*/\r
public class Sequence implements SequenceI\r
{\r
- protected String name;\r
- protected String sequence;\r
- protected String description;\r
- protected int start;\r
- protected int end;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- String pdbId;\r
+ SequenceI datasetSequence;\r
+ String name;\r
+ 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
+\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 = new Vector();\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
this.start = start;\r
this.end = end;\r
\r
+ parseId();\r
+\r
+ checkValidRange();\r
+ }\r
+\r
+ com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
+ "[/][0-9]{1,}[-][0-9]{1,}$");\r
+ com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
+ "[0-9]{1,}$");\r
+\r
+ void parseId()\r
+ {\r
+ // Does sequence have the /start-end signiature?\r
+ if(limitrx.search(name))\r
+ {\r
+ name = limitrx.left();\r
+ endrx.search(limitrx.stringMatched());\r
+ setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));\r
+ setEnd( Integer.parseInt( endrx.stringMatched() ));\r
+ }\r
+ }\r
+\r
+ void checkValidRange()\r
+ {\r
if (end < 1)\r
{\r
int endRes = 0;\r
this.end = endRes;\r
}\r
\r
- setDisplayId();\r
}\r
\r
/**\r
*/\r
public Sequence(String name, String sequence)\r
{\r
- this(name, sequence, 1, sequence.length());\r
+ this(name, sequence, 1, -1);\r
}\r
\r
/**\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
+ {\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
+ 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
+ public void addPDBId(PDBEntry entry)\r
+ {\r
+ if(pdbIds == null)\r
+ pdbIds = new Vector();\r
+\r
+ pdbIds.addElement(entry);\r
+ }\r
+\r
/**\r
* DOCUMENT ME!\r
*\r
* @param id DOCUMENT ME!\r
*/\r
- public void setPDBId(String id)\r
+ public void setPDBId(Vector id)\r
{\r
- pdbId = id;\r
+ pdbIds = id;\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String getPDBId()\r
+ public Vector getPDBId()\r
{\r
- return pdbId;\r
+ return pdbIds;\r
}\r
\r
/**\r
*\r
* @return DOCUMENT ME!\r
*/\r
- public String getDisplayId()\r
+ public String getDisplayId(boolean jvsuffix)\r
{\r
- return displayId;\r
- }\r
+ StringBuffer result = new StringBuffer(name);\r
+ if (jvsuffix)\r
+ {\r
+ result.append("/" + start + "-" + end);\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void setDisplayId()\r
- {\r
- displayId = name + "/" + start + "-" + end;\r
+ return result.toString();\r
}\r
\r
/**\r
*/\r
public void setName(String name)\r
{\r
- this.name = name;\r
- setDisplayId();\r
+ this.name = name;\r
+ this.parseId();\r
}\r
\r
/**\r
*/\r
public String getName()\r
{\r
- return this.name;\r
+ return this.name;\r
}\r
\r
/**\r
public void setStart(int start)\r
{\r
this.start = start;\r
- setDisplayId();\r
}\r
\r
/**\r
public void setEnd(int end)\r
{\r
this.end = end;\r
- setDisplayId();\r
}\r
\r
/**\r
public void setSequence(String seq)\r
{\r
this.sequence = seq;\r
+ checkValidRange();\r
}\r
\r
/**\r
\r
while ((i < sequence.length()) && (j <= end) && (j <= pos))\r
{\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
+ if (!jalview.util.Comparison.isGap(sequence.charAt(i)))\r
{\r
j++;\r
}\r
\r
while ((j < i) && (j < sequence.length()))\r
{\r
- char c = sequence.charAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
+ if (!jalview.util.Comparison.isGap((sequence.charAt(j))))\r
{\r
pos++;\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
{\r
return color;\r
}\r
+\r
+ public String getVamsasId()\r
+ {\r
+ return vamsasId;\r
+ }\r
+\r
+ public void setVamsasId(String id)\r
+ {\r
+ vamsasId = id;\r
+ }\r
+\r
+ public void setDBRef(Vector dbref)\r
+ {\r
+ dbrefs = dbref;\r
+ }\r
+ public Vector getDBRef()\r
+ {\r
+ return dbrefs;\r
+ }\r
+\r
+ public void addDBRef(DBRefEntry entry)\r
+ {\r
+ if(dbrefs == null)\r
+ dbrefs = new Vector();\r
+\r
+ dbrefs.addElement(entry);\r
+ }\r
+\r
+ public void setDatasetSequence(SequenceI seq)\r
+ {\r
+ datasetSequence = seq;\r
+ }\r
+\r
+ public SequenceI getDatasetSequence()\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
+ 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
git://source.jalview.org / jalview.git / blobdiff