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documentation and targets for building a working applet examples
[jalview.git]
/
src
/
jalview
/
io
/
FormatAdapter.java
diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
dc0526d
..
a71d645
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-1,5
+1,5
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
@@
-36,7
+36,7
@@
public class FormatAdapter extends AppletFormatAdapter
}
/**
}
/**
- * create sequences with each seuqence string replaced with the one given in
+ * create sequences with each sequence string replaced with the one given in
* omitHiddenCOlumns
*
* @param seqs
* omitHiddenCOlumns
*
* @param seqs
@@
-194,23
+194,27
@@
public class FormatAdapter extends AppletFormatAdapter
{
if (omitHidden != null)
{
{
if (omitHidden != null)
{
- //
- Alignment alv = new Alignment(replaceStrings(alignment
- .getSequencesArray(), omitHidden));
+ // TODO consider using AlignmentView to prune to visible region
+ // TODO prune sequence annotation and groups to visible region
+ Alignment alv = new Alignment(replaceStrings(
+ alignment.getSequencesArray(), omitHidden));
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
- for (int i = 0; i < ala.length; i++)
+ if (ala != null)
{
{
- AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
- if (selgp != null)
+ for (int i = 0; i < ala.length; i++)
{
{
- colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
- .getEndRes(), na);
+ AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
+ if (selgp != null)
+ {
+ colSel.makeVisibleAnnotation(selgp.getStartRes(),
+ selgp.getEndRes(), na);
+ }
+ else
+ {
+ colSel.makeVisibleAnnotation(na);
+ }
+ alv.addAnnotation(na);
}
}
- else
- {
- colSel.makeVisibleAnnotation(na);
- }
- alv.addAnnotation(na);
}
return this.formatSequences(format, alv, suffix);
}
}
return this.formatSequences(format, alv, suffix);
}