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omitHiddenColumns
author
amwaterhouse
<Andrew Waterhouse>
Tue, 18 Jul 2006 15:31:51 +0000
(15:31 +0000)
committer
amwaterhouse
<Andrew Waterhouse>
Tue, 18 Jul 2006 15:31:51 +0000
(15:31 +0000)
src/jalview/io/FormatAdapter.java
patch
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diff --git
a/src/jalview/io/FormatAdapter.java
b/src/jalview/io/FormatAdapter.java
index
0c8554a
..
84940a8
100755
(executable)
--- a/
src/jalview/io/FormatAdapter.java
+++ b/
src/jalview/io/FormatAdapter.java
@@
-20,8
+20,6
@@
package jalview.io;
\r
import jalview.datamodel.*;
\r
\r
\r
import jalview.datamodel.*;
\r
\r
-import java.util.Vector;
\r
-
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-31,6
+29,23
@@
import java.util.Vector;
*/
\r
public class FormatAdapter extends AppletFormatAdapter
\r
{
\r
*/
\r
public class FormatAdapter extends AppletFormatAdapter
\r
{
\r
+
\r
+ public String formatSequences(String format,
\r
+ SequenceI [] seqs,
\r
+ String [] omitHiddenColumns)
\r
+ {
\r
+ if(omitHiddenColumns!=null)
\r
+ {
\r
+ for(int i=0; i<seqs.length; i++)
\r
+ seqs [i] = new Sequence(
\r
+ seqs[i].getName(), omitHiddenColumns[i],
\r
+ seqs[i].getStart(), seqs[i].getEnd());
\r
+ }
\r
+
\r
+ return formatSequences(format, seqs);
\r
+ }
\r
+
\r
+
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
/**
\r
* DOCUMENT ME!
\r
*
\r
@@
-39,12
+54,9
@@
public class FormatAdapter extends AppletFormatAdapter
*
\r
* @return DOCUMENT ME!
\r
*/
\r
*
\r
* @return DOCUMENT ME!
\r
*/
\r
- public String formatSequences(String format, Vector seqs)
\r
+ public String formatSequences(String format,
\r
+ SequenceI [] seqs)
\r
{
\r
{
\r
- SequenceI[] s = new SequenceI[seqs.size()];
\r
-
\r
- for (int i = 0; i < seqs.size(); i++)
\r
- s[i] = (SequenceI) seqs.elementAt(i);
\r
\r
try
\r
{
\r
\r
try
\r
{
\r
@@
-93,7
+105,7
@@
public class FormatAdapter extends AppletFormatAdapter
jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
\r
}
\r
\r
jalview.bin.Cache.getDefault("PFAM_JVSUFFIX", true));
\r
}
\r
\r
- afile.setSeqs(s);
\r
+ afile.setSeqs(seqs);
\r
\r
return afile.print();
\r
}
\r
\r
return afile.print();
\r
}
\r