X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fwriters%2FPhylogenyWriter.java;h=911ebb5d8437f54cf9ed3fc21018deb1bd5e8519;hb=665e671efec73fcb36a9aac45f119330f290fa81;hp=c443842db2bc10396454adf17eee56553f32f3c9;hpb=eee996a6476a1e3d84c07f8f690dcde3ff4b2ef5;p=jalview.git
diff --git a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
index c443842..911ebb5 100644
--- a/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
+++ b/forester/java/src/org/forester/io/writers/PhylogenyWriter.java
@@ -21,13 +21,12 @@
// 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.io.writers;
import java.io.BufferedWriter;
import java.io.File;
-import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.StringWriter;
@@ -41,6 +40,7 @@ import org.forester.io.parsers.nexus.NexusConstants;
import org.forester.io.parsers.phyloxml.PhyloXmlMapping;
import org.forester.phylogeny.Phylogeny;
import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
import org.forester.phylogeny.data.PhylogenyDataUtil;
import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
import org.forester.phylogeny.iterators.PostOrderStackObject;
@@ -53,17 +53,17 @@ public final class PhylogenyWriter {
public final static String PHYLO_XML_INTENDATION_BASE = " ";
public final static String PHYLO_XML_VERSION_ENCODING_LINE = "";
public final static String PHYLO_XML_NAMESPACE_LINE = "";
+ + ForesterConstants.XML_SCHEMA_INSTANCE
+ + "\" xsi:schemaLocation=\""
+ + ForesterConstants.PHYLO_XML_LOCATION
+ + " "
+ + ForesterConstants.PHYLO_XML_LOCATION
+ + "/"
+ + ForesterConstants.PHYLO_XML_VERSION
+ + "/" + ForesterConstants.PHYLO_XML_XSD
+ + "\" " + "xmlns=\""
+ + ForesterConstants.PHYLO_XML_LOCATION
+ + "\">";
public final static String PHYLO_XML_END = "";
private boolean _saw_comma;
private StringBuffer _buffer;
@@ -71,8 +71,8 @@ public final class PhylogenyWriter {
private PhylogenyNode _root;
private boolean _has_next;
private Stack _stack;
- private boolean _simple_nh;
private boolean _nh_write_distance_to_parent;
+ NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_style;
private boolean _indent_phyloxml;
private int _node_level;
private int _phyloxml_level;
@@ -80,6 +80,7 @@ public final class PhylogenyWriter {
public PhylogenyWriter() {
setIndentPhyloxml( INDENT_PHYLOXML_DEAFULT );
+ setNhConversionSupportStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
}
private void appendPhylogenyLevelPhyloXml( final Writer writer, final Phylogeny tree ) throws IOException {
@@ -110,7 +111,7 @@ public final class PhylogenyWriter {
if ( tree.getConfidence() != null ) {
if ( ForesterUtil.isEmpty( tree.getConfidence().getType() ) ) {
PhylogenyDataUtil.appendElement( writer, PhyloXmlMapping.CONFIDENCE, tree.getConfidence().getValue()
- + "", indentation );
+ + "", indentation );
}
PhylogenyDataUtil.appendElement( writer,
PhyloXmlMapping.CONFIDENCE,
@@ -199,10 +200,6 @@ public final class PhylogenyWriter {
return _saw_comma;
}
- private boolean isSimpleNH() {
- return _simple_nh;
- }
-
private boolean isWriteDistanceToParentInNH() {
return _nh_write_distance_to_parent;
}
@@ -304,10 +301,6 @@ public final class PhylogenyWriter {
_saw_comma = saw_comma;
}
- private void setSimpleNH( final boolean simple_nh ) {
- _simple_nh = simple_nh;
- }
-
private void setStack( final Stack stack ) {
_stack = stack;
}
@@ -321,43 +314,53 @@ public final class PhylogenyWriter {
}
public void toNewHampshire( final List trees,
- final boolean simple_nh,
final boolean write_distance_to_parent,
final File out_file,
final String separator ) throws IOException {
