- 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
-\r
- public Vector sequenceFeatures = new Vector();\r
- public void setSequenceFeatures(Vector v)\r
- {\r
- sequenceFeatures = v;\r
- }\r
-\r
- public Vector getSequenceFeatures()\r
- {return sequenceFeatures; }\r
-\r
- public void setPDBId(String id)\r
- {\r
- pdbId = id;\r
- }\r
- public String getPDBId()\r
- {\r
- return pdbId;\r
- }\r
-\r
-\r
- public Sequence(String name, String sequence, int start, int end)\r
- {\r
-\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
-\r
- setDisplayId();\r
-\r
- }\r
-\r
- public Sequence(String name,String sequence) {\r
- this(name,sequence,1,sequence.length());\r
- }\r
- public Sequence(SequenceI seq) {\r
- this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());\r
- }\r
- public String getDisplayId() {\r
- return displayId;\r
- }\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
- }\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
- }\r
- public String getName() {\r
- return this.name;\r
- }\r
- public void setStart(int start) {\r
- this.start = start;\r
- setDisplayId();\r
- }\r
- public int getStart() {\r
- return this.start;\r
- }\r
- public void setEnd(int end) {\r
- this.end = end;\r
- setDisplayId();\r
- }\r
- public int getEnd() {\r
- return this.end;\r
- }\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
- public void setSequence(String seq) {\r
- this.sequence = seq;\r
- }\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
- public String getSequence(int start,int end) {\r
- if(end>sequence.length())\r
- end = sequence.length();\r
- return this.sequence.substring(start,end);\r
- }\r
-\r
- public char getCharAt(int i) {\r
- if (i < sequence.length()) {\r
- return sequence.charAt(i);\r
- } else {\r
- return ' ';\r
- }\r
- }\r
- public void setDescription(String desc) {\r
- this.description = desc;\r
- }\r
- public String getDescription() {\r
- return this.description;\r
- }\r
-\r
- public int findIndex(int pos) {\r
- // returns the alignment position for a residue\r
- int j = start;\r
- int i = 0;\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
- j++;\r
-\r
- i++;\r
- }\r
- if (j == end && j < pos)\r
- return end+1;\r
- else\r
- return i;\r
-\r
- }\r
-\r
- public int findPosition(int i) {\r
- // Returns the sequence position for an alignment position\r
- int j = 0;\r
- int pos = start;\r
-\r
- while (j < i && j<sequence.length())\r
- {\r
- char c = sequence.charAt(j);\r
- if (!jalview.util.Comparison.isGap((c)))\r
- pos++;\r
-\r
- j++;\r
- }\r
- return pos;\r
- }\r
-\r
- public int[] gapMap() {\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
- int[] map = new int[seq.length()];\r
- int j=0;\r
- int p=0;\r
- while (j<sequence.length()) {\r
- if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
- map[p++]=j;\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
+\r
+ /** DOCUMENT ME!! */\r
+ public Vector sequenceFeatures;\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ * @param sequence DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ */\r
+ public Sequence(String name, String sequence, int start, int end)\r
+ {\r
+ this.name = name;\r
+ this.sequence = sequence;\r
+ this.start = start;\r
+ this.end = end;\r
+\r
+ parseId();\r
+\r
+ checkValidRange();\r
+ }\r
+\r
+ static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(\r
+ "[/][0-9]{1,}[-][0-9]{1,}$");\r
+ static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(\r
+ "[0-9]{1,}$");\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
+ char ch;\r
+ for (int j = 0; j < sequence.length(); j++)\r
+ {\r
+ ch = sequence.charAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
+ {\r
+ endRes++;\r
+ }\r
+ }\r
+ if (endRes > 0)\r
+ {\r
+ endRes += start - 1;\r
+ }\r
+\r
+ this.end = endRes;\r
+ }\r
+\r
+ }\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param name DOCUMENT ME!\r
+ * @param sequence DOCUMENT ME!\r
+ */\r
+ public Sequence(String name, String sequence)\r
+ {\r
+ this(name, sequence, 1, -1);\r
+ }\r
+\r
+ /**\r
+ * Creates a new Sequence object.\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public Sequence(SequenceI seq)\r
+ {\r
+ this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param v DOCUMENT ME!\r
+ */\r
+ public void setSequenceFeatures(Vector v)\r
+ {\r
+ sequenceFeatures = v;\r
+ }\r
+\r
+ public void addSequenceFeature(SequenceFeature sf)\r
+ {\r
+ if(sequenceFeatures==null)\r
+ sequenceFeatures = new Vector();\r
+\r
+ sequenceFeatures.addElement(sf);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector 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(Vector id)\r
+ {\r
+ pdbIds = id;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Vector getPDBId()\r
+ {\r
+ return pdbIds;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public String getDisplayId(boolean jvsuffix)\r
+ {\r
+ StringBuffer result = new StringBuffer(name);\r
+ if (jvsuffix)\r
+ {\r
+ result.append("/" + start + "-" + end);\r