--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.tools.ConfidenceAssessor;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class confadd {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String FIRST_OPTION = "f";
+ final static private String LAST_OPTION = "l";
+ final static private String STRICT_OPTION = "s";
+ final static private String NORMALIZE_OPTION = "n";
+ final static private String PRG_NAME = "confadd";
+ final static private String PRG_VERSION = "1.01";
+ final static private String PRG_DATE = "2010.10.26";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( args.length < 4 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ if ( cla.getNumberOfNames() != 4 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( FIRST_OPTION );
+ allowed_options.add( LAST_OPTION );
+ allowed_options.add( STRICT_OPTION );
+ allowed_options.add( NORMALIZE_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final String confidence_type = cla.getName( 0 );
+ final File target_file = cla.getFile( 1 );
+ final File evaluators_file = cla.getFile( 2 );
+ final File outfile = cla.getFile( 3 );
+ if ( ForesterUtil.isEmpty( confidence_type ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "attempt to use empty confidence type" );
+ }
+ if ( outfile.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
+ }
+ if ( !target_file.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "target [" + target_file + "] does not exist" );
+ }
+ if ( !evaluators_file.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "evaluators [" + evaluators_file + "] does not exist" );
+ }
+ boolean strict = false;
+ int first = 0;
+ int last = 0;
+ double norm = 0;
+ try {
+ if ( cla.isOptionSet( STRICT_OPTION ) ) {
+ if ( cla.isOptionHasAValue( STRICT_OPTION ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "no value allowed for -" + STRICT_OPTION + " allowed" );
+ }
+ strict = true;
+ }
+ if ( cla.isOptionSet( FIRST_OPTION ) ) {
+ first = cla.getOptionValueAsInt( FIRST_OPTION );
+ }
+ if ( cla.isOptionSet( LAST_OPTION ) ) {
+ last = cla.getOptionValueAsInt( LAST_OPTION );
+ }
+ if ( cla.isOptionSet( NORMALIZE_OPTION ) ) {
+ norm = cla.getOptionValueAsDouble( NORMALIZE_OPTION );
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getLocalizedMessage() );
+ }
+ if ( ( first < 0 ) || ( last < 0 ) ) {
+ ForesterUtil
+ .fatalError( PRG_NAME,
+ "attempt to set first or last evaluator topology to use to a number less than zero" );
+ }
+ if ( norm < 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "illegal value for normalizer [" + norm + "]" );
+ }
+ Phylogeny[] targets = null;
+ Phylogeny[] evaluators = null;
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ try {
+ targets = factory.create( target_file, ForesterUtil.createParserDependingOnFileType( target_file, true ) );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read target phylogenies from [" + target_file + "]: "
+ + e.getLocalizedMessage() );
+ }
+ int counter = 0;
+ for( final Phylogeny target : targets ) {
+ try {
+ checkUniquenessOfExternalNodes( target, "target " + counter );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ counter++;
+ }
+ if ( targets.length == 1 ) {
+ ForesterUtil.programMessage( PRG_NAME, "read in one target" );
+ }
+ else {
+ ForesterUtil.programMessage( PRG_NAME, "read in a total of " + targets.length + " targets" );
+ }
+ try {
+ evaluators = factory.create( evaluators_file, ForesterUtil
+ .createParserDependingOnFileType( evaluators_file, true ) );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read evaluator topologies from [" + evaluators_file + "]: "
+ + e.getLocalizedMessage() );
+ }
+ counter = 0;
+ for( final Phylogeny evaluator : evaluators ) {
+ try {
+ checkUniquenessOfExternalNodes( evaluator, "evaluator " + counter );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ counter++;
+ }
+ ForesterUtil.programMessage( PRG_NAME, "read in a total of " + evaluators.length + " evaluator topologies" );
+ System.gc();
+ if ( last == 0 ) {
+ last = evaluators.length - 1;
+ }
+ if ( ( last >= evaluators.length ) || ( last <= first ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "illegal value for first or last evaluator topology to use [" + first
+ + ", " + last + "]" );
+ }
+ double value = 1;
+ if ( norm > 0 ) {
+ value = norm / ( 1 + last - first );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "first topology to use: " + first );
+ String is_last = "";
+ if ( last == ( evaluators.length - 1 ) ) {
+ is_last = " (corresponds to last topology in file)";
+ }
+ ForesterUtil.programMessage( PRG_NAME, "last topology to use : " + last + is_last );
+ ForesterUtil.programMessage( PRG_NAME, "sum of topologies used as evaluators: " + ( last - first + 1 ) );
+ if ( norm > 0 ) {
+ ForesterUtil.programMessage( PRG_NAME, "normalizer: " + norm + " (" + ForesterUtil.round( value, 6 ) + ")" );
+ }
+ else {
+ ForesterUtil.programMessage( PRG_NAME, "normalizer: n/a" );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "strict: " + strict );
+ for( final Phylogeny target : targets ) {
+ try {
+ ConfidenceAssessor.evaluate( confidence_type, evaluators, target, strict, value, first, last );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( targets, 0, outfile, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to write to [" + outfile + "]: " + e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "wrote output to: [" + outfile + "]" );
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( PRG_NAME
+ + " [options] <confidence type> <target tree file> <evaluators tree file> <outfile>" );
+ System.out.println();
+ System.out.println( "options:" );
+ System.out.println();
+ System.out.println( " -" + STRICT_OPTION
+ + " : strict [default: non-strict]: all nodes between 'target' and 'evaluators' must match" );
+ System.out.println( " -" + NORMALIZE_OPTION
+ + "=<d>: normalize to this value (e.g. 100 for most bootstrap analyses) [default: no normalization]" );
+ System.out.println( " -" + FIRST_OPTION + "=<i>: first evaluator topology to use (0-based) [default: 0]" );
+ System.out.println( " -" + LAST_OPTION
+ + "=<i>: last evaluator topology to use (0-based) [default: use all until final topology]" );
+ System.out.println();
+ }
+
+ private static void checkUniquenessOfExternalNodes( final Phylogeny phy, final String msg )
+ throws IllegalArgumentException {
+ final Set<PhylogenyNode> ext_nodes = new HashSet<PhylogenyNode>( phy.getNumberOfExternalNodes() );
+ for( final PhylogenyNodeIterator it = phy.iteratorExternalForward(); it.hasNext(); ) {
+ final PhylogenyNode node = it.next();
+ if ( ext_nodes.contains( node ) ) {
+ throw new IllegalArgumentException( "external node [" + node.toString() + "] of " + msg
+ + " is not unique" );
+ }
+ ext_nodes.add( node );
+ }
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.tools.SupportCount;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class count_support {
+
+ final static private String PRG_NAME = "count_support";
+ final static private String PRG_VERSION = "1.0";
+ final static private String PRG_DATE = "2008.03.04";
+ private final static boolean WRITE_EVALUATORS_AS_NHX = false;
+
+ public static void main( final String args[] ) {
+ ForesterUtil
+ .printProgramInformation( count_support.PRG_NAME, count_support.PRG_VERSION, count_support.PRG_DATE );
+ if ( ( args.length < 3 ) || ( args.length > 7 ) ) {
+ System.out.println();
+ System.out.println( count_support.PRG_NAME + ": wrong number of arguments" );
+ System.out.println();
+ System.out
+ .println( "Usage: \"count_support [options] <file containing phylogeny to be evaluated> <file with phylogenies to be used for evaluation> <outfile> [outfile for evaluator phylogenies, "
+ + "always unstripped if -t=<d> option is used, otherwise strippedness is dependent on -s option]\"\n" );
+ System.out
+ .println( " Options: -s strip external nodes from evaluator phylogenies not found in phylogeny to be evaluated" );
+ System.out.println( " : -t=<d> threshold for similarity (0.0 to 1.0)" );
+ System.out.println( " : -n no branch lengths in outfile for evaluator phylogenies" );
+ System.out.println();
+ System.exit( -1 );
+ }
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( "s" );
+ allowed_options.add( "t" );
+ allowed_options.add( "n" );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "Unknown option(s): " + dissallowed_options );
+ }
+ final File phylogeny_infile = cla.getFile( 0 );
+ final File evaluators_infile = cla.getFile( 1 );
+ final File phylogeny_outfile = cla.getFile( 2 );
+ File evaluators_outfile = null;
+ boolean branch_lengths_in_ev_out = true;
+ if ( cla.isOptionSet( "n" ) ) {
+ branch_lengths_in_ev_out = false;
+ }
+ if ( cla.getNumberOfNames() == 4 ) {
+ evaluators_outfile = cla.getFile( 3 );
+ }
+ else {
+ if ( !branch_lengths_in_ev_out ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME,
+ "Cannot use -n option if no outfile for evaluators specified" );
+ }
+ }
+ Phylogeny p = null;
+ Phylogeny[] ev = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+ p = factory.create( phylogeny_infile, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" ["
+ + e.getMessage() + "]" );
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( evaluators_infile, true );
+ ev = factory.create( evaluators_infile, pp );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "Could not read \"" + evaluators_infile + "\" ["
+ + e.getMessage() + "]" );
+ }
+ boolean strip = false;
+ if ( cla.isOptionSet( "s" ) ) {
+ strip = true;
+ }
+ double threshhold = -1.0;
+ if ( cla.isOptionSet( "t" ) ) {
+ try {
+ threshhold = cla.getOptionValueAsDouble( "t" );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "error in command line arguments: " + e.getMessage() );
+ }
+ if ( ( threshhold < 0 ) || ( threshhold > 1.0 ) ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME,
+ "support threshold has to be between 0.0 and 1.0 (inclusive)" );
+ }
+ }
+ List<Phylogeny> evaluator_phylogenies_above_threshold = null;
+ try {
+ if ( threshhold >= 0 ) {
+ evaluator_phylogenies_above_threshold = SupportCount.count( p, ev, strip, threshhold, true );
+ if ( evaluator_phylogenies_above_threshold.size() < 1 ) {
+ ForesterUtil.fatalError( "count_support", "appears like threshold for similarity is set too high" );
+ }
+ }
+ else {
+ SupportCount.count( p, ev, strip, true );
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "Failure during support counting: " + e.getMessage() );
+ }
+ if ( threshhold >= 0 ) {
+ count_support.normalizeSupport( p, 100, evaluator_phylogenies_above_threshold.size() );
+ System.out.println( evaluator_phylogenies_above_threshold.size() + " out of " + ev.length
+ + " evaluator phylogenies are above threshold of " + threshhold );
+ }
+ try {
+ final PhylogenyWriter w = new PhylogenyWriter();
+ w.toPhyloXML( phylogeny_outfile, p, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ System.out.println( "Wrote phylogeny with support values to: " + phylogeny_outfile );
+ if ( evaluators_outfile != null ) {
+ try {
+ final PhylogenyWriter w = new PhylogenyWriter();
+ if ( evaluator_phylogenies_above_threshold != null ) {
+ System.out.println( "Writing " + evaluator_phylogenies_above_threshold.size()
+ + " evaluator phylogenies above threshold of " + threshhold + " to: " + evaluators_outfile );
+ if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
+ w.toNewHampshireX( evaluator_phylogenies_above_threshold, evaluators_outfile, ";"
+ + ForesterUtil.getLineSeparator() );
+ }
+ else {
+ w.toNewHampshire( evaluator_phylogenies_above_threshold,
+ true,
+ branch_lengths_in_ev_out,
+ evaluators_outfile,
+ ";" + ForesterUtil.getLineSeparator() );
+ }
+ }
+ else {
+ System.out.println( "Writing " + ev.length + " evaluator phylogenies to :" + evaluators_outfile );
+ if ( count_support.WRITE_EVALUATORS_AS_NHX ) {
+ w.toNewHampshireX( Arrays.asList( ev ), evaluators_outfile, ";"
+ + ForesterUtil.getLineSeparator() );
+ }
+ else {
+ w.toNewHampshire( Arrays.asList( ev ), true, branch_lengths_in_ev_out, evaluators_outfile, ";"
+ + ForesterUtil.getLineSeparator() );
+ }
+ }
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( count_support.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
+ }
+ }
+ System.out.println();
+ System.out.println( "Done." );
+ System.out.println();
+ }
+
+ private static void normalizeSupport( final Phylogeny p, final double normalized_max, final int number_phylos ) {
+ double min = Double.MAX_VALUE;
+ double max = -Double.MAX_VALUE;
+ double sum = 0.0;
+ int n = 0;
+ for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( !node.isRoot() && !node.isExternal() ) {
+ final double b = PhylogenyMethods.getConfidenceValue( node );
+ if ( b > max ) {
+ max = b;
+ }
+ if ( ( b >= 0 ) && ( b < min ) ) {
+ min = b;
+ }
+ sum += b;
+ ++n;
+ }
+ }
+ double av = sum / n;
+ System.out.println( "Max support before normalization is : " + max );
+ System.out.println( "Min support before normalization is : " + min );
+ System.out.println( "Average support before normalization is: " + av + " (=" + sum + "/" + n + ")" );
+ System.out.println( "Normalizing so that theoretical maximum support value is: " + normalized_max );
+ System.out.println( "Number of phylogenies used in support analysis: " + number_phylos );
+ final double f = normalized_max / number_phylos;
+ min = Double.MAX_VALUE;
+ max = -Double.MAX_VALUE;
+ sum = 0.0;
+ n = 0;
+ for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.isRoot() || node.isExternal() ) {
+ PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
+ }
+ else {
+ double b = PhylogenyMethods.getConfidenceValue( node );
+ b = f * b;
+ PhylogenyMethods.setBootstrapConfidence( node, b );
+ if ( b > max ) {
+ max = b;
+ }
+ if ( ( b >= 0 ) && ( b < min ) ) {
+ min = b;
+ }
+ sum += b;
+ ++n;
+ }
+ }
+ av = sum / n;
+ System.out.println( "Max support after normalization is : " + max );
+ System.out.println( "Min support after normalization is : " + min );
+ System.out.println( "Average support after normalization is: " + av + " (=" + sum + "/" + n + ")" );
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.data.Identifier;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.tools.PhylogenyDecorator;
+import org.forester.tools.PhylogenyDecorator.FIELD;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public final class decorator {
+
+ private static final String SEQUENCE_NAME_FIELD = "s";
+ private static final String TAXONOMY_CODE_FIELD = "c";
+ private static final String TAXONOMY_SCIENTIFIC_NAME_FIELD = "sn";
+ private static final String DS_FILED = "d";
+ private static final String SEQUENCE_ANNOTATION_DESC = "a";
+ private static final String NODE_NAME_FIELD = "n";
+ final static private String PICKY_OPTION = "p";
+ final static private String FIELD_OPTION = "f";
+ final static private String MOVE_DOMAIN_NUMBER_OPTION = "mdn"; // Hidden expert option.
+ final static private String TREE_NAME_OPTION = "pn";
+ final static private String TREE_ID_OPTION = "pi";
+ final static private String TREE_DESC_OPTION = "pd";
+ final static private String EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION = "sn";
+ final static private String PROCESS_NAME_INTELLIGENTLY_OPTION = "x";
+ final static private String PROCESS_SIMILAR_TO_OPTION = "xs";
+ final static private String CUT_NAME_AFTER_FIRST_SPACE_OPTION = "c";
+ final static private String ALLOW_REMOVAL_OF_CHARS_OPTION = "r";
+ final static private String ADVANCED_TABLE_OPTION = "table";
+ final static private String KEY_COLUMN = "k";
+ final static private String VALUE_COLUMN = "v";
+ final static private String MAPPING_FILE_SEPARATOR_OPTION = "s";
+ final static private String MAPPING_FILE_SEPARATOR_DEFAULT = ":";
+ final static private boolean USE_FIRST_SEPARATOR_ONLY = true;
+ final static private String PRG_NAME = "decorator";
+ final static private String PRG_VERSION = "1.10";
+ final static private String PRG_DATE = "2009.10.08";
+
+ private static void argumentsError() {
+ System.out.println();
+ System.out.println( decorator.PRG_NAME + " -" + ADVANCED_TABLE_OPTION + " | -f=<c> <phylogenies infile> "
+ + "[mapping table file] <phylogenies outfile>" );
+ System.out.println();
+ System.out.println( "options:" );
+ System.out.println();
+ System.out.println( " -" + ADVANCED_TABLE_OPTION + " : table instead of one to one map (-f=<c>)" );
+ System.out.println( " -r=<n> : allow to remove up to n characters from the end of the names" );
+ System.out.println( " in phylogenies infile if not found (in map) otherwise" );
+ System.out.println( " -p : for picky, fails if node name not found in mapping table, default is off" );
+ System.out.println( " -" + TREE_NAME_OPTION + "=<s>: name for the phylogeny" );
+ System.out.println( " -" + TREE_ID_OPTION + "=<s>: identifier for the phylogeny (in the form provider:value)" );
+ System.out.println( " -" + TREE_DESC_OPTION + "=<s>: description for phylogenies" );
+ System.out.println();
+ System.out.println();
+ System.out.println( "advanced options, only available if -" + ADVANCED_TABLE_OPTION + " is not used:" );
+ System.out.println();
+ System.out.println( " -f=<c> : field to be replaced: " + NODE_NAME_FIELD + " : node name" );
+ System.out.println( " " + SEQUENCE_ANNOTATION_DESC
+ + " : sequence annotation description" );
+ System.out.println( " " + DS_FILED + " : domain structure" );
+ System.out.println( " " + TAXONOMY_CODE_FIELD + " : taxonomy code" );
+ System.out.println( " " + TAXONOMY_SCIENTIFIC_NAME_FIELD
+ + ": taxonomy scientific name" );
+ System.out.println( " " + SEQUENCE_NAME_FIELD + " : sequence name" );
+ System.out.println( " -k=<n> : key column in mapping table (0 based)," );
+ System.out.println( " names of the node to be decorated - default is 0" );
+ System.out.println( " -v=<n> : value column in mapping table (0 based)," );
+ System.out.println( " data which with to decorate - default is 1" );
+ System.out.println( " -" + EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION
+ + " : to extract bracketed scientific names" );
+ System.out.println( " -s=<c> : column separator in mapping file, default is \""
+ + decorator.MAPPING_FILE_SEPARATOR_DEFAULT + "\"" );
+ System.out.println( " -x : process name \"intelligently\" (only for -f=n)" );
+ System.out.println( " -" + decorator.PROCESS_SIMILAR_TO_OPTION
+ + " : process name \"intelligently\" and process information after \"similar to\" (only for -f=n)" );
+ System.out.println( " -c : cut name after first space (only for -f=n)" );
+ System.out.println();
+ System.exit( -1 );
+ }
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( decorator.PRG_NAME, decorator.PRG_VERSION, decorator.PRG_DATE );
+ if ( ( args.length < 4 ) || ( args.length > 12 ) ) {
+ decorator.argumentsError();
+ }
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( ( cla.getNumberOfNames() < 3 ) || ( cla.getNumberOfNames() > 4 ) ) {
+ decorator.argumentsError();
+ }
+ final File phylogenies_infile = cla.getFile( 0 );
+ final File mapping_infile = cla.getFile( 1 );
+ final File phylogenies_outfile = cla.getFile( 2 );
+ if ( phylogenies_outfile.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "[" + phylogenies_outfile + "] already exists" );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( decorator.ADVANCED_TABLE_OPTION );
+ allowed_options.add( decorator.PICKY_OPTION );
+ allowed_options.add( decorator.FIELD_OPTION );
+ allowed_options.add( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION );
+ allowed_options.add( decorator.PROCESS_SIMILAR_TO_OPTION );
+ allowed_options.add( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION );
+ allowed_options.add( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
+ allowed_options.add( decorator.KEY_COLUMN );
+ allowed_options.add( decorator.VALUE_COLUMN );
+ allowed_options.add( decorator.MAPPING_FILE_SEPARATOR_OPTION );
+ allowed_options.add( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION );
+ allowed_options.add( decorator.TREE_NAME_OPTION );
+ allowed_options.add( decorator.TREE_ID_OPTION );
+ allowed_options.add( decorator.TREE_DESC_OPTION );
+ allowed_options.add( decorator.MOVE_DOMAIN_NUMBER_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final boolean advanced_table = cla.isOptionSet( decorator.ADVANCED_TABLE_OPTION );
+ if ( !advanced_table ) {
+ final List<String> mandatory_options = new ArrayList<String>();
+ mandatory_options.add( decorator.FIELD_OPTION );
+ final String missing_options = cla.validateMandatoryOptionsAsString( mandatory_options );
+ if ( missing_options.length() > 0 ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "missing option(s): " + missing_options );
+ }
+ }
+ final boolean picky = cla.isOptionSet( decorator.PICKY_OPTION );
+ String separator = decorator.MAPPING_FILE_SEPARATOR_DEFAULT;
+ if ( cla.isOptionSet( decorator.MAPPING_FILE_SEPARATOR_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ separator = cla.getOptionValue( decorator.MAPPING_FILE_SEPARATOR_OPTION );
+ }
+ int key_column = 0;
+ int value_column = 1;
+ String field_str = "";
+ FIELD field = FIELD.NODE_NAME;
+ int numbers_of_chars_allowed_to_remove_if_not_found_in_map = -1;
+ boolean cut_name_after_space = false;
+ boolean process_name_intelligently = false;
+ boolean process_similar_to = false;
+ boolean extract_bracketed_scientific_name = false;
+ boolean move_domain_numbers_at_end_to_middle = false;
+ String tree_name = "";
+ String tree_id = "";
+ String tree_desc = "";
+ try {
+ if ( cla.isOptionSet( decorator.TREE_NAME_OPTION ) ) {
+ tree_name = cla.getOptionValueAsCleanString( decorator.TREE_NAME_OPTION );
+ }
+ if ( cla.isOptionSet( decorator.TREE_ID_OPTION ) ) {
+ tree_id = cla.getOptionValueAsCleanString( decorator.TREE_ID_OPTION );
+ }
+ if ( cla.isOptionSet( decorator.TREE_DESC_OPTION ) ) {
+ tree_desc = cla.getOptionValueAsCleanString( decorator.TREE_DESC_OPTION );
+ }
+ if ( cla.isOptionSet( decorator.EXTRACT_BRACKETED_SCIENTIC_NAME_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ extract_bracketed_scientific_name = true;
+ }
+ if ( cla.isOptionSet( decorator.KEY_COLUMN ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ key_column = cla.getOptionValueAsInt( decorator.KEY_COLUMN );
+ }
+ if ( cla.isOptionSet( decorator.VALUE_COLUMN ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ value_column = cla.getOptionValueAsInt( decorator.VALUE_COLUMN );
+ }
+ if ( cla.isOptionSet( decorator.CUT_NAME_AFTER_FIRST_SPACE_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ cut_name_after_space = true;
+ }
+ if ( cla.isOptionSet( decorator.PROCESS_NAME_INTELLIGENTLY_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ process_name_intelligently = true;
+ }
+ if ( cla.isOptionSet( decorator.PROCESS_SIMILAR_TO_OPTION ) ) {
+ if ( advanced_table ) {
+ argumentsError();
+ }
+ process_similar_to = true;
+ }
+ if ( cla.isOptionSet( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION ) ) {
+ numbers_of_chars_allowed_to_remove_if_not_found_in_map = cla
+ .getOptionValueAsInt( decorator.ALLOW_REMOVAL_OF_CHARS_OPTION );
+ }
+ if ( cla.isOptionSet( decorator.MOVE_DOMAIN_NUMBER_OPTION ) ) {
+ move_domain_numbers_at_end_to_middle = true;
+ }
+ if ( cla.isOptionSet( decorator.FIELD_OPTION ) ) {
+ field_str = cla.getOptionValue( decorator.FIELD_OPTION );
+ if ( field_str.equals( NODE_NAME_FIELD ) ) {
+ field = FIELD.NODE_NAME;
+ }
+ else if ( field_str.equals( SEQUENCE_ANNOTATION_DESC ) ) {
+ field = FIELD.SEQUENCE_ANNOTATION_DESC;
+ }
+ else if ( field_str.equals( DS_FILED ) ) {
+ field = FIELD.DOMAIN_STRUCTURE;
+ extract_bracketed_scientific_name = false;
+ }
+ else if ( field_str.equals( TAXONOMY_CODE_FIELD ) ) {
+ field = FIELD.TAXONOMY_CODE;
+ }
+ else if ( field_str.equals( SEQUENCE_NAME_FIELD ) ) {
+ field = FIELD.SEQUENCE_NAME;
+ }
+ else if ( field_str.equals( TAXONOMY_SCIENTIFIC_NAME_FIELD ) ) {
+ field = FIELD.TAXONOMY_SCIENTIFIC_NAME;
+ extract_bracketed_scientific_name = false;
+ }
+ else {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "unknown value for \"" + decorator.FIELD_OPTION
+ + "\" option: \"" + field_str + "\"" );
+ }
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "error in command line: " + e.getMessage() );
+ }
+ if ( ( field != FIELD.NODE_NAME ) && ( cut_name_after_space || process_name_intelligently ) ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x or -c option without -f=n" );
+ }
+ if ( ( field != FIELD.NODE_NAME ) && process_similar_to ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
+ + " option without -f=n" );
+ }
+ if ( cut_name_after_space && process_name_intelligently ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -x and -c option together" );
+ }
+ if ( process_similar_to && process_name_intelligently ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
+ + " and -x option together" );
+ }
+ if ( process_similar_to && cut_name_after_space ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "attempt to use -" + decorator.PROCESS_SIMILAR_TO_OPTION
+ + " and -c option together" );
+ }
+ Phylogeny[] phylogenies = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogenies_infile, true );
+ phylogenies = factory.create( phylogenies_infile, pp );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read phylgenies from [" + phylogenies_infile
+ + "] [" + e.getMessage() + "]" );
+ }
+ Map<String, String> map = null;
+ if ( !advanced_table ) {
+ BasicTable<String> mapping_table = null;
+ try {
+ mapping_table = BasicTableParser.parse( mapping_infile, separator, decorator.USE_FIRST_SEPARATOR_ONLY );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read [" + mapping_infile + "] ["
+ + e.getMessage() + "]" );
+ }
+ if ( ( key_column < 0 ) || ( key_column >= mapping_table.getNumberOfColumns() ) ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for key column" );
+ }
+ if ( ( value_column < 0 ) || ( value_column >= mapping_table.getNumberOfColumns() ) ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "illegal value for value column" );
+ }
+ map = mapping_table.getColumnsAsMap( key_column, value_column );
+ }
+ if ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id )
+ || !ForesterUtil.isEmpty( tree_desc ) ) {
+ if ( ( phylogenies.length > 1 )
+ && ( !ForesterUtil.isEmpty( tree_name ) || !ForesterUtil.isEmpty( tree_id ) ) ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME,
+ "attempt to set same name or id on more than one phylogeny" );
+ }
+ if ( !ForesterUtil.isEmpty( tree_name ) ) {
+ phylogenies[ 0 ].setName( tree_name );
+ }
+ if ( !ForesterUtil.isEmpty( tree_id ) ) {
+ final String[] s_ary = tree_id.split( ":" );
+ phylogenies[ 0 ].setIdentifier( new Identifier( s_ary[ 1 ], s_ary[ 0 ] ) );
+ }
+ if ( !ForesterUtil.isEmpty( tree_desc ) ) {
+ for( int i = 0; i < phylogenies.length; ++i ) {
+ phylogenies[ i ].setDescription( tree_desc );
+ }
+ }
+ }
+ try {
+ if ( advanced_table ) {
+ Map<String, Map<String, String>> table = null;
+ try {
+ table = PhylogenyDecorator.parseMappingTable( mapping_infile );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "failed to read \"" + mapping_infile + "\" ["
+ + e.getMessage() + "]" );
+ }
+ PhylogenyDecorator.decorate( phylogenies,
+ table,
+ picky,
+ numbers_of_chars_allowed_to_remove_if_not_found_in_map );
+ }
+ else {
+ PhylogenyDecorator.decorate( phylogenies,
+ map,
+ field,
+ extract_bracketed_scientific_name,
+ picky,
+ cut_name_after_space,
+ process_name_intelligently,
+ process_similar_to,
+ numbers_of_chars_allowed_to_remove_if_not_found_in_map,
+ move_domain_numbers_at_end_to_middle );
+ }
+ }
+ catch ( final NullPointerException e ) {
+ ForesterUtil.unexpectedFatalError( decorator.PRG_NAME, e );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "failed to map [" + e + "]" );
+ }
+ try {
+ final PhylogenyWriter w = new PhylogenyWriter();
+ w.toPhyloXML( phylogenies, 0, phylogenies_outfile, ForesterUtil.getLineSeparator() );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( decorator.PRG_NAME, "failed to write output [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "wrote: " + phylogenies_outfile );
+ ForesterUtil.programMessage( PRG_NAME, "OK." );
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.util.StringTokenizer;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.ForesterUtil;
+
+public class get_distances {
+
+ public static void main( final String args[] ) {
+ if ( args.length != 3 ) {
+ System.out.println( "\nget_distances: Wrong number of arguments.\n" );
+ System.out.println( "Usage: \"get_distances <phylogeny file> <file with node names> <outfile>\"\n" );
+ System.exit( -1 );
+ }
+ final File phylogeny_infile = new File( args[ 0 ] );
+ final File names_infile = new File( args[ 1 ] );
+ final File outfile = new File( args[ 2 ] );
+ Phylogeny p = null;
+ try {
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ p = factory.create( phylogeny_infile, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ System.out.println( "\nCould not read \"" + phylogeny_infile + "\" [" + e.getMessage() + "]\n" );
+ System.exit( -1 );
+ }
+ String line = "";
+ try {
+ final BufferedReader in = new BufferedReader( new FileReader( names_infile ) );
+ final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+ while ( ( line = in.readLine() ) != null ) {
+ if ( line.length() < 3 ) {
+ continue;
+ }
+ final StringTokenizer st = new StringTokenizer( line );
+ if ( st.countTokens() < 2 ) {
+ continue;
+ }
+ final double d = PhylogenyMethods.getInstance().calculateDistance( p.getNode( st.nextToken() ),
+ p.getNode( st.nextToken() ) );
+ out.write( line + " " + d );
+ out.newLine();
+ }
+ out.flush();
+ out.close();
+ in.close();
+ }
+ catch ( final IOException e ) {
+ System.out.println( "\nError during processing of \"" + names_infile + "\" [" + e.getMessage()
+ + "] at line \"" + line + "\"\n" );
+ System.exit( -1 );
+ }
+ System.out.println( "\nDone.\n" );
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2009 Christian M. Zmasek
+// Copyright (C) 2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.SortedMap;
+
+import org.forester.go.GoId;
+import org.forester.go.GoTerm;
+import org.forester.go.GoUtils;
+import org.forester.go.OBOparser;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterUtil;
+import org.forester.util.GeneralTable;
+
+public class goac {
+
+ private static final String ALL = "{ALL}";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String PRG_NAME = "goac";
+ final static private String PRG_VERSION = "1.03";
+ final static private String PRG_DATE = "2010.04.21";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/goac";
+
+ private static void addStats( final SortedMap<String, List<GoId>> data_to_be_analyzed,
+ final GeneralTable<String, Double> table ) {
+ for( final String go : table.getColumnIdentifiers() ) {
+ final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+ for( final String label : data_to_be_analyzed.keySet() ) {
+ if ( !label.equals( ALL ) ) {
+ final Double value = table.getValue( go, label );
+ stats.addValue( value == null ? 0.0 : value );
+ }
+ }
+ table.setValue( go, "{AVG}", stats.arithmeticMean() );
+ table.setValue( go, "{SUM}", stats.getSum() );
+ table.setValue( go, "{MED}", stats.median() );
+ if ( stats.getN() > 1 ) {
+ table.setValue( go, "{SD}", stats.sampleStandardDeviation() );
+ }
+ else {
+ table.setValue( go, "{SD}", new Double( 0 ) );
+ }
+ table.setValue( go, "{MIN}", stats.getMin() );
+ table.setValue( go, "{MAX}", stats.getMax() );
+ }
+ }
+
+ 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() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ if ( cla.getNumberOfNames() != 3 ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final File obofile = cla.getFile( 0 );
+ final File query_superterms_file = cla.getFile( 1 );
+ final File exp_file = cla.getFile( 2 );
+ final OBOparser parser = new OBOparser( obofile, OBOparser.ReturnType.BASIC_GO_TERM );
+ List<GoTerm> all_go_terms = null;
+ try {
+ all_go_terms = parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ }
+ final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( all_go_terms );
+ final List<GoId> query_superterms_ids = new ArrayList<GoId>();
+ SortedMap<String, List<GoId>> query_superterms_id_raw = null;
+ try {
+ query_superterms_id_raw = GoUtils.parseGoIds( query_superterms_file, "#", "" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, e.getMessage() );
+ System.exit( -1 );
+ }
+ final List<GoId> queries = query_superterms_id_raw.get( "" );
+ for( final GoId id : queries ) {
+ if ( !goid_to_term_map.containsKey( id ) ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, "\"" + id + "\" not present in \"" + obofile + "\"" );
+ System.exit( -1 );
+ }
+ query_superterms_ids.add( id );
+ }
+ SortedMap<String, List<GoId>> data_to_be_analyzed = null;
+ try {
+ data_to_be_analyzed = GoUtils.parseGoIds( exp_file, "#", ">" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, e.getMessage() );
+ System.exit( -1 );
+ }
+ final List<GoId> all_ids = new ArrayList<GoId>();
+ for( final String label : data_to_be_analyzed.keySet() ) {
+ final List<GoId> experiment_set_ids = data_to_be_analyzed.get( label );
+ for( final GoId go_id : experiment_set_ids ) {
+ if ( !goid_to_term_map.containsKey( go_id ) ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, "GO id [" + go_id + "] not found in GO id to term map" );
+ System.exit( -1 );
+ }
+ all_ids.add( go_id );
+ }
+ }
+ if ( data_to_be_analyzed.size() > 1 ) {
+ data_to_be_analyzed.put( ALL, all_ids );
+ }
+ final GeneralTable<String, Double> table_counts = new GeneralTable<String, Double>();
+ final GeneralTable<String, Double> table_percentage = new GeneralTable<String, Double>();
+ for( final String label : data_to_be_analyzed.keySet() ) {
+ System.out.println();
+ System.out.println( label + "\t\t\t\t" );
+ final List<GoId> experiment_set_ids = data_to_be_analyzed.get( label );
+ Map<GoId, Integer> counts_id = null;
+ try {
+ counts_id = GoUtils.countCategoriesId( query_superterms_ids, experiment_set_ids, goid_to_term_map );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, e.getMessage() );
+ System.exit( -1 );
+ }
+ int sum = 0;
+ for( final GoId id : counts_id.keySet() ) {
+ sum += counts_id.get( id );
+ }
+ if ( sum > 0 ) {
+ table_counts.setValue( "{total}", label, ( double ) sum );
+ }
+ for( final GoId id : counts_id.keySet() ) {
+ final int counts = counts_id.get( id );
+ double percentage = 0.0;
+ if ( sum > 0 ) {
+ percentage = 100.0 * counts / ( sum );
+ }
+ System.out.println( counts + "\t" + counts + "/" + sum + "\t" + percentage + "\t" + id + "\t"
+ + goid_to_term_map.get( id ).getName() );
+ table_counts.setValue( goid_to_term_map.get( id ).getName(), label, ( double ) counts );
+ table_percentage.setValue( goid_to_term_map.get( id ).getName(), label, percentage );
+ }
+ }
+ addStats( data_to_be_analyzed, table_counts );
+ addStats( data_to_be_analyzed, table_percentage );
+ System.out.println();
+ System.out.println();
+ System.out.println();
+ System.out.println( table_counts.toString( ForesterUtil.FORMATTER_3 ) );
+ System.out.println();
+ System.out.println();
+ System.out.println();
+ System.out.println( table_percentage.toString( ForesterUtil.FORMATTER_3 ) );
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out
+ .println( PRG_NAME
+ + " <file with all GO terms, in 'obo' format> <file with ancestral term ids> <file with go ids to be analyzed>" );
+ System.out.println();
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+import org.forester.go.etc.MetaOntologizer;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class meta_ontologizer {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String P_OPTION = "p";
+ final static private String PRG_NAME = "meta_ontologizer";
+ final static private String PRG_VERSION = "1.10";
+ final static private String PRG_DATE = "2009.04.29";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+ private static final String RESULT_FILE_PREFIX = "table";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( args.length < 4 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( P_OPTION );
+ final List<String> mandatory_options = new ArrayList<String>();
+ mandatory_options.add( P_OPTION );
+ if ( ( cla.getNumberOfNames() != 5 ) && ( cla.getNumberOfNames() != 6 ) ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final String missing = cla.validateMandatoryOptionsAsString( mandatory_options );
+ if ( missing.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "missing option(s): " + missing );
+ }
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final File obo_file = cla.getFile( 0 );
+ final File pfam2go_file = cla.getFile( 1 );
+ final File ontologizer_outdir = cla.getFile( 2 );