final Iterator it = trees.iterator();
final StringBuffer sb = new StringBuffer();
while ( it.hasNext() ) {
- sb.append( toNewHampshire( it.next(), simple_nh, write_distance_to_parent ) );
+ sb.append( toNewHampshire( it.next(), write_distance_to_parent ) );
sb.append( separator );
}
writeToFile( sb, out_file );
}
public StringBuffer toNewHampshire( final Phylogeny tree,
- final boolean simple_nh,
- final boolean nh_write_distance_to_parent ) throws IOException {
+ final boolean nh_write_distance_to_parent,
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
+ setOutputFormt( FORMAT.NH );
+ setNhConversionSupportStyle( svs );
+ setWriteDistanceToParentInNH( nh_write_distance_to_parent );
+ return getOutput( tree );
+ }
+
+ public StringBuffer toNewHampshire( final Phylogeny tree, final boolean nh_write_distance_to_parent )
+ throws IOException {
setOutputFormt( FORMAT.NH );
- setSimpleNH( simple_nh );
setWriteDistanceToParentInNH( nh_write_distance_to_parent );
return getOutput( tree );
}
+ public void toNewHampshire( final Phylogeny tree, final boolean write_distance_to_parent, final File out_file )
+ throws IOException {
+ writeToFile( toNewHampshire( tree, write_distance_to_parent ), out_file );
+ }
+
public void toNewHampshire( final Phylogeny tree,
- final boolean simple_nh,
final boolean write_distance_to_parent,
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs,
final File out_file ) throws IOException {
- writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent ), out_file );
+ writeToFile( toNewHampshire( tree, write_distance_to_parent, svs ), out_file );
}
public void toNewHampshire( final Phylogeny[] trees,
- final boolean simple_nh,
final boolean write_distance_to_parent,
final File out_file,
final String separator ) throws IOException {
final StringBuffer sb = new StringBuffer();
for( final Phylogeny element : trees ) {
- sb.append( toNewHampshire( element, simple_nh, write_distance_to_parent ) );
+ sb.append( toNewHampshire( element, write_distance_to_parent ) );
sb.append( separator );
}
writeToFile( sb, out_file );
@@ -393,34 +396,26 @@ public final class PhylogenyWriter {
writeToFile( sb, out_file );
}
- public void toNexus( final File out_file, final List trees ) throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
- writeNexusStart( writer );
- writeNexusTaxaBlock( writer, trees.get( 0 ) );
- writeNexusTreesBlock( writer, trees );
- writer.flush();
- writer.close();
- }
-
- public void toNexus( final File out_file, final Phylogeny tree ) throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
+ public void toNexus( final File out_file, final Phylogeny tree, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs )
+ throws IOException {
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) );
final List trees = new ArrayList( 1 );
trees.add( tree );
writeNexusStart( writer );
writeNexusTaxaBlock( writer, tree );
- writeNexusTreesBlock( writer, trees );
+ writeNexusTreesBlock( writer, trees, svs );
writer.flush();
writer.close();
}
- public StringBuffer toNexus( final Phylogeny tree ) throws IOException {
+ public StringBuffer toNexus( final Phylogeny tree, final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
final StringWriter string_writer = new StringWriter();
final Writer writer = new BufferedWriter( string_writer );
final List trees = new ArrayList( 1 );
trees.add( tree );
writeNexusStart( writer );
writeNexusTaxaBlock( writer, tree );
- writeNexusTreesBlock( writer, trees );
+ writeNexusTreesBlock( writer, trees, svs );
writer.flush();
