{\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
sequenceFeatures = features;\r
}\r
\r
- public void addSequenceFeature(SequenceFeature sf)\r
+ public synchronized void addSequenceFeature(SequenceFeature sf)\r
{\r
if(sequenceFeatures==null)\r
{\r
System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);\r
temp[sequenceFeatures.length] = sf;\r
\r
-\r
sequenceFeatures = temp;\r
}\r
\r
- SequenceFeature [] sfarray;\r
-\r
- public SequenceFeature[] getsfarray()\r
- {\r
- return sfarray;\r
- }\r
-\r
\r
/**\r
* DOCUMENT ME!\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
- dbrefs.addElement(entry);\r
+ temp[temp.length-1] = entry;\r
+\r
+ dbrefs = temp;\r
}\r
\r
public void setDatasetSequence(SequenceI seq)\r
public void showHiddenSequence(SequenceI seq)\r
{\r
hiddenSequences.deleteSequence(seq, false);\r
- if (hiddenSequences.getSize() < 1)\r
+ if (hiddenSequences.getSize(false) < 1)\r
{\r
hiddenSequences = null;\r
}\r
-\r
}\r
\r
public void changeCase(boolean toUpper, int start, int end)\r