--- /dev/null
+// $Id:
+//
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2011 Christian M Zmasek
+// Copyright (C) 2011 Sanford-Burnham Medical Research Institute
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: www.phylosoft.org/forester
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.List;
+
+import org.forester.archaeopteryx.Archaeopteryx;
+import org.forester.io.parsers.FastaParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.PropertiesMap;
+import org.forester.phylogeny.data.Property;
+import org.forester.phylogeny.data.Property.AppliesTo;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sequence.Sequence;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class map_lengths {
+
+ final static private String PRG_NAME = "map_lengths";
+
+ public static void main( final String[] args ) {
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhyloXmlParser xml_parser = new PhyloXmlParser();
+ final Phylogeny[] phylogenies_0 = factory.create( cla.getFile( 0 ), xml_parser );
+ final Phylogeny phy = phylogenies_0[ 0 ];
+ for( int i = 1; i < cla.getNumberOfNames(); i++ ) {
+ final String fasta_name = cla.getName( i );
+ final List<Sequence> seqs = FastaParser.parse( new File( fasta_name ) );
+ for( int s = 0; s < seqs.size(); s++ ) {
+ final Sequence seq = seqs.get( s );
+ final int actual_length = seq.getLength() - seq.getNumberOfGapResidues();
+ String node_name = "" + seq.getIdentifier();
+ node_name = node_name.substring( 0, node_name.indexOf( "/" ) );
+ final PhylogenyNode n = phy.getNode( node_name );
+ if ( n.getNodeData().getProperties() == null ) {
+ n.getNodeData().setProperties( new PropertiesMap() );
+ }
+ final PropertiesMap properties = n.getNodeData().getProperties();
+ final Property p = new Property( "r:" + i, "" + actual_length, "", "xsd:integer", AppliesTo.NODE );
+ properties.addProperty( p );
+ }
+ }
+ Archaeopteryx.createApplication( phy );
+ }
+ catch ( final IOException e ) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+}
public static void main( final String args[] ) {
File in = null;
- File out = null;
- if ( ( args.length != 2 ) ) {
- // System.exit( -1 );
- if ( ( args.length == 0 ) ) {
- in = new File( "C:\\Users\\zma\\dollo.xml" );
- out = null;
- }
- }
+ final File out = null;
try {
- System.out.println( "..." );
CommandLineArguments cla = null;
cla = new CommandLineArguments( args );
- // in = cla.getFile( 0 );
+ in = cla.getFile( 0 );
// out = cla.getFile( 1 );
// if ( out.exists() ) {
// System.out.println( out + " already exists" );
final static int show_taxonomy_scientific_names = 17;
final static int show_taxonomy_common_names = 18;
final static int color_according_to_annotation = 19;
- final static int show_property = 20;
- final static int show_gene_symbols = 21;
- final static int node_data_popup = 22;
- final static int show_relation_confidence = 23;
- final static int show_vector_data = 24;
- final static int show_taxonomy_images = 25;
+ final static int show_gene_symbols = 20;
+ final static int node_data_popup = 21;
+ final static int show_relation_confidence = 22;
+ final static int show_vector_data = 23;
+ final static int show_taxonomy_images = 24;
+ final static int show_properties = 25;
// ------------------
// Click-to options
// ------------------
{ "Prot/Gene Acc", "display", "no" }, { "Show Internal Data", "display", "yes" },
{ "Dyna Hide", "display", "yes" }, { "Taxonomy Scientific", "display", "yes" },
{ "Taxonomy Common", "display", "no" }, { "Annotation Colorize", "nodisplay", "no" },
- { "Property", "nodisplay", "no" }, { "Prot/Gene Symbol", "display", "yes" },
- { "Rollover", "display", "yes" }, { "Relation Confidence", "display", "no" },
- { "Vector Data", "display", "no" }, { "Taxonomy Images", "display", "no" } };
+ { "Prot/Gene Symbol", "display", "yes" }, { "Rollover", "display", "yes" },
+ { "Relation Confidence", "display", "no" }, { "Vector Data", "display", "no" },
+ { "Taxonomy Images", "display", "no" }, { "Properties", "display", "no" } };
final static String clickto_options[][] = {
{ "Display Node Data", "display" }, { "Collapse/Uncollapse", "display" }, { "Root/Reroot", "display" },
{ "Sub/Super Tree", "display" }, { "Swap Descendants", "display" }, { "Colorize Subtree", "display" },
else if ( key.equals( "color_according_to_annotation" ) ) {
key_index = Configuration.color_according_to_annotation;
}
- else if ( key.equals( "show_property" ) ) {
- key_index = Configuration.show_property;
- }
else if ( key.equals( "show_vector_data" ) ) {
key_index = Configuration.show_vector_data;
}
+ else if ( key.equals( "show_properties" ) ) {
+ key_index = Configuration.show_properties;
+ }
else if ( key.equals( "show_relation_confidence" ) ) {
key_index = Configuration.show_relation_confidence;
}
private JComboBox _show_sequence_relations;
private JComboBox _sequence_relation_type_box;
