git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
formatting
[jalview.git]
/
src
/
jalview
/
io
/
AppletFormatAdapter.java
diff --git
a/src/jalview/io/AppletFormatAdapter.java
b/src/jalview/io/AppletFormatAdapter.java
index
232de57
..
2e4ddc4
100755
(executable)
--- a/
src/jalview/io/AppletFormatAdapter.java
+++ b/
src/jalview/io/AppletFormatAdapter.java
@@
-20,9
+20,6
@@
\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
*
\r
@@
-38,8
+35,8
@@
};
\r
\r
public static final String [] WRITEABLE_FORMATS = new String[]
\r
};
\r
\r
public static final String [] WRITEABLE_FORMATS = new String[]
\r
- {
\r
- "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM"
\r
+ {
\r
+ "BLC", "CLUSTAL", "FASTA", "MSF", "PileUp", "PIR", "PFAM" //, "AMSA"
\r
};
\r
\r
\r
};
\r
\r
\r
@@
-175,14
+172,9
@@
* @return DOCUMENT ME!
\r
*/
\r
public String formatSequences(String format,
\r
* @return DOCUMENT ME!
\r
*/
\r
public String formatSequences(String format,
\r
- Vector seqs,
\r
+ AlignmentI alignment,
\r
boolean jvsuffix)
\r
{
\r
boolean jvsuffix)
\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
AlignFile afile = null;
\r
try
\r
{
\r
AlignFile afile = null;
\r
@@
-219,11
+211,14
@@
{
\r
afile = new StockholmFile();
\r
}
\r
{
\r
afile = new StockholmFile();
\r
}
\r
-
\r
+ else if (format.equals("AMSA"))
\r
+ {
\r
+ afile = new AMSAFile(alignment);
\r
+ }
\r
\r
afile.addJVSuffix(jvsuffix);
\r
\r
\r
afile.addJVSuffix(jvsuffix);
\r
\r
- afile.setSeqs(s);
\r
+ afile.setSeqs( alignment.getSequencesArray() );
\r
\r
return afile.print();
\r
}
\r
\r
return afile.print();
\r
}
\r