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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
annotator.java
diff --git
a/forester/java/src/org/forester/application/annotator.java
b/forester/java/src/org/forester/application/annotator.java
index
1614412
..
4374f53
100644
(file)
--- a/
forester/java/src/org/forester/application/annotator.java
+++ b/
forester/java/src/org/forester/application/annotator.java
@@
-94,8
+94,8
@@
public final class annotator {
}
catch ( final Exception e ) {
ForesterUtil
}
catch ( final Exception e ) {
ForesterUtil
- .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
- + "]" );
+ .fatalError( PRG_NAME, "failed to read phylgenies from [" + infile + "] [" + e.getMessage()
+ + "]" );
}
try {
obtainSeqInformation( phy );
}
try {
obtainSeqInformation( phy );
@@
-112,6
+112,7
@@
public final class annotator {
// catch ( final AncestralTaxonomyInferenceException e ) {
// ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
// }
// catch ( final AncestralTaxonomyInferenceException e ) {
// ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
// }
+ //phy.setRerootable( false );
try {
final PhylogenyWriter w = new PhylogenyWriter();
w.toPhyloXML( phy, 0, outfile );
try {
final PhylogenyWriter w = new PhylogenyWriter();
w.toPhyloXML( phy, 0, outfile );
@@
-128,7
+129,7
@@
public final class annotator {
}
private static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
}
private static void inferTaxonomyFromDescendents( final Phylogeny phy ) throws IOException,
- AncestralTaxonomyInferenceException {
+ AncestralTaxonomyInferenceException {
AncestralTaxonomyInference.inferTaxonomyFromDescendents( phy );
}
AncestralTaxonomyInference.inferTaxonomyFromDescendents( phy );
}