+ File domain_gain_loss_file = null;
+ String outfile_base = null;
+ String comment = null;
+ if ( cla.getNumberOfNames() == 6 ) {
+ domain_gain_loss_file = cla.getFile( 3 );
+ outfile_base = cla.getName( 4 );
+ comment = cla.getName( 5 );
+ }
+ else {
+ outfile_base = cla.getName( 3 );
+ comment = cla.getName( 4 );
+ }
+ double p_adjusted_upper_limit = -1;
+ try {
+ p_adjusted_upper_limit = cla.getOptionValueAsDouble( P_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ try {
+ final PfamToGoParser parser = new PfamToGoParser( pfam2go_file );
+ final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+ ForesterUtil.programMessage( PRG_NAME, "parsed " + pfam_to_go_mappings.size() + " Pfam to GO mappings" );
+ MetaOntologizer.reformat( ontologizer_outdir,
+ RESULT_FILE_PREFIX,
+ domain_gain_loss_file,
+ outfile_base,
+ obo_file,
+ p_adjusted_upper_limit,
+ comment,
+ pfam_to_go_mappings );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ e.printStackTrace();
+ }
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out
+ .println( PRG_NAME
+ + " -p=<adj P value limit> <obo file> <pfam to go file> <ontologizer outdir> [domain gain loss file] <base for meta ontologizer outfile> <comment>" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class nhx_too {
+
+ final static private String PRG_NAME = "nhx_too";
+ final static private String PRG_VERSION = "0.1";
+ final static private String PRG_DATE = "2008.03.04";
+ final static private String INT_NODE_NAME_IS_SUPPORT = "is";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( nhx_too.PRG_NAME, nhx_too.PRG_VERSION, nhx_too.PRG_DATE );
+ if ( ( args.length < 3 ) || ( args.length > 3 ) ) {
+ System.out.println();
+ System.out.println( nhx_too.PRG_NAME + ": wrong number of arguments" );
+ System.out.println();
+ System.out.println( "Usage: \"" + nhx_too.PRG_NAME + " [options] <infile> <outfile>\n" );
+ System.out.println( " Options: -" + nhx_too.INT_NODE_NAME_IS_SUPPORT
+ + ": internal node names are support values (i.e. MrBayes output)" );
+ System.out.println();
+ System.exit( -1 );
+ }
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( nhx_too.INT_NODE_NAME_IS_SUPPORT );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( nhx_too.PRG_NAME, "Unknown option(s): " + dissallowed_options );
+ }
+ final File phylogeny_infile = cla.getFile( 0 );
+ final File phylogeny_outfile = cla.getFile( 1 );
+ boolean int_node_name_is_support = false;
+ if ( cla.isOptionSet( nhx_too.INT_NODE_NAME_IS_SUPPORT ) ) {
+ int_node_name_is_support = true;
+ }
+ Phylogeny p = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogeny_infile, true );
+ p = factory.create( phylogeny_infile, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( nhx_too.PRG_NAME, "Could not read \"" + phylogeny_infile + "\" [" + e.getMessage()
+ + "]" );
+ }
+ if ( int_node_name_is_support ) {
+ try {
+ ForesterUtil.transferInternalNodeNamesToConfidence( p );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.unexpectedFatalError( nhx_too.PRG_NAME,
+ "Failure during moving of internal names to support values ["
+ + e.getMessage() + "]" );
+ }
+ }
+ try {
+ final PhylogenyWriter w = new PhylogenyWriter();
+ w.toNewHampshireX( p, phylogeny_outfile );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( nhx_too.PRG_NAME, "Failure to write output [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ System.out.println( "Done [wrote \"" + phylogeny_outfile + "\"]." );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.io.parsers.SymmetricalDistanceMatrixParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class nj {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String VERBOSE_OPTION = "v";
+ final static private String UPPER_TRIANGLE_OPTION = "u";
+ final static private String PRG_NAME = "nj";
+ final static private String PRG_VERSION = "0.0.1";
+ final static private String PRG_DATE = "2008.03.04";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( HELP_OPTION_1 );
+ allowed_options.add( HELP_OPTION_2 );
+ allowed_options.add( VERBOSE_OPTION );
+ allowed_options.add( UPPER_TRIANGLE_OPTION );
+ if ( ( args.length < 2 ) ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( cla.getNumberOfNames() != 2 ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ boolean verbose = false;
+ boolean upper_triangle = false;
+ if ( cla.isOptionSet( VERBOSE_OPTION ) ) {
+ verbose = true;
+ }
+ if ( cla.isOptionSet( UPPER_TRIANGLE_OPTION ) ) {
+ upper_triangle = true;
+ }
+ final File infile = cla.getFile( 0 );
+ final File outfile = cla.getFile( 1 );
+ final String error1 = ForesterUtil.isReadableFile( infile );
+ if ( !ForesterUtil.isEmpty( error1 ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "cannot read from infile [" + infile + "]: " + error1 );
+ }
+ if ( outfile.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "outfile [" + outfile + "] already exists" );
+ }
+ final String error2 = ForesterUtil.isWritableFile( outfile );
+ if ( !ForesterUtil.isEmpty( error2 ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "cannot write to outfile [" + outfile + "]: " + error2 );
+ }
+ final SymmetricalDistanceMatrixParser parser = SymmetricalDistanceMatrixParser.createInstance();
+ if ( upper_triangle ) {
+ parser.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.UPPER_TRIANGLE );
+ }
+ else {
+ parser.setInputMatrixType( SymmetricalDistanceMatrixParser.InputMatrixType.LOWER_TRIANGLE );
+ }
+ DistanceMatrix[] matrices = null;
+ try {
+ matrices = parser.parse( infile );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read from infile [" + infile + "]: " + e.getMessage() );
+ }
+ if ( verbose ) {
+ System.out.println( PRG_NAME + " > read " + matrices.length + " pairwise distance matrice(s) of size "
+ + matrices[ 0 ].getSize() );
+ }
+ final List<Phylogeny> ps = new ArrayList<Phylogeny>();
+ final NeighborJoining nj = NeighborJoining.createInstance();
+ nj.setVerbose( verbose );
+ final long start_time = new Date().getTime();
+ for( final DistanceMatrix matrix : matrices ) {
+ ps.add( nj.execute( matrix ) );
+ }
+ final long end_time = new Date().getTime();
+ final PhylogenyWriter w = new PhylogenyWriter();
+ try {
+ w.toPhyloXML( outfile, ps, 1, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
+ }
+ System.out.println();
+ System.out.println( PRG_NAME + " > OK [" + ( end_time - start_time ) + "ms]" );
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( "% java -cp forester.jar org.forester.applications." + PRG_NAME
+ + " [options] <pairwise distances infile> <out file>" );
+ System.out.println();
+ System.out.println( " Options: " );
+ System.out.println( VERBOSE_OPTION + ": verbose on" );
+ System.out.println( UPPER_TRIANGLE_OPTION + ": upper triangle option on (lower triangle is default)" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.go.GoTerm;
+import org.forester.go.OBOparser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class obo_tool {
+
+ private static final String IDS_TO_NAMES_SUFFIX = "_ids_to_names";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String GO_ID_TO_NAME_OPTION = "i";
+ final static private String PRG_NAME = "obo_tool";
+ final static private String PRG_VERSION = "1.00";
+ final static private String PRG_DATE = "2008.11.26";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( args.length < 3 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( GO_ID_TO_NAME_OPTION );
+ if ( cla.getNumberOfNames() != 2 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ boolean output_ids_to_names = false;
+ if ( cla.isOptionSet( GO_ID_TO_NAME_OPTION ) ) {
+ output_ids_to_names = true;
+ }
+ final File infile = cla.getFile( 0 );
+ final File outfile = cla.getFile( 1 );
+ final OBOparser parser = new OBOparser( infile, OBOparser.ReturnType.BASIC_GO_TERM );
+ List<GoTerm> go_terms = null;
+ try {
+ go_terms = parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "successfully read in " + go_terms.size() + " GO terms from [" + infile
+ + "]" );
+ if ( output_ids_to_names ) {
+ final File outfile_ids_to_names = new File( outfile + IDS_TO_NAMES_SUFFIX );
+ final String error = ForesterUtil.isWritableFile( outfile_ids_to_names );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( PRG_NAME, error );
+ }
+ try {
+ final Writer out = new BufferedWriter( new FileWriter( outfile_ids_to_names ) );
+ for( final GoTerm go_term : go_terms ) {
+ out.write( go_term.getGoId().getId() );
+ out.write( "\t" );
+ out.write( go_term.getDefinition() );
+ out.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ out.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.toString() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "wrote: [" + outfile_ids_to_names + "]" );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( PRG_NAME + " <options> <obo infile> <outfile>" );
+ System.out.println();
+ System.out.println( " options: " );
+ System.out.println();
+ System.out.println( " -" + GO_ID_TO_NAME_OPTION + ": output GO id to name map file" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.pccx.BasicExternalNodeBasedCoverageExtender;
+import org.forester.pccx.Coverage;
+import org.forester.pccx.CoverageCalculationOptions;
+import org.forester.pccx.CoverageCalculator;
+import org.forester.pccx.CoverageExtender;
+import org.forester.pccx.ExternalNodeBasedCoverageMethod;
+import org.forester.pccx.ExternalNodeBasedCoverageMethodOptions;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+/*
+ * @author Christian M. Zmasek
+ */
+public class pccx {
+
+ final static private int EXTEND_BY_DEFAULT = -100;
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String USE_REAL_BL_OPTION = "d";
+ final static private String USE_LOG_REAL_BL_OPTION = "ld";
+ final static private String EXTEND_BY_OPTION = "x";
+ final static private String OUTPUT_OPTION = "o";
+ final static private String INPUT_OPTION = "i";
+ final static private String OUTPUT_ANNOTATED_PHYLOGENIES_OPTION = "p";
+ final static private String PRG_NAME = "pccx";
+ final static private String PRG_VERSION = "1.0.0";
+ final static private String BRANCH_LENGTH_BASED_SCORING = "org.forester.tools.modeling.BranchLengthBasedScoringMethod";
+ final static private String BRANCH_COUNTING_BASED_SCORING = "org.forester.tools.modeling.BranchCountingBasedScoringMethod";
+ final static private String LOG_BRANCH_LENGTH_BASED_SCORING = "org.forester.tools.modeling.LogBranchLengthBasedScoringMethod";
+ final static private String PRG_DATE = "2008.03.04";
+ final static private String WWW = "www.phylosoft.org/forester/applications/pccx";
+ final static private String E_MAIL = "czmasek@burnham.org";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( pccx.PRG_NAME, pccx.PRG_VERSION, pccx.PRG_DATE, pccx.E_MAIL, pccx.WWW );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( pccx.HELP_OPTION_1 ) || cla.isOptionSet( pccx.HELP_OPTION_2 ) ) {
+ System.out.println();
+ pccx.printHelp();
+ System.exit( 0 );
+ }
+ if ( ( args.length < 2 ) ) {
+ System.out.println();
+ System.out.println( "Incorrect number of arguments." );
+ System.out.println();
+ pccx.printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ boolean use_bl = false;
+ boolean use_log_bl = false;
+ int extend_by = pccx.EXTEND_BY_DEFAULT;
+ allowed_options.add( pccx.USE_REAL_BL_OPTION );
+ allowed_options.add( pccx.USE_LOG_REAL_BL_OPTION );
+ allowed_options.add( pccx.EXTEND_BY_OPTION );
+ allowed_options.add( pccx.INPUT_OPTION );
+ allowed_options.add( pccx.OUTPUT_OPTION );
+ allowed_options.add( pccx.OUTPUT_ANNOTATED_PHYLOGENIES_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ if ( cla.getNumberOfNames() < 1 ) {
+ System.out.println();
+ System.out.println( "No phylogenies infile indicated." );
+ System.out.println();
+ pccx.printHelp();
+ System.exit( -1 );
+ }
+ final File phylogenies_infile = cla.getFile( 0 );
+ final List<String> external_otu_names = new ArrayList<String>();
+ if ( cla.getNumberOfNames() > 1 ) {
+ for( int i = 1; i < cla.getNumberOfNames(); ++i ) {
+ external_otu_names.add( cla.getName( i ) );
+ }
+ }
+ if ( cla.isOptionSet( pccx.USE_REAL_BL_OPTION ) ) {
+ use_bl = true;
+ }
+ if ( cla.isOptionSet( pccx.USE_LOG_REAL_BL_OPTION ) ) {
+ use_log_bl = true;
+ }
+ if ( use_bl && use_log_bl ) {
+ System.out.println();
+ pccx.printHelp();
+ System.exit( -1 );
+ }
+ if ( cla.isOptionSet( pccx.EXTEND_BY_OPTION ) ) {
+ extend_by = 0;
+ try {
+ extend_by = cla.getOptionValueAsInt( pccx.EXTEND_BY_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, e.getMessage() );
+ }
+ }
+ Phylogeny[] phylogenies = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( phylogenies_infile, true );
+ phylogenies = factory.create( phylogenies_infile, pp );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, "could not read \"" + phylogenies_infile + "\": " + e.getMessage() );
+ }
+ final List<Phylogeny> phylogenies_list = Arrays.asList( phylogenies );
+ File outfile = null;
+ PrintStream out = System.out;
+ if ( cla.isOptionSet( pccx.OUTPUT_OPTION ) ) {
+ try {
+ outfile = new File( cla.getOptionValue( pccx.OUTPUT_OPTION ) );
+ final String error = ForesterUtil.isWritableFile( outfile );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, error );
+ }
+ out = new PrintStream( outfile );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, e.getMessage() );
+ }
+ }
+ File infile = null;
+ BasicTable<String> intable = null;
+ if ( cla.isOptionSet( pccx.INPUT_OPTION ) ) {
+ try {
+ infile = new File( cla.getOptionValue( pccx.INPUT_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( infile );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, error );
+ }
+ intable = BasicTableParser.parse( infile, " ", false );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, "failed to read \"" + infile + "\" [" + e.getMessage() + "]" );
+ }
+ try {
+ for( int row = 0; row < intable.getNumberOfRows(); ++row ) {
+ System.out.println( "Adding external node: " + intable.getValueAsString( 0, row ) );
+ external_otu_names.add( intable.getValueAsString( 0, row ) );
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, e.getMessage() );
+ }
+ }
+ File annotated_phylogenies_outfile = null;
+ boolean output_annoted_phylogenies = false;
+ if ( cla.isOptionSet( pccx.OUTPUT_ANNOTATED_PHYLOGENIES_OPTION ) ) {
+ output_annoted_phylogenies = true;
+ annotated_phylogenies_outfile = new File( cla.getOptionValue( pccx.OUTPUT_ANNOTATED_PHYLOGENIES_OPTION ) );
+ final String error = ForesterUtil.isWritableFile( annotated_phylogenies_outfile );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, error );
+ }
+ }
+ try {
+ final CoverageCalculationOptions options;
+ if ( use_log_bl ) {
+ options = new ExternalNodeBasedCoverageMethodOptions( pccx.LOG_BRANCH_LENGTH_BASED_SCORING );
+ }
+ else if ( use_bl ) {
+ options = new ExternalNodeBasedCoverageMethodOptions( pccx.BRANCH_LENGTH_BASED_SCORING );
+ }
+ else {
+ options = new ExternalNodeBasedCoverageMethodOptions( pccx.BRANCH_COUNTING_BASED_SCORING );
+ }
+ final int s = phylogenies_list.get( 0 ).getNumberOfExternalNodes() - external_otu_names.size();
+ if ( extend_by > s ) {
+ extend_by = s;
+ }
+ System.out.println();
+ System.out.println( "Options: " + options.asString() );
+ System.out.println();
+ if ( extend_by != pccx.EXTEND_BY_DEFAULT ) {
+ if ( extend_by > 0 ) {
+ System.out.println( "Printing " + extend_by + " names to extend coverage in an optimal manner:" );
+ }
+ else {
+ System.out.println( "Printing names to completely extend coverage in an optimal manner:" );
+ }
+ System.out.println();
+ final CoverageCalculator cc = CoverageCalculator.getInstance( new ExternalNodeBasedCoverageMethod(),
+ options );
+ final CoverageExtender ce = new BasicExternalNodeBasedCoverageExtender();
+ Coverage cov = cc.calculateCoverage( phylogenies_list, external_otu_names, false );
+ System.out.println( " before:" );
+ System.out.println( cov.asString() );
+ System.out.println();
+ final List<String> result = ce.find( phylogenies_list, external_otu_names, extend_by, options, out );
+ final List<String> new_names = new ArrayList<String>( external_otu_names );
+ for( final Object element : result ) {
+ final String n = ( String ) element;
+ new_names.add( n );
+ }
+ cov = cc.calculateCoverage( phylogenies_list, new_names, output_annoted_phylogenies );
+ System.out.println();
+ System.out.println( " after:" );
+ System.out.println( cov.asString() );
+ }
+ else {
+ final CoverageCalculator cc = CoverageCalculator.getInstance( new ExternalNodeBasedCoverageMethod(),
+ options );
+ final Coverage cov = cc.calculateCoverage( phylogenies_list,
+ external_otu_names,
+ output_annoted_phylogenies );
+ System.out.println( cov.asString() );
+ }
+ System.out.println();
+ if ( output_annoted_phylogenies ) {
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( annotated_phylogenies_outfile, phylogenies_list.get( 0 ), 1 );
+ System.out.println( "Wrote annotated phylogeny to \"" + annotated_phylogenies_outfile + "\"" );
+ System.out.println();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, "Failed to write to \"" + annotated_phylogenies_outfile
+ + "\" [" + e.getMessage() + "]" );
+ }
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( pccx.PRG_NAME, e.toString() );
+ }
+ System.out.println();
+ System.out.println( pccx.PRG_NAME + ": successfully completed" );
+ System.out.println( "If this application is useful to you, please cite:" );
+ System.out.println( pccx.WWW );
+ System.out.println();
+ out.flush();
+ out.close();
+ }
+
+ private static void printHelp() {
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( pccx.PRG_NAME
+ + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
+ System.out.println();
+ System.out.println( " Options: " );
+ System.out.println();
+ System.out.println( " -d : 1/distance based scoring method (instead of branch counting based)" );
+ System.out.println( " -ld : -ln(distance) based scoring method (instead of branch counting based)" );
+ System.out.println( " -x[=<n>] : optimally extend coverage by <n> external nodes. Use none, 0," );
+ System.out.println( " or negative value for complete coverage extension." );
+ System.out.println( " -o=<file> : write output to <file>" );
+ System.out.println( " -i=<file> : read (new-line separated) external node names from <file>" );
+ System.out.println( " -" + pccx.OUTPUT_ANNOTATED_PHYLOGENIES_OPTION
+ + "=<file> : write output as annotated phylogeny to <file> (only first" );
+ System.out.println( " phylogeny in phylogenies infile is used)" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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
+
+package org.forester.application;
+
+import java.io.File;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.CommandLineArguments;
+
+public class perfume {
+
+ private final static String BASE = "b_";
+
+ public static void main( final String args[] ) {
+ if ( ( args.length != 2 ) ) {
+ System.exit( -1 );
+ }
+ try {
+ CommandLineArguments cla = null;
+ cla = new CommandLineArguments( args );
+ final File in = cla.getFile( 0 );
+ final File out = cla.getFile( 1 );
+ if ( out.exists() ) {
+ System.out.println( out + " already exists" );
+ System.exit( -1 );
+ }
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhyloXmlParser xml_parser = new PhyloXmlParser();
+ final Phylogeny[] phylogenies_0 = factory.create( in, xml_parser );
+ final Phylogeny phylogeny_0 = phylogenies_0[ 0 ];
+ final PhylogenyNodeIterator it = phylogeny_0.iteratorPostorder();
+ int i = 0;
+ while ( it.hasNext() ) {
+ final PhylogenyNode node = it.next();
+ processNode( node, i );
+ i++;
+ }
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( out, phylogeny_0, 0 );
+ }
+ catch ( final Exception e ) {
+ System.out.println( e.getLocalizedMessage() );
+ e.printStackTrace();
+ System.exit( -1 );
+ }
+ }
+
+ private static void processNode( final PhylogenyNode node, final int i ) {
+ node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+ if ( !node.isExternal() ) {
+ if ( ( node.getName() == null ) || node.getName().isEmpty() ) {
+ node.setName( BASE + i );
+ }
+ }
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2009 Christian M. Zmasek
+// Copyright (C) 2009 Burnham Institute for Medical Research
+// 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 java.util.Map;
+import java.util.Set;
+import java.util.SortedSet;
+import java.util.TreeSet;
+
+import org.forester.go.GoId;
+import org.forester.go.GoTerm;
+import org.forester.go.GoUtils;
+import org.forester.go.OBOparser;
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+import org.forester.surfacing.DomainId;
+
+public class pfam2go_extractor {
+
+ final static private String PRG_NAME = "pfam2go_extractor";
+
+ public static void main( final String args[] ) {
+ if ( args.length < 3 ) {
+ printHelp();
+ }
+ final PfamToGoParser p = new PfamToGoParser( new File( args[ 0 ] ) );
+ List<PfamToGoMapping> pfam2go = null;
+ try {
+ pfam2go = p.parse();
+ }
+ catch ( final IOException e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ final OBOparser parser = new OBOparser( new File( args[ 1 ] ), OBOparser.ReturnType.BASIC_GO_TERM );
+ List<GoTerm> all_go_terms = null;
+ try {
+ all_go_terms = parser.parse();
+ }
+ catch ( final IOException e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ final Map<GoId, GoTerm> goid_to_term_map = GoUtils.createGoIdToGoTermMap( all_go_terms );
+ System.out.println( "# pfam2go : " + args[ 0 ] );
+ System.out.println( "# OBO file: " + args[ 1 ] );
+ final GoId[] queries = new GoId[ args.length - 2 ];
+ for( int i = 2; i < args.length; ++i ) {
+ queries[ i - 2 ] = new GoId( args[ i ] );
+ System.out.println( "# " + ( i - 2 ) + ": " + queries[ i - 2 ].getId() + " = "
+ + goid_to_term_map.get( queries[ i - 2 ] ).getName() + " ("
+ + goid_to_term_map.get( queries[ i - 2 ] ).getDefinition() + ")" );
+ }
+ final SortedSet<String> pfams = new TreeSet<String>();
+ for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
+ final DomainId domain_id = pfam_to_go_mapping.getKey();
+ final GoId go_id = pfam_to_go_mapping.getValue();
+ final Set<GoId> supers = GoUtils.getAllSuperGoIds( go_id, goid_to_term_map );
+ supers.add( go_id );
+ for( int i = 0; i < queries.length; ++i ) {
+ if ( supers.contains( queries[ i ] ) ) {
+ pfams.add( domain_id.toString() );
+ }
+ }
+ }
+ for( final String pfam : pfams ) {
+ System.out.println( pfam );
+ }
+ }
+
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( PRG_NAME
+ + " <pfam2go mapping file> <file with all GO terms, in 'obo' format> <GO id> [more GO ids]" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2009 Christian M. Zmasek
+// Copyright (C) 2009 Burnham Institute for Medical Research
+// 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.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class pfam_go {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String PRG_NAME = "pfam2go";
+ final static private String PRG_VERSION = "1.00";
+ final static private String PRG_DATE = "2010.02.02";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org";
+
+ private static void doit( final File pfams_file, final List<PfamToGoMapping> mappings ) throws IOException {
+ final BufferedReader reader = ForesterUtil.obtainReader( pfams_file );
+ String line = "";
+ int found_count = 0;
+ int not_found_count = 0;
+ final Set<String> encountered_domains = new HashSet<String>();
+ while ( ( line = reader.readLine() ) != null ) {
+ line = line.trim();
+ if ( ForesterUtil.isEmpty( line ) || line.startsWith( "##" ) ) {
+ continue;
+ }
+ else if ( line.startsWith( "#" ) ) {
+ encountered_domains.clear();
+ line = line.replace( '#', '>' );
+ System.out.println( line );
+ }
+ else {
+ if ( !encountered_domains.contains( line ) ) {
+ encountered_domains.add( line );
+ boolean found = false;
+ for( final PfamToGoMapping mapping : mappings ) {
+ if ( mapping.getKey().getId().equals( line ) ) {
+ System.out.println( mapping.getValue() );
+ found = true;
+ }
+ }
+ if ( found ) {
+ found_count++;
+ }
+ else {
+ not_found_count++;
+ }
+ }
+ else {
+ System.err.println( "# duplicate domain: " + line );
+ }
+ }
+ }
+ System.out.println( "# pfams with mapping to GO : " + found_count );
+ System.out.println( "# pfams without mapping to GO: " + not_found_count );
+ reader.close();
+ }
+
+ 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() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ if ( cla.getNumberOfNames() != 2 ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final File pfam2go_file = cla.getFile( 0 );
+ final File pfams_file = cla.getFile( 1 );
+ final PfamToGoParser pfam2go_parser = new PfamToGoParser( pfam2go_file );
+ List<PfamToGoMapping> mappings = null;
+ try {
+ mappings = pfam2go_parser.parse();
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ try {
+ doit( pfams_file, mappings );
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( PRG_NAME + " <pfam2go file> <file with pfams>" );
+ System.out.println();
+ System.out.println();
+ }
+}
\ No newline at end of file
--- /dev/null
+// $Id:
+//
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2010 Christian M Zmasek
+// Copyright (C) 2010 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.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.util.List;
+
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+
+public class pfamacc2go {
+
+ final static private String PRG_NAME = "pfamacc2go";
+
+ public static void main( final String args[] ) {
+ if ( args.length != 2 ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ final PfamToGoParser p = new PfamToGoParser( new File( args[ 0 ] ) );
+ p.setUseAccessors( true );
+ List<PfamToGoMapping> pfam2go = null;
+ try {
+ pfam2go = p.parse();
+ }
+ catch ( final IOException e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ BufferedReader br = null;
+ try {
+ br = new BufferedReader( new FileReader( args[ 1 ] ) );
+ }
+ catch ( final FileNotFoundException e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ String line;
+ int total_pfam_ids = 0;
+ int mapped_pfam_ids = 0;
+ try {
+ while ( ( line = br.readLine() ) != null ) {
+ line = line.trim();
+ if ( ( line.length() > 0 ) && !line.startsWith( "#" ) ) {
+ String[] pfam_ids = null;
+ if ( line.contains( "," ) ) {
+ pfam_ids = line.split( "," );
+ }
+ else {
+ pfam_ids = new String[ 1 ];
+ pfam_ids[ 0 ] = line;
+ }
+ for( final String pfam_id : pfam_ids ) {
+ total_pfam_ids++;
+ boolean mapped = false;
+ for( final PfamToGoMapping pfam_to_go_mapping : pfam2go ) {
+ if ( pfam_to_go_mapping.getKey().getId().equals( pfam_id ) ) {
+ mapped = true;
+ System.out.println( pfam_to_go_mapping.getValue().toString() );
+ }
+ }
+ if ( mapped ) {
+ mapped_pfam_ids++;
+ }
+ }
+ }
+ }
+ }
+ catch ( final Exception e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ System.out.println( "# total pfam ids : " + total_pfam_ids );
+ System.out.println( "# pfam ids mapped: " + mapped_pfam_ids );
+ }
+
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( PRG_NAME
+ + " <pfam2go mapping file> <file with pfam accessors, newline and/or comma separated>" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+//
+// forester -- software libraries and applications
+// for genomics and evolutionary biology research.
+//
+// Copyright (C) 2010 Christian M Zmasek
+// Copyright (C) 2010 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.BufferedReader;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.util.HashMap;
+import java.util.Map;
+
+public class pfamacc2pfamid {
+
+ final static private String PRG_NAME = "pfamacc2pfamid";
+
+ public static void main( final String args[] ) {
+ if ( args.length != 2 ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ BufferedReader br = null;
+ try {
+ br = new BufferedReader( new FileReader( args[ 0 ] ) );
+ }
+ catch ( final FileNotFoundException e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ String line;
+ final Map<String, String> acc_id = new HashMap<String, String>();
+ String id = null;
+ try {
+ while ( ( line = br.readLine() ) != null ) {
+ if ( line.startsWith( "#=GF ID" ) ) {
+ if ( id != null ) {
+ System.err.println( "illegal format" );
+ System.exit( -1 );
+ }
+ id = line.substring( 7 ).trim();
+ }
+ else if ( line.startsWith( "#=GF AC" ) ) {
+ if ( id == null ) {
+ System.err.println( "illegal format" );
+ System.exit( -1 );
+ }
+ String acc = line.substring( 7 ).trim();
+ if ( acc.indexOf( '.' ) > 0 ) {
+ acc = acc.substring( 0, acc.indexOf( '.' ) );
+ }
+ acc_id.put( acc, id );
+ id = null;
+ }
+ else if ( line.startsWith( "//" ) ) {
+ if ( id != null ) {
+ System.err.println( "illegal format" );
+ System.exit( -1 );
+ }
+ }
+ }
+ }
+ catch ( final Exception e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ try {
+ br = new BufferedReader( new FileReader( args[ 1 ] ) );
+ }
+ catch ( final FileNotFoundException e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ int not_found = 0;
+ try {
+ while ( ( line = br.readLine() ) != null ) {
+ line = line.trim();
+ if ( ( line.length() > 0 ) && !line.startsWith( "#" ) ) {
+ String[] pfam_accs = null;
+ if ( line.contains( "," ) ) {
+ pfam_accs = line.split( "," );
+ }
+ else {
+ pfam_accs = new String[ 1 ];
+ pfam_accs[ 0 ] = line;
+ }
+ for( final String pfam_acc : pfam_accs ) {
+ if ( acc_id.containsKey( pfam_acc ) ) {
+ System.out.println( acc_id.get( pfam_acc ) );
+ }
+ else {
+ not_found++;
+ }
+ }
+ }
+ }
+ }
+ catch ( final Exception e ) {
+ printHelp();
+ e.printStackTrace();
+ }
+ System.err.println( "# not found: " + not_found );
+ }
+
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( PRG_NAME + " <Pfam full> <file with pfam accessors, newline and/or comma separated>" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+import org.forester.util.ForesterUtil.PhylogenyNodeField;
+
+public class phyloxml_converter {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String FIELD_OPTION = "f";
+ final static private String FIELD_CLADE_NAME = "nn";
+ final static private String FIELD_TAXONOMY_CODE = "tc";
+ final static private String FIELD_TAXONOMY_SCI_NAME = "sn";
+ final static private String FIELD_TAXONOMY_COMM_NAME = "cn";
+ final static private String FIELD_SEQUENCE_GENE_NAME = "gn";
+ final static private String FIELD_SEQUENCE_SYMBOL = "sy";
+ final static private String FIELD_DUMMY = "dummy";
+ final static private String INTERNAL_NAMES_ARE_BOOT_SUPPPORT = "i";
+ final static private String MIDPOINT_REROOT = "m";
+ final static private String EXTRACT_TAXONOMY = "xt";
+ final static private String EXTRACT_TAXONOMY_PF = "xp";
+ final static private String ORDER_SUBTREES = "o";
+ final static private String NO_TREE_LEVEL_INDENDATION = "ni";
+ final static private String REPLACE_UNDER_SCORES = "ru";
+ final static private String PRG_NAME = "phyloxml_converter";
+ final static private String PRG_VERSION = "1.21";
+ final static private String PRG_DATE = "2010.10.02";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+ final static private boolean SPECIAL = false;
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( args.length < 3 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( NO_TREE_LEVEL_INDENDATION );
+ allowed_options.add( FIELD_OPTION );
+ allowed_options.add( MIDPOINT_REROOT );
+ allowed_options.add( ORDER_SUBTREES );
+ allowed_options.add( INTERNAL_NAMES_ARE_BOOT_SUPPPORT );
+ allowed_options.add( REPLACE_UNDER_SCORES );
+ allowed_options.add( EXTRACT_TAXONOMY );
+ allowed_options.add( EXTRACT_TAXONOMY_PF );
+ if ( cla.getNumberOfNames() != 2 ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final List<String> mandatory_options = new ArrayList<String>();
+ mandatory_options.add( FIELD_OPTION );
+ final String missing_options = cla.validateMandatoryOptionsAsString( mandatory_options );
+ if ( missing_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "missing option(s): " + missing_options );
+ }
+ if ( !cla.isOptionValueSet( FIELD_OPTION ) ) {
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final String field_option_value = cla.getOptionValue( FIELD_OPTION );
+ PhylogenyNodeField field = null;
+ if ( field_option_value.equals( FIELD_CLADE_NAME ) ) {
+ field = PhylogenyNodeField.CLADE_NAME;
+ }
+ else if ( field_option_value.equals( FIELD_TAXONOMY_CODE ) ) {
+ field = PhylogenyNodeField.TAXONOMY_CODE;
+ }
+ else if ( field_option_value.equals( FIELD_TAXONOMY_SCI_NAME ) ) {
+ field = PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME;
+ }
+ else if ( field_option_value.equals( FIELD_TAXONOMY_COMM_NAME ) ) {
+ field = PhylogenyNodeField.TAXONOMY_COMMON_NAME;
+ }
+ else if ( field_option_value.equals( FIELD_SEQUENCE_GENE_NAME ) ) {
+ field = PhylogenyNodeField.SEQUENCE_NAME;
+ }
+ else if ( field_option_value.equals( FIELD_SEQUENCE_SYMBOL ) ) {
+ field = PhylogenyNodeField.SEQUENCE_SYMBOL;
+ }
+ else if ( field_option_value.equals( FIELD_DUMMY ) ) {
+ }
+ else {
+ ForesterUtil.fatalError( PRG_NAME, "unknown value for -\"" + FIELD_OPTION + "\" option: \""
+ + field_option_value + "\"" );
+ }
+ boolean int_values_are_boots = false;
+ if ( cla.isOptionSet( INTERNAL_NAMES_ARE_BOOT_SUPPPORT ) ) {
+ int_values_are_boots = true;
+ }
+ boolean midpoint_reroot = false;
+ if ( cla.isOptionSet( MIDPOINT_REROOT ) ) {
+ midpoint_reroot = true;
+ }
+ boolean order_subtrees = false;
+ if ( cla.isOptionSet( ORDER_SUBTREES ) ) {
+ order_subtrees = true;
+ }
+ boolean replace_underscores = false;
+ if ( cla.isOptionSet( REPLACE_UNDER_SCORES ) ) {
+ replace_underscores = true;
+ }
+ boolean no_indendation = false;
+ if ( cla.isOptionSet( NO_TREE_LEVEL_INDENDATION ) ) {
+ no_indendation = true;
+ }
+ boolean extr_taxonomy = false;
+ if ( cla.isOptionSet( EXTRACT_TAXONOMY ) ) {
+ extr_taxonomy = true;
+ }
+ boolean extr_taxonomy_pf_only = false;
+ if ( cla.isOptionSet( EXTRACT_TAXONOMY_PF ) ) {
+ extr_taxonomy_pf_only = true;
+ }
+ final File infile = cla.getFile( 0 );
+ final File outfile = cla.getFile( 1 );
+ if ( outfile.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "[" + outfile + "] already exists" );
+ }
+ if ( !infile.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "[" + infile + "] does not exist" );
+ }
+ Phylogeny[] phys = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser parser = ForesterUtil.createParserDependingOnFileType( infile, true );
+ if ( parser instanceof NHXParser ) {
+ if ( ( field != PhylogenyNodeField.TAXONOMY_CODE )
+ && ( field != PhylogenyNodeField.TAXONOMY_COMMON_NAME )
+ && ( field != PhylogenyNodeField.TAXONOMY_SCIENTIFIC_NAME ) ) {
+ if ( extr_taxonomy_pf_only ) {
+ ( ( NHXParser ) parser )
+ .setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.PFAM_STYLE_ONLY );
+ replace_underscores = false;
+ }
+ else if ( extr_taxonomy ) {
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.YES );
+ replace_underscores = false;
+ }
+ }
+ else {
+ ( ( NHXParser ) parser ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.NO );
+ }
+ ( ( NHXParser ) parser ).setReplaceUnderscores( replace_underscores );
+ ( ( NHXParser ) parser ).setIgnoreQuotes( false );
+ }
+ else if ( parser instanceof NexusPhylogeniesParser ) {
+ ( ( NexusPhylogeniesParser ) parser ).setReplaceUnderscores( replace_underscores );
+ ( ( NexusPhylogeniesParser ) parser ).setIgnoreQuotes( false );
+ }
+ phys = factory.create( infile, parser );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read phylogeny from [" + infile + "]: " + e.getMessage() );
+ }
+ if ( SPECIAL ) {
+ for( final Phylogeny phy : phys ) {
+ performSpecialProcessing( phy );
+ }
+ }
+ if ( int_values_are_boots ) {
+ for( final Phylogeny phy : phys ) {
+ ForesterUtil.transferInternalNamesToBootstrapSupport( phy );
+ }
+ }
+ if ( field != null ) {
+ for( final Phylogeny phy : phys ) {
+ ForesterUtil.transferNodeNameToField( phy, field );
+ }
+ }
+ if ( midpoint_reroot ) {
+ try {
+ for( final Phylogeny phy : phys ) {
+ PhylogenyMethods.midpointRoot( phy );
+ }
+ }
+ catch ( final Exception e ) {
+ System.out.println( "" );
+ ForesterUtil.printWarningMessage( PRG_NAME, "midpoint rerooting failed: " + e.getLocalizedMessage() );
+ }
+ }
+ if ( order_subtrees ) {
+ for( final Phylogeny phy : phys ) {
+ phy.orderAppearance( true );
+ }
+ }
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ if ( no_indendation ) {
+ writer.setIndentPhyloxml( false );
+ }
+ writer.toPhyloXML( phys, 0, outfile, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to write to [" + outfile + "]: " + e.getMessage() );
+ }
+ System.out.println( "[" + PRG_NAME + "] wrote: [" + outfile + "]" );
+ System.out.println( "[" + PRG_NAME + "] OK" );
+ System.out.println();
+ }
+
+ private static void performSpecialProcessing( final Phylogeny phy ) {
+ // Can place some kind of custom processing here.
