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[jalview.git]
/
src
/
jalview
/
io
/
JPredFile.java
diff --git
a/src/jalview/io/JPredFile.java
b/src/jalview/io/JPredFile.java
index
0ee41b8
..
92d5414
100755
(executable)
--- a/
src/jalview/io/JPredFile.java
+++ b/
src/jalview/io/JPredFile.java
@@
-1,6
+1,6
@@
/*
\r
* Jalview - A Sequence Alignment Editor and Viewer
\r
/*
\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
* This program is free software; you can redistribute it and/or
\r
* modify it under the terms of the GNU General Public License
\r
@@
-44,15
+44,6
@@
public class JPredFile extends AlignFile
Hashtable Symscores; // indexes of symbol annotation properties in sequenceI vector
\r
private int QuerySeqPosition;
\r
\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
/**
\r
* Creates a new JPredFile object.
\r
@@
-197,8
+188,8
@@
public class JPredFile extends AlignFile
\r
for (int j = 0; j < i; j++)
\r
{
\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
\r
scores.addElement((Object) ascore);
\r
@@
-220,7
+211,7
@@
public class JPredFile extends AlignFile
\r
for (int i = 0; i < numSymbols; i++)
\r
{
\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
else
\r
@@
-351,19
+342,19
@@
public class JPredFile extends AlignFile
int i=0;
\r
int j=seqs.size();
\r
for (; i<QuerySeqPosition; i++)
\r
int i=0;
\r
int j=seqs.size();
\r
for (; i<QuerySeqPosition; i++)
\r
- annotSeqs.add(seqs.get(i));
\r
+ annotSeqs.addElement(seqs.elementAt(i));
\r
// check that no stray annotations have been added at the end.
\r
{
\r
// check that no stray annotations have been added at the end.
\r
{
\r
- SequenceI sq = (SequenceI) seqs.get(j-1);
\r
+ SequenceI sq = (SequenceI) seqs.elementAt(j-1);
\r
if (sq.getName().toUpperCase().startsWith("JPRED")) {
\r
if (sq.getName().toUpperCase().startsWith("JPRED")) {
\r
- annotSeqs.add(sq);
\r
- seqs.remove(--j);
\r
+ annotSeqs.addElement(sq);
\r
+ seqs.removeElementAt(--j);
\r
}
\r
}
\r
for (; i<j; i++)
\r
}
\r
}
\r
for (; i<j; i++)
\r
- newseqs.add(seqs.get(i));
\r
+ newseqs.addElement(seqs.elementAt(i));
\r
\r
\r
- seqs.clear();
\r
+ seqs.removeAllElements();
\r
seqs = newseqs;
\r
}
\r
}
\r
seqs = newseqs;
\r
}
\r
}
\r