String description;\r
int start;\r
int end;\r
- String displayId;\r
Color color = Color.white;\r
- String pdbId;\r
+ Vector pdbIds;\r
String vamsasId;\r
Vector dbrefs;\r
\r
this.start = start;\r
this.end = end;\r
\r
+ parseId();\r
+\r
checkValidRange();\r
}\r
\r
+ void parseId()\r
+ {\r
+ // Remove /start-end from sequence\r
+ if (name.indexOf("/") > 0)\r
+ {\r
+ String limits = name.substring(name.lastIndexOf("/")+1);\r
+ try\r
+ {\r
+ StringTokenizer 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
+ // 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.lastIndexOf("/"));\r
+ }\r
+ catch (NumberFormatException ex)\r
+ { }\r
+ }\r
+\r
+ }\r
+\r
void checkValidRange()\r
{\r
if (end < 1)\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
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(boolean dbref, boolean jvsuffix)\r
+ public String getDisplayId(boolean jvsuffix)\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
- result.append(name);\r
-\r
+ StringBuffer result = new StringBuffer(name);\r
if (jvsuffix)\r
{\r
result.append("/" + start + "-" + end);\r
*/\r
public void setName(String name)\r
{\r
- this.name = name;\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
\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