/*\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
*/\r
package jalview.io;\r
\r
-import jalview.datamodel.*;\r
-\r
-import jalview.util.*;\r
-\r
import java.io.*;\r
-\r
import java.util.*;\r
\r
+import jalview.datamodel.*;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector\r
private int QuerySeqPosition;\r
\r
- /**\r
- * Creates a new JPredFile object.\r
- *\r
- * @param inStr DOCUMENT ME!\r
- */\r
- public JPredFile(String inStr)\r
- {\r
- super(inStr);\r
- }\r
\r
/**\r
* Creates a new JPredFile object.\r
\r
for (int j = 0; j < i; j++)\r
{\r
- scores.set(j,\r
- (Object) ((Float) scores.get(j)).toString());\r
+ scores.setElementAt(\r
+ (Object) ((Float) scores.elementAt(j)).toString(), j);\r
}\r
\r
scores.addElement((Object) ascore);\r
\r
for (int i = 0; i < numSymbols; i++)\r
{\r
- conf.set(i, (Object) symbols.nextToken());\r
+ conf.setElementAt( symbols.nextToken(), i);\r
}\r
}\r
else\r
}\r
}\r
}\r
-\r
+ /* leave it to the parser user to actually check this.\r
if (noSeqs < 1)\r
{\r
throw new IOException(\r
"JpredFile Parser: No sequence in the prediction!");\r
- }\r
+ }*/\r
\r
maxLength = seq_entries.elementAt(0).toString().length();\r
\r
if (!Symscores.containsKey(ids.elementAt(i)) &&\r
!isValidProteinSequence(newSeq.getSequence()))\r
{\r
- throw new IOException(\r
- "JPredConcise: Not a valid protein sequence - (" +\r
- ids.elementAt(i).toString() + ")");\r
+ throw new IOException("JPredConcise: "\r
+ +AppletFormatAdapter.INVALID_CHARACTERS +" : "\r
+ +ids.elementAt(i).toString() + ")");\r
}\r
\r
if (maxLength != seq_entries.elementAt(i).toString().length())\r
e.printStackTrace();\r
}\r
}\r
+ Vector annotSeqs=null;\r
+ /**\r
+ * removeNonSequences\r
+ */\r
+ public void removeNonSequences()\r
+ {\r
+ if (annotSeqs!=null)\r
+ return;\r
+ annotSeqs = new Vector();\r
+ Vector newseqs = new Vector();\r
+ int i=0;\r
+ int j=seqs.size();\r
+ for (; i<QuerySeqPosition; i++)\r
+ annotSeqs.addElement(seqs.elementAt(i));\r
+ // check that no stray annotations have been added at the end.\r
+ {\r
+ SequenceI sq = (SequenceI) seqs.elementAt(j-1);\r
+ if (sq.getName().toUpperCase().startsWith("JPRED")) {\r
+ annotSeqs.addElement(sq);\r
+ seqs.removeElementAt(--j);\r
+ }\r
+ }\r
+ for (; i<j; i++)\r
+ newseqs.addElement(seqs.elementAt(i));\r
+\r
+ seqs.removeAllElements();\r
+ seqs = newseqs;\r
+ }\r
}\r
\r
\r