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
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
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
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