public void parse() throws IOException\r
{\r
boolean idsFound = false;\r
- Vector ids = new Vector();\r
StringBuffer[] seqstrings;\r
- Vector starts = new Vector();\r
- Vector ends = new Vector();\r
\r
String line = null;\r
\r
\r
if (abracket > -1)\r
{\r
- if (line.indexOf(" ") > -1) //\r
- {\r
- line = line.substring(abracket + 1,\r
- line.indexOf(" ", abracket + 1));\r
- }\r
- else\r
- line = line.substring(abracket+1);\r
-\r
+ line = line.substring(abracket+1);\r
\r
Sequence seq = parseId(line);\r
- ids.addElement(seq.getName());\r
- starts.addElement(seq.getStart() + "");\r
- ends.addElement(seq.getEnd() + "");\r
+ seqs.addElement(seq);\r
}\r
}\r
while (!idsFound);\r
\r
int starCol = line.indexOf("*");\r
- seqstrings = new StringBuffer[ids.size()];\r
+ seqstrings = new StringBuffer[seqs.size()];\r
\r
- for (int i = 0; i < ids.size(); i++)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
if (seqstrings[i] == null)\r
{\r
\r
while ((line = nextLine()).indexOf("*") == -1)\r
{\r
- for (int i = 0; i < ids.size(); i++)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
if (line.length() > (i + starCol))\r
{\r
}\r
}\r
\r
- for (int i = 0; i < ids.size(); i++)\r
+ for (int i = 0; i < seqs.size(); i++)\r
{\r
- Sequence newSeq = new Sequence(ids.elementAt(i).toString(),\r
- seqstrings[i].toString(),\r
- Integer.parseInt(starts.elementAt(i).\r
- toString()),\r
- Integer.parseInt(ends.elementAt(i).toString()));\r
+ Sequence newSeq = (Sequence) seqs.elementAt(i);\r
\r
if (!isValidProteinSequence(newSeq.getSequence()))\r
{\r
throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
+" : "+ newSeq.getName()\r
+" : "+invalidCharacter);\r
-\r
}\r
\r
- seqs.addElement(newSeq);\r
+ newSeq.setSequence(seqstrings[i].toString());\r
}\r
\r
}\r
\r
while ((i < s.length) && (s[i] != null))\r
{\r
- out.append(">" + printId(s[i]) +"\n");\r
+ out.append(">" + printId(s[i]));\r
+ if(s[i].getDescription()!=null)\r
+ out.append(" "+s[i].getDescription());\r
+\r
+ out.append("\n");\r
\r
if (s[i].getSequence().length > max)\r
{\r