writer.close();
return string_writer.getBuffer();
@@ -430,14 +425,14 @@ public final class PhylogenyWriter {
final List trees,
final int phyloxml_level,
final String separator ) throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) );
toPhyloXML( writer, trees, phyloxml_level, separator );
writer.flush();
writer.close();
}
public void toPhyloXML( final File out_file, final Phylogeny tree, final int phyloxml_level ) throws IOException {
- final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file, ForesterConstants.UTF_8 ) );
writePhyloXmlStart( writer );
toPhyloXMLNoPhyloXmlSource( writer, tree, phyloxml_level );
writePhyloXmlEnd( writer );
@@ -468,6 +463,13 @@ public final class PhylogenyWriter {
writer.close();
}
+ public void toPhyloXML( final Phylogeny phy, final int phyloxml_level, final File out_file ) throws IOException {
+ final Writer writer = new BufferedWriter( new PrintWriter( out_file ) );
+ toPhyloXML( writer, phy, phyloxml_level );
+ writer.flush();
+ writer.close();
+ }
+
public void toPhyloXML( final Writer writer,
final List trees,
final int phyloxml_level,
@@ -538,12 +540,10 @@ public final class PhylogenyWriter {
}
PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE );
}
- if ( indentation != null ) {
- PhyloXmlNodeWriter.toPhyloXml( getWriter(), node, getPhyloXmlLevel(), indentation.toString() );
- }
- else {
- PhyloXmlNodeWriter.toPhyloXml( getWriter(), node, getPhyloXmlLevel(), "" );
- }
+ PhyloXmlNodeWriter.toPhyloXml( getWriter(),
+ node,
+ getPhyloXmlLevel(),
+ indentation != null ? indentation.toString() : "" );
if ( node.isExternal() ) {
getWriter().write( ForesterUtil.LINE_SEPARATOR );
if ( indentation != null ) {
@@ -556,10 +556,18 @@ public final class PhylogenyWriter {
getBuffer().append( node.toNewHampshireX() );
}
else if ( getOutputFormt() == FORMAT.NH ) {
- getBuffer().append( node.toNewHampshire( isSimpleNH(), isWriteDistanceToParentInNH() ) );
+ getBuffer().append( node.toNewHampshire( isWriteDistanceToParentInNH(), getNhConversionSupportStyle() ) );
}
}
+ private NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportStyle() {
+ return _nh_conversion_support_style;
+ }
+
+ private void setNhConversionSupportStyle( final NH_CONVERSION_SUPPORT_VALUE_STYLE nh_conversion_support_style ) {
+ _nh_conversion_support_style = nh_conversion_support_style;
+ }
+
private void writeOpenClade( final PhylogenyNode node ) throws IOException {
if ( !isSawComma() ) {
if ( !node.isRoot() && node.isFirstChildNode() ) {
@@ -570,7 +578,15 @@ public final class PhylogenyWriter {
if ( isIndentPhyloxml() ) {
getWriter().write( createIndentation().toString() );
}
- PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE );
+ if ( node.isCollapse() ) {
+ PhylogenyDataUtil.appendOpen( getWriter(),
+ PhyloXmlMapping.CLADE,
+ PhyloXmlMapping.NODE_COLLAPSE,
+ "true" );
+ }
+ else {
+ PhylogenyDataUtil.appendOpen( getWriter(), PhyloXmlMapping.CLADE );
+ }
}
else if ( ( getOutputFormt() == FORMAT.NHX ) || ( getOutputFormt() == FORMAT.NH ) ) {
getBuffer().append( "(" );
@@ -585,44 +601,24 @@ public final class PhylogenyWriter {
}
if ( tree != null ) {
reset( writer, tree );
- boolean rerootable = true;
String unit = "";
String type = "";
- String rooted = "false";
- if ( tree.isRooted() ) {
- rooted = "true";
- }
- if ( !tree.isRerootable() ) {
- rerootable = false;
- }
if ( !ForesterUtil.isEmpty( tree.getDistanceUnit() ) ) {
unit = tree.getDistanceUnit();
}
if ( !ForesterUtil.isEmpty( tree.getType() ) ) {
type = tree.getType();
}
- if ( rerootable ) {