+ // final List<PhylogenyNode> remove_us = new ArrayList<PhylogenyNode>();
+ // int counter = 0;
+ // for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+ // final PhylogenyNode node = it.next();
+ // final String name = node.getNodeName().toLowerCase();
+ // if ( name.startsWith( "environmental_samples" ) || name.startsWith( "unclassified" )
+ // || name.startsWith( "bacteria" ) || name.startsWith( "other" )
+ // || name.startsWith( "viroids" ) || name.startsWith( "viruses" ) ) {
+ // remove_us.add( node );
+ // System.out.println( counter++ );
+ // }
+ // }
+ // phy.hashIDs();
+ // for( final PhylogenyNode node : remove_us ) {
+ // if ( phy.getNode( node.getNodeId() ) != null ) {
+ // phy.deleteSubtree( node );
+ // System.out.println( "deleted: " + node );
+ // }
+ // }
+ // phy.hashIDs();
+ //
+ // for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+ // final PhylogenyNode node = it.next();
+ // node.getNodeData().setTaxonomy( null );
+ // }
+ // phy.reRoot( phy.getFirstExternalNode() );
+ // PhylogenyMethods.midpointRoot( phy );
+ // phy.orderAppearance( true );
+ for( final PhylogenyNodeIterator it = phy.iteratorPostorder(); it.hasNext(); ) {
+ final PhylogenyNode node = it.next();
+ final String name = node.getName();
+ if ( !ForesterUtil.isEmpty( name ) ) {
+ // final Taxonomy taxo = new Taxonomy();
+ // if ( node.isExternal() ) {
+ // taxo.setTaxonomyCode( name );
+ // node.getNodeData().setTaxonomy( taxo );
+ // }
+ // else if ( name.indexOf( '_' ) == -1 || name.length() > 6 ) {
+ // taxo.setScientificName( name );
+ // node.getNodeData().setTaxonomy( taxo );
+ // }
+ // node.setName( "" );
+ // if ( name.indexOf( "BF" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "BACFR" );
+ // }
+ // else if ( name.indexOf( "BT" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "BACTN" );
+ // }
+ // else if ( name.indexOf( "MXAN" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "MYXXD" );
+ // }
+ // else if ( name.indexOf( "STIAU" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "STIAU" );
+ // }
+ // else if ( name.indexOf( "BOVA" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "BACOV" );
+ // }
+ // else if ( name.indexOf( "BUNI" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "BACUN" );
+ // }
+ // else if ( name.indexOf( "Pgin" ) >= 0 ) {
+ // taxo.setTaxonomyCode( "PORGI" );
+ // }
+ // else if ( name.equals( "3CGH" ) || name.equals( "3CK7" ) ) {
+ // taxo.setTaxonomyCode( "BACTN" );
+ // }
+ // node.getNodeData().setTaxonomy( taxo );
+ }
+ }
+ }
+
+ private static void printHelp() {
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out
+ .println( PRG_NAME
+ + " -"
+ + FIELD_OPTION
+ + "=<field option> [options] <infile in New Hamphshire, NHX, Nexus, ToL XML, or phyloXML format> <outfile>" );
+ System.out.println();
+ System.out.println( " field options: " );
+ System.out.println();
+ System.out.println( " " + FIELD_CLADE_NAME + ": transfer name to node/clade name" );
+ System.out.println( " " + FIELD_TAXONOMY_CODE + ": transfer name to taxonomy code" );
+ System.out.println( " " + FIELD_TAXONOMY_SCI_NAME + ": transfer name to taxonomy scientific name" );
+ System.out.println( " " + FIELD_TAXONOMY_COMM_NAME + ": transfer name to taxonomy common name" );
+ System.out.println( " " + FIELD_SEQUENCE_GENE_NAME + ": transfer name to sequence name" );
+ System.out.println( " " + FIELD_SEQUENCE_SYMBOL + ": transfer name to sequence symbol" );
+ System.out.println();
+ System.out.println( " options: " );
+ System.out.println( " -" + INTERNAL_NAMES_ARE_BOOT_SUPPPORT
+ + " : internal names in NH or NHX tree are bootstrap support values" );
+ System.out.println( " -" + REPLACE_UNDER_SCORES + ": replace all underscores with spaces" );
+ System.out.println( " -" + MIDPOINT_REROOT + " : midpoint reroot" );
+ System.out.println( " -" + ORDER_SUBTREES + " : order subtrees" );
+ System.out
+ .println( " -"
+ + EXTRACT_TAXONOMY
+ + ": extract taxonomy to taxonomy code from \"seqname_TAXON\"-style names (cannot be used with the following field options: "
+ + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" );
+ System.out
+ .println( " -"
+ + EXTRACT_TAXONOMY_PF
+ + ": extract taxonomy to taxonomy code from Pfam (\"seqname_TAXON/x-y\") style names only (cannot be used with the following field options: "
+ + FIELD_TAXONOMY_CODE + ", " + FIELD_TAXONOMY_COMM_NAME + ", " + FIELD_TAXONOMY_SCI_NAME + ")" );
+ System.out.println( " -" + NO_TREE_LEVEL_INDENDATION + ": no tree level indendation in phyloXML output" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.FileWriter;
+import java.io.PrintWriter;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.ForesterUtil;
+
+public class printAllSpecies {
+
+ public static void main( final String args[] ) {
+ Phylogeny tree = null;
+ PhylogenyNode node = null;
+ PrintWriter out = null;
+ File infile = null, outfile = null;
+ if ( args.length != 2 ) {
+ System.err.println( "\nprintAllSpecies: Wrong number of arguments." );
+ System.err.println( "Usage: \"java printAllSpecies <infile> <outfile>\"\n" );
+ System.exit( -1 );
+ }
+ infile = new File( args[ 0 ] );
+ outfile = new File( args[ 1 ] );
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( infile, true );
+ tree = factory.create( infile, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ System.err.println( e + "\nCould not read " + infile + "\n" );
+ System.exit( -1 );
+ }
+ node = tree.getFirstExternalNode();
+ try {
+ out = new PrintWriter( new FileWriter( outfile ), true );
+ while ( node != null ) {
+ out.println( PhylogenyMethods.getSpecies( node ) );
+ node = node.getNextExternalNode();
+ }
+ }
+ catch ( final Exception e ) {
+ System.err.println( e + "\nException during writing.\n" );
+ System.exit( -1 );
+ }
+ finally {
+ out.close();
+ }
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.FileWriter;
+import java.io.PrintWriter;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.ForesterUtil;
+
+public class printSameOrder {
+
+ public static void main( final String args[] ) {
+ Phylogeny tree = null;
+ PhylogenyNode node = null;
+ PrintWriter out = null;
+ File infile = null, outfile = null;
+ if ( args.length != 2 ) {
+ System.err.println( "\nprintSameOrder: Wrong number of arguments." );
+ System.err.println( "Usage: \"java printSameOrder <infile> <outfile>\"\n" );
+ System.exit( -1 );
+ }
+ infile = new File( args[ 0 ] );
+ outfile = new File( args[ 1 ] );
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( infile, true );
+ tree = factory.create( infile, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ System.err.println( e + "\nCould not read " + infile + "\n" );
+ System.exit( -1 );
+ }
+ node = tree.getFirstExternalNode();
+ try {
+ out = new PrintWriter( new FileWriter( outfile ), true );
+ while ( node != null ) {
+ out.println( node.getName() );
+ node = node.getNextExternalNode();
+ }
+ }
+ catch ( final Exception e ) {
+ System.err.println( e + "\nException during writing.\n" );
+ System.exit( -1 );
+ }
+ finally {
+ out.close();
+ }
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// Copyright (C) 2000-2001 Washington University School of Medicine
+// and Howard Hughes Medical 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.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Vector;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PreorderTreeIterator;
+import org.forester.sdi.DistanceCalculator;
+import org.forester.sdi.RIO;
+import org.forester.sdi.SDIR;
+import org.forester.util.ForesterUtil;
+
+public class rio {
+
+ final static private String PRG_NAME = "RIO";
+ final static private String PRG_VERSION = "2.03 ALPHA";
+ final static private String PRG_DATE = "2010.01.15";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/";
+ final static private boolean TIME = true;
+ final static private boolean VERBOSE = true;
+ // For method getDistances -- calculation of distances.
+ final static private boolean MINIMIZE_COST = false;
+ // For method getDistances -- calculation of distances.
+ final static private boolean MINIMIZE_DUPS = true;
+ // For method getDistances -- calculation of distances.
+ final static private boolean MINIMIZE_HEIGHT = true;
+ final static private int WARN_NO_ORTHOS_DEFAULT = 2;
+ final static private int
+ // How many sd away from mean to root.
+ WARN_MORE_THAN_ONE_ORTHO_DEFAULT = 2;
+ // How many sd away from mean to LCA of orthos.
+ final static private double THRESHOLD_ULTRA_PARALOGS_DEFAULT = 50;
+ // How many sd away from mean to LCA of orthos.
+ final static private double WARN_ONE_ORTHO_DEFAULT = 2;
+
+ // Factor between the two distances to their LCA
+ // (larger/smaller).
+ // Factor between the two distances to their LCA
+ // (larger/smaller).
+ /**
+ * Calculates the mean and standard deviation of all nodes of Phylogeny t
+ * which have a bootstrap values zero or more. Returns null in case of
+ * failure (e.g t has no bootstrap values, or just one).
+ * <p>
+ *
+ * @param t
+ * reference to a tree with bootstrap values
+ * @return Array of doubles, [0] is the mean, [1] the standard deviation
+ */
+ private static double[] calculateMeanBoostrapValue( final Phylogeny t ) {
+ double b = 0;
+ int n = 0;
+ long sum = 0;
+ double x = 0.0, mean = 0.0;
+ final double[] da = new double[ 2 ];
+ final Vector<Double> bv = new Vector<Double>();
+ PhylogenyNode node = null;
+ PreorderTreeIterator i = null;
+ i = new PreorderTreeIterator( t );
+ // Calculates the mean.
+ while ( i.hasNext() ) {
+ node = i.next();
+ if ( !( ( node.getParent() != null ) && node.getParent().isRoot()
+ && ( PhylogenyMethods.getConfidenceValue( node.getParent().getChildNode1() ) > 0 )
+ && ( PhylogenyMethods.getConfidenceValue( node.getParent().getChildNode2() ) > 0 ) && ( node
+ .getParent().getChildNode2() == node ) ) ) {
+ b = PhylogenyMethods.getConfidenceValue( node );
+ if ( b > 0 ) {
+ sum += b;
+ bv.addElement( new Double( b ) );
+ n++;
+ }
+ }
+ // i.next();
+ }
+ if ( n < 2 ) {
+ return null;
+ }
+ mean = ( double ) sum / n;
+ // Calculates the standard deviation.
+ sum = 0;
+ for( int j = 0; j < n; ++j ) {
+ b = ( bv.elementAt( j ) ).intValue();
+ x = b - mean;
+ sum += ( x * x );
+ }
+ da[ 0 ] = mean;
+ da[ 1 ] = java.lang.Math.sqrt( sum / ( n - 1.0 ) );
+ return da;
+ }
+
+ private final static void errorInCommandLine() {
+ System.out.println( "\nrio: Error in command line.\n" );
+ printHelp();
+ System.exit( -1 );
+ }
+
+ // Uses DistanceCalculator to calculate distances.
+ private final static StringBuffer getDistances( final File tree_file_for_dist_val,
+ final File outfile,
+ final Phylogeny species_tree,
+ final String seq_name,
+ final ArrayList<String> al_ortholog_names_for_dc,
+ final HashMap<String, Integer> ortholog_hashmap,
+ final HashMap<String, Integer> super_ortholog_hashmap,
+ final int warn_more_than_one_ortho,
+ final int warn_no_orthos,
+ final double warn_one_ortho,
+ final int bootstraps,
+ final double t_orthologs_dc ) throws IOException {
+ Phylogeny consensus_tree = null;
+ Phylogeny
+ // to be a consensus tree.
+ assigned_cons_tree = null;
+ final SDIR sdiunrooted = new SDIR();
+ final ArrayList<PhylogenyNode> al_ortholog_nodes = new ArrayList<PhylogenyNode>();
+ double m = 0.0;
+ double sd = 0.0;
+ double d = 0.0;
+ int n = 0;
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ consensus_tree = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ];
+ PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, consensus_tree );
+ assigned_cons_tree = sdiunrooted.infer( consensus_tree,
+ species_tree,
+ rio.MINIMIZE_COST,
+ rio.MINIMIZE_DUPS,
+ rio.MINIMIZE_HEIGHT,
+ true,
+ 1 )[ 0 ];
+ final DistanceCalculator dc = new DistanceCalculator();
+ final StringBuffer sb = new StringBuffer();
+ sb.append( "Given the threshold for distance calculations (" + ForesterUtil.roundToInt( t_orthologs_dc )
+ + "): " );
+ // No orthologs.
+ if ( al_ortholog_names_for_dc.size() == 0 ) {
+ dc.setTree( assigned_cons_tree );
+ // Remark. Calculation of mean and sd _does_ include the node
+ // with seq_name.
+ m = dc.getMean();
+ sd = dc.getStandardDeviation();
+ d = dc.getDistanceToRoot( seq_name );
+ n = dc.getN();
+ sb.append( "No sequence is considered orthologous to query."
+ + "\ndistance of query to root = " + ForesterUtil.FORMATTER_06.format( d )
+ + "\nmean of distances (for all sequences) to root = " + ForesterUtil.FORMATTER_06.format( m )
+ + "\nsd of distances (for all sequences) to root = " + ForesterUtil.FORMATTER_06.format( sd )
+ + "\nn (sum of sequences in alignment plus query) = " + n );
+ if ( !( ( ( m - ( warn_no_orthos * sd ) ) < d ) && ( ( m + ( warn_no_orthos * sd ) ) > d ) ) ) {
+ sb.append( "\nWARNING: distance of query to root is outside of mean+/-" + warn_no_orthos + "*sd!" );
+ }
+ }
+ // One ortholog.
+ else if ( al_ortholog_names_for_dc.size() == 1 ) {
+ final String name_of_ortholog = al_ortholog_names_for_dc.get( 0 );
+ al_ortholog_nodes.add( assigned_cons_tree.getNode( name_of_ortholog ) );
+ al_ortholog_nodes.add( assigned_cons_tree.getNode( seq_name ) );
+ dc.setTreeAndExtNodes( assigned_cons_tree, al_ortholog_nodes );
+ // Remark. Calculation of mean _does_ include the node
+ // with seq_name.
+ d = dc.getDistanceToLCA( seq_name );
+ final double d_o = dc.getDistanceToLCA( name_of_ortholog );
+ sb.append( "One sequence is considered orthologous to query." + "\nLCA is LCA of query and its ortholog."
+ + "\ndistance of query to LCA = " + ForesterUtil.FORMATTER_06.format( d )
+ + "\ndistance of ortholog to LCA = " + ForesterUtil.FORMATTER_06.format( d_o ) );
+ if ( ( d_o > 0.0 )
+ && ( d > 0.0 )
+ && ( ( ( d_o >= d ) && ( ( d_o / d ) > warn_one_ortho ) ) || ( ( d_o < d ) && ( ( d / d_o ) > warn_one_ortho ) ) ) ) {
+ sb.append( "\nWARNING: Ratio of distances to LCA is greater than " + warn_one_ortho + "!" );
+ }
+ else if ( ( ( d_o == 0.0 ) || ( d == 0.0 ) ) && ( ( d_o != 0.0 ) || ( d != 0.0 ) ) ) {
+ sb.append( "\nWARNING: Ratio could not be calculated, " + " one distance is 0.0!" );
+ }
+ }
+ // More than one ortholog.
+ else {
+ for( int i = 0; i < al_ortholog_names_for_dc.size(); ++i ) {
+ al_ortholog_nodes.add( assigned_cons_tree.getNodeViaSequenceName( al_ortholog_names_for_dc.get( i ) ) );
+ }
+ al_ortholog_nodes.add( assigned_cons_tree.getNodesViaSequenceName( seq_name ).get( 0 ) );
+ dc.setTreeAndExtNodes( assigned_cons_tree, al_ortholog_nodes );
+ // Remark. Calculation of mean and sd _does_ include the node
+ // with seq_name.
+ m = dc.getMean();
+ sd = dc.getStandardDeviation();
+ d = dc.getDistanceToLCA( seq_name );
+ n = dc.getN();
+ sb.append( "More than one sequence is considered orthologous to query."
+ + "\nLCA is LCA of query and its orthologs."
+ + "\ndistance of query to LCA = "
+ + ForesterUtil.FORMATTER_06.format( d )
+ + "\nmean of distances (for query and its orthologs) to LCA = "
+ + ForesterUtil.FORMATTER_06.format( m )
+ + "\nsd of distances (for query and its orthologs) to LCA = "
+ + ForesterUtil.FORMATTER_06.format( sd )
+ + "\nn (sum of orthologs plus query) = " + n );
+ if ( !( ( ( m - ( warn_more_than_one_ortho * sd ) ) < d ) && ( ( m + ( warn_more_than_one_ortho * sd ) ) > d ) ) ) {
+ sb.append( "\n!WARNING: distance of query to LCA is outside of mean+/-" + warn_more_than_one_ortho
+ + "*sd!" );
+ }
+ }
+ return sb;
+ }
+
+ public static void main( final String[] args ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ File species_tree_file = null;
+ File multiple_trees_file = null;
+ File outfile = null;
+ File distance_matrix_file = null;
+ File tree_file_for_dist_val = null;
+ File tree_file_for_avg_bs = null;
+ String seq_name = "";
+ String arg = "";
+ boolean output_ultraparalogs = false;
+ ArrayList<String> orthologs_al_for_dc = null;
+ double t_orthologs = 0.0;
+ double t_sn = 0.0;
+ double t_orthologs_dc = 0.0;
+ double[] bs_mean_sd = null;
+ int sort = 13;
+ Phylogeny species_tree = null;
+ RIO rio_instance = null;
+ PrintWriter out = null;
+ long time = 0;
+ int warn_no_orthos = WARN_NO_ORTHOS_DEFAULT;
+ int warn_more_than_one_ortho = WARN_MORE_THAN_ONE_ORTHO_DEFAULT;
+ double warn_one_ortho = WARN_ONE_ORTHO_DEFAULT;
+ double threshold_ultra_paralogs = THRESHOLD_ULTRA_PARALOGS_DEFAULT;
+ if ( args.length < 2 ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ else if ( ( args.length < 3 ) || ( args.length > 18 ) ) {
+ errorInCommandLine();
+ }
+ for( int i = 0; i < args.length; ++i ) {
+ if ( args[ i ].trim().charAt( 0 ) != 'p' ) {
+ if ( args[ i ].trim().length() < 3 ) {
+ errorInCommandLine();
+ }
+ else {
+ arg = args[ i ].trim().substring( 2 );
+ }
+ }
+ try {
+ switch ( args[ i ].trim().charAt( 0 ) ) {
+ case 'M':
+ multiple_trees_file = new File( arg );
+ break;
+ case 'N':
+ seq_name = arg;
+ break;
+ case 'S':
+ species_tree_file = new File( arg );
+ break;
+ case 'O':
+ outfile = new File( arg );
+ break;
+ case 'D':
+ distance_matrix_file = new File( arg );
+ break;
+ case 'T':
+ tree_file_for_dist_val = new File( arg );
+ break;
+ case 't':
+ tree_file_for_avg_bs = new File( arg );
+ break;
+ case 'p':
+ output_ultraparalogs = true;
+ break;
+ case 'P':
+ sort = Integer.parseInt( arg );
+ if ( ( sort < 0 ) || ( sort > 17 ) ) {
+ errorInCommandLine();
+ }
+ break;
+ case 'L':
+ t_orthologs = Double.parseDouble( arg );
+ break;
+ case 'B':
+ t_sn = Double.parseDouble( arg );
+ break;
+ case 'U':
+ t_orthologs_dc = Double.parseDouble( arg );
+ break;
+ case 'v':
+ threshold_ultra_paralogs = Double.parseDouble( arg );
+ break;
+ case 'X':
+ warn_more_than_one_ortho = Integer.parseInt( arg );
+ break;
+ case 'Y':
+ warn_no_orthos = Integer.parseInt( arg );
+ break;
+ case 'Z':
+ warn_one_ortho = Double.parseDouble( arg );
+ break;
+ default:
+ errorInCommandLine();
+ }
+ }
+ catch ( final Exception e ) {
+ errorInCommandLine();
+ }
+ }
+ if ( ( seq_name == "" ) || ( species_tree_file == null ) || ( multiple_trees_file == null )
+ || ( outfile == null ) ) {
+ errorInCommandLine();
+ }
+ if ( ( sort < 0 ) || ( sort > 17 ) ) {
+ errorInCommandLine();
+ }
+ if ( ( sort > 2 ) && ( distance_matrix_file == null ) ) {
+ errorInCommandLine();
+ }
+ if ( VERBOSE ) {
+ System.out.println( "\nMultiple trees file: " + multiple_trees_file );
+ System.out.println( "Seq name: " + seq_name );
+ System.out.println( "Species tree file: " + species_tree_file );
+ System.out.println( "Outfile: " + outfile );
+ if ( distance_matrix_file != null ) {
+ System.out.println( "Distance matrix file: " + distance_matrix_file );
+ }
+ if ( tree_file_for_dist_val != null ) {
+ if ( tree_file_for_avg_bs == null ) {
+ System.out.println( "Phy to read dists and calc mean support from: " + tree_file_for_dist_val );
+ }
+ else {
+ System.out.println( "Phylogeny to read dist values from: " + tree_file_for_dist_val );
+ }
+ }
+ if ( tree_file_for_avg_bs != null ) {
+ System.out.println( "Phylogeny to calc mean bootstrap from: " + tree_file_for_avg_bs );
+ }
+ System.out.println( "Sort: " + sort );
+ System.out.println( "Threshold orthologs: " + t_orthologs );
+ System.out.println( "Threshold subtree neighborings: " + t_sn );
+ System.out.println( "Threshold orthologs for distance calc.: " + t_orthologs_dc );
+ if ( output_ultraparalogs ) {
+ System.out.println( "Threshold ultra paralogs: " + threshold_ultra_paralogs );
+ }
+ System.out.println( "More than one ortholog sd diff: " + warn_more_than_one_ortho );
+ System.out.println( "No orthologs sd diff: " + warn_no_orthos );
+ System.out.println( "One ortholog factor : " + warn_one_ortho + "\n" );
+ }
+ if ( TIME && VERBOSE ) {
+ time = System.currentTimeMillis();
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace();
+ System.exit( -1 );
+ }
+ if ( !species_tree.isRooted() ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not rooted" );
+ System.exit( -1 );
+ }
+ if ( !species_tree.isCompletelyBinary() ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, "Species tree is not completely binary" );
+ System.exit( -1 );
+ }
+ rio_instance = new RIO();
+ final StringBuffer output = new StringBuffer();
+ try {
+ if ( distance_matrix_file != null ) {
+ rio_instance.readDistanceMatrix( distance_matrix_file );
+ }
+ rio_instance.inferOrthologs( multiple_trees_file, species_tree.copy(), seq_name );
+ output.append( rio_instance.inferredOrthologsToString( seq_name, sort, t_orthologs, t_sn ) );
+ if ( tree_file_for_dist_val != null ) {
+ orthologs_al_for_dc = rio_instance.inferredOrthologsToArrayList( seq_name, t_orthologs_dc );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ if ( tree_file_for_avg_bs != null ) {
+ final Phylogeny p = factory.create( tree_file_for_avg_bs, new PhyloXmlParser() )[ 0 ];
+ bs_mean_sd = calculateMeanBoostrapValue( p );
+ }
+ else {
+ final Phylogeny p = factory.create( tree_file_for_dist_val, new PhyloXmlParser() )[ 0 ];
+ bs_mean_sd = calculateMeanBoostrapValue( p );
+ }
+ if ( ( bs_mean_sd != null ) && ( bs_mean_sd.length == 2 ) ) {
+ final double bs_mean = bs_mean_sd[ 0 ];
+ final double bs_sd = bs_mean_sd[ 1 ];
+ output.append( "\n\nMean bootstrap value of consensus tree (sd): "
+ + ForesterUtil.roundToInt( ( bs_mean * 100.0 ) / rio_instance.getBootstraps() ) + "% (+/-"
+ + ForesterUtil.roundToInt( ( bs_sd * 100.0 ) / rio_instance.getBootstraps() ) + "%)\n" );
+ }
+ output.append( "\n\nDistance values:\n" );
+ output.append( getDistances( tree_file_for_dist_val,
+ outfile,
+ species_tree,
+ seq_name,
+ orthologs_al_for_dc,
+ rio_instance.getInferredOrthologs( seq_name ),
+ rio_instance.getInferredSuperOrthologs( seq_name ),
+ warn_more_than_one_ortho,
+ warn_no_orthos,
+ warn_one_ortho,
+ rio_instance.getBootstraps(),
+ t_orthologs_dc ) );
+ }
+ if ( output_ultraparalogs ) {
+ output.append( "\n\nUltra paralogs:\n" );
+ output.append( rio_instance
+ .inferredUltraParalogsToString( seq_name, sort > 2, threshold_ultra_paralogs ) );
+ }
+ output.append( "\n\nSort priority: " + RIO.getOrder( sort ) );
+ output.append( "\nExt nodes : " + rio_instance.getExtNodesOfAnalyzedGeneTrees() );
+ output.append( "\nSamples : " + rio_instance.getBootstraps() + "\n" );
+ out = new PrintWriter( new FileWriter( outfile ), true );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.printErrorMessage( PRG_NAME, e.getLocalizedMessage() );
+ e.printStackTrace();
+ System.exit( -1 );
+ }
+ out.println( output );
+ out.close();
+ ForesterUtil.programMessage( PRG_NAME, "wrote results to \"" + outfile + "\"" );
+ if ( TIME && VERBOSE ) {
+ time = System.currentTimeMillis() - time;
+ ForesterUtil.programMessage( PRG_NAME, "time: " + time + "ms" );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "OK." );
+ System.exit( 0 );
+ }
+
+ private final static void printHelp() {
+ System.out.println( "M= (String) Multiple gene tree file (mandatory)" );
+ System.out.println( "N= (String) Query sequence name (mandatory)" );
+ System.out.println( "S= (String) Species tree file (mandatory)" );
+ System.out.println( "O= (String) Output file name -- overwritten without warning! (mandatory)" );
+ System.out.println( "D= (String) Distance matrix file for pairwise distances" );
+ System.out.println( "T= (String) Phylogeny file for distances of query to LCA" );
+ System.out.println( " of orthologs and for mean bootstrap value (if t= is not used)," );
+ System.out.println( " must be binary )" );
+ System.out.println( "t= (String) Phylogeny file for mean bootstrap value (if this option is used," );
+ System.out.println( " the mean bootstrap value is not calculated from the tree read in" );
+ System.out.println( " with T=), not necessary binary" );
+ System.out.println( "p To output ultra paralogs" );
+ System.out.println( "P= (int) Sort priority" );
+ System.out.println( "L= (double) Threshold orthologs for output" );
+ System.out.println( "U= (double) Threshold orthologs for distance calculation" );
+ System.out.println( "X= (int) More than one ortholog: " );
+ System.out.println( " numbers of sd the dist. to LCA has to differ from mean to generate a warning" );
+ System.out.println( "Y= (int) No orthologs:" );
+ System.out.println( " Numbers of sd the dist to root has to differ from mean to generate a warning" );
+ System.out.println( "Z= (double) One ortholog:" );
+ System.out.println( " threshold for factor between the two distances to their LCA (larger/smaller)" );
+ System.out.println( " to generate a warning" );
+ System.out.println();
+ System.out.println( " Sort priority (\"P=\"):" );
+ System.out.println( RIO.getOrderHelp().toString() );
+ System.out.println();
+ System.out
+ .println( " Example: \"rio M=gene_trees.xml N=bcl2_NEMVE S=species_tree.xml D=distances P=13 p O=out\"" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.SDI;
+import org.forester.sdi.SDIse;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public final class sdi {
+
+ final static private String STRIP_OPTION = "s";
+ final static private String GSDI_OPTION = "g";
+ final static private String MOST_PARSIMONIOUS_OPTION = "m";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String DEFAULT_OUTFILE = "sdi_out.xml";
+ final static private String PRG_NAME = "sdi";
+ final static private String PRG_VERSION = "beta 0.4";
+ final static private String PRG_DATE = "2009.01.22";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( sdi.PRG_NAME, sdi.PRG_VERSION, sdi.PRG_DATE );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( sdi.HELP_OPTION_1 ) || cla.isOptionSet( sdi.HELP_OPTION_2 ) ) {
+ System.out.println();
+ sdi.print_help();
+ System.exit( 0 );
+ }
+ else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
+ System.out.println();
+ System.out.println( "Wrong number of arguments." );
+ System.out.println();
+ sdi.print_help();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( sdi.STRIP_OPTION );
+ allowed_options.add( sdi.GSDI_OPTION );
+ allowed_options.add( sdi.MOST_PARSIMONIOUS_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ boolean use_sdise = true;
+ boolean strip = false;
+ boolean most_parsimonous_duplication_model = false;
+ if ( cla.isOptionSet( sdi.STRIP_OPTION ) ) {
+ strip = true;
+ }
+ if ( cla.isOptionSet( sdi.GSDI_OPTION ) ) {
+ use_sdise = false;
+ }
+ if ( cla.isOptionSet( sdi.MOST_PARSIMONIOUS_OPTION ) ) {
+ if ( use_sdise ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
+ }
+ most_parsimonous_duplication_model = true;
+ }
+ Phylogeny species_tree = null;
+ Phylogeny gene_tree = null;
+ File gene_tree_file = null;
+ File species_tree_file = null;
+ File out_file = null;
+ try {
+ gene_tree_file = cla.getFile( 0 );
+ species_tree_file = cla.getFile( 1 );
+ if ( cla.getNumberOfNames() == 3 ) {
+ out_file = cla.getFile( 2 );
+ }
+ else {
+ out_file = new File( sdi.DEFAULT_OUTFILE );
+ }
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "error in command line: " + e.getMessage() );
+ }
+ if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
+ }
+ if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
+ }
+ if ( ForesterUtil.isWritableFile( out_file ) != null ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "Failed to read species tree from \"" + gene_tree_file + "\" ["
+ + e.getMessage() + "]" );
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "Failed to read gene tree from \"" + gene_tree_file + "\" ["
+ + e.getMessage() + "]" );
+ }
+ gene_tree.setRooted( true );
+ species_tree.setRooted( true );
+ if ( !gene_tree.isCompletelyBinary() ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "gene tree (\"" + gene_tree_file + "\") is not completely binary." );
+ }
+ if ( use_sdise ) {
+ if ( !species_tree.isCompletelyBinary() ) {
+ ForesterUtil.fatalError( sdi.PRG_NAME, "species tree (\"" + species_tree_file
+ + "\") is not completely binary." );
+ }
+ }
+ // For timing.
+ // gene_tree = Helper.createBalancedTree( 10 );
+ // species_tree = Helper.createBalancedTree( 13 );
+ // species_tree = Helper.createUnbalancedTree( 1024 );
+ // gene_tree = Helper.createUnbalancedTree( 8192 );
+ // species_tree = gene_tree.copyTree();
+ // gene_tree = species_tree.copyTree();
+ // Helper.numberSpeciesInOrder( species_tree );
+ // Helper.numberSpeciesInOrder( gene_tree );
+ // Helper.randomizeSpecies( 1, 8192, gene_tree );
+ // Helper.intervalNumberSpecies( gene_tree, 4096 );
+ // Helper.numberSpeciesInDescOrder( gene_tree );
+ System.out.println();
+ System.out.println( "Strip species tree: " + strip );
+ SDI sdi = null;
+ final long start_time = new Date().getTime();
+ try {
+ if ( use_sdise ) {
+ System.out.println();
+ System.out.println( "Using SDIse algorithm." );
+ sdi = new SDIse( gene_tree, species_tree );
+ }
+ else {
+ System.out.println();
+ System.out.println( "Using GSDI algorithm." );
+ System.out.println();
+ System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
+ sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model );
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ System.out.println();
+ System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( out_file, gene_tree, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "Failed to write to \"" + out_file + "\" [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
+ System.out.println();
+ if ( use_sdise ) {
+ sdi.computeMappingCostL();
+ System.out.println( "Mapping cost : " + sdi.computeMappingCostL() );
+ }
+ System.out.println( "Number of duplications : " + sdi.getDuplicationsSum() );
+ if ( !use_sdise && !most_parsimonous_duplication_model ) {
+ System.out.println( "Number of potential duplications: "
+ + ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum() );
+ }
+ if ( !use_sdise ) {
+ System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() );
+ }
+ System.out.println();
+ } // main( final String args[] )
+
+ private static void print_help() {
+ System.out.println( "Usage: \"" + sdi.PRG_NAME
+ + " [-options] <gene tree in phyloXML format> <species tree in phyloXML format> [outfile]\"" );
+ System.out.println();
+ System.out.println( "Options:" );
+ System.out.println( " -" + sdi.STRIP_OPTION + ": to strip the species tree prior to duplication inference" );
+ System.out.println( " -" + sdi.GSDI_OPTION
+ + ": to use GSDI algorithm instead of SDIse algorithm (under development, not recommended)" );
+ System.out
+ .println( " -" + sdi.MOST_PARSIMONIOUS_OPTION + ": use most parimonious duplication model for GSDI: " );
+ System.out.println( " assign nodes as speciations which would otherwise be assiged" );
+ System.out.println( " as unknown because of polytomies in the species tree" );
+ System.out.println();
+ System.out.println( "Species tree:" );
+ System.out.println( " In phyloXML format, with taxonomy data in appropriate fields." );
+ System.out.println();
+ System.out.println( "Gene tree:" );
+ System.out.println( " In phyloXM format, with taxonomy and sequence data in appropriate fields." );
+ System.out.println();
+ System.out
+ .println( "!! WARNING: GSDI algorithm is under development (and possibly not correct), please use SDIse instead !!" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// Copyright (C) 2000-2001 Washington University School of Medicine
+// and Howard Hughes Medical 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.FileWriter;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.util.Arrays;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.SDIR;
+import org.forester.sdi.SDIse;
+import org.forester.util.ForesterUtil;
+
+/*
+ * Allows to infer duplications - speciations on all (rooted or unrooted) gene
+ * trees in a directory by using method "infer" of class SDIunrooted. <p> The
+ * output of this is a (re)rooted tree with speciation - duplication assigned
+ * for each tree (in "gene tree directory" with suffix "suffix for gene trees"),
+ * as well as a summary list ("outputfile name"). <p> The summary list contains
+ * the following. The number in brackets indicates how many external nodes of
+ * the gene tree had to be removed since the associated species was not found in
+ * the species tree. "en" indicates the number of external nodes in the
+ * resulting (analyzed and returned) gene tree. "d" are the number of
+ * duplications, "L=" the mapping cost, "h=" the height, "d=" the minimal
+ * difference in tree heights (of the two subtrees at the root; this number is
+ * 0.0 for a midpoint rooted tree) of the resulting, analyzed and rooted gene
+ * tree(s). <p> The output file ending with "_Sdist" is a file which lists the
+ * distribution of trees sizes, "_Ddist" lists the distribution of the sums of
+ * duplications (up to a certain maximal size, set with final variables
+ * MAX_EXT_NODE_DIST and MAX_DUP_DIST).
+ *
+ * @see SDIunrooted
+ *
+ * @author Christian M. Zmasek
+ */
+public class sdi_dir {
+
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org";
+ final static private String PRG_NAME = "sdi_dir";
+ final static private String PRG_VERSION = "2.00";
+ final static private String PRG_DATE = "2010.04.26";
+
+ private static void errorInCommandLine() {
+ System.out.println( "\nsdi_dir: Error in command line.\n" );
+ System.out.print( "Usage: % sdi_dir [-options] <gene tree directory> <suffix for gene trees>" );
+ System.out.println( " <species tree file name> <output directory> <outputfile name>" );
+ System.out.println( "\nOptions:" );
+ System.out.println( " -l to root by minimizing the mapping cost L (and also the sum of duplications)" );
+ System.out.println( " -d to root by minimizing the sum of duplications" );
+ System.out.println( " -h to root by minimizing tree height (can be used together with -l or -d)" );
+ System.out.println( " -w to write assigned gene trees into output directory" );
+ System.out.println( "\nGene tree directory" );
+ System.out.println( " The directory from which to read phyloXML formatted gene trees which" );
+ System.out.println( " contain taxonomic information in appropriate sub-elements of taxonomy" );
+ System.out.println( " (see: www.phyloxml.org)." );
+ System.out.println( " The gene trees can either be rooted, in which case no rooting with -l, -d, or -h " );
+ System.out.println( " is necessary, or they can be unrooted, in which case rooting is mandatory." );
+ System.out.println( "\nSuffix for gene trees" );
+ System.out.println( " Suffix of the gene trees to analyze (e.g. \".phyloxml\")." );
+ System.out.println( "\nSpecies tree file" );
+ System.out.println( " In phyloXML format, taxonomic information in appropriate sub-elements of taxonomy." );
+ System.out.println( " (see: www.phyloxml.org)." );
+ System.out.println( "\nOutput directory" );
+ System.out.println( " The directory into which the assigned gene trees will be written." );
+ System.out.println( "\nOutputfile name" );
+ System.out.println( " File name for summary output files." );
+ System.out.println( "" );
+ System.exit( -1 );
+ }
+
+ /**
+ * Runs method "infer" of class SDIunrooted on all gene trees in directory
+ * indir.
