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JAL-429 remove pointless code from phylip parser
features/JAL-653_rebased_gffalignments
author
Jim Procter
<jprocter@issues.jalview.org>
Sun, 7 Jun 2015 18:06:27 +0000
(19:06 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Sun, 7 Jun 2015 18:06:27 +0000
(19:06 +0100)
src/jalview/io/PhylipFile.java
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diff --git
a/src/jalview/io/PhylipFile.java
b/src/jalview/io/PhylipFile.java
index
ce65eea
..
d7f6dbc
100644
(file)
--- a/
src/jalview/io/PhylipFile.java
+++ b/
src/jalview/io/PhylipFile.java
@@
-3,7
+3,6
@@
*/
package jalview.io;
*/
package jalview.io;
-import jalview.datamodel.Alignment;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
@@
-171,13
+170,6
@@
public class PhylipFile extends AlignFile
seqs.add(sequenceElements[i]);
}
seqs.add(sequenceElements[i]);
}
- // create an alignment based on the sequences
- Alignment a = new Alignment(sequenceElements);
- // add annotations - although comments say addAnnotations
- // is used by AppletFormatAdapter, it doesn't say other
- // classes should/can not use it
- addAnnotations(a);
-
} catch (IOException e)
{
System.err.println("Exception parsing PHYLIP file " + e);
} catch (IOException e)
{
System.err.println("Exception parsing PHYLIP file " + e);