{\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
+ 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
+ public synchronized void addSequenceFeature(SequenceFeature sf)\r
{\r
if(sequenceFeatures==null)\r
- sequenceFeatures = new Vector();\r
+ {\r
+ sequenceFeatures = new SequenceFeature[0];\r
+ }\r
+\r
+ for(int i=0; i<sequenceFeatures.length; i++)\r
+ {\r
+ if(sequenceFeatures[i].equals(sf))\r
+ {\r
+ return;\r
+ }\r
+ }\r
\r
- sequenceFeatures.addElement(sf);\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 = temp;\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
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
}\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
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
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
+ 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(false) < 1)\r
+ {\r
+ hiddenSequences = null;\r
+ }\r
+ }\r
+\r
+ public void changeCase(boolean toUpper, int start, int end)\r
+ {\r
+ StringBuffer newSeq = new StringBuffer();\r
+\r
+ if(end>sequence.length())\r
+ end = sequence.length();\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
+ public void toggleCase(int start, int end)\r
+ {\r
+ StringBuffer newSeq = new StringBuffer();\r
+\r
+ if(end>sequence.length())\r
+ end = sequence.length();\r
+\r
+ if (start > 0)\r
+ {\r
+ newSeq.append(sequence.substring(0, start));\r
+ }\r
+\r
+ char nextChar;\r
+ for(int c=start; c<end; c++)\r
+ {\r
+ nextChar = sequence.charAt(c);\r
+ if(Character.isLetter(nextChar))\r
+ {\r
+ if(Character.isUpperCase(nextChar))\r
+ nextChar = Character.toLowerCase(nextChar);\r
+ else\r
+ nextChar = Character.toUpperCase(nextChar);\r
+ }\r
+\r
+\r
+ newSeq.append(nextChar);\r
+ }\r
+\r
+ if (end < sequence.length())\r
+ newSeq.append(sequence.substring(end));\r
+\r
+ sequence = newSeq.toString();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff