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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
phylogeny
/
Phylogeny.java
diff --git
a/forester/java/src/org/forester/phylogeny/Phylogeny.java
b/forester/java/src/org/forester/phylogeny/Phylogeny.java
index
3679cd5
..
115e885
100644
(file)
--- a/
forester/java/src/org/forester/phylogeny/Phylogeny.java
+++ b/
forester/java/src/org/forester/phylogeny/Phylogeny.java
@@
-38,6
+38,7
@@
import java.util.Map;
import java.util.NoSuchElementException;
import java.util.Vector;
import java.util.NoSuchElementException;
import java.util.Vector;
+import org.forester.io.parsers.nhx.NHXParser;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BranchData;
import org.forester.io.writers.PhylogenyWriter;
import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.BranchData;
@@
-47,6
+48,8
@@
import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
import org.forester.phylogeny.data.Sequence;
import org.forester.phylogeny.data.SequenceRelation;
import org.forester.phylogeny.data.SequenceRelation.SEQUENCE_RELATION_TYPE;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
import org.forester.phylogeny.iterators.ExternalForwardIterator;
import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.ExternalForwardIterator;
import org.forester.phylogeny.iterators.LevelOrderTreeIterator;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
@@
-304,6
+307,11
@@
public class Phylogeny {
return _distance_unit;
}
return _distance_unit;
}
+ public final static Phylogeny createInstanceFromNhxString( final String nhx ) throws IOException {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ return factory.create( nhx, new NHXParser() )[ 0 ];
+ }
+
/**
*
* Warning. The order of the returned nodes is random
/**
*
* Warning. The order of the returned nodes is random
@@
-1090,14
+1098,12
@@
public class Phylogeny {
}
public String toNewHampshire() {
}
public String toNewHampshire() {
- return toNewHampshire( false, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
+ return toNewHampshire( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
}
}
- public String toNewHampshire( final boolean simple_nh,
- final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
+ public String toNewHampshire( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
try {
try {
- return new PhylogenyWriter().toNewHampshire( this, simple_nh, true, nh_conversion_support_style )
- .toString();
+ return new PhylogenyWriter().toNewHampshire( this, true, nh_conversion_support_style ).toString();
}
catch ( final IOException e ) {
throw new Error( "this should not have happend: " + e.getMessage() );
}
catch ( final IOException e ) {
throw new Error( "this should not have happend: " + e.getMessage() );