*/\r
package jalview.datamodel;\r
\r
-import MCview.*;\r
-\r
-import jalview.analysis.*;\r
-\r
import java.awt.*;\r
\r
import java.util.*;\r
*/\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
\r
/** DOCUMENT ME!! */\r
- public Vector sequenceFeatures = new Vector();\r
+ public Vector sequenceFeatures;\r
\r
/**\r
* Creates a new Sequence object.\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
+ 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
- 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
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 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
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
}\r