*/\r
package jalview.datamodel;\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 shortName;\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 Sequence(String name, String sequence, int start, int end)\r
{\r
this.name = name;\r
+ parseId();\r
+\r
this.sequence = sequence;\r
this.start = start;\r
this.end = end;\r
\r
+ checkValidRange();\r
+ }\r
+\r
+ void parseId()\r
+ {\r
+ // Read in any DB refs first\r
+ StringTokenizer st = new StringTokenizer(name, "|");\r
+ if(st.countTokens()<1)\r
+ {\r
+ shortName = name;\r
+ return;\r
+ }\r
+\r
+ while (st.countTokens() > 1)\r
+ {\r
+ String a = st.nextToken();\r
+ String b = st.nextToken();\r
+ addDBRef(new DBRefEntry(a, "0", b));\r
+ }\r
+\r
+ if (st.hasMoreTokens())\r
+ shortName = st.nextToken();\r
+\r
+ // Remove /start-end from sequence\r
+ if (shortName.indexOf("/") > 0)\r
+ {\r
+ st = new StringTokenizer(shortName, "/");\r
+ String limits = null;\r
+ try\r
+ {\r
+ if (st.countTokens() == 2)\r
+ {\r
+\r
+ shortName = st.nextToken();\r
+\r
+ limits = st.nextToken();\r
+\r
+ st = new StringTokenizer(limits, "-");\r
+\r
+ if (st.countTokens() == 2)\r
+ {\r
+ setStart(Integer.valueOf(st.nextToken()).intValue());\r
+ setEnd(Integer.valueOf(st.nextToken()).intValue());\r
+ }\r
+ }\r
+\r
+ // If we're still in this loop, parsing of start and end was ok\r
+ // Therefore remove it from the sequence name\r
+ name = name.substring(0, name.indexOf("/"));\r
+ }\r
+ catch (NumberFormatException ex)\r
+ {\r
+ // Problem parsing sequence limits. Just add it back to the\r
+ // Id so we dont lose this info\r
+ shortName += "/" + limits;\r
+ }\r
+ }\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
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 dbref, boolean jvsuffix)\r
{\r
- return displayId;\r
- }\r
+ StringBuffer result = new StringBuffer();\r
+ if (dbref && dbrefs != null)\r
+ {\r
+ for (int i = 0; i < dbrefs.size(); i++)\r
+ {\r
+ DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);\r
+ result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");\r
+ }\r
+ }\r
\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void setDisplayId()\r
- {\r
- displayId = name + "/" + start + "-" + end;\r
+ result.append(shortName);\r
+\r
+ if (jvsuffix)\r
+ {\r
+ result.append("/" + start + "-" + end);\r
+ }\r
+\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
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 String getShortName()\r
+ {\r
+ return shortName;\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff