{\r
SequenceI datasetSequence;\r
String name;\r
- String shortName;\r
String sequence;\r
String description;\r
int start;\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
- this.sequence = sequence;\r
-\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
+ if (name.indexOf("/") > 0)\r
{\r
- st = new StringTokenizer(shortName, "/");\r
- String limits = null;\r
+ String limits = name.substring(name.lastIndexOf("/")+1);\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
+ 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
\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
+ name = name.substring(0, name.lastIndexOf("/"));\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
*\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(shortName);\r
-\r
+ StringBuffer result = new StringBuffer(name);\r
if (jvsuffix)\r
{\r
result.append("/" + start + "-" + end);\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
return datasetSequence;\r
}\r
\r
- public String getShortName()\r
- {\r
- return shortName;\r
- }\r
-\r
}\r