String vamsasId;\r
Vector dbrefs;\r
\r
+ /** This annotation is displayed below the alignment but the\r
+ * positions are tied to the residues of this sequence */\r
+ Vector annotation;\r
\r
/** DOCUMENT ME!! */\r
- public Vector sequenceFeatures;\r
+ public SequenceFeature [] sequenceFeatures;\r
\r
/**\r
* Creates a new Sequence object.\r
*\r
* @param v DOCUMENT ME!\r
*/\r
- public void setSequenceFeatures(Vector v)\r
+ public void setSequenceFeatures(SequenceFeature [] features)\r
{\r
- sequenceFeatures = v;\r
+ sequenceFeatures = features;\r
}\r
\r
public void addSequenceFeature(SequenceFeature sf)\r
{\r
if(sequenceFeatures==null)\r
- sequenceFeatures = new Vector();\r
+ {\r
+ sequenceFeatures = new SequenceFeature[0];\r
+ }\r
+\r
+ SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];\r
+ System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);\r
+ temp[sequenceFeatures.length] = sf;\r
\r
- sequenceFeatures.addElement(sf);\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
*\r
* @return DOCUMENT ME!\r
*/\r
- public Vector getSequenceFeatures()\r
+ public SequenceFeature [] getSequenceFeatures()\r
{\r
return sequenceFeatures;\r
}\r
return datasetSequence;\r
}\r
\r
+ public AlignmentAnnotation [] getAnnotation()\r
+ {\r
+ if(annotation==null)\r
+ return null;\r
+\r
+ AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];\r
+ for(int r = 0; r<ret.length; r++)\r
+ ret[r] = (AlignmentAnnotation)annotation.elementAt(r);\r
+\r
+ return ret;\r
+ }\r
+\r
+ public void addAlignmentAnnotation(AlignmentAnnotation annotation)\r
+ {\r
+ if(this.annotation==null)\r
+ this.annotation = new Vector();\r
+\r
+ this.annotation.addElement( annotation );\r
+ }\r
+\r
}\r