- PhylogenyDataUtil.appendOpen( writer,
- PhyloXmlMapping.PHYLOGENY,
- PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR,
- rooted,
- PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR,
- unit,
- PhyloXmlMapping.PHYLOGENY_TYPE_ATTR,
- type );
- }
- else {
- PhylogenyDataUtil.appendOpen( writer,
- PhyloXmlMapping.PHYLOGENY,
- PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR,
- rooted,
- PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR,
- unit,
- PhyloXmlMapping.PHYLOGENY_TYPE_ATTR,
- type,
- PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR,
- "false" );
- }
+ PhylogenyDataUtil.appendOpen( writer,
+ PhyloXmlMapping.PHYLOGENY,
+ PhyloXmlMapping.PHYLOGENY_IS_ROOTED_ATTR,
+ tree.isRooted() + "",
+ PhyloXmlMapping.PHYLOGENY_BRANCHLENGTH_UNIT_ATTR,
+ unit,
+ PhyloXmlMapping.PHYLOGENY_TYPE_ATTR,
+ type,
+ PhyloXmlMapping.PHYLOGENY_IS_REROOTABLE_ATTR,
+ tree.isRerootable() + "" );
appendPhylogenyLevelPhyloXml( writer, tree );
while ( isHasNext() ) {
next();
@@ -636,18 +632,8 @@ public final class PhylogenyWriter {
if ( out_file.exists() ) {
throw new IOException( "attempt to overwrite existing file \"" + out_file.getAbsolutePath() + "\"" );
}
- final PrintWriter out = new PrintWriter( new FileWriter( out_file ), true );
- if ( getOutputFormt() == FORMAT.PHYLO_XML ) {
- out.print( PHYLO_XML_VERSION_ENCODING_LINE );
- out.print( ForesterUtil.LINE_SEPARATOR );
- out.print( PHYLO_XML_NAMESPACE_LINE );
- out.print( ForesterUtil.LINE_SEPARATOR );
- }
+ final PrintWriter out = new PrintWriter( out_file, ForesterConstants.UTF_8 );
out.print( sb );
- if ( getOutputFormt() == FORMAT.PHYLO_XML ) {
- out.print( ForesterUtil.LINE_SEPARATOR );
- out.print( PHYLO_XML_END );
- }
out.flush();
out.close();
}
@@ -691,19 +677,19 @@ public final class PhylogenyWriter {
else if ( !ForesterUtil.isEmpty( node.getNodeData().getTaxonomy().getCommonName() ) ) {
data = node.getNodeData().getTaxonomy().getCommonName();
}
- else if ( node.getNodeData().getTaxonomy().getTaxonomyCode() != null ) {
- data = node.getNodeData().getTaxonomy().getTaxonomyCode();
- }
}
else if ( node.getNodeData().isHasSequence() ) {
if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getName() ) ) {
data = node.getNodeData().getSequence().getName();
}
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getSymbol() ) ) {
+ data = node.getNodeData().getSequence().getSymbol();
+ }
+ else if ( !ForesterUtil.isEmpty( node.getNodeData().getSequence().getGeneName() ) ) {
+ data = node.getNodeData().getSequence().getGeneName();
+ }
}
- if ( data.length() > 0 ) {
- data = data.replaceAll( " ", "_" );
- }
- writer.write( data );
+ writer.write( ForesterUtil.santitizeStringForNH( data ).toString() );
}
writer.write( ";" );
writer.write( ForesterUtil.LINE_SEPARATOR );
@@ -711,7 +697,9 @@ public final class PhylogenyWriter {
writer.write( ForesterUtil.LINE_SEPARATOR );
}
- public static void writeNexusTreesBlock( final Writer writer, final List trees ) throws IOException {
+ public static void writeNexusTreesBlock( final Writer writer,
+ final List trees,
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
writer.write( NexusConstants.BEGIN_TREES );
writer.write( ForesterUtil.LINE_SEPARATOR );
int i = 1;
@@ -735,7 +723,7 @@ public final class PhylogenyWriter {
else {
writer.write( "[&U]" );
}
- writer.write( phylogeny.toNewHampshire( false ) );
+ writer.write( phylogeny.toNewHampshire( svs ) );
writer.write( ForesterUtil.LINE_SEPARATOR );
i++;
}
@@ -759,3 +747,7 @@ public final class PhylogenyWriter {
NH, NHX, PHYLO_XML, NEXUS;
}
}
+
+
+
+