+ * <p>
+ * Trees are rooted by minimizing either the sum of duplications, the
+ * mapping cost L, or the tree height (or combinations thereof). One
+ * resulting tree for each (out of possibly many) is stored in outdir and a
+ * summary outfile is created. The distributions of the tree sizes (name of
+ * outfile + _Ddist) and the distributions of the sum of duplications per
+ * tree (name of outfile + _Sdist) are written out as well.
+ * <p>
+ * If both minimize_sum_of_dup and minimize_mapping_cost are true, trees are
+ * rooted by minimizing by minimizing the mapping cost L.
+ * <p>
+ * If minimize_sum_of_dup, minimize_mapping_cost, and minimize_height are
+ * false trees are assumed to be alreadty rooted.
+ * <p>
+ * (Last modified: 02/02/01)
+ *
+ * @see SDIR#infer(Phylogeny,Phylogeny,boolean,boolean,boolean,boolean,int,boolean)
+ * @param indir
+ * a directory containing gene trees in NHX format
+ * @param species_tree_file
+ * a species tree file in NHX format
+ * @param outdir
+ * a directory where to write trees
+ * @param outfile
+ * a file name for the summary file
+ * @param suffix
+ * a suffix for the trees to read (e.g. nhx), is case sensitive
+ * @param write_trees
+ * set to true to write out one tree with minmal duplications or
+ * L each
+ * @param minimize_mapping_cost
+ * set to true to root by minimizing the mapping cost L
+ * @param minimize_sum_of_dup
+ * set to true to root by minimizing the sum of duplications
+ * @param minimize_height
+ * set to true to root by minimizing the tree height -- if
+ * minimize_mapping_cost is set to true or minimize_sum_of_dup is
+ * set to true, then out of the resulting trees with minimal
+ * mapping cost or minimal number of duplications the tree with
+ * the minimal height is chosen
+ */
+ public static void infer( final File indir,
+ final File species_tree_file,
+ final File outdir,
+ final File outfile,
+ String suffix,
+ final boolean write_trees,
+ final boolean minimize_mapping_cost,
+ boolean minimize_sum_of_dup,
+ final boolean minimize_height ) throws IOException {
+ final int MIN_EXT_NODES = 4; // Minimal size of trees [in ext nodes]
+ // to be analyzed.
+ final int MAX_EXT_NODES = 5000; // Maximal size of trees [in ext nodes]
+ // to be analyzed.
+ final int MAX_DUP_DIST = 50; // Max number of dups to output in dup
+ // distribution ("_Ddist").
+ final int MAX_EXT_NODE_DIST = 1000; // Max number of ext nodes to output
+ // in size
+ // distribution ("_Sdist").
+ int successful = 0, number_of_too_small_trees = 0, number_of_too_large_trees = 0, dups = 0, c = 0, ext_nodes = 0, removed = 0;
+ final int nodecount0 = 0;
+ int j = 0;
+ long total_number_of_d = 0, total_number_of_ext_nodes = 0, sum_costs = 0;
+ double sum_tree_heights = 0.0, sum_subtree_diff = 0.0;
+ Phylogeny species_tree = null;
+ String filename = null;
+ String[] filenames = null;
+ Phylogeny[] trees = null;
+ final int[] duplications = new int[ MAX_EXT_NODES - 1 ], // For dup
+ // distribution.
+ sizes = new int[ MAX_EXT_NODES - 1 ]; // For ext nodes dist.of
+ // successfully assigned trees.
+ File outtree = null;
+ PrintWriter out = null, out_ddist = null, out_sdist = null;
+ final File ddist_outfile = new File( outfile + "_Ddist" ), sdist_outfile = new File( outfile + "_Sdist" );
+ final java.text.DecimalFormat df = new java.text.DecimalFormat( "0.0#####" );
+ df.setDecimalSeparatorAlwaysShown( true );
+ if ( !indir.exists() || !indir.isDirectory() ) {
+ throw new IllegalArgumentException( indir + " does not exist or is not a directory." );
+ }
+ if ( !outdir.exists() || !outdir.isDirectory() ) {
+ throw new IllegalArgumentException( outdir + " does not exist or is not a directory." );
+ }
+ if ( outfile.exists() ) {
+ throw new IllegalArgumentException( outfile + " does already exist." );
+ }
+ if ( ddist_outfile.exists() ) {
+ throw new IllegalArgumentException( ddist_outfile + " does already exist." );
+ }
+ if ( sdist_outfile.exists() ) {
+ throw new IllegalArgumentException( sdist_outfile + " does already exist." );
+ }
+ if ( !species_tree_file.exists() || !species_tree_file.isFile() ) {
+ throw new IllegalArgumentException( species_tree_file + " does not exist or is not a file." );
+ }
+ if ( minimize_mapping_cost && minimize_sum_of_dup ) {
+ minimize_sum_of_dup = false;
+ }
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ species_tree = factory.create( species_tree_file, new PhyloXmlParser() )[ 0 ];
+ filenames = indir.list();
+ Arrays.sort( filenames );
+ suffix = suffix.trim();
+ out = new PrintWriter( new FileWriter( outfile ), true );
+ //nodecount0 = PhylogenyNode.getNodeCount();
+ for( int i = 0; i < filenames.length; ++i ) {
+ filename = filenames[ i ];
+ if ( ( suffix.length() < 1 ) || filename.endsWith( suffix ) ) {
+ final File gene_tree_file = new File( indir.getPath(), filename );
+ if ( gene_tree_file.exists() && gene_tree_file.isFile() ) {
+ out.print( j + "\t" + filename );
+ System.out.println( j + ": " + filename );
+ j++;
+ Phylogeny gene_tree = null;
+ gene_tree = factory.create( gene_tree_file, new PhyloXmlParser() )[ 0 ];
+ // Removes from gene_tree all species not found in
+ // species_tree.
+ removed = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree );
+ if ( filename.length() < 8 ) {
+ out.print( "\t\t\t[-" + removed + "]" );
+ }
+ else if ( filename.length() < 16 ) {
+ out.print( "\t\t[-" + removed + "]" );
+ }
+ else {
+ out.print( "\t[-" + removed + "]" );
+ }
+ if ( gene_tree.getNumberOfExternalNodes() < MIN_EXT_NODES ) {
+ out.print( "\t<" + MIN_EXT_NODES + "en\n" );
+ number_of_too_small_trees++;
+ }
+ else if ( gene_tree.getNumberOfExternalNodes() > MAX_EXT_NODES ) {
+ out.print( "\t>" + MAX_EXT_NODES + "en\n" );
+ number_of_too_large_trees++;
+ }
+ else {
+ SDIR sdiunrooted = null;
+ // PhylogenyNode.setNodeCount( nodecount0 );
+ sdiunrooted = new SDIR();
+ if ( minimize_mapping_cost || minimize_sum_of_dup || minimize_height ) {
+ trees = sdiunrooted.infer( gene_tree,
+ species_tree,
+ minimize_mapping_cost,
+ minimize_sum_of_dup,
+ minimize_height,
+ write_trees,
+ 1 );
+ dups = sdiunrooted.getMinimalDuplications();
+ }
+ else {
+ final SDIse sdi = new SDIse( gene_tree, species_tree );
+ trees = new Phylogeny[ 1 ];
+ trees[ 0 ] = gene_tree;
+ dups = sdi.getDuplicationsSum();
+ c = sdi.computeMappingCostL();
+ sum_costs += c;
+ out.print( "\t L=" + c );
+ }
+ successful++;
+ ext_nodes = gene_tree.getNumberOfExternalNodes();
+ total_number_of_ext_nodes += ext_nodes;
+ sizes[ ext_nodes ]++;
+ out.print( "\t " + ext_nodes + "en" );
+ total_number_of_d += dups;
+ duplications[ dups ]++;
+ out.print( "\t " + dups + "d" );
+ if ( minimize_mapping_cost ) {
+ c = sdiunrooted.getMinimalMappingCost();
+ sum_costs += c;
+ out.print( "\t L=" + c );
+ }
+ if ( minimize_height ) {
+ out.print( "\t h=" + df.format( sdiunrooted.getMinimalTreeHeight() ) );
+ out.print( "\t d=" + df.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
+ sum_tree_heights += sdiunrooted.getMinimalTreeHeight();
+ sum_subtree_diff += sdiunrooted.getMinimalDiffInSubTreeHeights();
+ }
+ out.println();
+ if ( write_trees ) {
+ outtree = new File( outdir, new File( filenames[ i ] ).getName() );
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( outtree, trees[ 0 ], 1 );
+ }
+ }
+ }
+ }
+ }
+ //PhylogenyNode.setNodeCount( nodecount0 );
+ if ( minimize_mapping_cost ) {
+ out.println( "\nRooted by minimizing mapping cost L." );
+ System.out.println( "\nRooted by minimizing mapping cost L." );
+ if ( minimize_height ) {
+ out.println( "Selected tree(s) with minimal height out of resulting trees." );
+ System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
+ }
+ }
+ else if ( minimize_sum_of_dup ) {
+ out.println( "\nRooted by minimizing sum of duplications." );
+ System.out.println( "\nRooted by minimizing sum of duplications." );
+ if ( minimize_height ) {
+ out.println( "Selected tree(s) with minimal height out of resulting trees." );
+ System.out.println( "Selected tree(s) with minimal height out of resulting trees." );
+ }
+ }
+ else if ( minimize_height ) {
+ out.println( "\nRooted by minimizing tree height." );
+ System.out.println( "\nRooted by minimizing tree height." );
+ }
+ else {
+ out.println( "\nNo (re) rooting was performed." );
+ System.out.println( "\nNo (re) rooting was performed." );
+ }
+ out.println( "\nTrees directory : " + indir );
+ out.println( "Suffix for trees : " + suffix );
+ out.println( "Species tree : " + species_tree_file );
+ out.println( "Output directory : " + outdir );
+ out.println( "Output file : " + outfile );
+ out.println( "\nTotal number of attempts (tree files read) : " + j );
+ out.println( "Total number of successfully assigned trees : " + successful );
+ out.println( "Number of too small trees : " + number_of_too_small_trees );
+ out.println( "Number of too large trees : " + number_of_too_large_trees );
+ out.println( "\nSum of duplications : " + total_number_of_d );
+ if ( minimize_mapping_cost ) {
+ out.println( "Sum of mapping costs L : " + sum_costs );
+ }
+ if ( minimize_height ) {
+ out.println( "Sum of tree heights : " + sum_tree_heights );
+ out.println( "Sum of differences in subtree heights : " + sum_subtree_diff );
+ }
+ out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
+ out.close();
+ System.out.println( "\nTotal number of attempts (tree files read) : " + j );
+ System.out.println( "Total number of successfully assigned trees : " + successful );
+ System.out.println( "Number of too small trees : " + number_of_too_small_trees );
+ System.out.println( "Number of too large trees : " + number_of_too_large_trees );
+ System.out.println( "\nSum of duplications : " + total_number_of_d );
+ if ( minimize_mapping_cost ) {
+ System.out.println( "Sum of mapping costs L : " + sum_costs );
+ }
+ if ( minimize_height ) {
+ System.out.println( "Sum of tree heights : " + sum_tree_heights );
+ System.out.println( "Sum of differences in subtree heights : " + sum_subtree_diff );
+ }
+ System.out.println( "Sum of external nodes (in successfully assigned trees): " + total_number_of_ext_nodes );
+ out_ddist = new PrintWriter( new FileWriter( ddist_outfile ), true );
+ for( int i = 0; ( i < duplications.length ) && ( i <= MAX_DUP_DIST ); ++i ) {
+ out_ddist.println( i + " " + duplications[ i ] );
+ }
+ out_ddist.close();
+ out_sdist = new PrintWriter( new FileWriter( sdist_outfile ), true );
+ for( int i = 0; ( i < sizes.length ) && ( i <= MAX_EXT_NODE_DIST ); ++i ) {
+ out_sdist.println( i + " " + sizes[ i ] );
+ }
+ out_sdist.close();
+ } // infer
+
+ /**
+ * Main method for this class.
+ * <p>
+ * (Last modified: 04/26/10)
+ *
+ * @param [args[0]
+ * -l to root by minimizing mapping cost L]
+ * @param [args[0]
+ * -d to root by minimizing sum of duplications]
+ * @param [args[0]
+ * -w to write out trees into outdir]
+ * @param [args[0]
+ * -h to root by minimizing tree height]
+ * @param [args[0]
+ * -n input trees are in New Hampshire format instead of NHX --
+ * or gene tree is in NHX, but species information in gene tree
+ * is only present in the form of SWISS-PROT sequence names]
+ * @param args[0or1]
+ * trees directory name
+ * @param args[1or2]
+ * suffix for gene trees
+ * @param args[2or3]
+ * speciestree file name
+ * @param args[3or4]
+ * output directory name
+ * @param args[4or5]
+ * output file name
+ */
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ // These are the default values.
+ boolean minimize_mapping_cost = false;
+ boolean minimize_sum_of_dup = false;
+ boolean minimize_height = false;
+ boolean write_trees = false;
+ File indir = null;
+ File speciestree_file = null;
+ File outdir = null;
+ File outfile = null;
+ String suffix = null;
+ if ( args.length == 5 ) {
+ indir = new File( args[ 0 ] );
+ suffix = args[ 1 ];
+ speciestree_file = new File( args[ 2 ] );
+ outdir = new File( args[ 3 ] );
+ outfile = new File( args[ 4 ] );
+ }
+ else if ( args.length == 6 ) {
+ if ( args[ 0 ].startsWith( "-" ) ) {
+ minimize_mapping_cost = false;
+ minimize_sum_of_dup = false;
+ minimize_height = false;
+ write_trees = false;
+ if ( args[ 0 ].toLowerCase().indexOf( "w" ) != -1 ) {
+ write_trees = true;
+ }
+ if ( args[ 0 ].toLowerCase().indexOf( "l" ) != -1 ) {
+ minimize_mapping_cost = true;
+ }
+ if ( args[ 0 ].toLowerCase().indexOf( "d" ) != -1 ) {
+ minimize_sum_of_dup = true;
+ }
+ if ( args[ 0 ].toLowerCase().indexOf( "h" ) != -1 ) {
+ minimize_height = true;
+ }
+ }
+ else {
+ sdi_dir.errorInCommandLine();
+ }
+ indir = new File( args[ 1 ] );
+ suffix = args[ 2 ];
+ speciestree_file = new File( args[ 3 ] );
+ outdir = new File( args[ 4 ] );
+ outfile = new File( args[ 5 ] );
+ }
+ else {
+ sdi_dir.errorInCommandLine();
+ }
+ if ( minimize_mapping_cost && minimize_sum_of_dup ) {
+ minimize_sum_of_dup = false;
+ }
+ try {
+ sdi_dir.infer( indir,
+ speciestree_file,
+ outdir,
+ outfile,
+ suffix,
+ write_trees,
+ minimize_mapping_cost,
+ minimize_sum_of_dup,
+ minimize_height );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, "error: " + e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "OK." );
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.SDIR;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class sdi_r {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String MIN_MAPPING_COST_OPTION = "ml";
+ final static private String MIN_DUPS_OPTION = "md";
+ final static private String MIN_HEIGHT_OPTION = "mh";
+ final static private String PRG_NAME = "sdi_r";
+ final static private String PRG_VERSION = "1.11";
+ final static private String PRG_DATE = "2009.06.19";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org";
+ // How many resulting trees "main" should return/display.
+ private final static int TREES_TO_RETURN = 5;
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) || ( args.length == 0 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( ( args.length < 3 ) || ( cla.getNumberOfNames() != 2 ) ) {
+ System.out.println();
+ System.out.println( "[" + PRG_NAME + "] incorrect number of arguments" );
+ System.out.println();
+ printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( MIN_MAPPING_COST_OPTION );
+ allowed_options.add( MIN_DUPS_OPTION );
+ allowed_options.add( MIN_HEIGHT_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final File outfile = new File( "sdir_outfile.xml" );
+ if ( outfile.exists() ) {
+ ForesterUtil.fatalError( PRG_NAME, "outfile \"" + outfile + "\" already exists" );
+ }
+ final File gene_tree_file = cla.getFile( 0 );
+ final File species_tree_file = cla.getFile( 1 );
+ boolean minimize_cost = false;
+ if ( cla.isOptionSet( MIN_MAPPING_COST_OPTION ) ) {
+ minimize_cost = true;
+ }
+ boolean minimize_sum_of_dup = false;
+ if ( cla.isOptionSet( MIN_DUPS_OPTION ) ) {
+ minimize_sum_of_dup = true;
+ }
+ boolean minimize_height = false;
+ if ( cla.isOptionSet( MIN_HEIGHT_OPTION ) ) {
+ minimize_height = true;
+ }
+ int r = 0;
+ Phylogeny[] gene_trees = null;
+ Phylogeny species_tree = null;
+ if ( minimize_cost && minimize_sum_of_dup ) {
+ minimize_sum_of_dup = false;
+ }
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ try {
+ final PhylogenyParser pp = new PhyloXmlParser();
+ species_tree = factory.create( species_tree_file, pp )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read species tree [" + species_tree_file + "]: "
+ + e.getLocalizedMessage() );
+ }
+ if ( !species_tree.isRooted() ) {
+ ForesterUtil.fatalError( PRG_NAME, "species tree [" + species_tree_file + "] is not rooted" );
+ }
+ try {
+ final PhylogenyParser pp = new PhyloXmlParser();
+ gene_trees = factory.create( gene_tree_file, pp );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read gene trees [" + gene_tree_file + "]: "
+ + e.getLocalizedMessage() );
+ }
+ // Removes from gene_tree all species not found in species_tree.
+ int gene_tree_counter = 0;
+ final List<Phylogeny> all_result_trees = new ArrayList<Phylogeny>();
+ for( final Phylogeny gene_tree : gene_trees ) {
+ r = PhylogenyMethods.taxonomyBasedDeletionOfExternalNodes( species_tree, gene_tree );
+ ForesterUtil.programMessage( PRG_NAME, "Removed " + r + " external nodes from gene tree" );
+ final SDIR sdiunrooted = new SDIR();
+ final long start_time = new Date().getTime();
+ Phylogeny[] result_trees = null;
+ try {
+ result_trees = sdiunrooted.infer( gene_tree,
+ species_tree,
+ minimize_cost,
+ minimize_sum_of_dup,
+ minimize_height,
+ true,
+ sdi_r.TREES_TO_RETURN );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ final long time_req = new Date().getTime() - start_time;
+ if ( minimize_cost ) {
+ ForesterUtil.programMessage( PRG_NAME, "Rooted by minimizing mapping cost L" );
+ if ( minimize_height ) {
+ ForesterUtil.programMessage( PRG_NAME,
+ "Selected tree(s) with minimal height out of resulting trees" );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Number differently rooted trees minimizing criterion : "
+ + sdiunrooted.getCount() );
+ ForesterUtil.programMessage( PRG_NAME, "Minimal cost : "
+ + sdiunrooted.getMinimalMappingCost() );
+ ForesterUtil.programMessage( PRG_NAME, "Minimal duplications : "
+ + sdiunrooted.getMinimalDuplications() );
+ if ( minimize_height ) {
+ ForesterUtil.programMessage( PRG_NAME, "Phylogeny height : "
+ + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalTreeHeight() ) );
+ ForesterUtil.programMessage( PRG_NAME, "Difference in subtree heights : "
+ + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
+ }
+ }
+ else if ( minimize_sum_of_dup ) {
+ ForesterUtil.programMessage( PRG_NAME, "Rooted by minimizing sum of duplications" );
+ if ( minimize_height ) {
+ ForesterUtil.programMessage( PRG_NAME,
+ "Selected tree(s) with minimal height out of resulting trees" );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Number differently rooted trees minimizing criterion : "
+ + sdiunrooted.getCount() );
+ ForesterUtil.programMessage( PRG_NAME, "Minimal duplications : "
+ + sdiunrooted.getMinimalDuplications() );
+ if ( minimize_height ) {
+ ForesterUtil.programMessage( PRG_NAME,
+ "Phylogeny height : "
+ + ForesterUtil.FORMATTER_06.format( sdiunrooted
+ .getMinimalTreeHeight() ) );
+ ForesterUtil.programMessage( PRG_NAME,
+ "Difference in subtree heights : "
+ + ForesterUtil.FORMATTER_06.format( sdiunrooted
+ .getMinimalDiffInSubTreeHeights() ) );
+ }
+ }
+ else if ( minimize_height ) {
+ ForesterUtil.programMessage( PRG_NAME, "Rooted by minimizing tree height (midpoint rooting)." );
+ ForesterUtil.programMessage( PRG_NAME, "Minimal tree height : "
+ + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalTreeHeight() ) );
+ ForesterUtil.programMessage( PRG_NAME, "Minimal difference in subtree heights: "
+ + ForesterUtil.FORMATTER_06.format( sdiunrooted.getMinimalDiffInSubTreeHeights() ) );
+ ForesterUtil.programMessage( PRG_NAME, "Duplications in midpoint rooted tree : "
+ + sdiunrooted.getMinimalDuplications() );
+ }
+ else {
+ ForesterUtil.programMessage( PRG_NAME, "No (re) rooting was performed." );
+ ForesterUtil.programMessage( PRG_NAME, "Duplications in tree: " + sdiunrooted.getMinimalDuplications() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Time requirement (minus I/O) : "
+ + time_req + "ms" );
+ for( int i = 0; i < result_trees.length; ++i ) {
+ final String name = result_trees[ i ].getName();
+ if ( ForesterUtil.isEmpty( name ) ) {
+ result_trees[ i ].setName( "SDIR result [gene tree + " + gene_tree_counter + "]" + " " + i );
+ }
+ else {
+ result_trees[ i ].setName( name + " SDIR result [gene tree + " + gene_tree_counter + "]" + " " + i );
+ }
+ all_result_trees.add( result_trees[ i ] );
+ }
+ ++gene_tree_counter;
+ } // for( final Phylogeny gene_tree : gene_trees )
+ try {
+ final PhylogenyWriter w = new PhylogenyWriter();
+ w.toPhyloXML( outfile, all_result_trees, 0, ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failure to write output to [" + outfile + "]: "
+ + e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Wrote: " + outfile );
+ ForesterUtil.programMessage( PRG_NAME, "OK." );
+ }
+
+ private static void printHelp() {
+ System.out.println( "Usage: " + PRG_NAME
+ + " <options> <gene tree(s) in phyloXML format> <species tree in phyloXML format>\"" );
+ System.out.println( "\nOptions:" );
+ System.out.println( " -" + MIN_MAPPING_COST_OPTION
+ + " to root by minimizing the mapping cost L (and also the sum of duplications)" );
+ System.out.println( " -" + MIN_DUPS_OPTION + " to root by minimizing the sum of duplications" );
+ System.out.println( " -" + MIN_HEIGHT_OPTION
+ + " to root by minimizing tree height (can be used together with -" + MIN_MAPPING_COST_OPTION + " or -"
+ + MIN_DUPS_OPTION + ")" );
+ System.out.println( "" );
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.FilenameFilter;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.forester.io.parsers.phyloxml.PhyloXmlParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.Shin;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class shin {
+
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String DEFAULT_OUTFILE = "out";
+ final static private String PRG_NAME = "shin";
+ final static private String PRG_VERSION = "0.001 alpha";
+ final static private String PRG_DATE = "2009.10.14";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE );
+ System.out.println();
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
+ System.out.println();
+ print_help();
+ System.exit( 0 );
+ }
+ else if ( ( args.length != 3 ) ) {
+ System.out.println();
+ System.out.println( "wrong number of arguments" );
+ System.out.println();
+ print_help();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ File gene_trees_dir = null;
+ File species_trees_file = null;
+ //File out_file = null;
+ File out_dir = null;
+ Phylogeny[] species_trees = null;
+ try {
+ gene_trees_dir = cla.getFile( 0 );
+ species_trees_file = cla.getFile( 1 );
+ out_dir = cla.getFile( 2 );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
+ }
+ if ( ForesterUtil.isReadableFile( species_trees_file ) != null ) {
+ ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isReadableFile( species_trees_file ) );
+ }
+ if ( !gene_trees_dir.isDirectory() || !gene_trees_dir.canRead() ) {
+ ForesterUtil.fatalError( PRG_NAME, "cannot read gene trees from [" + gene_trees_dir + "]" );
+ }
+ // if ( ForesterUtil.isWritableFile( out_file ) != null ) {
+ // ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
+ // }
+ if ( !out_dir.exists() ) {
+ boolean success = false;
+ try {
+ success = out_dir.mkdir();
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to create [" + out_dir + "] [" + e.getMessage() + "]" );
+ }
+ if ( !success ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to create [" + out_dir + "]" );
+ }
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ species_trees = factory.create( species_trees_file, new PhyloXmlParser() );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read species trees from [" + species_trees_file + "] ["
+ + e.getMessage() + "]" );
+ }
+ if ( ( species_trees == null ) || ( species_trees.length < 1 ) ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to read species trees from [" + species_trees_file + "]" );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "read in " + species_trees.length + " species trees from ["
+ + species_trees_file + "]" );
+ final FilenameFilter filter = new FilenameFilter() {
+
+ public boolean accept( final File dir, final String name ) {
+ return ( !name.startsWith( "." ) && !name.startsWith( "00_" ) && name.endsWith( ".xml" ) );
+ }
+ };
+ final String[] gene_tree_names = gene_trees_dir.list( filter );
+ Arrays.sort( gene_tree_names );
+ final List<File> gene_tree_files = new ArrayList<File>();
+ for( final String gene_tree_name : gene_tree_names ) {
+ final File gene_tree_file = new File( gene_trees_dir + ForesterUtil.FILE_SEPARATOR + gene_tree_name );
+ if ( !gene_tree_file.isDirectory() ) {
+ gene_tree_files.add( gene_tree_file );
+ }
+ }
+ ForesterUtil.programMessage( PRG_NAME, "going to analyze " + gene_tree_files.size() + " gene trees from ["
+ + gene_trees_dir + "]" );
+ final Shin shin = new Shin();
+ try {
+ shin.method1( gene_tree_files, species_trees, out_dir );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ e.printStackTrace();
+ }
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ // System.out.println();
+ // System.out.println( "Strip species tree: " + strip );
+ // SDI sdi = null;
+ // final long start_time = new Date().getTime();
+ // try {
+ // if ( use_sdise ) {
+ // System.out.println();
+ // System.out.println( "Using SDIse algorithm." );
+ // sdi = new SDIse( gene_tree, species_tree );
+ // }
+ // else {
+ // System.out.println();
+ // System.out.println( "Using GSDI algorithm." );
+ // System.out.println();
+ // System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
+ // sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model );
+ // }
+ // }
+ // catch ( final Exception e ) {
+ // ForesterUtil.unexpectedFatalError( PRG_NAME, e );
+ // }
+ // System.out.println();
+ // System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
+ // try {
+ // final PhylogenyWriter writer = new PhylogenyWriter();
+ // writer.toPhyloXML( out_file, gene_tree, 1 );
+ // }
+ // catch ( final IOException e ) {
+ // ForesterUtil.fatalError( PRG_NAME, "Failed to write to \"" + out_file + "\" [" + e.getMessage() + "]" );
+ // }
+ // System.out.println();
+ // System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
+ // System.out.println();
+ // System.out.println();
+ }
+
+ private static void print_help() {
+ System.out.println( "Usage: " + PRG_NAME + " [-options] <gene trees dir> <species tree file name> <outdir>" );
+ System.out.println();
+ System.out.println( "Options:" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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 org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.util.ForesterUtil;
+
+public class strip {
+
+ public static void main( final String args[] ) {
+ if ( args.length < 4 ) {
+ System.out.println( "\nstrip: Wrong number of arguments.\n" );
+ System.out
+ .println( "Usage: \"strip <infile> <outfile> <options> [name1] [name2] ... OR [phylogenyfile]\"\n" );
+ System.out.println( " Options: -k to keep listed nodes" );
+ System.out.println( " -r to remove listed nodes" );
+ System.out.println( " -kp to keep nodes found in [phylogenyfile]" );
+ System.out.println( " -rp to remove nodes found in [phylogenyfile]\n" );
+ System.exit( -1 );
+ }
+ final File infile = new File( args[ 0 ] );
+ final File outfile = new File( args[ 1 ] );
+ final String options = args[ 2 ];
+ Phylogeny p = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( infile, true );
+ p = factory.create( infile, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ System.out.println( "\nCould not read \"" + infile + "\" [" + e.getMessage() + "]\n" );
+ System.exit( -1 );
+ }
+ boolean keep = false;
+ boolean from_p0 = false;
+ if ( options.trim().toLowerCase().equals( "-k" ) ) {
+ keep = true;
+ }
+ else if ( options.trim().toLowerCase().equals( "-kp" ) ) {
+ keep = true;
+ from_p0 = true;
+ }
+ else if ( options.trim().toLowerCase().equals( "-rp" ) ) {
+ from_p0 = true;
+ }
+ else if ( !options.trim().toLowerCase().equals( "-r" ) ) {
+ System.out.println( "\nUnknown option \"" + options + "\"\n" );
+ System.exit( -1 );
+ }
+ String[] names = null;
+ if ( from_p0 ) {
+ names = strip.readInNamesFromPhylogeny( args[ 3 ] );
+ }
+ else {
+ names = new String[ args.length - 3 ];
+ for( int i = 0; i < args.length - 3; ++i ) {
+ names[ i ] = args[ i + 3 ];
+ }
+ }
+ if ( keep ) {
+ PhylogenyMethods.deleteExternalNodesPositiveSelection( names, p );
+ }
+ else {
+ PhylogenyMethods.deleteExternalNodesNegativeSelection( names, p );
+ }
+ try {
+ final PhylogenyWriter w = new PhylogenyWriter();
+ w.toPhyloXML( outfile, p, 1 );
+ }
+ catch ( final IOException e ) {
+ System.out.println( "\nFailure to write output [" + e.getMessage() + "]\n" );
+ System.exit( -1 );
+ }
+ }
+
+ private static String[] readInNamesFromPhylogeny( final String file ) {
+ Phylogeny p0 = null;
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final File f = new File( file );
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( f, true );
+ p0 = factory.create( f, pp )[ 0 ];
+ }
+ catch ( final Exception e ) {
+ System.out.println( "\nCould not read \"" + file + "\" [" + e.getMessage() + "]\n" );
+ System.exit( -1 );
+ }
+ return p0.getAllExternalNodeNames();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.io.PrintWriter;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.BasicDescriptiveStatistics;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterUtil;
+
+public final class support_statistics {
+
+ final static private int PLACES = 2;
+ final static private String HELP_OPTION = "help";
+ final static private String OUTPUTFILE_OPTION = "o";
+ final static private String PRG_NAME = "support_statistics";
+ final static private String PRG_VERSION = "1.0";
+ final static private String PRG_DATE = "2008.08.29";
+
+ private static StringBuffer analyze( final File[] phylogenies_infiles, final Phylogeny[] phylogenies ) {
+ final DescriptiveStatistics[] dss = new DescriptiveStatistics[ phylogenies.length ];
+ for( int i = 0; i < phylogenies.length; i++ ) {
+ dss[ i ] = new BasicDescriptiveStatistics();
+ final Phylogeny p = phylogenies[ i ];
+ for( final PhylogenyNodeIterator iter = p.iteratorPostorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( !node.isRoot() && !node.isExternal() ) {
+ double s = PhylogenyMethods.getConfidenceValue( node );
+ if ( s < 0.0 ) {
+ s = 0.0;
+ }
+ dss[ i ].addValue( s );
+ }
+ }
+ }
+ DescriptiveStatistics dss_comp = null;
+ if ( dss.length > 2 ) {
+ dss_comp = new BasicDescriptiveStatistics();
+ for( final DescriptiveStatistics element : dss ) {
+ dss_comp.addValue( element.arithmeticMean() );
+ }
+ }
+ int max_length = 30;
+ for( int i = 0; i < phylogenies.length; i++ ) {
+ final int l = phylogenies_infiles[ i ].getName().length();
+ if ( l > max_length ) {
+ max_length = l;
+ }
+ }
+ final StringBuffer sb = new StringBuffer();
+ sb.append( "\t" + ForesterUtil.normalizeString( "name:", max_length, true, ' ' ) + "\t" );
+ sb.append( "median:" + "\t" );
+ sb.append( "mean:" + "\t" );
+ sb.append( "sd:" + "\t" );
+ sb.append( "min:" + "\t" );
+ sb.append( "max:" + "\t" );
+ sb.append( "n:" + "\t" );
+ if ( dss_comp != null ) {
+ sb.append( "\"z-score\":" );
+ }
+ sb.append( ForesterUtil.getLineSeparator() );
+ for( int i = 0; i < phylogenies.length; i++ ) {
+ sb.append( i + 1 + ":\t"
+ + ForesterUtil.normalizeString( phylogenies_infiles[ i ].getName(), max_length, true, ' ' ) + "\t" );
+ sb.append( ForesterUtil.round( dss[ i ].median(), support_statistics.PLACES ) + "\t" );
+ sb.append( ForesterUtil.round( dss[ i ].arithmeticMean(), support_statistics.PLACES ) + "\t" );
+ try {
+ sb.append( ForesterUtil.round( dss[ i ].sampleStandardDeviation(), support_statistics.PLACES ) + "\t" );
+ }
+ catch ( final ArithmeticException ex ) {
+ sb.append( "n/a\t" );
+ }
+ sb.append( ForesterUtil.round( dss[ i ].getMin(), support_statistics.PLACES ) + "\t" );
+ sb.append( ForesterUtil.round( dss[ i ].getMax(), support_statistics.PLACES ) + "\t" );
+ sb.append( dss[ i ].getN() + "\t" );
+ if ( dss_comp != null ) {
+ final double z_score = dss_comp.sampleStandardUnit( dss[ i ].arithmeticMean() );
+ sb.append( ForesterUtil.round( z_score, support_statistics.PLACES ) + "\t" );
+ }
+ sb.append( ForesterUtil.getLineSeparator() );
+ }
+ if ( dss_comp != null ) {
+ sb.append( ForesterUtil.getLineSeparator() );
+ sb.append( "\t" + ForesterUtil.normalizeString( "values for support means:", max_length, true, ' ' )
+ + "\t\t" );
+ sb.append( ForesterUtil.round( dss_comp.arithmeticMean(), support_statistics.PLACES ) + "\t" );
+ sb.append( ForesterUtil.round( dss_comp.sampleStandardDeviation(), support_statistics.PLACES ) + "\t" );
+ sb.append( ForesterUtil.round( dss_comp.getMin(), support_statistics.PLACES ) + "\t" );
+ sb.append( ForesterUtil.round( dss_comp.getMax(), support_statistics.PLACES ) + "\t" );
+ }
+ return sb;
+ }
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( support_statistics.PRG_NAME,
+ support_statistics.PRG_VERSION,
+ support_statistics.PRG_DATE );
+ if ( ( args.length < 1 ) ) {
+ System.out.println();
+ System.out.println( "wrong number of arguments" );
+ System.out.println();
+ support_statistics.printHelp();
+ System.exit( -1 );
+ }
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( support_statistics.HELP_OPTION ) ) {
+ System.out.println();
+ support_statistics.printHelp();
+ System.exit( 0 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( support_statistics.OUTPUTFILE_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( support_statistics.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ final File[] phylogenies_infiles = new File[ cla.getNumberOfNames() ];
+ for( int i = 0; i < phylogenies_infiles.length; ++i ) {
+ phylogenies_infiles[ i ] = cla.getFile( i );
+ }
+ File outfile = null;
+ if ( cla.isOptionSet( support_statistics.OUTPUTFILE_OPTION ) ) {
+ try {
+ outfile = new File( cla.getOptionValue( support_statistics.OUTPUTFILE_OPTION ) );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( support_statistics.PRG_NAME, "error in command line: " + e.getMessage() );
+ }
+ final String error = ForesterUtil.isWritableFile( outfile );
+ if ( error != null ) {
+ ForesterUtil.fatalError( support_statistics.PRG_NAME, error );
+ }
+ }
+ final Phylogeny[] phylogenies = new Phylogeny[ phylogenies_infiles.length ];
+ for( int i = 0; i < phylogenies_infiles.length; i++ ) {
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil
+ .createParserDependingOnFileType( phylogenies_infiles[ i ], true );
+ phylogenies[ i ] = factory.create( phylogenies_infiles[ i ], pp )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( support_statistics.PRG_NAME, "could not read \"" + phylogenies_infiles[ i ]
+ + "\": " + e.getMessage() );
+ }
+ }
+ final StringBuffer sb = support_statistics.analyze( phylogenies_infiles, phylogenies );
+ System.out.println();
+ System.out.println( sb );
+ System.out.println();
+ if ( outfile != null ) {
+ try {
+ final PrintWriter out = new PrintWriter( outfile );
+ out.println( sb );
+ out.flush();
+ out.close();
+ System.out.println( "wrote file: " + outfile );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( support_statistics.PRG_NAME, "failed to write output: " + e.getMessage() );
+ }
+ }
+ System.out.println( support_statistics.PRG_NAME + ": successfully completed" );
+ System.out.println();
+ }
+
+ private static void printHelp() {
+ System.out.println( "usage:" );
+ System.out.println();
+ System.out.println( support_statistics.PRG_NAME + " [-o=<outfile>] <phylogeny infile 1> "
+ + "<phylogeny infile 2> <phylogeny infile 3> ..." );
+ System.out.println();
+ System.out.println( " options: " );
+ System.out.println();
+ System.out.println( " -o=<outfile> : write output to file" );
+ System.out.println();
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.io.parsers.PhylogenyParser;
+import org.forester.io.parsers.nhx.NHXParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.util.ForesterUtil;
+
+public final class support_transfer {
+
+ /**
+ * Transfers branch length values from one Phylogeny to another. It is
+ * mainly a "main method" for method "copyBranchLengthValuesFrom( Phylogeny )"
+ * of org.forester.phylogeny.Phylogeny, to be used in other (Perl) programs.
