/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
public class PIRFile\r
extends AlignFile\r
{\r
+ public static boolean useModellerOutput = false;\r
+\r
Vector words = new Vector(); //Stores the words in a line after splitting\r
\r
public PIRFile()\r
{\r
}\r
\r
- public PIRFile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
-\r
public PIRFile(String inFile, String type)\r
throws IOException\r
{\r
{\r
StringBuffer sequence;\r
String line = null;\r
+ ModellerDescription md;\r
\r
while ( (line = nextLine()) != null)\r
{\r
{\r
sequence.setLength(sequence.length() - 1);\r
newSeq.setSequence(sequence.toString());\r
- if (!isValidProteinSequence(newSeq.getSequence()))\r
- {\r
- throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
- +" : "+ newSeq.getName()\r
- +" : "+invalidCharacter);\r
- }\r
\r
seqs.addElement(newSeq);\r
- ModellerDescription md = new ModellerDescription(newSeq.\r
- getDescription());\r
+\r
+ md = new ModellerDescription(newSeq.\r
+ getDescription());\r
md.updateSequenceI(newSeq);\r
}\r
}\r
int len = 72;\r
StringBuffer out = new StringBuffer();\r
int i = 0;\r
+ ModellerDescription md;\r
\r
while ( (i < s.length) && (s[i] != null))\r
{\r
- String seq = s[i].getSequence();\r
+ String seq = s[i].getSequenceAsString();\r
seq = seq + "*";\r
\r
+\r
if (is_NA)\r
{\r
- // modeller doesn't really do nucleotides, so we don't do anything fancy\r
- // Nucleotide sequence tags should have a >DL; prefix\r
- out.append(">P1;" + s[i].getName() + "\n"); // JBPNote Should change >P to >N\r
+ // modeller doesn't really do nucleotides, so we don't do anything fancy\r
+ // Official tags area as follows, for now we'll use P1 and DL\r
+ // Protein (complete) P1\r
+ // Protein (fragment) F1\r
+ // DNA (linear) Dl\r
+ // DNA (circular) DC\r
+ // RNA (linear) RL\r
+ // RNA (circular) RC\r
+ // tRNA N3\r
+ // other functional RNA N1\r
+\r
+ out.append(">N1;" + s[i].getName() + "\n");\r
if (s[i].getDescription() == null)\r
{\r
out.append(s[i].getName() + " " +\r
}\r
else\r
{\r
- out.append(">P1;" + s[i].getName() + "\n");\r
- ModellerDescription md = new ModellerDescription(s[i]);\r
- out.append(md.getDescriptionLine() + "\n");\r
+\r
+ if(useModellerOutput)\r
+ {\r
+ out.append(">P1;" + s[i].getName() + "\n");\r
+ md = new ModellerDescription(s[i]);\r
+ out.append(md.getDescriptionLine() + "\n");\r
+ }\r
+ else\r
+ {\r
+ out.append(">P1;" + printId(s[i]) + "\n");\r
+ if (s[i].getDescription() != null)\r
+ out.append(s[i].getDescription() + "\n");\r
+ else\r
+ out.append(s[i].getName() + " "\r
+ + (s[i].getEnd() - s[i].getStart() + 1)\r
+ + " residues\n");\r
+ }\r
}\r
int nochunks = (seq.length() / len) + 1;\r
\r