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more tests for isDuplication() and isSpecation() added
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
application
/
support_transfer.java
diff --git
a/forester/java/src/org/forester/application/support_transfer.java
b/forester/java/src/org/forester/application/support_transfer.java
index
82817e9
..
340bcf4
100644
(file)
--- a/
forester/java/src/org/forester/application/support_transfer.java
+++ b/
forester/java/src/org/forester/application/support_transfer.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;
@@
-37,6
+37,7
@@
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Confidence;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
@@
-47,7
+48,7
@@
public final class support_transfer {
* Transfers branch length values from one Phylogeny to another. It is
* mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )"
* of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.
* Transfers branch length values from one Phylogeny to another. It is
* mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )"
* of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.
- *
+ *
* @param args[0]
* Filename (String) for Phylogeny which has correct branch
* length values
* @param args[0]
* Filename (String) for Phylogeny which has correct branch
* length values
@@
-59,8
+60,8
@@
public final class support_transfer {
* @param args[2]
* String Filename (String) for outputfile
* @param args[3]
* @param args[2]
* String Filename (String) for outputfile
* @param args[3]
- * String [number of tree with correct bl to use in case treefile contains more than one, default 0]
-
+ * String [number of tree with correct bl to use in case treefile contains more than one, default 0]
+
*/
public static void main( final String args[] ) {
Phylogeny phylogeny_w_bl = null; // Has correct branch lengths
*/
public static void main( final String args[] ) {
Phylogeny phylogeny_w_bl = null; // Has correct branch lengths
@@
-94,7
+95,7
@@
public final class support_transfer {
final PhylogenyParser pp_bl = ParserUtils.createParserDependingOnFileType( infile_bl, true );
final PhylogenyParser pp_s = ParserUtils.createParserDependingOnFileType( infile_support_vals, true );
if ( pp_bl instanceof NHXParser ) {
final PhylogenyParser pp_bl = ParserUtils.createParserDependingOnFileType( infile_bl, true );
final PhylogenyParser pp_s = ParserUtils.createParserDependingOnFileType( infile_support_vals, true );
if ( pp_bl instanceof NHXParser ) {
- ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( PhylogenyMethods.TAXONOMY_EXTRACTION.YES );
+ ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.NO );
}
phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];
}
phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];
@@
-137,7
+138,7
@@
public final class support_transfer {
else {
PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
}
else {
PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
}
- node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+ node.setDistanceToParent( PhylogenyDataUtil.BRANCH_LENGTH_DEFAULT );
}
} // moveBranchLengthsToBootstrap()
}
} // moveBranchLengthsToBootstrap()
@@
-146,7
+147,7
@@
public final class support_transfer {
* Important (but obvious): The topology of both trees needs to be the same.
* The method is not robust, and might produce wrong results if the internal
* topology differs or if the external node names are not unique.
* Important (but obvious): The topology of both trees needs to be the same.
* The method is not robust, and might produce wrong results if the internal
* topology differs or if the external node names are not unique.
- *
+ *
* @param from
* the Phylogeny to copy the support values from
* @param to
* @param from
* the Phylogeny to copy the support values from
* @param to