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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
gene_tree_preprocess.java
diff --git
a/forester/java/src/org/forester/application/gene_tree_preprocess.java
b/forester/java/src/org/forester/application/gene_tree_preprocess.java
index
bcb93f4
..
581381c
100644
(file)
--- a/
forester/java/src/org/forester/application/gene_tree_preprocess.java
+++ b/
forester/java/src/org/forester/application/gene_tree_preprocess.java
@@
-21,7
+21,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.application;
package org.forester.application;
@@
-73,7
+73,7
@@
public class gene_tree_preprocess {
"failed to read phylogeny from [" + in + "]: " + e.getLocalizedMessage() );
}
final File outtree = new File( ForesterUtil.removeSuffix( in.toString() )
"failed to read phylogeny from [" + in + "]: " + e.getLocalizedMessage() );
}
final File outtree = new File( ForesterUtil.removeSuffix( in.toString() )
- + "_preprocessed_gene_tree.phylo.xml" );
+ + "_preprocessed_gene_tree.phylo.xml" );
final File removed_nodes = new File( ForesterUtil.removeSuffix( in.toString() ) + "_removed_nodes.txt" );
final File present_species = new File( ForesterUtil.removeSuffix( in.toString() ) + "_species_present.txt" );
checkForOutputFileWriteability( outtree );
final File removed_nodes = new File( ForesterUtil.removeSuffix( in.toString() ) + "_removed_nodes.txt" );
final File present_species = new File( ForesterUtil.removeSuffix( in.toString() ) + "_species_present.txt" );
checkForOutputFileWriteability( outtree );
@@
-81,7
+81,7
@@
public class gene_tree_preprocess {
checkForOutputFileWriteability( present_species );
if ( phy.getNumberOfExternalNodes() < 2 ) {
ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
checkForOutputFileWriteability( present_species );
if ( phy.getNumberOfExternalNodes() < 2 ) {
ForesterUtil.fatalError( PRG_NAME, "phylogeny has " + phy.getNumberOfExternalNodes()
- + " external node(s), aborting" );
+ + " external node(s), aborting" );
}
final SortedSet<String> not_found = SequenceDbWsTools.obtainSeqInformation( phy,
true,
}
final SortedSet<String> not_found = SequenceDbWsTools.obtainSeqInformation( phy,
true,