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work on: add ability to perform GSDI in applets
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
archaeopteryx
/
AptxUtil.java
diff --git
a/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
b/forester/java/src/org/forester/archaeopteryx/AptxUtil.java
index
bc7a693
..
89a0cda
100644
(file)
--- a/
forester/java/src/org/forester/archaeopteryx/AptxUtil.java
+++ b/
forester/java/src/org/forester/archaeopteryx/AptxUtil.java
@@
-75,6
+75,7
@@
import org.forester.io.parsers.tol.TolParser;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
import org.forester.io.parsers.util.ParserUtils;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyMethods.DESCENDANT_SORT_PRIORITY;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BranchColor;
import org.forester.phylogeny.PhylogenyNode;
import org.forester.phylogeny.data.Accession;
import org.forester.phylogeny.data.BranchColor;
@@
-1027,8
+1028,9
@@
public final class AptxUtil {
final boolean phyloxml_validate_against_xsd,
final boolean replace_underscores,
final boolean internal_numbers_are_confidences,
final boolean phyloxml_validate_against_xsd,
final boolean replace_underscores,
final boolean internal_numbers_are_confidences,
- final TAXONOMY_EXTRACTION taxonomy_extraction )
- throws FileNotFoundException, IOException {
+ final TAXONOMY_EXTRACTION taxonomy_extraction,
+ final boolean midpoint_reroot ) throws FileNotFoundException,
+ IOException {
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser parser;
boolean nhx_or_nexus = false;
final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
final PhylogenyParser parser;
boolean nhx_or_nexus = false;
@@
-1057,6
+1059,12
@@
public final class AptxUtil {
PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
PhylogenyMethods.transferInternalNodeNamesToConfidence( phy );
}
}
+ if ( midpoint_reroot ) {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ PhylogenyMethods.orderAppearance( phy.getRoot(), true, true, DESCENDANT_SORT_PRIORITY.NODE_NAME );
+ }
+ }
return phys;
}
return phys;
}