// 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 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;
private Stack<PostOrderStackObject> _stack;
private boolean _simple_nh;
private boolean _nh_write_distance_to_parent;
- private boolean _write_conf_values_in_branckets_in_nh;
+ NH_CONVERSION_SUPPORT_VALUE_STYLE _nh_conversion_support_style;
private boolean _indent_phyloxml;
private int _node_level;
private int _phyloxml_level;
public PhylogenyWriter() {
setIndentPhyloxml( INDENT_PHYLOXML_DEAFULT );
- setWriteConfidenceValuesInBracketsInNH( false );
+ setNhConversionSupportStyle( NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
}
private void appendPhylogenyLevelPhyloXml( final Writer writer, final Phylogeny tree ) throws IOException {
public StringBuffer toNewHampshire( final Phylogeny tree,
final boolean simple_nh,
final boolean nh_write_distance_to_parent,
- final boolean write_conf_values_in_branckets_in_nh ) throws IOException {
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
setOutputFormt( FORMAT.NH );
- setWriteConfidenceValuesInBracketsInNH( write_conf_values_in_branckets_in_nh );
+ setNhConversionSupportStyle( svs );
setSimpleNH( simple_nh );
setWriteDistanceToParentInNH( nh_write_distance_to_parent );
return getOutput( tree );
public void toNewHampshire( final Phylogeny tree,
final boolean simple_nh,
final boolean write_distance_to_parent,
- final boolean use_brackets_for_confidence,
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs,
final File out_file ) throws IOException {
- writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent, use_brackets_for_confidence ), out_file );
+ writeToFile( toNewHampshire( tree, simple_nh, write_distance_to_parent, svs ), out_file );
}
public void toNewHampshire( final Phylogeny[] trees,
writeToFile( sb, out_file );
}
- public void toNexus( final File out_file, final Phylogeny tree, final boolean write_conf_values_in_branckets_in_nh )
+ 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 ) );
final List<Phylogeny> trees = new ArrayList<Phylogeny>( 1 );
trees.add( tree );
writeNexusStart( writer );
writeNexusTaxaBlock( writer, tree );
- writeNexusTreesBlock( writer, trees, write_conf_values_in_branckets_in_nh );
+ writeNexusTreesBlock( writer, trees, svs );
writer.flush();
writer.close();
}
- public StringBuffer toNexus( final Phylogeny tree, final boolean write_conf_values_in_branckets_in_nh )
- 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<Phylogeny> trees = new ArrayList<Phylogeny>( 1 );
trees.add( tree );
writeNexusStart( writer );
writeNexusTaxaBlock( writer, tree );
- writeNexusTreesBlock( writer, trees, write_conf_values_in_branckets_in_nh );
+ writeNexusTreesBlock( writer, trees, svs );
writer.flush();
writer.close();
return string_writer.getBuffer();
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<Phylogeny> trees,
final int phyloxml_level,
}
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 ) {
else if ( getOutputFormt() == FORMAT.NH ) {
getBuffer().append( node.toNewHampshire( isSimpleNH(),
isWriteDistanceToParentInNH(),
- isWriteConfidenceValuesInBracketsInNH() ) );
+ getNhConversionSupportStyle() ) );
}
}
- private boolean isWriteConfidenceValuesInBracketsInNH() {
- return _write_conf_values_in_branckets_in_nh;
+ private NH_CONVERSION_SUPPORT_VALUE_STYLE getNhConversionSupportStyle() {
+ return _nh_conversion_support_style;
}
- private void setWriteConfidenceValuesInBracketsInNH( final boolean write_conf_values_in_branckets_in_nh ) {
- _write_conf_values_in_branckets_in_nh = write_conf_values_in_branckets_in_nh;
+ 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 ( 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( "(" );
}
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();
public static void writeNexusTreesBlock( final Writer writer,
final List<Phylogeny> trees,
- final boolean write_conf_values_in_branckets_in_nh ) throws IOException {
+ final NH_CONVERSION_SUPPORT_VALUE_STYLE svs ) throws IOException {
writer.write( NexusConstants.BEGIN_TREES );
writer.write( ForesterUtil.LINE_SEPARATOR );
int i = 1;
else {
writer.write( "[&U]" );
}
- writer.write( phylogeny.toNewHampshire( false, write_conf_values_in_branckets_in_nh ) );
+ writer.write( phylogeny.toNewHampshire( false, svs ) );
writer.write( ForesterUtil.LINE_SEPARATOR );
i++;
}
git://source.jalview.org / jalview.git / blobdiff