+ *
+ * @param args[0]
+ * Filename (String) for Phylogeny which has correct branch
+ * length values
+ * @param args[1]
+ * String Filename (String) for Phylogeny to which the branch
+ * lengths of the first Phylogeny are to be copied, both Trees
+ * must only differ in their branch length values, i.e. topology
+ * and sequence names, etc. must be the same
+ * @param args[2]
+ * String Filename (String) for outputfile
+ * @param args[3]
+ * String [number of tree with correct bl to use in case treefile contains more than one, default 0]
+
+ */
+ public static void main( final String args[] ) {
+ Phylogeny phylogeny_w_bl = null; // Has correct branch lengths
+ Phylogeny phylogeny_w_support_vals = null; // Has bootsrap in the b.l.
+ // field (will be
+ // transferred
+ // to the bootstrap field by the Phylogeny constructor) or
+ // has regular boostraps (NHX, :B=...).
+ File infile_bl = null;
+ File infile_support_vals = null;
+ File outfile = null;
+ int index_of_tree_w_bl = 0;
+ if ( ( args.length != 3 ) && ( args.length != 4 ) ) {
+ System.err.println( "SupportTransfer: Wrong number" + " of arguments. Usage: \"java transfersBranchLenghts"
+ + " <treefile with correct b.l.> <treefile with bootstraps>" + "<outputfile> "
+ + "[number of tree with correct bl to use in case treefile contains more than one, default 0]\"" );
+ System.exit( -1 );
+ }
+ if ( args.length == 4 ) {
+ index_of_tree_w_bl = ( new Integer( args[ 3 ] ) ).intValue();
+ }
+ try {
+ infile_bl = new File( args[ 0 ] );
+ infile_support_vals = new File( args[ 1 ] );
+ outfile = new File( args[ 2 ] );
+ if ( outfile.exists() ) {
+ System.out.println( "transfersBranchLenghts: " + outfile.getAbsolutePath() + " does already exist." );
+ System.exit( -1 );
+ }
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp_bl = ForesterUtil.createParserDependingOnFileType( infile_bl, true );
+ final PhylogenyParser pp_s = ForesterUtil.createParserDependingOnFileType( infile_support_vals, true );
+ if ( pp_bl instanceof NHXParser ) {
+ ( ( NHXParser ) pp_bl ).setTaxonomyExtraction( ForesterUtil.TAXONOMY_EXTRACTION.YES );
+ }
+ phylogeny_w_bl = factory.create( infile_bl, pp_bl )[ index_of_tree_w_bl ];
+ phylogeny_w_support_vals = factory.create( infile_support_vals, pp_s )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ System.out.println( "SupportTransfer: Could not read tree(s): " + e );
+ System.exit( -1 );
+ }
+ try {
+ final double max_bs = PhylogenyMethods.getMaximumConfidenceValue( phylogeny_w_support_vals );
+ PhylogenyMethods.normalizeBootstrapValues( phylogeny_w_support_vals, max_bs, 100 );
+ support_transfer.transferSupportValues( phylogeny_w_support_vals, phylogeny_w_bl );
+ }
+ catch ( final IllegalArgumentException e ) {
+ System.out.println( e.getMessage() );
+ System.exit( -1 );
+ }
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( outfile, phylogeny_w_bl, 0 );
+ }
+ catch ( final IOException e ) {
+ System.out.println( "Failure to write phylogeny \'" + outfile + "\" [" + e.getMessage() + "]" );
+ System.exit( -1 );
+ }
+ }
+
+ /**
+ * Moves the values in the branch length field to the bootstrap field, for
+ * each PhylogenyNode of this Phylogeny. Converts a Phylogeny originating
+ * from a phylip treefile after bootstrapping and which therefore has its
+ * bootstrap values where the branch lenghts would be.
+ */
+ public final static void moveBranchLengthsToBootstrap( final Phylogeny p ) {
+ for( final PhylogenyNodeIterator iter = p.iteratorPreorder(); iter.hasNext(); ) {
+ final PhylogenyNode node = iter.next();
+ if ( node.isInternal() && ( node.getDistanceToParent() > 0 ) ) {
+ PhylogenyMethods.setBootstrapConfidence( node, node.getDistanceToParent() );
+ }
+ else {
+ PhylogenyMethods.setBootstrapConfidence( node, Confidence.CONFIDENCE_DEFAULT_VALUE );
+ }
+ node.setDistanceToParent( PhylogenyNode.DISTANCE_DEFAULT );
+ }
+ } // moveBranchLengthsToBootstrap()
+
+ /**
+ * Modifies Phylogeny to with the support values from Phylogeny from.
+ * Important (but obvious): The topology of both trees needs to be the same.
+ * The method is not robust, and might produce wrong results if the internal
+ * topology differs or if the external node names are not unique.
+ *
+ * @param from
+ * the Phylogeny to copy the support values from
+ * @param to
+ * the Phylogeny to copy the support values to
+ */
+ public final static void transferSupportValues( final Phylogeny from, final Phylogeny to ) {
+ to: for( final PhylogenyNodeIterator it_to = to.iteratorPostorder(); it_to.hasNext(); ) {
+ final PhylogenyNode node_to = it_to.next();
+ if ( !node_to.isExternal() ) {
+ final List<String> ext_children_to = node_to.getAllExternalDescendantsNames();
+ for( final PhylogenyNodeIterator it_from = from.iteratorPostorder(); it_from.hasNext(); ) {
+ final PhylogenyNode node_from = it_from.next();
+ final List<String> ext_children_from = node_from.getAllExternalDescendantsNames();
+ if ( ( ext_children_from.size() == ext_children_to.size() )
+ && ext_children_from.containsAll( ext_children_to ) ) {
+ PhylogenyMethods.setBootstrapConfidence( node_to, PhylogenyMethods
+ .getConfidenceValue( node_from ) );
+ continue to;
+ }
+ }
+ final String message = "Attempt to transfer support values from nonidentical topologies";
+ throw new IllegalArgumentException( message );
+ }
+ }
+ }
+}
\ No newline at end of file
--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.forester.evoinference.matrix.character.CharacterStateMatrix;
+import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
+import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
+import org.forester.io.parsers.nexus.NexusCharactersParser;
+import org.forester.io.parsers.nexus.NexusPhylogeniesParser;
+import org.forester.io.parsers.nexus.PaupLogParser;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.surfacing.DomainParsimonyCalculator;
+import org.forester.surfacing.SurfacingUtil;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class surf_paup {
+
+ final static private String PRG_VERSION = "0.90";
+ final static private String PRG_DATE = "2008.03.28";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ private static final String PRG_NAME = "surf_paup";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE, E_MAIL, WWW );
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( HELP_OPTION_1 );
+ allowed_options.add( HELP_OPTION_2 );
+ if ( ( args.length < 2 ) ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
+ printHelp();
+ System.exit( 0 );
+ }
+ if ( cla.getNumberOfNames() != 3 ) {
+ printHelp();
+ System.exit( -1 );
+ }
+ final File surfacing_nexus_outfile = cla.getFile( 0 );
+ final File paup_log_file = cla.getFile( 1 );
+ final String outfile_name = cla.getFile( 2 ).toString();
+ final NexusCharactersParser nex_char_parser = new NexusCharactersParser();
+ try {
+ nex_char_parser.setSource( surfacing_nexus_outfile );
+ nex_char_parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "problem with parsing character labels from ["
+ + surfacing_nexus_outfile + "]: " + e.getMessage() );
+ e.printStackTrace();
+ }
+ final String[] labels = nex_char_parser.getCharStateLabels();
+ ForesterUtil.programMessage( PRG_NAME, "read in " + labels.length + " character labels" );
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final NexusPhylogeniesParser phylogeny_parser = new NexusPhylogeniesParser();
+ Phylogeny[] phylogenies = null;
+ try {
+ phylogenies = factory.create( surfacing_nexus_outfile, phylogeny_parser );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "problem with parsing phylogeny [" + surfacing_nexus_outfile + "]: "
+ + e.getMessage() );
+ e.printStackTrace();
+ }
+ if ( phylogenies.length != 1 ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to parse one phylogeny from [" + surfacing_nexus_outfile
+ + "], got " + phylogenies.length + " instead" );
+ }
+ final Phylogeny phylogeny = phylogenies[ 0 ];
+ if ( !phylogeny.isRooted() ) {
+ ForesterUtil.fatalError( PRG_NAME, "phylogeny from [" + surfacing_nexus_outfile + "] is not rooted" );
+ }
+ ForesterUtil.postOrderRelabelInternalNodes( phylogeny, phylogeny.getNumberOfExternalNodes() + 1 );
+ CharacterStateMatrix<BinaryStates> matrix = null;
+ final PaupLogParser paup_log_parser = new PaupLogParser();
+ try {
+ paup_log_parser.setSource( paup_log_file );
+ matrix = paup_log_parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to parse matrix from [" + paup_log_file + "]: "
+ + e.getMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "read in character state matrix of size "
+ + matrix.getNumberOfIdentifiers() + "x" + matrix.getNumberOfCharacters() );
+ final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( phylogeny );
+ domain_parsimony.executeOnGivenBinaryStatesMatrix( matrix, labels );
+ final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
+ SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(),
+ outfile_name + "_paup_gl",
+ Format.FORESTER );
+ SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(),
+ outfile_name + "_paup_glc",
+ Format.FORESTER );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.GAIN,
+ outfile_name + "_paup_gains",
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+ CharacterStateMatrix.GainLossStates.LOSS,
+ outfile_name + "_paup_losses",
+ sep,
+ ForesterUtil.LINE_SEPARATOR,
+ null );
+ SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
+ + "_paup_present", sep, ForesterUtil.LINE_SEPARATOR, null );
+ final String date_time = ForesterUtil.getCurrentDateTime();
+ SurfacingUtil.preparePhylogeny( phylogeny, domain_parsimony, date_time, "parsimony (paup)", "paup_"
+ + outfile_name, "" );
+ SurfacingUtil.writePhylogenyToFile( phylogeny, outfile_name + "_paup.xml" );
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ }
+
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out
+ .println( "% java -cp forester.jar org.forester.applications."
+ + PRG_NAME
+ + " <surfacing nexus outfile with character labels and tree> <paup log file with reconstructed states matrix> <outfile name base>" );
+ System.out.println();
+ }
+}
\ No newline at end of file
--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.go.GoId;
+import org.forester.go.GoNameSpace;
+import org.forester.go.GoTerm;
+import org.forester.go.GoUtils;
+import org.forester.go.OBOparser;
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+import org.forester.io.parsers.HmmscanPerDomainTableParser;
+import org.forester.io.parsers.HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.PhylogenyNode;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
+import org.forester.surfacing.BasicDomainSimilarityCalculator;
+import org.forester.surfacing.BasicGenomeWideCombinableDomains;
+import org.forester.surfacing.BasicSpecies;
+import org.forester.surfacing.BinaryDomainCombination;
+import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
+import org.forester.surfacing.DomainCountsDifferenceUtil;
+import org.forester.surfacing.DomainId;
+import org.forester.surfacing.DomainLengthsTable;
+import org.forester.surfacing.DomainParsimonyCalculator;
+import org.forester.surfacing.DomainSimilarity;
+import org.forester.surfacing.DomainSimilarityCalculator;
+import org.forester.surfacing.GenomeWideCombinableDomains;
+import org.forester.surfacing.MappingResults;
+import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.PairwiseGenomeComparator;
+import org.forester.surfacing.PrintableDomainSimilarity;
+import org.forester.surfacing.Protein;
+import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.Species;
+import org.forester.surfacing.SurfacingUtil;
+import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
+import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
+import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
+import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+
+public class surfacing {
+
+ public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out";
+ public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot";
+ public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc";
+ // gain/loss:
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc";
+ // gain/loss counts:
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc";
+ // tables:
+ // public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc";
+ // public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html";
+ // public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc";
+ // public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html";
+ // public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc";
+ // public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html";
+ // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d";
+ // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D = "_dollo_gains_goid_d";
+ // public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html";
+ // public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d";
+ //public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html";
+ // public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D = "_dollo_present_goid_d";
+ //public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html";
+ public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex";
+ public final static String BDC_PRESENT_NEXUS = "_dc.nex";
+ // ---
+ public final static String PRG_NAME = "surfacing";
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex";
+ public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex";
+ public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex";
+ public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features";
+ public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
+ public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String OUTPUT_DIR_OPTION = "out_dir";
+ final static private String SCORING_OPTION = "scoring";
+ private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ final static private String SCORING_DOMAIN_COUNT_BASED = "domains";
+ final static private String SCORING_PROTEIN_COUNT_BASED = "proteins";
+ final static private String SCORING_COMBINATION_BASED = "combinations";
+ final static private String DETAILEDNESS_OPTION = "detail";
+ private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ final static private String SPECIES_MATRIX_OPTION = "smatrix";
+ final static private String DETAILEDNESS_BASIC = "basic";
+ final static private String DETAILEDNESS_LIST_IDS = "list_ids";
+ final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious";
+ final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort";
+ private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ final static private String DOMAIN_SIMILARITY_SORT_MIN = "min";
+ final static private String DOMAIN_SIMILARITY_SORT_MAX = "max";
+ final static private String DOMAIN_SIMILARITY_SORT_SD = "sd";
+ final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean";
+ final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff";
+ final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species";
+ final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first";
+ final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort";
+ private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot";
+ final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb";
+ final static private String CUTOFF_SCORE_FILE_OPTION = "cos";
+ final static private String NOT_IGNORE_DUFS_OPTION = "dufs";
+ final static private String MAX_E_VALUE_OPTION = "e";
+ final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
+ final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
+ final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
+ final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
+ final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
+ final static private String OUTPUT_FILE_OPTION = "o";
+ final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g";
+ final static private String GO_OBO_FILE_USE_OPTION = "obo";
+ final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component";
+ final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output";
+ private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML;
+ final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains";
+ final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids";
+ final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false;
+ final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains";
+ final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false;
+ final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd";
+ final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd";
+ final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd";
+ final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String DISPLAY_M_HISTOGRAMS_OPTION = "mhisto";
+ // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false;
+ final static private String JACKNIFE_OPTION = "jack";
+ final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
+ final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
+ private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
+ final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
+ final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
+ //final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference";
+ final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh";
+ final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh";
+ final static private String FILTER_POSITIVE_OPTION = "pos_filter";
+ final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
+ final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
+ final static private String INPUT_FILES_FROM_FILE_OPTION = "input";
+ final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
+ final static private String SEQ_EXTRACT_OPTION = "prot_extract";
+ final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
+ final static private String PRG_VERSION = "2.003";
+ final static private String PRG_DATE = "2010.12.03";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
+ final static private boolean IGNORE_DUFS_DEFAULT = true;
+ final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
+ final static private double MAX_E_VALUE_DEFAULT = -1;
+ final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
+ final static private String DEFAULT_SEARCH_PARAMETER = "ls";
+ final private static boolean VERBOSE_DEFAULT = true;
+ private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
+ private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
+ private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
+ private static final String SEQ_EXTRACT_SUFFIX = ".prot";
+ private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
+ private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
+ private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
+ private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
+ private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
+ private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
+ private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
+ private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
+ private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
+ private static final boolean VERBOSE = false;
+ private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
+ private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
+ private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis";
+ private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true;
+ public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams";
+ public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation";
+ public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary";
+ public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains";
+ public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains";
+ public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc";
+ public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc";
+ public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS";
+ public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS";
+ public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities";
+ private static final String LOG_FILE_SUFFIX = "_log.txt";
+ private static final String DATA_FILE_SUFFIX = "_domain_combination_data.txt";
+ private static final String DATA_FILE_DESC = "#SPECIES\tPRTEIN_ID\tN_TERM_DOMAIN\tC_TERM_DOMAIN\tN_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tC_TERM_DOMAIN_PER_DOMAIN_E_VALUE\tN_TERM_DOMAIN_COUNTS_PER_PROTEIN\tC_TERM_DOMAIN_COUNTS_PER_PROTEIN";
+ private static final INDIVIDUAL_SCORE_CUTOFF INDIVIDUAL_SCORE_CUTOFF_DEFAULT = INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE;
+
+ // final String error = ForesterUtil.isReadableFile( new File(
+ // input_file_properties[ i ][ 0 ] ) );
+ // if ( !ForesterUtil.isEmpty( error ) ) {
+ // ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ // }
+ private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final String[][] input_file_properties,
+ final String automated_pairwise_comparison_suffix,
+ final File outdir ) {
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ final String species_i = input_file_properties[ i ][ 1 ];
+ final String species_j = input_file_properties[ j ][ 1 ];
+ String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
+ + species_j + automated_pairwise_comparison_suffix;
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+ pairwise_similarities_output_file_str += ".html";
+ }
+ break;
+ }
+ final String error = ForesterUtil
+ .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
+ + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
+ }
+ }
+ }
+
+ private static StringBuilder createParametersAsString( final boolean ignore_dufs,
+ final double e_value_max,
+ final int max_allowed_overlap,
+ final boolean no_engulfing_overlaps,
+ final File cutoff_scores_file,
+ final BinaryDomainCombination.DomainCombinationType dc_type ) {
+ final StringBuilder parameters_sb = new StringBuilder();
+ parameters_sb.append( "E-value: " + e_value_max );
+ if ( cutoff_scores_file != null ) {
+ parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+ }
+ else {
+ parameters_sb.append( ", Cutoff-scores-file: not-set" );
+ }
+ if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
+ }
+ else {
+ parameters_sb.append( ", Max-overlap: not-set" );
+ }
+ if ( no_engulfing_overlaps ) {
+ parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
+ }
+ else {
+ parameters_sb.append( ", Engulfing-overlaps: allowed" );
+ }
+ if ( ignore_dufs ) {
+ parameters_sb.append( ", Ignore-dufs: true" );
+ }
+ else {
+ parameters_sb.append( ", Ignore-dufs: false" );
+ }
+ parameters_sb.append( ", DC type (if applicable): " + dc_type );
+ return parameters_sb;
+ }
+
+ /**
+ * Warning: This sideeffects 'all_bin_domain_combinations_encountered'!
+ *
+ *
+ * @param output_file
+ * @param all_bin_domain_combinations_changed
+ * @param sum_of_all_domains_encountered
+ * @param all_bin_domain_combinations_encountered
+ * @param is_gains_analysis
+ * @throws IOException
+ */
+ private static void executeFitchGainsAnalysis( final File output_file,
+ final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
+ final int sum_of_all_domains_encountered,
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
+ final boolean is_gains_analysis ) throws IOException {
+ SurfacingUtil.checkForOutputFileWriteability( output_file );
+ final Writer out = ForesterUtil.createBufferedWriter( output_file );
+ final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
+ .listToSortedCountsMap( all_bin_domain_combinations_changed );
+ final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
+ final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
+ int above_one = 0;
+ int one = 0;
+ for( final Object bdc_object : bdc_to_counts.keySet() ) {
+ final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
+ final int count = bdc_to_counts.get( bdc_object );
+ if ( count < 1 ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
+ }
+ out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ if ( count > 1 ) {
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
+ above_one++;
+ }
+ else if ( count == 1 ) {
+ all_domains_in_combination_changed_only_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_only_once.add( bdc.getId1() );
+ one++;
+ }
+ }
+ final int all = all_bin_domain_combinations_encountered.size();
+ int never_lost = -1;
+ if ( !is_gains_analysis ) {
+ all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
+ never_lost = all_bin_domain_combinations_encountered.size();
+ for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
+ out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ if ( is_gains_analysis ) {
+ out.write( "Sum of all distinct domain combinations appearing once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ out.write( "Sum of all distinct domain combinations never lost : " + never_lost
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ out.write( "All binary combinations : " + all
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "All domains : "
+ + sum_of_all_domains_encountered );
+ out.close();
+ ForesterUtil.programMessage( surfacing.PRG_NAME,
+ "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
+ + "\"" );
+ }
+
+ private static void executePlusMinusAnalysis( final File output_file,
+ final List<String> plus_minus_analysis_high_copy_base,
+ final List<String> plus_minus_analysis_high_copy_target,
+ final List<String> plus_minus_analysis_low_copy,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final List<Object> plus_minus_analysis_numbers ) {
+ final Set<String> all_spec = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_spec.add( gwcd.getSpecies().getSpeciesId() );
+ }
+ final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
+ final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
+ final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
+ final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
+ final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
+ final File proteins_file_base = new File( output_file + "" );
+ final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
+ final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
+ try {
+ DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
+ protein_lists_per_species,
+ plus_minus_analysis_high_copy_base,
+ plus_minus_analysis_high_copy_target,
+ plus_minus_analysis_low_copy,
+ min_diff,
+ factor,
+ plain_out_dom,
+ html_out_dom,
+ html_out_dc,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ all_domains_go_ids_out_dom,
+ passing_domains_go_ids_out_dom,
+ proteins_file_base );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + html_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + plain_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
+ + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
+ + passing_domains_go_ids_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
+ + all_domains_go_ids_out_dom + "\"" );
+ }
+
+ private static Phylogeny[] getIntrees( final File[] intree_files,
+ final int number_of_genomes,
+ final String[][] input_file_properties ) {
+ final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
+ int i = 0;
+ for( final File intree_file : intree_files ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
+ + error );
+ }
+ try {
+ final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
+ .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
+ if ( p_array.length < 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ + "] does not contain any phylogeny in phyloXML format" );
+ }
+ else if ( p_array.length > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+ + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = p_array[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
+ + "]: " + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "number of external nodes ["
+ + intree.getNumberOfExternalNodes() + "] of input tree [" + intree_file
+ + "] is smaller than the number of genomes the be analyzed [" + number_of_genomes + "]" );
+ }
+ final StringBuilder parent_names = new StringBuilder();
+ final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
+ if ( nodes_lacking_name > 0 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
+ + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
+ }
+ preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
+ if ( !intree.isCompletelyBinary() ) {
+ ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
+ + "] is not completely binary" );
+ }
+ intrees[ i++ ] = intree;
+ }
+ return intrees;
+ }
+
+ private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
+ final NeighborJoining nj = NeighborJoining.createInstance();
+ final List<Phylogeny> phylogenies = nj.execute( distances_list );
+ final PhylogenyWriter w = new PhylogenyWriter();
+ try {
+ w.toNewHampshire( phylogenies, true, true, outfile, ";" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
+ }
+ return phylogenies;
+ }
+
+ private static void log( final String msg, final Writer w ) {
+ try {
+ w.write( msg );
+ w.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ public static void main( final String args[] ) {
+ final long start_time = new Date().getTime();
+ // final StringBuffer log = new StringBuffer();
+ final StringBuilder html_desc = new StringBuilder();
+ ForesterUtil.printProgramInformation( surfacing.PRG_NAME,
+ surfacing.PRG_VERSION,
+ surfacing.PRG_DATE,
+ surfacing.E_MAIL,
+ surfacing.WWW );
+ final String nl = ForesterUtil.LINE_SEPARATOR;
+ html_desc.append( "<table>" + nl );
+ html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing.PRG_NAME + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Version:</td><td>" + surfacing.PRG_VERSION + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing.PRG_DATE + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Contact:</td><td>" + surfacing.E_MAIL + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>WWW:</td><td>" + surfacing.WWW + "</td></tr>" + nl );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( surfacing.HELP_OPTION_1 ) || cla.isOptionSet( surfacing.HELP_OPTION_2 ) ) {
+ surfacing.printHelp();
+ System.exit( 0 );
+ }
+ if ( ( args.length < 1 ) ) {
+ surfacing.printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( surfacing.NOT_IGNORE_DUFS_OPTION );
+ allowed_options.add( surfacing.MAX_E_VALUE_OPTION );
+ allowed_options.add( surfacing.DETAILEDNESS_OPTION );
+ allowed_options.add( surfacing.OUTPUT_FILE_OPTION );
+ allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_OPTION );
+ allowed_options.add( surfacing.SPECIES_MATRIX_OPTION );
+ allowed_options.add( surfacing.SCORING_OPTION );
+ allowed_options.add( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
+ allowed_options.add( surfacing.NO_ENGULFING_OVERLAP_OPTION );
+ allowed_options.add( surfacing.DOMAIN_COUNT_SORT_OPTION );
+ allowed_options.add( surfacing.CUTOFF_SCORE_FILE_OPTION );
+ allowed_options.add( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
+ allowed_options.add( surfacing.OUTPUT_DIR_OPTION );
+ allowed_options.add( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION );
+ allowed_options.add( surfacing.PFAM_TO_GO_FILE_USE_OPTION );
+ allowed_options.add( surfacing.GO_OBO_FILE_USE_OPTION );
+ allowed_options.add( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION );
+ allowed_options.add( surfacing.GO_NAMESPACE_LIMIT_OPTION );
+ allowed_options.add( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
+ allowed_options.add( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
+ allowed_options.add( surfacing.DISPLAY_M_HISTOGRAMS_OPTION );
+ allowed_options.add( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
+ allowed_options.add( JACKNIFE_OPTION );
+ allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
+ allowed_options.add( JACKNIFE_RATIO_OPTION );
+ allowed_options.add( INPUT_SPECIES_TREE_OPTION );
+ //allowed_options.add( INFER_SPECIES_TREES_OPTION );
+ allowed_options.add( FILTER_POSITIVE_OPTION );
+ allowed_options.add( FILTER_NEGATIVE_OPTION );
+ allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
+ allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
+ allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
+ allowed_options.add( IGNORE_VIRAL_IDS );
+ allowed_options.add( SEQ_EXTRACT_OPTION );
+ allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
+ allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
+ allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
+ allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
+ allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
+ boolean ignore_dufs = surfacing.IGNORE_DUFS_DEFAULT;
+ boolean ignore_combination_with_same = surfacing.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
+ double e_value_max = surfacing.MAX_E_VALUE_DEFAULT;
+ int max_allowed_overlap = surfacing.MAX_ALLOWED_OVERLAP_DEFAULT;
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ boolean output_binary_domain_combinationsfor_graph_analysis = false;
+ if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
+ output_binary_domain_combinationsfor_graph_analysis = true;
+ }
+ if ( cla.isOptionSet( surfacing.MAX_E_VALUE_OPTION ) ) {
+ try {
+ e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_E_VALUE_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for E-value maximum" );
+ }
+ }
+ if ( cla.isOptionSet( surfacing.MAX_ALLOWED_OVERLAP_OPTION ) ) {
+ try {
+ max_allowed_overlap = cla.getOptionValueAsInt( surfacing.MAX_ALLOWED_OVERLAP_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for maximal allowed domain overlap" );
+ }
+ }
+ boolean no_engulfing_overlaps = false;
+ if ( cla.isOptionSet( surfacing.NO_ENGULFING_OVERLAP_OPTION ) ) {
+ no_engulfing_overlaps = true;
+ }
+ boolean ignore_virus_like_ids = false;
+ if ( cla.isOptionSet( surfacing.IGNORE_VIRAL_IDS ) ) {
+ ignore_virus_like_ids = true;
+ }
+ if ( cla.isOptionSet( surfacing.NOT_IGNORE_DUFS_OPTION ) ) {
+ ignore_dufs = false;
+ }
+ if ( cla.isOptionSet( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
+ ignore_combination_with_same = true;
+ }
+ boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
+ if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
+ ignore_domains_without_combs_in_all_spec = true;
+ }
+ boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
+ if ( cla.isOptionSet( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
+ ignore_species_specific_domains = true;
+ }
+ File output_file = null;
+ if ( cla.isOptionSet( surfacing.OUTPUT_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.OUTPUT_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "no value for domain combinations similarities output file: -"
+ + surfacing.OUTPUT_FILE_OPTION + "=<file>" );
+ }
+ output_file = new File( cla.getOptionValue( surfacing.OUTPUT_FILE_OPTION ) );
+ SurfacingUtil.checkForOutputFileWriteability( output_file );
+ }
+ File cutoff_scores_file = null;
+ Map<String, Double> individual_score_cutoffs = null;
+ if ( cla.isOptionSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.CUTOFF_SCORE_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for individual domain score cutoffs file: -"
+ + surfacing.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
+ }
+ cutoff_scores_file = new File( cla.getOptionValue( surfacing.CUTOFF_SCORE_FILE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read individual domain score cutoffs file: "
+ + error );
+ }
+ try {
+ final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
+ individual_score_cutoffs = scores_table.getColumnsAsMapDouble( 0, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from individual score cutoffs file: " + e );
+ }
+ }
+ BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
+ if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
+ dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
+ }
+ if ( cla.isOptionSet( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
+ dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
+ }
+ File out_dir = null;
+ if ( cla.isOptionSet( surfacing.OUTPUT_DIR_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.OUTPUT_DIR_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for output directory: -"
+ + surfacing.OUTPUT_DIR_OPTION + "=<dir>" );
+ }
+ out_dir = new File( cla.getOptionValue( surfacing.OUTPUT_DIR_OPTION ) );
+ if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
+ }
+ if ( !out_dir.exists() ) {
+ final boolean success = out_dir.mkdir();
+ if ( !success || !out_dir.exists() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to create \"" + out_dir + "\"" );
+ }
+ }
+ if ( !out_dir.canWrite() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
+ }
+ }
+ File positive_filter_file = null;
+ File negative_filter_file = null;
+ File negative_domains_filter_file = null;
+ if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) && cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use both negative and positive protein filter" );
+ }
+ if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION )
+ && ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) || cla
+ .isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) ) {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
+ }
+ if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative filter: -"
+ + surfacing.FILTER_NEGATIVE_OPTION + "=<file>" );
+ }
+ negative_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( negative_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
+ + msg );
+ }
+ }
+ else if ( cla.isOptionSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.FILTER_POSITIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for positive filter: -"
+ + surfacing.FILTER_POSITIVE_OPTION + "=<file>" );
+ }
+ positive_filter_file = new File( cla.getOptionValue( surfacing.FILTER_POSITIVE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( positive_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
+ + msg );
+ }
+ }
+ else if ( cla.isOptionSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for negative domains filter: -"
+ + surfacing.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
+ }
+ negative_domains_filter_file = new File( cla.getOptionValue( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + negative_domains_filter_file
+ + "\": " + msg );
+ }
+ }
+ final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
+ final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
+ final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
+ final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
+ processPlusMinusAnalysisOption( cla,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ plus_minus_analysis_numbers );
+ File input_files_file = null;
+ String[] input_file_names_from_file = null;
+ if ( cla.isOptionSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -"
+ + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ }
+ input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( input_files_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg );
+ }
+ try {
+ input_file_names_from_file = ForesterUtil.file2array( input_files_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e );
+ }
+ }
+ if ( ( cla.getNumberOfNames() < 1 )
+ && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "No hmmpfam output file indicated is input: use comand line directly or "
+ + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ }
+ DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
+ if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.SCORING_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "no value for scoring method for domain combinations similarity calculation: -"
+ + surfacing.SCORING_OPTION + "=<"
+ + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
+ + surfacing.SCORING_PROTEIN_COUNT_BASED + "|"
+ + surfacing.SCORING_COMBINATION_BASED + ">\"" );
+ }
+ final String scoring_str = cla.getOptionValue( surfacing.SCORING_OPTION );
+ if ( scoring_str.equals( surfacing.SCORING_DOMAIN_COUNT_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
+ }
+ else if ( scoring_str.equals( surfacing.SCORING_COMBINATION_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ }
+ else if ( scoring_str.equals( surfacing.SCORING_PROTEIN_COUNT_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + scoring_str
+ + "\" for scoring method for domain combinations similarity calculation: \"-"
+ + surfacing.SCORING_OPTION + "=<" + surfacing.SCORING_DOMAIN_COUNT_BASED + "|"
+ + surfacing.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing.SCORING_COMBINATION_BASED + ">\"" );
+ }
+ }
+ boolean sort_by_species_count_first = false;
+ if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
+ sort_by_species_count_first = true;
+ }
+ boolean species_matrix = false;
+ if ( cla.isOptionSet( surfacing.SPECIES_MATRIX_OPTION ) ) {
+ species_matrix = true;
+ }
+ boolean output_protein_lists_for_all_domains = false;
+ if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
+ output_protein_lists_for_all_domains = true;
+ }
+ Detailedness detailedness = DETAILEDNESS_DEFAULT;
+ if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.DETAILEDNESS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for -" + surfacing.DETAILEDNESS_OPTION + "=<"
+ + surfacing.DETAILEDNESS_BASIC + "|" + surfacing.DETAILEDNESS_LIST_IDS + "|"
+ + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
+ }
+ final String detness = cla.getOptionValue( surfacing.DETAILEDNESS_OPTION ).toLowerCase();
+ if ( detness.equals( surfacing.DETAILEDNESS_BASIC ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
+ }
+ else if ( detness.equals( surfacing.DETAILEDNESS_LIST_IDS ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
+ }
+ else if ( detness.equals( surfacing.DETAILEDNESS_PUNCTILIOUS ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + detness + "\" for detailedness: \"-"
+ + surfacing.DETAILEDNESS_OPTION + "=<" + surfacing.DETAILEDNESS_BASIC + "|"
+ + surfacing.DETAILEDNESS_LIST_IDS + "|" + surfacing.DETAILEDNESS_PUNCTILIOUS + ">\"" );
+ }
+ }
+ String automated_pairwise_comparison_suffix = null;
+ boolean perform_pwc = false;
+ boolean write_pwc_files = false;
+ if ( cla.isOptionSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
+ perform_pwc = true;
+ if ( !cla.isOptionValueSet( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
+ write_pwc_files = false;
+ }
+ else {
+ write_pwc_files = true;
+ automated_pairwise_comparison_suffix = "_"
+ + cla.getOptionValue( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
+ }
+ }
+ String query_domain_ids = null;
+ if ( cla.isOptionSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.SEQ_EXTRACT_OPTION ) ) {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "no domain ids given for sequences with given domains to be extracted : -"
+ + surfacing.SEQ_EXTRACT_OPTION
+ + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
+ }
+ query_domain_ids = cla.getOptionValue( surfacing.SEQ_EXTRACT_OPTION );
+ }
+ DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
+ DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
+ if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for domain combinations similarities sorting: -"
+ + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
+ + ">\"" );
+ }
+ final String sort_str = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
+ if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MAX ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MIN ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_SD ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ }
+ else if ( sort_str.equals( surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort_str
+ + "\" for domain combinations similarities sorting: \"-"
+ + surfacing.DOMAIN_SIMILARITY_SORT_OPTION + "=<" + surfacing.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_MAX + "|" + surfacing.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
+ + surfacing.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|" + surfacing.DOMAIN_SIMILARITY_SORT_SD
+ + ">\"" );
+ }
+ }
+ PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
+ if ( cla.isOptionSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for print option: -"
+ + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
+ }
+ final String sort = cla.getOptionValue( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
+ if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
+ domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
+ }
+ else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
+ // domain_similarity_print_option =
+ // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
+ }
+ else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
+ domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
+ + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ + surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
+ }
+ }
+ GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
+ if ( cla.isOptionSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.DOMAIN_COUNT_SORT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for sorting of domain counts: -"
+ + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|"
+ + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
+ }
+ final String sort = cla.getOptionValue( surfacing.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
+ if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_ALPHA ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ }
+ else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
+ }
+ else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
+ }
+ else if ( sort.equals( surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + sort
+ + "\" for sorting of domain counts: \"-" + surfacing.DOMAIN_COUNT_SORT_OPTION + "=<"
+ + surfacing.DOMAIN_COUNT_SORT_ALPHA + "|" + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ + surfacing.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
+ }
+ }
+ String[][] input_file_properties = null;
+ if ( input_file_names_from_file != null ) {
+ input_file_properties = surfacing.processInputFileNames( input_file_names_from_file );
+ }
+ else {
+ input_file_properties = surfacing.processInputFileNames( cla.getNames() );
+ }
+ final int number_of_genomes = input_file_properties.length;
+ if ( number_of_genomes < 2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot analyze less than two files" );
+ }
+ if ( ( number_of_genomes < 3 ) && perform_pwc ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use : -"
+ + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix> to turn on pairwise analyses with less than three input files" );
+ }
+ checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
+ input_file_properties,
+ automated_pairwise_comparison_suffix,
+ out_dir );
+ for( int i = 0; i < number_of_genomes; i++ ) {
+ File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
+ + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+ if ( out_dir != null ) {
+ dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
+ }
+ SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
+ }
+ File pfam_to_go_file = null;
+ Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
+ int domain_id_to_go_ids_count = 0;
+ if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
+ + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
+ }
+ pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
+ }
+ try {
+ final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
+ final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+ domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
+ if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
+ "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
+ }
+ domain_id_to_go_ids_count = parser.getMappingCount();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+ }
+ }
+ File go_obo_file = null;
+ List<GoTerm> go_terms = null;
+ if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
+ + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
+ }
+ if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
+ + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
+ + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
+ }
+ go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( go_obo_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
+ }
+ try {
+ final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
+ go_terms = parser.parse();
+ if ( parser.getGoTermCount() != go_terms.size() ) {
+ ForesterUtil
+ .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
+ }
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
+ }
+ }
+ Map<GoId, GoTerm> go_id_to_term_map = null;
+ if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
+ && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
+ go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
+ }
+ GoNameSpace go_namespace_limit = null;
+ if ( cla.isOptionSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
+ if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO namespace limit (-"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
+ + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
+ + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
+ }
+ if ( !cla.isOptionValueSet( surfacing.GO_NAMESPACE_LIMIT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO namespace limit: \"-"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
+ }
+ final String go_namespace_limit_str = cla.getOptionValue( surfacing.GO_NAMESPACE_LIMIT_OPTION )
+ .toLowerCase();
+ if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
+ go_namespace_limit = GoNameSpace.createMolecularFunction();
+ }
+ else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
+ go_namespace_limit = GoNameSpace.createBiologicalProcess();
+ }
+ else if ( go_namespace_limit_str.equals( surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
+ go_namespace_limit = GoNameSpace.createCellularComponent();
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "unknown value \"" + go_namespace_limit_str
