@ -560,11 +560,12 @@ public class Sequence implements SequenceI
       vamsasId = id;\r
     }\r
 \r
-    public void setDBRef(Vector dbref)\r
+    public void setDBRef(DBRefEntry [] dbref)\r
     {\r
       dbrefs = dbref;\r
     }\r
-    public Vector getDBRef()\r
+\r
+    public DBRefEntry [] getDBRef()\r
     {\r
       return dbrefs;\r
     }\r
@@ -572,9 +573,14 @@ public class Sequence implements SequenceI
     public void addDBRef(DBRefEntry entry)\r
     {\r
       if(dbrefs == null)\r
-        dbrefs = new Vector();\r
+        dbrefs = new DBRefEntry[0];\r
+\r
+      DBRefEntry [] temp = new DBRefEntry[dbrefs.length+1];\r
+      System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length);\r
+\r
+      temp[temp.length-1] = entry;\r
 \r
-      dbrefs.addElement(entry);\r
+      dbrefs = temp;\r
     }\r
 \r
     public void setDatasetSequence(SequenceI seq)\r