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
checkValidRange();\r
}\r
\r
- static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
+ com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
"[/][0-9]{1,}[-][0-9]{1,}$");\r
- static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
"[0-9]{1,}$");\r
\r
void parseId()\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