Vector annotation;\r
\r
/** DOCUMENT ME!! */\r
- public Vector sequenceFeatures;\r
+ public SequenceFeature [] sequenceFeatures;\r
+\r
+ /** This array holds hidden sequences\r
+ * of which this sequence is the representitive member of a group\r
+ */\r
+ SequenceGroup hiddenSequences;\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
- sequenceFeatures.addElement(sf);\r
+ for(int i=0; i<sequenceFeatures.length; i++)\r
+ {\r
+ if(sequenceFeatures[i].equals(sf))\r
+ {\r
+ return;\r
+ }\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
+\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
}\r
}\r
\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- * @param c DOCUMENT ME!\r
- */\r
- public void insertCharAt(int i, char c)\r
- {\r
- insertCharAt(i, c, true);\r
- }\r
\r
/**\r
* DOCUMENT ME!\r
* @param c DOCUMENT ME!\r
* @param chop DOCUMENT ME!\r
*/\r
- public void insertCharAt(int i, char c, boolean chop)\r
+ public void insertCharAt(int i, char c)\r
{\r
String tmp = new String(sequence);\r
\r
this.annotation.addElement( annotation );\r
}\r
\r
+ public SequenceGroup getHiddenSequences()\r
+ {\r
+ return hiddenSequences;\r
+ }\r
+\r
+ public void addHiddenSequence(SequenceI seq)\r
+ {\r
+ if(hiddenSequences==null)\r
+ {\r
+ hiddenSequences = new SequenceGroup();\r
+ }\r
+ hiddenSequences.addSequence(seq, false);\r
+ }\r
+\r
+ public void showHiddenSequence(SequenceI seq)\r
+ {\r
+ hiddenSequences.deleteSequence(seq, false);\r
+ if (hiddenSequences.getSize() < 1)\r
+ {\r
+ hiddenSequences = null;\r
+ }\r
+\r
+ }\r
+\r
+ public void changeCase(boolean toUpper, int start, int end)\r
+ {\r
+ StringBuffer newSeq = new StringBuffer();\r
+\r
+\r
+ if (start > 0)\r
+ {\r
+ newSeq.append(sequence.substring(0, start));\r
+ }\r
+\r
+ if (toUpper)\r
+ newSeq.append(sequence.substring(start, end).toUpperCase());\r
+ else\r
+ newSeq.append(sequence.substring(start, end).toLowerCase());\r
+\r
+ if (end < sequence.length())\r
+ newSeq.append(sequence.substring(end));\r
+\r
+ sequence = newSeq.toString();\r
+ }\r
+\r
}\r