+ + "\" for GO namespace limit: \"-" + surfacing.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ + surfacing.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
+ }
+ }
+ if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
+ && ( number_of_genomes > 2 ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ }
+ boolean jacknifed_distances = false;
+ int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
+ double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
+ long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
+ if ( cla.isOptionSet( surfacing.JACKNIFE_OPTION ) ) {
+ if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use jacknife resampling analysis (-"
+ + surfacing.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
+ + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix for pairwise comparison output files>)" );
+ }
+ jacknifed_distances = true;
+ if ( cla.isOptionHasAValue( surfacing.JACKNIFE_OPTION ) ) {
+ try {
+ jacknife_resamplings = cla.getOptionValueAsInt( surfacing.JACKNIFE_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for number of resamplings" );
+ }
+ if ( jacknife_resamplings < 2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use less than 2 resamplings" );
+ }
+ }
+ if ( cla.isOptionSet( surfacing.JACKNIFE_RATIO_OPTION )
+ && cla.isOptionHasAValue( surfacing.JACKNIFE_RATIO_OPTION ) ) {
+ try {
+ jacknife_ratio = cla.getOptionValueAsDouble( surfacing.JACKNIFE_RATIO_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for jacknife ratio" );
+ }
+ if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "attempt to use illegal value for jacknife ratio: "
+ + jacknife_ratio );
+ }
+ }
+ if ( cla.isOptionSet( surfacing.JACKNIFE_RANDOM_SEED_OPTION )
+ && cla.isOptionHasAValue( surfacing.JACKNIFE_RANDOM_SEED_OPTION ) ) {
+ try {
+ random_seed = cla.getOptionValueAsLong( surfacing.JACKNIFE_RANDOM_SEED_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for random generator seed" );
+ }
+ }
+ }
+ // boolean infer_species_trees = false;
+ // if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
+ // if ( ( output_file == null ) || ( number_of_genomes < 3 )
+ // || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
+ // ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
+ // + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
+ // + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ // + "=<suffix for pairwise comparison output files>)" );
+ // }
+ // infer_species_trees = true;
+ // }
+ File[] intree_files = null;
+ Phylogeny[] intrees = null;
+ if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
+ // TODO FIXME if jacknife.... maybe not
+ if ( number_of_genomes < 3 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer gains and losses on input species trees (-"
+ + surfacing.INPUT_SPECIES_TREE_OPTION + " without pairwise analyses ("
+ + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix for pairwise comparison output files>)" );
+ }
+ if ( !cla.isOptionValueSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input tree: -"
+ + surfacing.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
+ }
+ final String intrees_str = cla.getOptionValue( surfacing.INPUT_SPECIES_TREE_OPTION );
+ if ( intrees_str.indexOf( "#" ) > 0 ) {
+ final String[] intrees_strs = intrees_str.split( "#" );
+ intree_files = new File[ intrees_strs.length ];
+ int i = 0;
+ for( final String s : intrees_strs ) {
+ intree_files[ i++ ] = new File( s.trim() );
+ }
+ }
+ else {
+ intree_files = new File[ 1 ];
+ intree_files[ 0 ] = new File( intrees_str );
+ }
+ intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
+ }
+ long random_number_seed_for_fitch_parsimony = 0l;
+ boolean radomize_fitch_parsimony = false;
+ if ( cla.isOptionSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for random number seed: -"
+ + surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
+ }
+ try {
+ random_number_seed_for_fitch_parsimony = cla
+ .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ radomize_fitch_parsimony = true;
+ }
+ SortedSet<DomainId> filter = null;
+ if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
+ || ( negative_domains_filter_file != null ) ) {
+ filter = new TreeSet<DomainId>();
+ if ( positive_filter_file != null ) {
+ processFilter( positive_filter_file, filter );
+ }
+ else if ( negative_filter_file != null ) {
+ processFilter( negative_filter_file, filter );
+ }
+ else if ( negative_domains_filter_file != null ) {
+ processFilter( negative_domains_filter_file, filter );
+ }
+ }
+ Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
+ File[] secondary_features_map_files = null;
+ final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
+ if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
+ SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
+ }
+ if ( cla.isOptionSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
+ if ( !cla.isOptionValueSet( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for secondary features map file: -"
+ + surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
+ }
+ final String[] secondary_features_map_files_strs = cla
+ .getOptionValue( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
+ secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
+ domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
+ int i = 0;
+ for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
+ secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
+ final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: " + error );
+ }
+ try {
+ domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
+ .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read secondary features map file: "
+ + e.getMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "problem with contents of features map file ["
+ + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
+ }
+ i++;
+ }
+ }
+ if ( out_dir == null ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no output directory indicated (-"
+ + surfacing.OUTPUT_DIR_OPTION + "=<dir>)" );
+ }
+ if ( output_file == null ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no name for (main) output file indicated (-"
+ + surfacing.OUTPUT_FILE_OPTION + "=<file>)" );
+ }
+ if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
+ + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
+ }
+ if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
+ + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
+ }
+ boolean display_histograms = false;
+ if ( cla.isOptionSet( surfacing.DISPLAY_M_HISTOGRAMS_OPTION ) ) {
+ display_histograms = true;
+ }
+ System.out.println( "Output directory : " + out_dir );
+ if ( input_file_names_from_file != null ) {
+ System.out.println( "Input files names from : " + input_files_file + " ["
+ + input_file_names_from_file.length + " input files]" );
+ html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
+ + input_file_names_from_file.length + " input files]</td></tr>" + nl );
+ }
+ if ( positive_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
+ + " domain ids]</td></tr>" + nl );
+ }
+ if ( negative_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
+ + " domain ids]</td></tr>" + nl );
+ }
+ if ( negative_domains_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
+ + filter_size + " domain ids]</td></tr>" + nl );
+ }
+ if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
+ String plus0 = "";
+ for( final String s : plus_minus_analysis_high_copy_base_species ) {
+ plus0 += "+" + s + " ";
+ }
+ String plus1 = "";
+ for( final String s : plus_minus_analysis_high_copy_target_species ) {
+ plus1 += "*" + s + " ";
+ }
+ String minus = "";
+ for( final String s : plus_minus_analysis_high_low_copy_species ) {
+ minus += "-" + s + " ";
+ }
+ System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus );
+ html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
+ + "</td></tr>" + nl );
+ }
+ if ( cutoff_scores_file != null ) {
+ System.out.println( "Cutoff scores file : " + cutoff_scores_file );
+ html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
+ }
+ if ( e_value_max >= 0.0 ) {
+ System.out.println( "E-value maximum (inclusive) : " + e_value_max );
+ html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
+ }
+ System.out.println( "Ignore DUFs : " + ignore_dufs );
+ if ( ignore_virus_like_ids ) {
+ System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids );
+ html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
+ + ignore_virus_like_ids + "</td></tr>" + nl );
+ }
+ html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
+ if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ System.out.println( "Max allowed domain overlap : " + max_allowed_overlap );
+ html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
+ }
+ if ( no_engulfing_overlaps ) {
+ System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps );
+ html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
+ + "</td></tr>" + nl );
+ }
+ System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec );
+ html_desc
+ .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
+ + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
+ System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
+ html_desc
+ .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
+ + ignore_species_specific_domains + "</td></tr>" + nl );
+ System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
+ html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
+ + ignore_combination_with_same + "</td></tr>" + nl );
+ ;
+ System.out.println( "Consider directedness : "
+ + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
+ html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
+ + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
+ if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
+ System.out.println( "Consider adjacency : "
+ + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
+ html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
+ + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
+ + nl );
+ }
+ System.out.print( "Domain counts sort order : " );
+ switch ( dc_sort_order ) {
+ case ALPHABETICAL_KEY_ID:
+ System.out.println( "alphabetical" );
+ break;
+ case KEY_DOMAIN_COUNT:
+ System.out.println( "domain count" );
+ break;
+ case KEY_DOMAIN_PROTEINS_COUNT:
+ System.out.println( "domain proteins count" );
+ break;
+ case COMBINATIONS_COUNT:
+ System.out.println( "domain combinations count" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for dc sort order" );
+ }
+ if ( domain_id_to_go_ids_map != null ) {
+ System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
+ + " mappings]" );
+ html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
+ + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
+ }
+ if ( go_terms != null ) {
+ System.out.println( "GO terms from : " + go_obo_file + " [" + go_terms.size() + " terms]" );
+ html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
+ + "</td></tr>" + nl );
+ }
+ if ( go_namespace_limit != null ) {
+ System.out.println( "Limit GO terms to : " + go_namespace_limit.toString() );
+ html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
+ }
+ if ( perform_pwc ) {
+ System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix );
+ html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
+ + "</td></tr>" + nl );
+ }
+ if ( out_dir != null ) {
+ System.out.println( "Output directory : " + out_dir );
+ }
+ if ( query_domain_ids != null ) {
+ System.out.println( "Query domains (ordered) : " + query_domain_ids );
+ html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
+ }
+ System.out.println( "Write similarities to : " + output_file );
+ System.out.print( " Scoring method : " );
+ html_desc.append( "<tr><td>Scoring method:</td><td>" );
+ switch ( scoring ) {
+ case COMBINATIONS:
+ System.out.println( "domain combinations based" );
+ html_desc.append( "domain combinations based" + "</td></tr>" + nl );
+ break;
+ case DOMAINS:
+ System.out.println( "domain counts based" );
+ html_desc.append( "domain counts based" + "</td></tr>" + nl );
+ break;
+ case PROTEINS:
+ System.out.println( "domain proteins counts based" );
+ html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
+ }
+ System.out.print( " Sort by : " );
+ html_desc.append( "<tr><td>Sort by:</td><td>" );
+ switch ( domain_similarity_sort_field ) {
+ case MIN:
+ System.out.print( "score minimum" );
+ html_desc.append( "score minimum" );
+ break;
+ case MAX:
+ System.out.print( "score maximum" );
+ html_desc.append( "score maximum" );
+ break;
+ case MEAN:
+ System.out.print( "score mean" );
+ html_desc.append( "score mean" );
+ break;
+ case SD:
+ System.out.print( "score standard deviation" );
+ html_desc.append( "score standard deviation" );
+ break;
+ case SPECIES_COUNT:
+ System.out.print( "species number" );
+ html_desc.append( "species number" );
+ break;
+ case DOMAIN_ID:
+ System.out.print( "alphabetical domain identifier" );
+ html_desc.append( "alphabetical domain identifier" );
+ break;
+ case MAX_DIFFERENCE:
+ System.out.print( "(maximal) difference" );
+ html_desc.append( "(maximal) difference" );
+ break;
+ case ABS_MAX_COUNTS_DIFFERENCE:
+ System.out.print( "absolute (maximal) counts difference" );
+ html_desc.append( "absolute (maximal) counts difference" );
+ break;
+ case MAX_COUNTS_DIFFERENCE:
+ System.out.print( "(maximal) counts difference" );
+ html_desc.append( "(maximal) counts difference" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
+ }
+ if ( sort_by_species_count_first ) {
+ System.out.println( " (sort by species count first)" );
+ html_desc.append( " (sort by species count first)" );
+ }
+ else {
+ System.out.println();
+ }
+ html_desc.append( "</td></tr>" + nl );
+ System.out.print( " Detailedness : " );
+ switch ( detailedness ) {
+ case BASIC:
+ System.out.println( "basic" );
+ break;
+ case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
+ System.out.println( "list combining domains for each species" );
+ break;
+ case PUNCTILIOUS:
+ System.out.println( "punctilious" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for detailedness" );
+ }
+ System.out.print( " Print option : " );
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ System.out.println( "HTML" );
+ break;
+ case SIMPLE_TAB_DELIMITED:
+ System.out.println( "simple tab delimited" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for print option" );
+ }
+ System.out.print( " Species matrix : " + species_matrix );
+ System.out.println();
+ final File dc_data_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + DATA_FILE_SUFFIX );
+ System.out.println( "Domain comb data output : " + dc_data_file );
+ html_desc.append( "<tr><td>Domain combination data output:</td><td> " + dc_data_file + " </td></tr>" );
+ System.out.println();
+ if ( perform_pwc ) {
+ System.out.println( "Pairwise comparisons: " );
+ html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
+ System.out.print( " Sort by : " );
+ html_desc.append( "<tr><td>Sort by:</td><td>" );
+ switch ( domain_similarity_sort_field_for_automated_pwc ) {
+ case MEAN:
+ System.out.print( "score mean" );
+ html_desc.append( "score mean" );
+ break;
+ case DOMAIN_ID:
+ System.out.print( "alphabetical domain identifier" );
+ html_desc.append( "alphabetical domain identifier" );
+ break;
+ case MAX_DIFFERENCE:
+ System.out.print( "difference" );
+ html_desc.append( "difference" );
+ break;
+ case ABS_MAX_COUNTS_DIFFERENCE:
+ System.out.print( "absolute counts difference" );
+ html_desc.append( "absolute counts difference" );
+ break;
+ case MAX_COUNTS_DIFFERENCE:
+ System.out.print( "counts difference" );
+ html_desc.append( "counts difference" );
+ break;
+ default:
+ ForesterUtil
+ .unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for similarities" );
+ }
+ System.out.println();
+ html_desc.append( "</td></tr>" + nl );
+ if ( jacknifed_distances ) {
+ html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
+ html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
+ + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
+ System.out.println( " Jacknife : " + jacknife_resamplings + " resamplings" );
+ System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) );
+ System.out.println( " Random number seed : " + random_seed );
+ }
+ // if ( infer_species_trees ) {
+ // html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
+ // System.out.println( " Infer species trees : true" );
+ // }
+ if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
+ for( final File intree_file : intree_files ) {
+ html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
+ + "</td></tr>" + nl );
+ System.out.println( " Intree for gain/loss pars.: " + intree_file );
+ }
+ }
+ if ( radomize_fitch_parsimony ) {
+ html_desc.append( "<tr><td> Random number seed for Fitch parsimony analysis:</td><td>"
+ + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
+ System.out.println( " Random number seed : " + random_number_seed_for_fitch_parsimony );
+ }
+ if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
+ for( int i = 0; i < secondary_features_map_files.length; i++ ) {
+ html_desc.append( "<tr><td>Secondary features map file:</td><td>"
+ + secondary_features_map_files[ i ] + "</td></tr>" + nl );
+ System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
+ + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
+ if ( VERBOSE ) {
+ System.out.println();
+ System.out.println( "Domain ids to secondary features map:" );
+ for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
+ System.out.print( domain_id.getId() );
+ System.out.print( " => " );
+ for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
+ System.out.print( sec );
+ System.out.print( " " );
+ }
+ System.out.println();
+ }
+ }
+ }
+ }
+ } // if ( perform_pwc ) {
+ System.out.println();
+ html_desc.append( "<tr><td>Command line:</td><td>" + cla.getCommandLineArgsAsString() + "</td></tr>" + nl );
+ System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
+ BufferedWriter[] query_domains_writer_ary = null;
+ List<DomainId>[] query_domain_ids_array = null;
+ if ( query_domain_ids != null ) {
+ final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
+ query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
+ query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
+ for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
+ String query_domain_ids_str = query_domain_ids_str_array[ i ];
+ final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
+ final List<DomainId> query = new ArrayList<DomainId>();
+ for( final String element : query_domain_ids_str_ary ) {
+ query.add( new DomainId( element ) );
+ }
+ query_domain_ids_array[ i ] = query;
+ query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
+ String protein_names_writer_str = query_domain_ids_str + surfacing.SEQ_EXTRACT_SUFFIX;
+ if ( out_dir != null ) {
+ protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
+ }
+ try {
+ query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "Could not open [" + protein_names_writer_str + "]: "
+ + e.getLocalizedMessage() );
+ }
+ }
+ }
+ SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
+ boolean need_protein_lists_per_species = false;
+ if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
+ need_protein_lists_per_species = true;
+ }
+ if ( need_protein_lists_per_species ) {
+ protein_lists_per_species = new TreeMap<Species, List<Protein>>();
+ }
+ final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
+ final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
+ List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
+ List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
+ if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
+ all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
+ all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
+ }
+ final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
+ final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
+ + output_file + D_PROMISCUITY_FILE_SUFFIX );
+ BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
+ try {
+ per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
+ per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
+ + ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
+ }
+ final File log_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file + LOG_FILE_SUFFIX );
+ BufferedWriter log_writer = null;
+ try {
+ log_writer = new BufferedWriter( new FileWriter( log_file ) );
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
+ }
+ BufferedWriter dc_data_writer = null;
+ try {
+ dc_data_writer = new BufferedWriter( new FileWriter( dc_data_file ) );
+ dc_data_writer.write( DATA_FILE_DESC );
+ dc_data_writer.write( ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getMessage() );
+ }
+ for( int i = 0; i < number_of_genomes; ++i ) {
+ System.out.println();
+ System.out.println( ( i + 1 ) + "/" + number_of_genomes );
+ log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
+ System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] );
+ log( "Genome : " + input_file_properties[ i ][ 0 ], log_writer );
+ HmmscanPerDomainTableParser parser = null;
+ INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
+ if ( individual_score_cutoffs != null ) {
+ ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF_DEFAULT;
+ }
+ if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
+ || ( negative_domains_filter_file != null ) ) {
+ HmmscanPerDomainTableParser.FilterType filter_type = HmmscanPerDomainTableParser.FilterType.NONE;
+ if ( positive_filter_file != null ) {
+ filter_type = HmmscanPerDomainTableParser.FilterType.POSITIVE_PROTEIN;
+ }
+ else if ( negative_filter_file != null ) {
+ filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_PROTEIN;
+ }
+ else if ( negative_domains_filter_file != null ) {
+ filter_type = HmmscanPerDomainTableParser.FilterType.NEGATIVE_DOMAIN;
+ }
+ parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
+ input_file_properties[ i ][ 1 ],
+ filter,
+ filter_type,
+ ind_score_cutoff );
+ }
+ else {
+ parser = new HmmscanPerDomainTableParser( new File( input_file_properties[ i ][ 0 ] ),
+ input_file_properties[ i ][ 1 ],
+ ind_score_cutoff );
+ }
+ if ( e_value_max >= 0.0 ) {
+ parser.setEValueMaximum( e_value_max );
+ }
+ parser.setIgnoreDufs( ignore_dufs );
+ parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
+ parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
+ if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parser.setMaxAllowedOverlap( max_allowed_overlap );
+ }
+ parser
+ .setReturnType( HmmscanPerDomainTableParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
+ if ( individual_score_cutoffs != null ) {
+ parser.setIndividualScoreCutoffs( individual_score_cutoffs );
+ }
+ List<Protein> protein_list = null;
+ try {
+ protein_list = parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, e.getMessage(), e );
+ }
+ if ( VERBOSE ) {
+ System.out.println( "Domains ignored due to negative domain filter: " );
+ ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
+ System.out.println( "Domains ignored due to virus like id: " );
+ ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
+ }
+ System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
+ log( "Number of proteins encountered : " + parser.getProteinsEncountered(), log_writer );
+ System.out.println( "Number of proteins stored : " + protein_list.size() );
+ log( "Number of proteins stored : " + protein_list.size(), log_writer );
+ System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
+ log( "Domains encountered : " + parser.getDomainsEncountered(), log_writer );
+ System.out.println( "Domains stored : " + parser.getDomainsStored() );
+ log( "Domains stored : " + parser.getDomainsStored(), log_writer );
+ System.out.println( "Distinct domains stored : "
+ + parser.getDomainsStoredSet().size() );
+ log( "Distinct domains stored : " + parser.getDomainsStoredSet().size(), log_writer );
+ System.out.println( "Domains ignored due to individual score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
+ log( "Domains ignored due to individual score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff(), log_writer );
+ System.out.println( "Domains ignored due to E-value : "
+ + parser.getDomainsIgnoredDueToEval() );
+ log( "Domains ignored due to E-value : " + parser.getDomainsIgnoredDueToEval(), log_writer );
+ System.out.println( "Domains ignored due to DUF designation : "
+ + parser.getDomainsIgnoredDueToDuf() );
+ log( "Domains ignored due to DUF designation : " + parser.getDomainsIgnoredDueToDuf(), log_writer );
+ if ( ignore_virus_like_ids ) {
+ System.out.println( "Domains ignored due virus like ids : "
+ + parser.getDomainsIgnoredDueToVirusLikeIds() );
+ log( "Domains ignored due virus like ids : " + parser.getDomainsIgnoredDueToVirusLikeIds(),
+ log_writer );
+ }
+ System.out.println( "Domains ignored due negative domain filter : "
+ + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
+ log( "Domains ignored due negative domain filter : "
+ + parser.getDomainsIgnoredDueToNegativeDomainFilter(), log_writer );
+ System.out.println( "Domains ignored due to overlap : "
+ + parser.getDomainsIgnoredDueToOverlap() );
+ log( "Domains ignored due to overlap : " + parser.getDomainsIgnoredDueToOverlap(),
+ log_writer );
+ if ( negative_filter_file != null ) {
+ System.out.println( "Proteins ignored due to negative filter : "
+ + parser.getProteinsIgnoredDueToFilter() );
+ log( "Proteins ignored due to negative filter : " + parser.getProteinsIgnoredDueToFilter(),
+ log_writer );
+ }
+ if ( positive_filter_file != null ) {
+ System.out.println( "Proteins ignored due to positive filter : "
+ + parser.getProteinsIgnoredDueToFilter() );
+ log( "Proteins ignored due to positive filter : " + parser.getProteinsIgnoredDueToFilter(),
+ log_writer );
+ }
+ System.out.println( "Time for processing : " + parser.getTime() + "ms" );
+ log( "", log_writer );
+ html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
+ + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
+ + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
+ + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
+ + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
+ + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
+ + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
+ if ( negative_filter_file != null ) {
+ html_desc.append( "; proteins ignored due to negative filter: "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ if ( positive_filter_file != null ) {
+ html_desc.append( "; proteins ignored due to positive filter: "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ html_desc.append( "</td></tr>" + nl );
+ // domain_partner_counts_array[ i ] =
+ // Methods.getDomainPartnerCounts( protein_domain_collections_array[
+ // i ],
+ // false, input_file_properties[ i ][ 1 ] );
+ try {
+ int count = 0;
+ for( final Protein protein : protein_list ) {
+ dc_data_writer.write( SurfacingUtil.proteinToDomainCombinations( protein, count + "", "\t" )
+ .toString() );
+ ++count;
+ }
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
+ }
+ gwcd_list.add( BasicGenomeWideCombinableDomains
+ .createInstance( protein_list,
+ ignore_combination_with_same,
+ new BasicSpecies( input_file_properties[ i ][ 1 ] ),
+ domain_id_to_go_ids_map,
+ dc_type ) );
+ domain_lengths_table.addLengths( protein_list );
+ if ( gwcd_list.get( i ).getSize() > 0 ) {
+ SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
+ out_dir,
+ per_genome_domain_promiscuity_statistics_writer,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ if ( output_binary_domain_combinationsfor_graph_analysis ) {
+ SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
+ out_dir,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ }
+ SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
+ SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
+ all_bin_domain_combinations_encountered );
+ }
+ if ( query_domains_writer_ary != null ) {
+ for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ try {
+ SurfacingUtil.extractProteinNames( protein_list,
+ query_domain_ids_array[ j ],
+ query_domains_writer_ary[ j ],
+ "\t" );
+ query_domains_writer_ary[ j ].flush();
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
+ }
+ if ( need_protein_lists_per_species ) {
+ protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
+ }
+ try {
+ log_writer.flush();
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
+ }
+ System.gc();
+ } // for( int i = 0; i < number_of_genomes; ++i ) {
+ try {
+ per_genome_domain_promiscuity_statistics_writer.flush();
+ per_genome_domain_promiscuity_statistics_writer.close();
+ dc_data_writer.flush();
+ dc_data_writer.close();
+ log_writer.flush();
+ log_writer.close();
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e2.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ + per_genome_domain_promiscuity_statistics_file );
+ if ( query_domains_writer_ary != null ) {
+ for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ try {
+ query_domains_writer_ary[ j ].close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.toString() );
+ }
+ }
+ }
+ if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
+ try {
+ SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
+ number_of_genomes,
+ domain_lengths_table,
+ domain_lengths_analysis_outfile );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e1.toString() );
+ }
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
+ System.out.println();
+ }
+ final long analysis_start_time = new Date().getTime();
+ PairwiseDomainSimilarityCalculator pw_calc = null;
+ // double[] values_for_all_scores_histogram = null;
+ final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
+ sort_by_species_count_first,
+ number_of_genomes == 2 );
+ switch ( scoring ) {
+ case COMBINATIONS:
+ pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
+ break;
+ case DOMAINS:
+ pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
+ break;
+ case PROTEINS:
+ pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "unknown value for sorting for scoring" );
+ }
+ DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
+ if ( domain_id_to_go_ids_map != null ) {
+ go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
+ }
+ final SortedSet<DomainSimilarity> similarities = calc
+ .calculateSimilarities( pw_calc,
+ gwcd_list,
+ ignore_domains_without_combs_in_all_spec,
+ ignore_species_specific_domains );
+ SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
+ detailedness,
+ go_annotation_output,
+ go_id_to_term_map,
+ go_namespace_limit );
+ DescriptiveStatistics pw_stats = null;
+ try {
+ String my_outfile = output_file.toString();
+ if ( !my_outfile.endsWith( ".html" ) ) {
+ my_outfile += ".html";
+ }
+ final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir
+ + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
+ List<Species> species_order = null;
+ if ( species_matrix ) {
+ species_order = new ArrayList<Species>();
+ for( int i = 0; i < number_of_genomes; i++ ) {
+ species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
+ }
+ }
+ html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
+ + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
+ + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Analysis date/time:</td><td>"
+ + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
+ + "</td></tr>" + nl );
+ html_desc.append( "</table>" + nl );
+ pw_stats = SurfacingUtil
+ .writeDomainSimilaritiesToFile( html_desc,
+ new StringBuilder( number_of_genomes + " genomes" ),
+ writer,
+ similarities,
+ number_of_genomes == 2,
+ species_order,
+ domain_similarity_print_option,
+ domain_similarity_sort_field,
+ scoring,
+ true );
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote main output (includes domain similarities) to: \""
+ + ( out_dir == null ? my_outfile : out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "Failed to write similarites to: \"" + output_file + "\" ["
+ + e.getMessage() + "]" );
+ }
+ System.out.println();
+ // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
+ final Species[] species = new Species[ number_of_genomes ];
+ for( int i = 0; i < number_of_genomes; ++i ) {
+ species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
+ }
+ List<Phylogeny> inferred_trees = null;
+ if ( ( number_of_genomes > 2 ) && perform_pwc ) {
+ final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
+ pwgc.performPairwiseComparisons( html_desc,
+ sort_by_species_count_first,
+ detailedness,
+ ignore_domains_without_combs_in_all_spec,
+ ignore_species_specific_domains,
+ domain_similarity_sort_field_for_automated_pwc,
+ domain_similarity_print_option,
+ scoring,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ species,
+ number_of_genomes,
+ gwcd_list,
+ pw_calc,
+ automated_pairwise_comparison_suffix,
+ true,
+ surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
+ surfacing.PRG_NAME,
+ display_histograms,
+ out_dir,
+ write_pwc_files );
+ String matrix_output_file = new String( output_file.toString() );
+ if ( matrix_output_file.indexOf( '.' ) > 1 ) {
+ matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
+ }
+ if ( out_dir != null ) {
+ matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
+ output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
+ }
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances() );
+ final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc.getDomainDistanceScoresMeans()
+ .get( 0 ) );
+ final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
+ final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances().get( 0 ) );
+ inferred_trees = new ArrayList<Phylogeny>();
+ inferred_trees.add( nj_gd );
+ inferred_trees.add( nj_bc );
+ inferred_trees.add( nj_d );
+ // final List<HistogramData> histogram_datas = pwgc.getHistogramDatas();
+ // if ( infer_species_trees ) {
+ // inferred_trees = new ArrayList<Phylogeny>();
+ // final List<Phylogeny> inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedBinaryCombinationsBasedDistances() );
+ // final List<Phylogeny> inferred_trees_d = inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedDomainsBasedDistances() );
+ // inferred_trees.addAll( inferred_trees_bc );
+ // inferred_trees.addAll( inferred_trees_d );
+ // }
+ if ( jacknifed_distances ) {
+ pwgc.performPairwiseComparisonsJacknifed( species,
+ number_of_genomes,
+ gwcd_list,
+ true,
+ jacknife_resamplings,
+ jacknife_ratio,
+ random_seed );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ + surfacing.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ + surfacing.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances() );
+ // if ( infer_species_trees ) {
+ // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
+ // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedBinaryCombinationsBasedDistances() );
+ // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
+ // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
+ // }
+ }
+ if ( display_histograms ) {
+ // final List<HistogramData> histogram_datas_all = new ArrayList<HistogramData>();
+ // histogram_datas_all.add( new HistogramData( "all",
+ // values_for_all_scores_histogram,
+ // null,
+ // 20 ) );
+ // final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all );
+ // final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
+ // hf_all.setVisible( true );
+ // hf.setVisible( true );
+ }
+ } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
+ if ( ( out_dir != null ) && ( !perform_pwc ) ) {
+ output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
+ }
+ writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
+ final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ e_value_max,
+ max_allowed_overlap,
+ no_engulfing_overlaps,
+ cutoff_scores_file,
+ dc_type );
+ String s = "_";
+ if ( radomize_fitch_parsimony ) {
+ s += random_number_seed_for_fitch_parsimony + "_";
+ }
+ int i = 0;
+ for( final Phylogeny intree : intrees ) {
+ final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
+ + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
+ final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
+ gwcd_list );
+ SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
+ radomize_fitch_parsimony,
+ outfile_name,
+ domain_parsimony,
+ intree,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ parameters_sb.toString(),
+ domain_id_to_secondary_features_maps,
+ positive_filter_file == null ? null : filter,
+ output_binary_domain_combinationsfor_graph_analysis,
+ all_bin_domain_combinations_gained_fitch,
+ all_bin_domain_combinations_lost_fitch,
+ dc_type );
+ // Listing of all domain combinations gained is only done if only one input tree is used.
+ if ( ( domain_id_to_secondary_features_maps != null )
+ && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
+ int j = 0;
+ for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
+ final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
+ final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
+ .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
+ SurfacingUtil
+ .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
+ + "_"
+ + secondary_features_map_files[ j++ ],
+ secondary_features_parsimony,
+ intree,
+ parameters_sb.toString(),
+ mapping_results_map );
+ if ( i == 0 ) {
+ System.out.println();
+ System.out.println( "Mapping to secondary features:" );
+ for( final Species spec : mapping_results_map.keySet() ) {
+ final MappingResults mapping_results = mapping_results_map.get( spec );
+ final int total_domains = mapping_results.getSumOfFailures()
+ + mapping_results.getSumOfSuccesses();
+ System.out.print( spec + ":" );
+ System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
+ System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
+ if ( total_domains > 0 ) {
+ System.out.println( ", mapped ratio = "
+ + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" );
+ }
+ else {
+ System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
+ }
+ }
+ }
+ }
+ }
+ i++;
+ } // for( final Phylogeny intree : intrees ) {
+ }
+ if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
+ executePlusMinusAnalysis( output_file,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ gwcd_list,
+ protein_lists_per_species,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ plus_minus_analysis_numbers );
+ }
+ if ( output_protein_lists_for_all_domains ) {
+ writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list );
+ }
+ // if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) {
+ // final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ // e_value_max,
+ // max_allowed_overlap,
+ // no_engulfing_overlaps,
+ // cutoff_scores_file );
+ // String s = "_";
+ // if ( radomize_fitch_parsimony ) {
+ // s += random_number_seed_for_fitch_parsimony + "_";
+ // }
+ // int i = 0;
+ // for( final Phylogeny inferred_tree : inferred_trees ) {
+ // if ( !inferred_tree.isRooted() ) {
+ // intrees[ 0 ].getRoot().getName();
+ // inferred_tree.r
+ // }
+ // final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s;
+ // final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator
+ // .createInstance( inferred_tree, gwcd_list );
+ // SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
+ // radomize_fitch_parsimony,
+ // outfile_name,
+ // domain_parsimony,
+ // inferred_tree,
+ // domain_id_to_go_ids_map,
+ // go_id_to_term_map,
+ // go_namespace_limit,
+ // parameters_sb.toString() );
+ // i++;
+ // }
+ // }
+ if ( all_bin_domain_combinations_gained_fitch != null ) {
+ try {
+ executeFitchGainsAnalysis( new File( output_file
+ + surfacing.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_gained_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ true );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ if ( all_bin_domain_combinations_lost_fitch != null ) {
+ try {
+ executeFitchGainsAnalysis( new File( output_file
+ + surfacing.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_lost_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ false );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ final Runtime rt = java.lang.Runtime.getRuntime();
+ final long free_memory = rt.freeMemory() / 1000000;
+ final long total_memory = rt.totalMemory() / 1000000;
+ System.out.println();
+ System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" );
+ System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
+ System.out.println( "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" );
+ System.out.println();
+ System.out.println( "If this application is useful to you, please cite:" );
+ System.out.println( surfacing.WWW );
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println();
+ }
+
+ private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
+ final String[][] input_file_properties ) {
+ final String[] genomes = new String[ input_file_properties.length ];
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] is not unique in input tree " + intree.getName() );
+ }
+ genomes[ i ] = input_file_properties[ i ][ 1 ];
+ }
+ //
+ final PhylogenyNodeIterator it = intree.iteratorPostorder();
+ while ( it.hasNext() ) {
+ final PhylogenyNode n = it.next();
+ if ( ForesterUtil.isEmpty( n.getName() ) ) {
+ if ( n.getNodeData().isHasTaxonomy()
+ && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+ n.setName( n.getNodeData().getTaxonomy().getScientificName() );
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "node without both name and scientific taxonomy name found" );
+ }
+ }
+ }
+ //
+ final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
+ if ( igns.size() > 0 ) {
+ System.out.println( "Not using the following " + igns.size() + " nodes:" );
+ for( int i = 0; i < igns.size(); ++i ) {
+ System.out.println( " " + i + ": " + igns.get( i ) );
+ }
+ System.out.println( "--" );
+ }
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ try {
+ intree.getNode( input_file_properties[ i ][ 1 ] );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] not present/not unique in input tree" );
+ }
+ }
+ }
+
+ // public static StringBuffer stringCombinableDomainsMapToStringBuffer(
+ // final SortedMap<String, CombinableDomains> map ) {
+ // final StringBuffer sb = new StringBuffer();
+ // for( final Iterator<String> iter = map.keySet().iterator();
+ // iter.hasNext(); ) {
+ // final Object key = iter.next();
+ // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ',
+ // false ) );
+ // final CombinableDomains domain_combination = map.get( key );
+ // sb.append( ForesterUtil.pad( new StringBuffer( "" +
+ // domain_combination.getNumberOfCombiningDomains() ), 8,
+ // ' ', false ) );
+ // sb.append( domain_combination.toStringBuffer() );
+ // sb.append( ForesterUtil.getLineSeparator() );
+ // }
+ // return sb;
+ // }
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications." + surfacing.PRG_NAME
+ + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
+ System.out.println();
+ System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
+ System.out
+ .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
+ System.out.println();
+ System.out.println( " Options: " );
+ System.out.println( surfacing.DETAILEDNESS_OPTION + ": level of detail for similarities output file (default:"
+ + DETAILEDNESS_DEFAULT + ")" );
+ System.out.println( surfacing.IGNORE_COMBINATION_WITH_SAME_OPTION
+ + ": to ignore combinations with self (default: not to ignore)" );
+ System.out
+ .println( surfacing.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
+ + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
+ System.out
+ .println( surfacing.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
+ + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
+ System.out.println( surfacing.NOT_IGNORE_DUFS_OPTION
+ + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
+ System.out
+ .println( surfacing.IGNORE_VIRAL_IDS
+ + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
+ System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
+ + DOMAIN_SORT_FILD_DEFAULT + ")" );
+ System.out.println( surfacing.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
+ System.out.println( surfacing.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
+ System.out.println( surfacing.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
+ System.out.println( surfacing.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
+ System.out.println( surfacing.SPECIES_MATRIX_OPTION + ": species matrix" );
+ System.out.println( surfacing.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
+ System.out.println( surfacing.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
+ + DOMAINS_SORT_ORDER_DEFAULT + ")" );
+ System.out.println( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
+ + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
+ System.out.println( surfacing.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
+ System.out.println( surfacing.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
+ + ": sort by species count first" );
+ System.out.println( surfacing.OUTPUT_DIR_OPTION + ": output directory" );
+ System.out.println( surfacing.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
+ System.out.println( surfacing.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
+ System.out.println( surfacing.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
+ System.out.println( surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
+ System.out.println( surfacing.INPUT_SPECIES_TREE_OPTION
+ + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
+ System.out
+ .println( surfacing.DISPLAY_M_HISTOGRAMS_OPTION + ": to display multiple histograms (using fluorite)" );
+ System.out
+ .println( JACKNIFE_OPTION
+ + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
+ + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
+ System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
+ + JACKNIFE_RATIO_DEFAULT + "]" );
+ System.out.println( JACKNIFE_RANDOM_SEED_OPTION
+ + ": seed for random number generator for jacknife resampling [default: "
+ + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
+ // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
+ // + ": to infer NJ species trees based on shared domains/binary domain combinations" );
+ System.out
+ .println( surfacing.INPUT_SPECIES_TREE_OPTION
+ + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
+ System.out.println( surfacing.FILTER_POSITIVE_OPTION
+ + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
+ System.out.println( surfacing.FILTER_NEGATIVE_OPTION
+ + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
+ System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
+ + "=<file>: to filter out (ignore) domains listed in <file>" );
+ System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
+ System.out
+ .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
+ + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
+ System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
+ + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
+ System.out.println( surfacing.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
+ + ": to consider directedness and adjacency in binary combinations" );
+ System.out
+ .println( surfacing.SEQ_EXTRACT_OPTION
+ + "=<domain ids (Pfam names)>: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" );
+ System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
+ + "=<file>: to perfom parsimony analysis on secondary features" );
+ System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
+ System.out.println( surfacing.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
+ + ": to output binary domain combinations for (downstream) graph analysis" );
+ System.out.println( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
+ System.out.println();
+ System.out.println();
+ System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
+ + "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
+ + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
+ + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
+ + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
+ + "=50 human mouse brafl strpu" );
+ System.out.println();
+ }
+
+ private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
+ SortedSet<String> filter_str = null;
+ try {
+ filter_str = ForesterUtil.file2set( filter_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( filter_str != null ) {
+ for( final String string : filter_str ) {
+ filter.add( new DomainId( string ) );
+ }
+ }
+ if ( VERBOSE ) {
+ System.out.println( "Filter:" );
+ for( final DomainId domainId : filter ) {
+ System.out.println( domainId.getId() );
+ }
+ }
+ }
+
+ private static String[][] processInputFileNames( final String[] names ) {
+ final String[][] input_file_properties = new String[ names.length ][];
+ for( int i = 0; i < names.length; ++i ) {
+ if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
+ input_file_properties[ i ] = new String[ 2 ];
+ input_file_properties[ i ][ 0 ] = names[ i ];
+ input_file_properties[ i ][ 1 ] = names[ i ];
+ }
+ else {
+ input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" );
+ if ( input_file_properties[ i ].length != 3 ) {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "properties for the input files (hmmpfam output) are expected "
+ + "to be in the following format \"<hmmpfam output file>#<species>\" (or just one word, which is both the filename and the species id), instead received \""
+ + names[ i ] + "\"" );
+ }
+ }
+ final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ }
+ }
+ return input_file_properties;
+ }
+
+ private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
+ + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
+ }
+ final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( plus_minus_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
+ }
+ processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
+ }
+ }
+
+ // First numbers is minimal difference, second is factor.