private JCheckBox _show_vector_data_cb;
+ private JCheckBox _show_properties_cb;
private JLabel _click_to_label;
private JLabel _zoom_label;
private JLabel _domain_display_label;
addJCheckBox( _show_vector_data_cb, ch_panel );
add( ch_panel );
break;
+ case Configuration.show_properties:
+ _show_properties_cb = new JCheckBox( title );
+ addJCheckBox( _show_properties_cb, ch_panel );
+ add( ch_panel );
+ break;
default:
throw new RuntimeException( "unknown checkbox: " + which );
}
return ( ( _show_vector_data_cb != null ) && _show_vector_data_cb.isSelected() );
}
+ public boolean isShowProperties() {
+ return ( ( _show_properties_cb != null ) && _show_properties_cb.isSelected() );
+ }
+
boolean isShowGeneSymbols() {
return ( ( _show_gene_symbols != null ) && _show_gene_symbols.isSelected() );
}
return ( ( _show_node_names != null ) && _show_node_names.isSelected() );
}
- boolean isShowProperty() {
- return ( ( _show_annotation != null ) && _show_annotation.isSelected() );
- }
-
boolean isShowSequenceAcc() {
return ( ( _show_sequence_acc != null ) && _show_sequence_acc.isSelected() );
}
_show_vector_data_cb.setSelected( state );
}
break;
+ case Configuration.show_properties:
+ if ( _show_properties_cb != null ) {
+ _show_properties_cb.setSelected( state );
+ }
+ break;
case Configuration.show_sequence_acc:
if ( _show_sequence_acc != null ) {
_show_sequence_acc.setSelected( state );
_configuration.getDisplayTitle( Configuration.show_vector_data ) );
setCheckbox( Configuration.show_vector_data, _configuration.doCheckOption( Configuration.show_vector_data ) );
}
+ if ( _configuration.doDisplayOption( Configuration.show_properties ) ) {
+ addCheckbox( Configuration.show_properties, _configuration.getDisplayTitle( Configuration.show_properties ) );
+ setCheckbox( Configuration.show_properties, _configuration.doCheckOption( Configuration.show_properties ) );
+ }
}
void setupSearchTools() {
sum += getTreeFontSet()._fm_large_italic.stringWidth( tax.getCommonName() + " ()" );
}
}
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ sum += getTreeFontSet()._fm_large.stringWidth( propertiesToString( node ).toString() );
+ }
if ( getControlPanel().isShowBinaryCharacters() && node.getNodeData().isHasBinaryCharacters() ) {
sum += getTreeFontSet()._fm_large.stringWidth( node.getNodeData().getBinaryCharacters()
.getGainedCharactersAsStringBuffer().toString() );
_sb.append( node.getNodeData().getSequence().getAccession().getValue() );
}
}
+ if ( getControlPanel().isShowProperties() && node.getNodeData().isHasProperties() ) {
+ if ( _sb.length() > 0 ) {
+ _sb.append( " " );
+ }
+ _sb.append( propertiesToString( node ) );
+ }
g.setFont( getTreeFontSet().getLargeFont() );
if ( is_in_found_nodes ) {
g.setFont( getTreeFontSet().getLargeFont().deriveFont( Font.BOLD ) );
}
}
+ private StringBuffer propertiesToString( final PhylogenyNode node ) {
+ final PropertiesMap properties = node.getNodeData().getProperties();
+ final StringBuffer sb = new StringBuffer();
+ boolean first = true;
+ for( final String ref : properties.getPropertyRefs() ) {
+ if ( first ) {
+ first = false;
+ }
+ else {
+ sb.append( " " );
+ }
+ sb.append( properties.getProperty( ref ).asText() );
+ }
+ return sb;
+ }
+
private double drawTaxonomyImage( final double x, final double y, final PhylogenyNode node, final Graphics2D g ) {
final List<Uri> us = new ArrayList<Uri>();
for( final Taxonomy t : node.getNodeData().getTaxonomies() ) {
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
return false;
}
+ static public Msa parseMsa( final File f ) throws IOException {
+ return parseMsa( new FileInputStream( f ) );
+ }
+
static public Msa parseMsa( final InputStream is ) throws IOException {
return BasicMsa.createInstance( parse( is ) );
}
return parseMsa( new ByteArrayInputStream( bytes ) );
}
+ static public List<Sequence> parse( final File f ) throws IOException {
+ return parse( new FileInputStream( f ) );
+ }
+
static public List<Sequence> parse( final InputStream is ) throws IOException {
final BufferedReader reader = new BufferedReader( new InputStreamReader( is, "UTF-8" ) );
String line = null;
}
public boolean isHasProperties() {
- return getProperties() != null;
+ return ( getProperties() != null ) && ( getProperties().size() > 0 );
}
public boolean isHasReference() {
}
@Override
+ public int getNumberOfGapResidues() {
+ int gaps = 0;
+ for( int i = 0; i < _mol_sequence.length; ++i ) {
+ if ( _mol_sequence[ i ] == GAP ) {
+ ++gaps;
+ }
+ }
+ return gaps;
+ }
+
+ @Override
public String toString() {
final StringBuffer sb = new StringBuffer();
sb.append( _identifier.toString() );
public abstract int getLength();
+ public abstract int getNumberOfGapResidues();
+
public abstract char[] getMolecularSequence();
public abstract char getResidueAt( final int position );
git://source.jalview.org / jalview.git / commitdiff