+ private static void processPlusMinusFile( final File plus_minus_file,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ Set<String> species_set = null;
+ int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
+ double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
+ try {
+ species_set = ForesterUtil.file2set( plus_minus_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+ }
+ if ( species_set != null ) {
+ for( final String species : species_set ) {
+ final String species_trimmed = species.substring( 1 );
+ if ( species.startsWith( "+" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_base.add( species_trimmed );
+ }
+ else if ( species.startsWith( "*" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_target.add( species_trimmed );
+ }
+ else if ( species.startsWith( "-" ) ) {
+ if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ low_copy.add( species_trimmed );
+ }
+ else if ( species.startsWith( "$D" ) ) {
+ try {
+ min_diff = Integer.parseInt( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME,
+ "could not parse integer value for minimal difference from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "$F" ) ) {
+ try {
+ factor = Double.parseDouble( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "#" ) ) {
+ // Comment, ignore.
+ }
+ else {
+ ForesterUtil
+ .fatalError( surfacing.PRG_NAME,
+ "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
+ + species + "\"" );
+ }
+ numbers.add( new Integer( min_diff + "" ) );
+ numbers.add( new Double( factor + "" ) );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
+ }
+ }
+
+ private static void writePresentToNexus( final File output_file,
+ final File positive_filter_file,
+ final SortedSet<DomainId> filter,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ try {
+ SurfacingUtil
+ .writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
+ : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
+ SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
+ + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ private static void writeProteinListsForAllSpecies( final File output_dir,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_domains.addAll( gwcd.getAllDomainIds() );
+ }
+ for( final DomainId domain : all_domains ) {
+ final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
+ SurfacingUtil.checkForOutputFileWriteability( out );
+ try {
+ final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+ SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
+ proteins_file_writer.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+ }
+ }
+}
--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.go.GoId;
+import org.forester.go.GoNameSpace;
+import org.forester.go.GoTerm;
+import org.forester.go.GoUtils;
+import org.forester.go.OBOparser;
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+import org.forester.io.parsers.HmmPfamOutputParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.surfacing.BasicDomainSimilarityCalculator;
+import org.forester.surfacing.BasicGenomeWideCombinableDomains;
+import org.forester.surfacing.BasicSpecies;
+import org.forester.surfacing.BinaryDomainCombination;
+import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
+import org.forester.surfacing.DomainCountsDifferenceUtil;
+import org.forester.surfacing.DomainId;
+import org.forester.surfacing.DomainLengthsTable;
+import org.forester.surfacing.DomainParsimonyCalculator;
+import org.forester.surfacing.DomainSimilarity;
+import org.forester.surfacing.DomainSimilarityCalculator;
+import org.forester.surfacing.GenomeWideCombinableDomains;
+import org.forester.surfacing.MappingResults;
+import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.PairwiseGenomeComparator;
+import org.forester.surfacing.PrintableDomainSimilarity;
+import org.forester.surfacing.Protein;
+import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.Species;
+import org.forester.surfacing.SurfacingUtil;
+import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
+import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
+import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
+import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+
+public class surfacing_hmmpfam {
+
+ public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out";
+ public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot";
+ public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc";
+ // gain/loss:
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc";
+ // gain/loss counts:
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc";
+ // tables:
+ public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D = "_dollo_gains_goid_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D = "_dollo_present_goid_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html";
+ public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex";
+ public final static String BDC_PRESENT_NEXUS = "_dc.nex";
+ // ---
+ public final static String PRG_NAME = "surfacing";
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex";
+ public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex";
+ public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex";
+ public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features";
+ public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
+ public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String OUTPUT_DIR_OPTION = "out_dir";
+ final static private String SCORING_OPTION = "scoring";
+ private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ final static private String SCORING_DOMAIN_COUNT_BASED = "domains";
+ final static private String SCORING_PROTEIN_COUNT_BASED = "proteins";
+ final static private String SCORING_COMBINATION_BASED = "combinations";
+ final static private String DETAILEDNESS_OPTION = "detail";
+ private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ final static private String SPECIES_MATRIX_OPTION = "smatrix";
+ final static private String DETAILEDNESS_BASIC = "basic";
+ final static private String DETAILEDNESS_LIST_IDS = "list_ids";
+ final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious";
+ final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort";
+ private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ final static private String DOMAIN_SIMILARITY_SORT_MIN = "min";
+ final static private String DOMAIN_SIMILARITY_SORT_MAX = "max";
+ final static private String DOMAIN_SIMILARITY_SORT_SD = "sd";
+ final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean";
+ final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff";
+ final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species";
+ final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first";
+ final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort";
+ private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot";
+ final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb";
+ final static private String CUTOFF_SCORE_FILE_OPTION = "cos";
+ final static private String NOT_IGNORE_DUFS_OPTION = "dufs";
+ final static private String MAX_E_VALUE_OPTION = "e";
+ final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
+ final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
+ final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
+ final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
+ final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
+ final static private String OUTPUT_FILE_OPTION = "o";
+ final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g";
+ final static private String GO_OBO_FILE_USE_OPTION = "obo";
+ final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component";
+ final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output";
+ private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML;
+ final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains";
+ final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids";
+ final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false;
+ final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains";
+ final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false;
+ final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd";
+ final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd";
+ final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd";
+ final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String DISPLAY_M_HISTOGRAMS_OPTION = "mhisto";
+ // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false;
+ final static private String JACKNIFE_OPTION = "jack";
+ final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
+ final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
+ private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
+ final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
+ final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
+ //final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference";
+ final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh";
+ final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh";
+ final static private String FILTER_POSITIVE_OPTION = "pos_filter";
+ final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
+ final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
+ final static private String INPUT_FILES_FROM_FILE_OPTION = "input";
+ final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
+ final static private String SEQ_EXTRACT_OPTION = "prot_extract";
+ final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
+ final static private String PRG_VERSION = "1.00";
+ final static private String PRG_DATE = "2009.07.06";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
+ final static private boolean IGNORE_DUFS_DEFAULT = true;
+ final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
+ final static private double MAX_E_VALUE_DEFAULT = -1;
+ final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
+ final static private String DEFAULT_SEARCH_PARAMETER = "ls";
+ final private static boolean ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT = true;
+ final private static boolean VERBOSE_DEFAULT = true;
+ private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
+ private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
+ private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
+ private static final String SEQ_EXTRACT_SUFFIX = ".prot";
+ private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
+ private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
+ private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
+ private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
+ private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
+ private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
+ private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
+ private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
+ private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
+ private static final boolean VERBOSE = false;
+ private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
+ private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
+ private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis";
+ private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true;
+ public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams";
+ public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation";
+ public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary";
+ public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains";
+ public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains";
+ public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc";
+ public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc";
+ public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS";
+ public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS";
+ public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities";
+
+ // final String error = ForesterUtil.isReadableFile( new File(
+ // input_file_properties[ i ][ 0 ] ) );
+ // if ( !ForesterUtil.isEmpty( error ) ) {
+ // ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ // }
+ private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final String[][] input_file_properties,
+ final String automated_pairwise_comparison_suffix,
+ final File outdir ) {
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ final String species_i = input_file_properties[ i ][ 1 ];
+ final String species_j = input_file_properties[ j ][ 1 ];
+ String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
+ + species_j + automated_pairwise_comparison_suffix;
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+ pairwise_similarities_output_file_str += ".html";
+ }
+ break;
+ }
+ final String error = ForesterUtil
+ .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
+ + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, error );
+ }
+ }
+ }
+ }
+
+ private static StringBuilder createParametersAsString( final boolean ignore_dufs,
+ final double e_value_max,
+ final int max_allowed_overlap,
+ final boolean no_engulfing_overlaps,
+ final File cutoff_scores_file,
+ final BinaryDomainCombination.DomainCombinationType dc_type ) {
+ final StringBuilder parameters_sb = new StringBuilder();
+ parameters_sb.append( "E-value: " + e_value_max );
+ if ( cutoff_scores_file != null ) {
+ parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+ }
+ else {
+ parameters_sb.append( ", Cutoff-scores-file: not-set" );
+ }
+ if ( max_allowed_overlap != surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
+ }
+ else {
+ parameters_sb.append( ", Max-overlap: not-set" );
+ }
+ if ( no_engulfing_overlaps ) {
+ parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
+ }
+ else {
+ parameters_sb.append( ", Engulfing-overlaps: allowed" );
+ }
+ if ( ignore_dufs ) {
+ parameters_sb.append( ", Ignore-dufs: true" );
+ }
+ else {
+ parameters_sb.append( ", Ignore-dufs: false" );
+ }
+ parameters_sb.append( ", DC type (if applicable): " + dc_type );
+ return parameters_sb;
+ }
+
+ /**
+ * Warning: This sideeffects 'all_bin_domain_combinations_encountered'!
+ *
+ *
+ * @param output_file
+ * @param all_bin_domain_combinations_changed
+ * @param sum_of_all_domains_encountered
+ * @param all_bin_domain_combinations_encountered
+ * @param is_gains_analysis
+ * @throws IOException
+ */
+ private static void executeFitchGainsAnalysis( final File output_file,
+ final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
+ final int sum_of_all_domains_encountered,
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
+ final boolean is_gains_analysis ) throws IOException {
+ SurfacingUtil.checkForOutputFileWriteability( output_file );
+ final Writer out = ForesterUtil.createBufferedWriter( output_file );
+ final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
+ .listToSortedCountsMap( all_bin_domain_combinations_changed );
+ final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
+ final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
+ int above_one = 0;
+ int one = 0;
+ for( final Object bdc_object : bdc_to_counts.keySet() ) {
+ final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
+ final int count = bdc_to_counts.get( bdc_object );
+ if ( count < 1 ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
+ }
+ out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ if ( count > 1 ) {
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
+ above_one++;
+ }
+ else if ( count == 1 ) {
+ all_domains_in_combination_changed_only_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_only_once.add( bdc.getId1() );
+ one++;
+ }
+ }
+ final int all = all_bin_domain_combinations_encountered.size();
+ int never_lost = -1;
+ if ( !is_gains_analysis ) {
+ all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
+ never_lost = all_bin_domain_combinations_encountered.size();
+ for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
+ out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ if ( is_gains_analysis ) {
+ out.write( "Sum of all distinct domain combinations appearing once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ out.write( "Sum of all distinct domain combinations never lost : " + never_lost
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ out.write( "All binary combinations : " + all
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "All domains : "
+ + sum_of_all_domains_encountered );
+ out.close();
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
+ "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
+ + "\"" );
+ }
+
+ private static void executePlusMinusAnalysis( final File output_file,
+ final List<String> plus_minus_analysis_high_copy_base,
+ final List<String> plus_minus_analysis_high_copy_target,
+ final List<String> plus_minus_analysis_low_copy,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final List<Object> plus_minus_analysis_numbers ) {
+ final Set<String> all_spec = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_spec.add( gwcd.getSpecies().getSpeciesId() );
+ }
+ final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
+ final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
+ final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
+ final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
+ final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
+ final File proteins_file_base = new File( output_file + "" );
+ final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
+ final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
+ try {
+ DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
+ protein_lists_per_species,
+ plus_minus_analysis_high_copy_base,
+ plus_minus_analysis_high_copy_target,
+ plus_minus_analysis_low_copy,
+ min_diff,
+ factor,
+ plain_out_dom,
+ html_out_dom,
+ html_out_dc,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ all_domains_go_ids_out_dom,
+ passing_domains_go_ids_out_dom,
+ proteins_file_base );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + html_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + plain_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + html_out_dc + "\"" );
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
+ "Wrote plus minus domain analysis based passing GO ids to \""
+ + passing_domains_go_ids_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
+ "Wrote plus minus domain analysis based all GO ids to \""
+ + all_domains_go_ids_out_dom + "\"" );
+ }
+
+ private static Phylogeny[] getIntrees( final File[] intree_files,
+ final int number_of_genomes,
+ final String[][] input_file_properties ) {
+ final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
+ int i = 0;
+ for( final File intree_file : intree_files ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read input tree file [" + intree_file
+ + "]: " + error );
+ }
+ try {
+ final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
+ .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
+ if ( p_array.length < 1 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
+ + "] does not contain any phylogeny in phyloXML format" );
+ }
+ else if ( p_array.length > 1 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "file [" + intree_file
+ + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = p_array[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "failed to read input tree from file ["
+ + intree_file + "]: " + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "number of external nodes ["
+ + intree.getNumberOfExternalNodes() + "] of input tree [" + intree_file
+ + "] is smaller than the number of genomes the be analyzed [" + number_of_genomes + "]" );
+ }
+ final StringBuilder parent_names = new StringBuilder();
+ final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
+ if ( nodes_lacking_name > 0 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file + "] has "
+ + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
+ }
+ preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
+ if ( !intree.isCompletelyBinary() ) {
+ ForesterUtil.printWarningMessage( surfacing_hmmpfam.PRG_NAME, "input tree [" + intree_file
+ + "] is not completely binary" );
+ }
+ intrees[ i++ ] = intree;
+ }
+ return intrees;
+ }
+
+ private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
+ final NeighborJoining nj = NeighborJoining.createInstance();
+ final List<Phylogeny> phylogenies = nj.execute( distances_list );
+ final PhylogenyWriter w = new PhylogenyWriter();
+ try {
+ w.toNewHampshire( phylogenies, true, true, outfile, ";" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
+ }
+ return phylogenies;
+ }
+
+ public static void main( final String args[] ) {
+ final long start_time = new Date().getTime();
+ // final StringBuffer log = new StringBuffer();
+ final StringBuilder html_desc = new StringBuilder();
+ ForesterUtil.printProgramInformation( surfacing_hmmpfam.PRG_NAME,
+ surfacing_hmmpfam.PRG_VERSION,
+ surfacing_hmmpfam.PRG_DATE,
+ surfacing_hmmpfam.E_MAIL,
+ surfacing_hmmpfam.WWW );
+ final String nl = ForesterUtil.LINE_SEPARATOR;
+ html_desc.append( "<table>" + nl );
+ html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing_hmmpfam.PRG_NAME + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Version:</td><td>" + surfacing_hmmpfam.PRG_VERSION + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing_hmmpfam.PRG_DATE + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Contact:</td><td>" + surfacing_hmmpfam.E_MAIL + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>WWW:</td><td>" + surfacing_hmmpfam.WWW + "</td></tr>" + nl );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.HELP_OPTION_1 ) || cla.isOptionSet( surfacing_hmmpfam.HELP_OPTION_2 ) ) {
+ surfacing_hmmpfam.printHelp();
+ System.exit( 0 );
+ }
+ if ( ( args.length < 1 ) ) {
+ surfacing_hmmpfam.printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( surfacing_hmmpfam.NOT_IGNORE_DUFS_OPTION );
+ allowed_options.add( surfacing_hmmpfam.MAX_E_VALUE_OPTION );
+ allowed_options.add( surfacing_hmmpfam.DETAILEDNESS_OPTION );
+ allowed_options.add( surfacing_hmmpfam.OUTPUT_FILE_OPTION );
+ allowed_options.add( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION );
+ allowed_options.add( surfacing_hmmpfam.SPECIES_MATRIX_OPTION );
+ allowed_options.add( surfacing_hmmpfam.SCORING_OPTION );
+ allowed_options.add( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION );
+ allowed_options.add( surfacing_hmmpfam.NO_ENGULFING_OVERLAP_OPTION );
+ allowed_options.add( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION );
+ allowed_options.add( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION );
+ allowed_options.add( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
+ allowed_options.add( surfacing_hmmpfam.OUTPUT_DIR_OPTION );
+ allowed_options.add( surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_OPTION );
+ allowed_options.add( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION );
+ allowed_options.add( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION );
+ allowed_options.add( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION );
+ allowed_options.add( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION );
+ allowed_options.add( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
+ allowed_options.add( surfacing_hmmpfam.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
+ allowed_options.add( surfacing_hmmpfam.DISPLAY_M_HISTOGRAMS_OPTION );
+ allowed_options.add( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
+ allowed_options.add( JACKNIFE_OPTION );
+ allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
+ allowed_options.add( JACKNIFE_RATIO_OPTION );
+ allowed_options.add( INPUT_SPECIES_TREE_OPTION );
+ //allowed_options.add( INFER_SPECIES_TREES_OPTION );
+ allowed_options.add( FILTER_POSITIVE_OPTION );
+ allowed_options.add( FILTER_NEGATIVE_OPTION );
+ allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
+ allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
+ allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
+ allowed_options.add( IGNORE_VIRAL_IDS );
+ allowed_options.add( SEQ_EXTRACT_OPTION );
+ allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
+ allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
+ allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
+ allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
+ allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
+ boolean ignore_dufs = surfacing_hmmpfam.IGNORE_DUFS_DEFAULT;
+ boolean ignore_combination_with_same = surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
+ double e_value_max = surfacing_hmmpfam.MAX_E_VALUE_DEFAULT;
+ int max_allowed_overlap = surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT;
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ boolean output_binary_domain_combinationsfor_graph_analysis = false;
+ if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
+ output_binary_domain_combinationsfor_graph_analysis = true;
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.MAX_E_VALUE_OPTION ) ) {
+ try {
+ e_value_max = cla.getOptionValueAsDouble( surfacing_hmmpfam.MAX_E_VALUE_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no acceptable value for E-value maximum" );
+ }
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION ) ) {
+ try {
+ max_allowed_overlap = cla.getOptionValueAsInt( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no acceptable value for maximal allowed domain overlap" );
+ }
+ }
+ boolean no_engulfing_overlaps = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.NO_ENGULFING_OVERLAP_OPTION ) ) {
+ no_engulfing_overlaps = true;
+ }
+ boolean ignore_virus_like_ids = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_VIRAL_IDS ) ) {
+ ignore_virus_like_ids = true;
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.NOT_IGNORE_DUFS_OPTION ) ) {
+ ignore_dufs = false;
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
+ ignore_combination_with_same = true;
+ }
+ boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
+ ignore_domains_without_combs_in_all_spec = true;
+ }
+ boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
+ ignore_species_specific_domains = true;
+ }
+ File output_file = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.OUTPUT_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.OUTPUT_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no value for domain combinations similarities output file: -"
+ + surfacing_hmmpfam.OUTPUT_FILE_OPTION + "=<file>" );
+ }
+ output_file = new File( cla.getOptionValue( surfacing_hmmpfam.OUTPUT_FILE_OPTION ) );
+ SurfacingUtil.checkForOutputFileWriteability( output_file );
+ }
+ File cutoff_scores_file = null;
+ Map<String, String> individual_domain_score_cutoffs = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no value for individual domain score cutoffs file: -"
+ + surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
+ }
+ cutoff_scores_file = new File( cla.getOptionValue( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "cannot read individual domain score cutoffs file: " + error );
+ }
+ try {
+ final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
+ individual_domain_score_cutoffs = scores_table.getColumnsAsMap( 0, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "cannot read from individual domain score cutoffs file: " + e );
+ }
+ }
+ BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
+ if ( cla.isOptionSet( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
+ dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
+ dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
+ }
+ File out_dir = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.OUTPUT_DIR_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.OUTPUT_DIR_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for output directory: -"
+ + surfacing_hmmpfam.OUTPUT_DIR_OPTION + "=<dir>" );
+ }
+ out_dir = new File( cla.getOptionValue( surfacing_hmmpfam.OUTPUT_DIR_OPTION ) );
+ if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "\"" + out_dir
+ + "\" aready exists and is not empty" );
+ }
+ if ( !out_dir.exists() ) {
+ final boolean success = out_dir.mkdir();
+ if ( !success || !out_dir.exists() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "failed to create \"" + out_dir + "\"" );
+ }
+ }
+ if ( !out_dir.canWrite() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
+ }
+ }
+ File positive_filter_file = null;
+ File negative_filter_file = null;
+ File negative_domains_filter_file = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION )
+ && cla.isOptionSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "attempt to use both negative and positive protein filter" );
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION )
+ && ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) || cla
+ .isOptionSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) ) {
+ ForesterUtil
+ .fatalError( surfacing_hmmpfam.PRG_NAME,
+ "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for negative filter: -"
+ + surfacing_hmmpfam.FILTER_NEGATIVE_OPTION + "=<file>" );
+ }
+ negative_filter_file = new File( cla.getOptionValue( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( negative_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + negative_filter_file
+ + "\": " + msg );
+ }
+ }
+ else if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for positive filter: -"
+ + surfacing_hmmpfam.FILTER_POSITIVE_OPTION + "=<file>" );
+ }
+ positive_filter_file = new File( cla.getOptionValue( surfacing_hmmpfam.FILTER_POSITIVE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( positive_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + positive_filter_file
+ + "\": " + msg );
+ }
+ }
+ else if ( cla.isOptionSet( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for negative domains filter: -"
+ + surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
+ }
+ negative_domains_filter_file = new File( cla
+ .getOptionValue( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \""
+ + negative_domains_filter_file + "\": " + msg );
+ }
+ }
+ final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
+ final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
+ final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
+ final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
+ processPlusMinusAnalysisOption( cla,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ plus_minus_analysis_numbers );
+ File input_files_file = null;
+ String[] input_file_names_from_file = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for input files file: -"
+ + surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ }
+ input_files_file = new File( cla.getOptionValue( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( input_files_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + input_files_file + "\": "
+ + msg );
+ }
+ try {
+ input_file_names_from_file = ForesterUtil.file2array( input_files_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "failed to read from \"" + input_files_file
+ + "\": " + e );
+ }
+ }
+ if ( ( cla.getNumberOfNames() < 1 )
+ && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "No hmmpfam output file indicated is input: use comand line directly or "
+ + surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ }
+ DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.SCORING_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.SCORING_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no value for scoring method for domain combinations similarity calculation: -"
+ + surfacing_hmmpfam.SCORING_OPTION + "=<"
+ + surfacing_hmmpfam.SCORING_DOMAIN_COUNT_BASED + "|"
+ + surfacing_hmmpfam.SCORING_PROTEIN_COUNT_BASED + "|"
+ + surfacing_hmmpfam.SCORING_COMBINATION_BASED + ">\"" );
+ }
+ final String scoring_str = cla.getOptionValue( surfacing_hmmpfam.SCORING_OPTION );
+ if ( scoring_str.equals( surfacing_hmmpfam.SCORING_DOMAIN_COUNT_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
+ }
+ else if ( scoring_str.equals( surfacing_hmmpfam.SCORING_COMBINATION_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ }
+ else if ( scoring_str.equals( surfacing_hmmpfam.SCORING_PROTEIN_COUNT_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + scoring_str
+ + "\" for scoring method for domain combinations similarity calculation: \"-"
+ + surfacing_hmmpfam.SCORING_OPTION + "=<" + surfacing_hmmpfam.SCORING_DOMAIN_COUNT_BASED + "|"
+ + surfacing_hmmpfam.SCORING_PROTEIN_COUNT_BASED + "|"
+ + surfacing_hmmpfam.SCORING_COMBINATION_BASED + ">\"" );
+ }
+ }
+ boolean sort_by_species_count_first = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
+ sort_by_species_count_first = true;
+ }
+ boolean species_matrix = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.SPECIES_MATRIX_OPTION ) ) {
+ species_matrix = true;
+ }
+ boolean output_protein_lists_for_all_domains = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
+ output_protein_lists_for_all_domains = true;
+ }
+ Detailedness detailedness = DETAILEDNESS_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.DETAILEDNESS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.DETAILEDNESS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for -"
+ + surfacing_hmmpfam.DETAILEDNESS_OPTION + "=<" + surfacing_hmmpfam.DETAILEDNESS_BASIC + "|"
+ + surfacing_hmmpfam.DETAILEDNESS_LIST_IDS + "|" + surfacing_hmmpfam.DETAILEDNESS_PUNCTILIOUS
+ + ">\"" );
+ }
+ final String detness = cla.getOptionValue( surfacing_hmmpfam.DETAILEDNESS_OPTION ).toLowerCase();
+ if ( detness.equals( surfacing_hmmpfam.DETAILEDNESS_BASIC ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
+ }
+ else if ( detness.equals( surfacing_hmmpfam.DETAILEDNESS_LIST_IDS ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
+ }
+ else if ( detness.equals( surfacing_hmmpfam.DETAILEDNESS_PUNCTILIOUS ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + detness
+ + "\" for detailedness: \"-" + surfacing_hmmpfam.DETAILEDNESS_OPTION + "=<"
+ + surfacing_hmmpfam.DETAILEDNESS_BASIC + "|" + surfacing_hmmpfam.DETAILEDNESS_LIST_IDS + "|"
+ + surfacing_hmmpfam.DETAILEDNESS_PUNCTILIOUS + ">\"" );
+ }
+ }
+ String automated_pairwise_comparison_suffix = null;
+ boolean perform_pwc = false;
+ boolean write_pwc_files = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
+ perform_pwc = true;
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
+ write_pwc_files = false;
+ }
+ else {
+ write_pwc_files = true;
+ automated_pairwise_comparison_suffix = "_"
+ + cla.getOptionValue( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
+ }
+ }
+ String query_domain_ids = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.SEQ_EXTRACT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.SEQ_EXTRACT_OPTION ) ) {
+ ForesterUtil
+ .fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no domain ids given for sequences with given domains to be extracted : -"
+ + surfacing_hmmpfam.SEQ_EXTRACT_OPTION
+ + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
+ }
+ query_domain_ids = cla.getOptionValue( surfacing_hmmpfam.SEQ_EXTRACT_OPTION );
+ }
+ DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
+ DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no value for domain combinations similarities sorting: -"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MAX + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MEAN + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
+ }
+ final String sort_str = cla.getOptionValue( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
+ if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MAX ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MIN ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SD ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ }
+ else if ( sort_str.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + sort_str
+ + "\" for domain combinations similarities sorting: \"-"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MAX + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_MEAN + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
+ }
+ }
+ PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for print option: -"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
+ }
+ final String sort = cla.getOptionValue( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
+ if ( sort.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
+ domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
+ }
+ else if ( sort.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
+ // domain_similarity_print_option =
+ // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "simple HTML output not implemented yet :(" );
+ }
+ else if ( sort.equals( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
+ domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + sort
+ + "\" for print option: -" + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML
+ + "|" + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ + surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
+ }
+ }
+ GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for sorting of domain counts: -"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing_hmmpfam.DOMAIN_COUNT_SORT_ALPHA
+ + "|" + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
+ }
+ final String sort = cla.getOptionValue( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
+ if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_ALPHA ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ }
+ else if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
+ }
+ else if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
+ }
+ else if ( sort.equals( surfacing_hmmpfam.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + sort
+ + "\" for sorting of domain counts: \"-" + surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION + "=<"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_ALPHA + "|"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ + surfacing_hmmpfam.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
+ }
+ }
+ String[][] input_file_properties = null;
+ if ( input_file_names_from_file != null ) {
+ input_file_properties = surfacing_hmmpfam.processInputFileNames( input_file_names_from_file );
+ }
+ else {
+ input_file_properties = surfacing_hmmpfam.processInputFileNames( cla.getNames() );
+ }
+ final int number_of_genomes = input_file_properties.length;
+ if ( number_of_genomes < 2 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot analyze less than two files" );
+ }
+ if ( ( number_of_genomes < 3 ) && perform_pwc ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use : -"
+ + surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix> to turn on pairwise analyses with less than three input files" );
+ }
+ checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
+ input_file_properties,
+ automated_pairwise_comparison_suffix,
+ out_dir );
+ for( int i = 0; i < number_of_genomes; i++ ) {
+ File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
+ + surfacing_hmmpfam.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+ if ( out_dir != null ) {
+ dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
+ }
+ SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
+ }
+ File pfam_to_go_file = null;
+ Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
+ int domain_id_to_go_ids_count = 0;
+ if ( cla.isOptionSet( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for Pfam to GO mapping file: -"
+ + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
+ }
+ pfam_to_go_file = new File( cla.getOptionValue( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
+ }
+ try {
+ final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
+ final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+ domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
+ if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
+ "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
+ }
+ domain_id_to_go_ids_count = parser.getMappingCount();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+ }
+ }
+ File go_obo_file = null;
+ List<GoTerm> go_terms = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for GO OBO file: -"
+ + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>" );
+ }
+ if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use GO OBO file (-"
+ + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
+ + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
+ }
+ go_obo_file = new File( cla.getOptionValue( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( go_obo_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read GO OBO file: " + error );
+ }
+ try {
+ final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
+ go_terms = parser.parse();
+ if ( parser.getGoTermCount() != go_terms.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
+ "parser.getGoTermCount() != go_terms.size()" );
+ }
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read from GO OBO file: "
+ + e.getLocalizedMessage() );
+ }
+ }
+ Map<GoId, GoTerm> go_id_to_term_map = null;
+ if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
+ && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
+ go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
+ }
+ GoNameSpace go_namespace_limit = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION ) ) {
+ if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use GO namespace limit (-"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION
+ + "=<namespace>) without Pfam to GO mapping file ("
+ + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
+ + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>)" );
+ }
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for GO namespace limit: \"-"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
+ }
+ final String go_namespace_limit_str = cla.getOptionValue( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION )
+ .toLowerCase();
+ if ( go_namespace_limit_str.equals( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
+ go_namespace_limit = GoNameSpace.createMolecularFunction();
+ }
+ else if ( go_namespace_limit_str.equals( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
+ go_namespace_limit = GoNameSpace.createBiologicalProcess();
+ }
+ else if ( go_namespace_limit_str.equals( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
+ go_namespace_limit = GoNameSpace.createCellularComponent();
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "unknown value \"" + go_namespace_limit_str
+ + "\" for GO namespace limit: \"-" + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ + surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
+ }
+ }
+ if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
+ && ( number_of_genomes > 2 ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ }
+ boolean jacknifed_distances = false;
+ int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
+ double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
+ long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
+ if ( cla.isOptionSet( surfacing_hmmpfam.JACKNIFE_OPTION ) ) {
+ if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot use jacknife resampling analysis (-"
+ + surfacing_hmmpfam.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
+ + surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix for pairwise comparison output files>)" );
+ }
+ jacknifed_distances = true;
+ if ( cla.isOptionHasAValue( surfacing_hmmpfam.JACKNIFE_OPTION ) ) {
+ try {
+ jacknife_resamplings = cla.getOptionValueAsInt( surfacing_hmmpfam.JACKNIFE_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "illegal format for number of resamplings" );
+ }
+ if ( jacknife_resamplings < 2 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "attempt to use less than 2 resamplings" );
+ }
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.JACKNIFE_RATIO_OPTION )
+ && cla.isOptionHasAValue( surfacing_hmmpfam.JACKNIFE_RATIO_OPTION ) ) {
+ try {
+ jacknife_ratio = cla.getOptionValueAsDouble( surfacing_hmmpfam.JACKNIFE_RATIO_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "illegal format for jacknife ratio" );
+ }
+ if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "attempt to use illegal value for jacknife ratio: " + jacknife_ratio );
+ }
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.JACKNIFE_RANDOM_SEED_OPTION )
+ && cla.isOptionHasAValue( surfacing_hmmpfam.JACKNIFE_RANDOM_SEED_OPTION ) ) {
+ try {
+ random_seed = cla.getOptionValueAsLong( surfacing_hmmpfam.JACKNIFE_RANDOM_SEED_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "illegal format for random generator seed" );
+ }
+ }
+ }
+ // boolean infer_species_trees = false;
+ // if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
+ // if ( ( output_file == null ) || ( number_of_genomes < 3 )
+ // || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
+ // ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
+ // + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
+ // + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ // + "=<suffix for pairwise comparison output files>)" );
+ // }
+ // infer_species_trees = true;
+ // }
+ File[] intree_files = null;
+ Phylogeny[] intrees = null;
+ if ( cla.isOptionSet( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION ) ) {
+ // TODO FIXME if jacknife.... maybe not
+ if ( number_of_genomes < 3 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "cannot infer gains and losses on input species trees (-"
+ + surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION
+ + " without pairwise analyses ("
+ + surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix for pairwise comparison output files>)" );
+ }
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for input tree: -"
+ + surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
+ }
+ final String intrees_str = cla.getOptionValue( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION );
+ if ( intrees_str.indexOf( "#" ) > 0 ) {
+ final String[] intrees_strs = intrees_str.split( "#" );
+ intree_files = new File[ intrees_strs.length ];
+ int i = 0;
+ for( final String s : intrees_strs ) {
+ intree_files[ i++ ] = new File( s.trim() );
+ }
+ }
+ else {
+ intree_files = new File[ 1 ];
+ intree_files[ 0 ] = new File( intrees_str );
+ }
+ intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
+ }
+ long random_number_seed_for_fitch_parsimony = 0l;
+ boolean radomize_fitch_parsimony = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for random number seed: -"
+ + surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
+ }
+ try {
+ random_number_seed_for_fitch_parsimony = cla
+ .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
+ }
+ radomize_fitch_parsimony = true;
+ }
+ SortedSet<DomainId> filter = null;
+ if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
+ || ( negative_domains_filter_file != null ) ) {
+ filter = new TreeSet<DomainId>();
+ if ( positive_filter_file != null ) {
+ processFilter( positive_filter_file, filter );
+ }
+ else if ( negative_filter_file != null ) {
+ processFilter( negative_filter_file, filter );
+ }
+ else if ( negative_domains_filter_file != null ) {
+ processFilter( negative_domains_filter_file, filter );
+ }
+ }
+ Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
+ File[] secondary_features_map_files = null;
+ final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
+ if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
+ SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
+ }
+ if ( cla.isOptionSet( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for secondary features map file: -"
+ + surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
+ }
+ final String[] secondary_features_map_files_strs = cla
+ .getOptionValue( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
+ secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
+ domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
+ int i = 0;
+ for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
+ secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
+ final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read secondary features map file: "
+ + error );
+ }
+ try {
+ domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
+ .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "cannot read secondary features map file: "
+ + e.getMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "problem with contents of features map file ["
+ + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
+ }
+ i++;
+ }
+ }
+ if ( out_dir == null ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no output directory indicated (-"
+ + surfacing_hmmpfam.OUTPUT_DIR_OPTION + "=<dir>)" );
+ }
+ if ( output_file == null ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no name for (main) output file indicated (-"
+ + surfacing_hmmpfam.OUTPUT_FILE_OPTION + "=<file>)" );
+ }
+ if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
+ + surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
+ }
+ if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
+ + surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + "=<file>)" );
+ }
+ boolean display_histograms = false;
+ if ( cla.isOptionSet( surfacing_hmmpfam.DISPLAY_M_HISTOGRAMS_OPTION ) ) {
+ display_histograms = true;
+ }
+ System.out.println( "Output directory : " + out_dir );
+ if ( input_file_names_from_file != null ) {
+ System.out.println( "Input files names from : " + input_files_file + " ["
+ + input_file_names_from_file.length + " input files]" );
+ html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
+ + input_file_names_from_file.length + " input files]</td></tr>" + nl );
+ }
+ if ( positive_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
+ + " domain ids]</td></tr>" + nl );
+ }
+ if ( negative_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
+ + " domain ids]</td></tr>" + nl );
+ }
+ if ( negative_domains_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
+ + filter_size + " domain ids]</td></tr>" + nl );
+ }
+ if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
+ String plus0 = "";
+ for( final String s : plus_minus_analysis_high_copy_base_species ) {
+ plus0 += "+" + s + " ";
+ }
+ String plus1 = "";
+ for( final String s : plus_minus_analysis_high_copy_target_species ) {
+ plus1 += "*" + s + " ";
+ }
+ String minus = "";
+ for( final String s : plus_minus_analysis_high_low_copy_species ) {
+ minus += "-" + s + " ";
+ }
+ System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus );
+ html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
+ + "</td></tr>" + nl );
+ }
+ if ( cutoff_scores_file != null ) {
+ System.out.println( "Cutoff scores file : " + cutoff_scores_file );
+ html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
+ }
+ if ( e_value_max >= 0.0 ) {
+ System.out.println( "E-value maximum (inclusive) : " + e_value_max );
+ html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
+ }
+ System.out.println( "Ignore DUFs : " + ignore_dufs );
+ if ( ignore_virus_like_ids ) {
+ System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids );
+ html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
+ + ignore_virus_like_ids + "</td></tr>" + nl );
+ }
+ html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
+ if ( max_allowed_overlap != surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ System.out.println( "Max allowed domain overlap : " + max_allowed_overlap );
+ html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
+ }
+ if ( no_engulfing_overlaps ) {
+ System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps );
+ html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
+ + "</td></tr>" + nl );
+ }
+ System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec );
+ html_desc
+ .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
+ + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
+ System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
+ html_desc
+ .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
+ + ignore_species_specific_domains + "</td></tr>" + nl );
+ System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
+ html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
+ + ignore_combination_with_same + "</td></tr>" + nl );
+ ;
+ System.out.println( "Consider directedness : "
+ + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
+ html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
+ + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
+ if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
+ System.out.println( "Consider adjacency : "
+ + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
+ html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
+ + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
+ + nl );
+ }
+ System.out.print( "Domain counts sort order : " );
+ switch ( dc_sort_order ) {
+ case ALPHABETICAL_KEY_ID:
+ System.out.println( "alphabetical" );
+ break;
+ case KEY_DOMAIN_COUNT:
+ System.out.println( "domain count" );
+ break;
+ case KEY_DOMAIN_PROTEINS_COUNT:
+ System.out.println( "domain proteins count" );
+ break;
+ case COMBINATIONS_COUNT:
+ System.out.println( "domain combinations count" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for dc sort order" );
+ }
+ if ( domain_id_to_go_ids_map != null ) {
+ System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
+ + " mappings]" );
+ html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
+ + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
+ }
+ if ( go_terms != null ) {
+ System.out.println( "GO terms from : " + go_obo_file + " [" + go_terms.size() + " terms]" );
+ html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
+ + "</td></tr>" + nl );
+ }
+ if ( go_namespace_limit != null ) {
+ System.out.println( "Limit GO terms to : " + go_namespace_limit.toString() );
+ html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
+ }
+ if ( perform_pwc ) {
+ System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix );
+ html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
+ + "</td></tr>" + nl );
+ }
+ if ( out_dir != null ) {
+ System.out.println( "Output directory : " + out_dir );
+ }
+ if ( query_domain_ids != null ) {
+ System.out.println( "Query domains (ordered) : " + query_domain_ids );
+ html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
+ }
+ System.out.println( "Write similarities to : " + output_file );
+ System.out.print( " Scoring method : " );
+ html_desc.append( "<tr><td>Scoring method:</td><td>" );
+ switch ( scoring ) {
+ case COMBINATIONS:
+ System.out.println( "domain combinations based" );
+ html_desc.append( "domain combinations based" + "</td></tr>" + nl );
+ break;
+ case DOMAINS:
+ System.out.println( "domain counts based" );
+ html_desc.append( "domain counts based" + "</td></tr>" + nl );
+ break;
+ case PROTEINS:
+ System.out.println( "domain proteins counts based" );
+ html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for sorting for scoring" );
+ }
+ System.out.print( " Sort by : " );
+ html_desc.append( "<tr><td>Sort by:</td><td>" );
+ switch ( domain_similarity_sort_field ) {
+ case MIN:
+ System.out.print( "score minimum" );
+ html_desc.append( "score minimum" );
+ break;
+ case MAX:
+ System.out.print( "score maximum" );
+ html_desc.append( "score maximum" );
+ break;
+ case MEAN:
+ System.out.print( "score mean" );
+ html_desc.append( "score mean" );
+ break;
+ case SD:
+ System.out.print( "score standard deviation" );
+ html_desc.append( "score standard deviation" );
+ break;
+ case SPECIES_COUNT:
+ System.out.print( "species number" );
+ html_desc.append( "species number" );
+ break;
+ case DOMAIN_ID:
+ System.out.print( "alphabetical domain identifier" );
+ html_desc.append( "alphabetical domain identifier" );
+ break;
+ case MAX_DIFFERENCE:
+ System.out.print( "(maximal) difference" );
+ html_desc.append( "(maximal) difference" );
+ break;
+ case ABS_MAX_COUNTS_DIFFERENCE:
+ System.out.print( "absolute (maximal) counts difference" );
+ html_desc.append( "absolute (maximal) counts difference" );
+ break;
+ case MAX_COUNTS_DIFFERENCE:
+ System.out.print( "(maximal) counts difference" );
+ html_desc.append( "(maximal) counts difference" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
+ "unknown value for sorting for similarities" );
+ }
+ if ( sort_by_species_count_first ) {
+ System.out.println( " (sort by species count first)" );
+ html_desc.append( " (sort by species count first)" );
+ }
+ else {
+ System.out.println();
+ }
+ html_desc.append( "</td></tr>" + nl );
+ System.out.print( " Detailedness : " );
+ switch ( detailedness ) {
+ case BASIC:
+ System.out.println( "basic" );
+ break;
+ case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
+ System.out.println( "list combining domains for each species" );
+ break;
+ case PUNCTILIOUS:
+ System.out.println( "punctilious" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
+ "unknown value for sorting for detailedness" );
+ }
+ System.out.print( " Print option : " );
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ System.out.println( "HTML" );
+ break;
+ case SIMPLE_TAB_DELIMITED:
+ System.out.println( "simple tab delimited" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for print option" );
+ }
+ System.out.print( " Species matrix : " + species_matrix );
+ System.out.println();
+ if ( perform_pwc ) {
+ System.out.println( "Pairwise comparisons: " );
+ html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
+ System.out.print( " Sort by : " );
+ html_desc.append( "<tr><td>Sort by:</td><td>" );
+ switch ( domain_similarity_sort_field_for_automated_pwc ) {
+ case MEAN:
+ System.out.print( "score mean" );
+ html_desc.append( "score mean" );
+ break;
+ case DOMAIN_ID:
+ System.out.print( "alphabetical domain identifier" );
+ html_desc.append( "alphabetical domain identifier" );
+ break;
+ case MAX_DIFFERENCE:
+ System.out.print( "difference" );
+ html_desc.append( "difference" );
+ break;
+ case ABS_MAX_COUNTS_DIFFERENCE:
+ System.out.print( "absolute counts difference" );
+ html_desc.append( "absolute counts difference" );
+ break;
+ case MAX_COUNTS_DIFFERENCE:
+ System.out.print( "counts difference" );
+ html_desc.append( "counts difference" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME,
+ "unknown value for sorting for similarities" );
+ }
+ System.out.println();
+ html_desc.append( "</td></tr>" + nl );
+ if ( jacknifed_distances ) {
+ html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
+ html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
+ + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
+ System.out.println( " Jacknife : " + jacknife_resamplings + " resamplings" );
+ System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) );
+ System.out.println( " Random number seed : " + random_seed );
+ }
+ // if ( infer_species_trees ) {
+ // html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
+ // System.out.println( " Infer species trees : true" );
+ // }
+ if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
+ for( final File intree_file : intree_files ) {
+ html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
+ + "</td></tr>" + nl );
+ System.out.println( " Intree for gain/loss pars.: " + intree_file );
+ }
+ }
+ if ( radomize_fitch_parsimony ) {
+ html_desc.append( "<tr><td> Random number seed for Fitch parsimony analysis:</td><td>"
+ + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
+ System.out.println( " Random number seed : " + random_number_seed_for_fitch_parsimony );
+ }
+ if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
+ for( int i = 0; i < secondary_features_map_files.length; i++ ) {
+ html_desc.append( "<tr><td>Secondary features map file:</td><td>"
+ + secondary_features_map_files[ i ] + "</td></tr>" + nl );
+ System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
+ + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
+ if ( VERBOSE ) {
+ System.out.println();
+ System.out.println( "Domain ids to secondary features map:" );
+ for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
+ System.out.print( domain_id.getId() );
+ System.out.print( " => " );
+ for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
+ System.out.print( sec );
+ System.out.print( " " );
+ }
+ System.out.println();
+ }
+ }
+ }
+ }
+ } // if ( perform_pwc ) {
+ System.out.println();
+ html_desc.append( "<tr><td>Command line:</td><td>" + cla.getCommandLineArgsAsString() + "</td></tr>" + nl );
+ System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
+ BufferedWriter[] query_domains_writer_ary = null;
+ List<DomainId>[] query_domain_ids_array = null;
+ if ( query_domain_ids != null ) {
+ final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
+ query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
+ query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
+ for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
+ String query_domain_ids_str = query_domain_ids_str_array[ i ];
+ final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
+ final List<DomainId> query = new ArrayList<DomainId>();
+ for( final String element : query_domain_ids_str_ary ) {
+ query.add( new DomainId( element ) );
+ }
+ query_domain_ids_array[ i ] = query;
+ query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
+ String protein_names_writer_str = query_domain_ids_str + surfacing_hmmpfam.SEQ_EXTRACT_SUFFIX;
+ if ( out_dir != null ) {
+ protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
+ }
+ try {
+ query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "Could not open [" + protein_names_writer_str
+ + "]: " + e.getLocalizedMessage() );
+ }
+ }
+ }
+ SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
+ boolean need_protein_lists_per_species = false;
+ if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
+ need_protein_lists_per_species = true;
+ }
+ if ( need_protein_lists_per_species ) {
+ protein_lists_per_species = new TreeMap<Species, List<Protein>>();
+ }
+ final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
+ final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
+ List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
+ List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
+ if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
+ all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
+ all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
+ }
+ final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
+ final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
+ + output_file + D_PROMISCUITY_FILE_SUFFIX );
+ BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
+ try {
+ per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
+ per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
+ + ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e2.getMessage() );
+ }
+ for( int i = 0; i < number_of_genomes; ++i ) {
+ System.out.println();
+ System.out.println( ( i + 1 ) + "/" + number_of_genomes );
+ System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] );
+ HmmPfamOutputParser parser = null;
+ if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
+ || ( negative_domains_filter_file != null ) ) {
+ HmmPfamOutputParser.FilterType filter_type = HmmPfamOutputParser.FilterType.NONE;
+ if ( positive_filter_file != null ) {
+ filter_type = HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN;
+ }
+ else if ( negative_filter_file != null ) {
+ filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN;
+ }
+ else if ( negative_domains_filter_file != null ) {
+ filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN;
+ }
+ parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
+ input_file_properties[ i ][ 1 ],
+ input_file_properties[ i ][ 2 ],
+ filter,
+ filter_type );
+ }
+ else {
+ parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
+ input_file_properties[ i ][ 1 ],
+ input_file_properties[ i ][ 2 ] );
+ }
+ if ( e_value_max >= 0.0 ) {
+ parser.setEValueMaximum( e_value_max );
+ }
+ parser.setIgnoreDufs( ignore_dufs );
+ parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
+ parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
+ if ( max_allowed_overlap != surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parser.setMaxAllowedOverlap( max_allowed_overlap );
+ }
+ parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
+ if ( individual_domain_score_cutoffs != null ) {
+ parser.setIndividualDomainScoreCutoffs( individual_domain_score_cutoffs );
+ }
+ parser.setAllowNonUniqueQuery( ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT );
+ parser.setVerbose( VERBOSE_DEFAULT );
+ List<Protein> protein_list = null;
+ try {
+ protein_list = parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage(), e );
+ }
+ if ( VERBOSE ) {
+ System.out.println( "Domains ignored due to negative domain filter: " );
+ ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
+ System.out.println( "Domains ignored due to virus like id: " );
+ ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
+ }
+ System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
+ System.out.println( "Number of proteins stored : " + protein_list.size() );
+ System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
+ System.out.println( "Domains stored : " + parser.getDomainsStored() );
+ System.out.println( "Distinct domains stored : "
+ + parser.getDomainsStoredSet().size() );
+ System.out.println( "Domains ignored due to individual score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
+ System.out.println( "Domains ignored due to E-value : "
+ + parser.getDomainsIgnoredDueToEval() );
+ System.out.println( "Domains ignored due to DUF designation : "
+ + parser.getDomainsIgnoredDueToDuf() );
+ if ( ignore_virus_like_ids ) {
+ System.out.println( "Domains ignored due virus like ids : "
+ + parser.getDomainsIgnoredDueToVirusLikeIds() );
+ }
+ System.out.println( "Domains ignored due negative domain filter : "
+ + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
+ System.out.println( "Domains ignored due to overlap : "
+ + parser.getDomainsIgnoredDueToOverlap() );
+ if ( negative_filter_file != null ) {
+ System.out.println( "Proteins ignored due to negative filter : "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ if ( positive_filter_file != null ) {
+ System.out.println( "Proteins ignored due to positive filter : "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ System.out.println( "Time for processing : " + parser.getTime() + "ms" );
+ html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
+ + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
+ + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
+ + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
+ + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
+ + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
+ + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
+ if ( negative_filter_file != null ) {
+ html_desc.append( "; proteins ignored due to negative filter: "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ if ( positive_filter_file != null ) {
+ html_desc.append( "; proteins ignored due to positive filter: "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ html_desc.append( "</td></tr>" + nl );
+ // domain_partner_counts_array[ i ] =
+ // Methods.getDomainPartnerCounts( protein_domain_collections_array[
+ // i ],
+ // false, input_file_properties[ i ][ 1 ] );
+ gwcd_list.add( BasicGenomeWideCombinableDomains
+ .createInstance( protein_list,
+ ignore_combination_with_same,
+ new BasicSpecies( input_file_properties[ i ][ 1 ] ),
+ domain_id_to_go_ids_map,
+ dc_type ) );
+ domain_lengths_table.addLengths( protein_list );
+ if ( gwcd_list.get( i ).getSize() > 0 ) {
+ SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
+ out_dir,
+ per_genome_domain_promiscuity_statistics_writer,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ if ( output_binary_domain_combinationsfor_graph_analysis ) {
+ SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
+ out_dir,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ }
+ SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
+ SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
+ all_bin_domain_combinations_encountered );
+ }
+ if ( query_domains_writer_ary != null ) {
+ for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ try {
+ SurfacingUtil.extractProteinNames( protein_list,
+ query_domain_ids_array[ j ],
+ query_domains_writer_ary[ j ],
+ "\t" );
+ query_domains_writer_ary[ j ].flush();
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
+ }
+ if ( need_protein_lists_per_species ) {
+ protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
+ }
+ System.gc();
+ } // for( int i = 0; i < number_of_hmmpfam_files_to_analyze; ++i ) {
+ try {
+ per_genome_domain_promiscuity_statistics_writer.flush();
+ per_genome_domain_promiscuity_statistics_writer.close();
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e2.toString() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ + per_genome_domain_promiscuity_statistics_file );
+ if ( query_domains_writer_ary != null ) {
+ for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ try {
+ query_domains_writer_ary[ j ].close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.toString() );
+ }
+ }
+ }
+ if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
+ try {
+ SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
+ number_of_genomes,
+ domain_lengths_table,
+ domain_lengths_analysis_outfile );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e1.toString() );
+ }
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
+ System.out.println();
+ }
+ final long analysis_start_time = new Date().getTime();
+ PairwiseDomainSimilarityCalculator pw_calc = null;
+ // double[] values_for_all_scores_histogram = null;
+ final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
+ sort_by_species_count_first,
+ number_of_genomes == 2 );
+ switch ( scoring ) {
+ case COMBINATIONS:
+ pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
+ break;
+ case DOMAINS:
+ pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
+ break;
+ case PROTEINS:
+ pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_hmmpfam.PRG_NAME, "unknown value for sorting for scoring" );
+ }
+ DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
+ if ( domain_id_to_go_ids_map != null ) {
+ go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
+ }
+ final SortedSet<DomainSimilarity> similarities = calc
+ .calculateSimilarities( pw_calc,
+ gwcd_list,
+ ignore_domains_without_combs_in_all_spec,
+ ignore_species_specific_domains );
+ SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
+ detailedness,
+ go_annotation_output,
+ go_id_to_term_map,
+ go_namespace_limit );
+ DescriptiveStatistics pw_stats = null;
+ try {
+ String my_outfile = output_file.toString();
+ if ( !my_outfile.endsWith( ".html" ) ) {
+ my_outfile += ".html";
+ }
+ final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir
+ + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
+ List<Species> species_order = null;
+ if ( species_matrix ) {
+ species_order = new ArrayList<Species>();
+ for( int i = 0; i < number_of_genomes; i++ ) {
+ species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
+ }
+ }
+ html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
+ + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
+ + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Analysis date/time:</td><td>"
+ + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
+ + "</td></tr>" + nl );
+ html_desc.append( "</table>" + nl );
+ pw_stats = SurfacingUtil
+ .writeDomainSimilaritiesToFile( html_desc,
+ new StringBuilder( number_of_genomes + " genomes" ),
+ writer,
+ similarities,
+ number_of_genomes == 2,
+ species_order,
+ domain_similarity_print_option,
+ domain_similarity_sort_field,
+ scoring,
+ true );
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME,
+ "Wrote main output (includes domain similarities) to: \""
+ + ( out_dir == null ? my_outfile : out_dir
+ + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "Failed to write similarites to: \"" + output_file
+ + "\" [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
+ final Species[] species = new Species[ number_of_genomes ];
+ for( int i = 0; i < number_of_genomes; ++i ) {
+ species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
+ }
+ List<Phylogeny> inferred_trees = null;
+ if ( ( number_of_genomes > 2 ) && perform_pwc ) {
+ final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
+ pwgc.performPairwiseComparisons( html_desc,
+ sort_by_species_count_first,
+ detailedness,
+ ignore_domains_without_combs_in_all_spec,
+ ignore_species_specific_domains,
+ domain_similarity_sort_field_for_automated_pwc,
+ domain_similarity_print_option,
+ scoring,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ species,
+ number_of_genomes,
+ gwcd_list,
+ pw_calc,
+ automated_pairwise_comparison_suffix,
+ true,
+ surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
+ surfacing_hmmpfam.PRG_NAME,
+ display_histograms,
+ out_dir,
+ write_pwc_files );
+ String matrix_output_file = new String( output_file.toString() );
+ if ( matrix_output_file.indexOf( '.' ) > 1 ) {
+ matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
+ }
+ if ( out_dir != null ) {
+ matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
+ output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
+ }
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing_hmmpfam.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getDomainDistanceScoresMeans() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances() );
+ final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing_hmmpfam.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getDomainDistanceScoresMeans().get( 0 ) );
+ final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing_hmmpfam.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
+ final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing_hmmpfam.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances().get( 0 ) );
+ inferred_trees = new ArrayList<Phylogeny>();
+ inferred_trees.add( nj_gd );
+ inferred_trees.add( nj_bc );
+ inferred_trees.add( nj_d );
+ // final List<HistogramData> histogram_datas = pwgc.getHistogramDatas();
+ // if ( infer_species_trees ) {
+ // inferred_trees = new ArrayList<Phylogeny>();
+ // final List<Phylogeny> inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedBinaryCombinationsBasedDistances() );
+ // final List<Phylogeny> inferred_trees_d = inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedDomainsBasedDistances() );
+ // inferred_trees.addAll( inferred_trees_bc );
+ // inferred_trees.addAll( inferred_trees_d );
+ // }
+ if ( jacknifed_distances ) {
+ pwgc.performPairwiseComparisonsJacknifed( species,
+ number_of_genomes,
+ gwcd_list,
+ true,
+ jacknife_resamplings,
+ jacknife_ratio,
+ random_seed );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ + surfacing_hmmpfam.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ + surfacing_hmmpfam.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances() );
+ // if ( infer_species_trees ) {
+ // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
+ // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedBinaryCombinationsBasedDistances() );
+ // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
+ // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
+ // }
+ }
+ if ( display_histograms ) {
+ // final List<HistogramData> histogram_datas_all = new ArrayList<HistogramData>();
+ // histogram_datas_all.add( new HistogramData( "all",
+ // values_for_all_scores_histogram,
+ // null,
+ // 20 ) );
+ // final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all );
+ // final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
+ // hf_all.setVisible( true );
+ // hf.setVisible( true );
+ }
+ } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
+ if ( ( out_dir != null ) && ( !perform_pwc ) ) {
+ output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
+ }
+ // writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
+ final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ e_value_max,
+ max_allowed_overlap,
+ no_engulfing_overlaps,
+ cutoff_scores_file,
+ dc_type );
+ String s = "_";
+ if ( radomize_fitch_parsimony ) {
+ s += random_number_seed_for_fitch_parsimony + "_";
+ }
+ int i = 0;
+ for( final Phylogeny intree : intrees ) {
+ final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
+ + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
+ final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
+ gwcd_list );
+ SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
+ radomize_fitch_parsimony,
+ outfile_name,
+ domain_parsimony,
+ intree,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ parameters_sb.toString(),
+ domain_id_to_secondary_features_maps,
+ positive_filter_file == null ? null : filter,
+ output_binary_domain_combinationsfor_graph_analysis,
+ all_bin_domain_combinations_gained_fitch,
+ all_bin_domain_combinations_lost_fitch,
+ dc_type );
+ // Listing of all domain combinations gained is only done if only one input tree is used.
+ if ( ( domain_id_to_secondary_features_maps != null )
+ && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
+ int j = 0;
+ for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
+ final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
+ final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
+ .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
+ SurfacingUtil
+ .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
+ + "_"
+ + secondary_features_map_files[ j++ ],
+ secondary_features_parsimony,
+ intree,
+ parameters_sb.toString(),
+ mapping_results_map );
+ if ( i == 0 ) {
+ System.out.println();
+ System.out.println( "Mapping to secondary features:" );
+ for( final Species spec : mapping_results_map.keySet() ) {
+ final MappingResults mapping_results = mapping_results_map.get( spec );
+ final int total_domains = mapping_results.getSumOfFailures()
+ + mapping_results.getSumOfSuccesses();
+ System.out.print( spec + ":" );
+ System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
+ System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
+ if ( total_domains > 0 ) {
+ System.out.println( ", mapped ratio = "
+ + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" );
+ }
+ else {
+ System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
+ }
+ }
+ }
+ }
+ }
+ i++;
+ } // for( final Phylogeny intree : intrees ) {
+ }
+ if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
+ executePlusMinusAnalysis( output_file,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ gwcd_list,
+ protein_lists_per_species,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ plus_minus_analysis_numbers );
+ }
+ if ( output_protein_lists_for_all_domains ) {
+ writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list );
+ }
+ // if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) {
+ // final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ // e_value_max,
+ // max_allowed_overlap,
+ // no_engulfing_overlaps,
+ // cutoff_scores_file );
+ // String s = "_";
+ // if ( radomize_fitch_parsimony ) {
+ // s += random_number_seed_for_fitch_parsimony + "_";
+ // }
+ // int i = 0;
+ // for( final Phylogeny inferred_tree : inferred_trees ) {
+ // if ( !inferred_tree.isRooted() ) {
+ // intrees[ 0 ].getRoot().getName();
+ // inferred_tree.r
+ // }
+ // final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s;
+ // final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator
+ // .createInstance( inferred_tree, gwcd_list );
+ // SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
+ // radomize_fitch_parsimony,
+ // outfile_name,
+ // domain_parsimony,
+ // inferred_tree,
+ // domain_id_to_go_ids_map,
+ // go_id_to_term_map,
+ // go_namespace_limit,
+ // parameters_sb.toString() );
+ // i++;
+ // }
+ // }
+ if ( all_bin_domain_combinations_gained_fitch != null ) {
+ try {
+ executeFitchGainsAnalysis( new File( output_file
+ + surfacing_hmmpfam.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_gained_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ true );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ if ( all_bin_domain_combinations_lost_fitch != null ) {
+ try {
+ executeFitchGainsAnalysis( new File( output_file
+ + surfacing_hmmpfam.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_lost_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ false );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ final Runtime rt = java.lang.Runtime.getRuntime();
+ final long free_memory = rt.freeMemory() / 1000000;
+ final long total_memory = rt.totalMemory() / 1000000;
+ System.out.println();
+ System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" );
+ System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
+ System.out.println( "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" );
+ System.out.println();
+ System.out.println( "If this application is useful to you, please cite:" );
+ System.out.println( surfacing_hmmpfam.WWW );
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println();
+ }
+
+ private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
+ final String[][] input_file_properties ) {
+ final String[] genomes = new String[ input_file_properties.length ];
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] is not unique in input tree " + intree.getName() );
+ }
+ genomes[ i ] = input_file_properties[ i ][ 1 ];
+ }
+ PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ try {
+ intree.getNode( input_file_properties[ i ][ 1 ] );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] not present/not unique in input tree" );
+ }
+ }
+ }
+
+ // public static StringBuffer stringCombinableDomainsMapToStringBuffer(
+ // final SortedMap<String, CombinableDomains> map ) {
+ // final StringBuffer sb = new StringBuffer();
+ // for( final Iterator<String> iter = map.keySet().iterator();
+ // iter.hasNext(); ) {
+ // final Object key = iter.next();
+ // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ',
+ // false ) );
+ // final CombinableDomains domain_combination = map.get( key );
+ // sb.append( ForesterUtil.pad( new StringBuffer( "" +
+ // domain_combination.getNumberOfCombiningDomains() ), 8,
+ // ' ', false ) );
+ // sb.append( domain_combination.toStringBuffer() );
+ // sb.append( ForesterUtil.getLineSeparator() );
+ // }
+ // return sb;
+ // }
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications."
+ + surfacing_hmmpfam.PRG_NAME
+ + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
+ System.out.println();
+ System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
+ System.out
+ .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
+ System.out.println();
+ System.out.println( " Options: " );
+ System.out.println( surfacing_hmmpfam.DETAILEDNESS_OPTION
+ + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" );
+ System.out.println( surfacing_hmmpfam.IGNORE_COMBINATION_WITH_SAME_OPTION
+ + ": to ignore combinations with self (default: not to ignore)" );
+ System.out
+ .println( surfacing_hmmpfam.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
+ + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
+ System.out
+ .println( surfacing_hmmpfam.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
+ + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
+ System.out.println( surfacing_hmmpfam.NOT_IGNORE_DUFS_OPTION
+ + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
+ System.out
+ .println( surfacing_hmmpfam.IGNORE_VIRAL_IDS
+ + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
+ System.out.println( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
+ + DOMAIN_SORT_FILD_DEFAULT + ")" );
+ System.out.println( surfacing_hmmpfam.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
+ System.out.println( surfacing_hmmpfam.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
+ System.out.println( surfacing_hmmpfam.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
+ System.out.println( surfacing_hmmpfam.NO_ENGULFING_OVERLAP_OPTION
+ + ": to ignore engulfed lower confidence domains" );
+ System.out.println( surfacing_hmmpfam.SPECIES_MATRIX_OPTION + ": species matrix" );
+ System.out.println( surfacing_hmmpfam.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
+ System.out.println( surfacing_hmmpfam.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
+ + DOMAINS_SORT_ORDER_DEFAULT + ")" );
+ System.out.println( surfacing_hmmpfam.DOMAIN_SIMILARITY_PRINT_OPTION
+ + ": domain similarity print option (default:" + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
+ System.out.println( surfacing_hmmpfam.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
+ System.out.println( surfacing_hmmpfam.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
+ + ": sort by species count first" );
+ System.out.println( surfacing_hmmpfam.OUTPUT_DIR_OPTION + ": output directory" );
+ System.out.println( surfacing_hmmpfam.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
+ System.out.println( surfacing_hmmpfam.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
+ System.out.println( surfacing_hmmpfam.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
+ System.out.println( surfacing_hmmpfam.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
+ System.out.println( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION
+ + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
+ System.out.println( surfacing_hmmpfam.DISPLAY_M_HISTOGRAMS_OPTION
+ + ": to display multiple histograms (using fluorite)" );
+ System.out
+ .println( JACKNIFE_OPTION
+ + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
+ + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
+ System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
+ + JACKNIFE_RATIO_DEFAULT + "]" );
+ System.out.println( JACKNIFE_RANDOM_SEED_OPTION
+ + ": seed for random number generator for jacknife resampling [default: "
+ + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
+ // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
+ // + ": to infer NJ species trees based on shared domains/binary domain combinations" );
+ System.out
+ .println( surfacing_hmmpfam.INPUT_SPECIES_TREE_OPTION
+ + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
+ System.out.println( surfacing_hmmpfam.FILTER_POSITIVE_OPTION
+ + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
+ System.out.println( surfacing_hmmpfam.FILTER_NEGATIVE_OPTION
+ + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
+ System.out.println( surfacing_hmmpfam.FILTER_NEGATIVE_DOMAINS_OPTION
+ + "=<file>: to filter out (ignore) domains listed in <file>" );
+ System.out
+ .println( surfacing_hmmpfam.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
+ System.out
+ .println( surfacing_hmmpfam.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
+ + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
+ System.out.println( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
+ + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
+ System.out.println( surfacing_hmmpfam.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
+ + ": to consider directedness and adjacency in binary combinations" );
+ System.out
+ .println( surfacing_hmmpfam.SEQ_EXTRACT_OPTION
+ + "=<domain ids (Pfam names)>: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" );
+ System.out.println( surfacing_hmmpfam.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
+ + "=<file>: to perfom parsimony analysis on secondary features" );
+ System.out.println( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION
+ + "=<file>: to presence/absence genome analysis" );
+ System.out.println( surfacing_hmmpfam.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
+ + ": to output binary domain combinations for (downstream) graph analysis" );
+ System.out.println( surfacing_hmmpfam.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS
+ + ": to output all proteins per domain" );
+ System.out.println();
+ System.out.println();
+ System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
+ + "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
+ + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
+ + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
+ + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
+ + "=50 human mouse brafl strpu" );
+ System.out.println();
+ }
+
+ private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
+ SortedSet<String> filter_str = null;
+ try {
+ filter_str = ForesterUtil.file2set( filter_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
+ }
+ if ( filter_str != null ) {
+ for( final String string : filter_str ) {
+ filter.add( new DomainId( string ) );
+ }
+ }
+ if ( VERBOSE ) {
+ System.out.println( "Filter:" );
+ for( final DomainId domainId : filter ) {
+ System.out.println( domainId.getId() );
+ }
+ }
+ }
+
+ private static String[][] processInputFileNames( final String[] names ) {
+ final String[][] input_file_properties = new String[ names.length ][];
+ for( int i = 0; i < names.length; ++i ) {
+ if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
+ input_file_properties[ i ] = new String[ 3 ];
+ input_file_properties[ i ][ 0 ] = names[ i ];
+ input_file_properties[ i ][ 1 ] = names[ i ];
+ input_file_properties[ i ][ 2 ] = DEFAULT_SEARCH_PARAMETER;
+ }
+ else {
+ input_file_properties[ i ] = names[ i ].split( surfacing_hmmpfam.SEPARATOR_FOR_INPUT_VALUES + "" );
+ if ( input_file_properties[ i ].length != 3 ) {
+ ForesterUtil
+ .fatalError( surfacing_hmmpfam.PRG_NAME,
+ "properties for the input files (hmmpfam output) are expected "
+ + "to be in the following format \"<hmmpfam output file>#<species>#<search"
+ + " parameter>\" (or just one word, which is both the filename and the species id), instead received \""
+ + names[ i ] + "\"" );
+ }
+ }
+ final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, error );
+ }
+ }
+ return input_file_properties;
+ }
+
+ private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ if ( cla.isOptionSet( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "no value for 'plus-minus' file: -"
+ + surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
+ }
+ final File plus_minus_file = new File( cla.getOptionValue( surfacing_hmmpfam.PLUS_MINUS_ANALYSIS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( plus_minus_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "can not read from \"" + plus_minus_file + "\": "
+ + msg );
+ }
+ processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
+ }
+ }
+
+ // First numbers is minimal difference, second is factor.
+ private static void processPlusMinusFile( final File plus_minus_file,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ Set<String> species_set = null;
+ int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
+ double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
+ try {
+ species_set = ForesterUtil.file2set( plus_minus_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getMessage() );
+ }
+ if ( species_set != null ) {
+ for( final String species : species_set ) {
+ final String species_trimmed = species.substring( 1 );
+ if ( species.startsWith( "+" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_base.add( species_trimmed );
+ }
+ else if ( species.startsWith( "*" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_target.add( species_trimmed );
+ }
+ else if ( species.startsWith( "-" ) ) {
+ if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ low_copy.add( species_trimmed );
+ }
+ else if ( species.startsWith( "$D" ) ) {
+ try {
+ min_diff = Integer.parseInt( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "could not parse integer value for minimal difference from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "$F" ) ) {
+ try {
+ factor = Double.parseDouble( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME,
+ "could not parse double value for factor from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "#" ) ) {
+ // Comment, ignore.
+ }
+ else {
+ ForesterUtil
+ .fatalError( surfacing_hmmpfam.PRG_NAME,
+ "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
+ + species + "\"" );
+ }
+ numbers.add( new Integer( min_diff + "" ) );
+ numbers.add( new Double( factor + "" ) );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, "'plus minus' file [" + plus_minus_file
+ + "] appears empty" );
+ }
+ }
+
+ private static void writeProteinListsForAllSpecies( final File output_dir,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_domains.addAll( gwcd.getAllDomainIds() );
+ }
+ for( final DomainId domain : all_domains ) {
+ final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
+ SurfacingUtil.checkForOutputFileWriteability( out );
+ try {
+ final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+ SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
+ proteins_file_writer.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_hmmpfam.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing_hmmpfam.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+ }
+ }
+}
--- /dev/null
+// $Id:
+//
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.Writer;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.SortedMap;
+import java.util.SortedSet;
+import java.util.TreeMap;
+import java.util.TreeSet;
+
+import org.forester.evoinference.distance.NeighborJoining;
+import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
+import org.forester.evoinference.matrix.distance.DistanceMatrix;
+import org.forester.go.GoId;
+import org.forester.go.GoNameSpace;
+import org.forester.go.GoTerm;
+import org.forester.go.GoUtils;
+import org.forester.go.OBOparser;
+import org.forester.go.PfamToGoMapping;
+import org.forester.go.PfamToGoParser;
+import org.forester.io.parsers.HmmPfamOutputParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.PhylogenyMethods;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.surfacing.BasicDomainSimilarityCalculator;
+import org.forester.surfacing.BasicGenomeWideCombinableDomains;
+import org.forester.surfacing.BasicSpecies;
+import org.forester.surfacing.BinaryDomainCombination;
+import org.forester.surfacing.CombinationsBasedPairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.DomainCountsBasedPairwiseSimilarityCalculator;
+import org.forester.surfacing.DomainCountsDifferenceUtil;
+import org.forester.surfacing.DomainId;
+import org.forester.surfacing.DomainLengthsTable;
+import org.forester.surfacing.DomainParsimonyCalculator;
+import org.forester.surfacing.DomainSimilarity;
+import org.forester.surfacing.DomainSimilarityCalculator;
+import org.forester.surfacing.GenomeWideCombinableDomains;
+import org.forester.surfacing.MappingResults;
+import org.forester.surfacing.PairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.PairwiseGenomeComparator;
+import org.forester.surfacing.PrintableDomainSimilarity;
+import org.forester.surfacing.Protein;
+import org.forester.surfacing.ProteinCountsBasedPairwiseDomainSimilarityCalculator;
+import org.forester.surfacing.Species;
+import org.forester.surfacing.SurfacingUtil;
+import org.forester.surfacing.DomainSimilarity.DomainSimilarityScoring;
+import org.forester.surfacing.DomainSimilarity.DomainSimilaritySortField;
+import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
+import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
+import org.forester.util.BasicTable;
+import org.forester.util.BasicTableParser;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.DescriptiveStatistics;
+import org.forester.util.ForesterConstants;
+import org.forester.util.ForesterUtil;
+
+public class surfacing_old {
+
+ public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out";
+ public final static String DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_dc.dot";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS = "_fitch_present_dc.dot";
+ public final static String DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX = ".dcc";
+ // gain/loss:
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS = "_dollo_gl_d";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_gl_dc";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_DOMAINS = "_fitch_gl_d";
+ public final static String PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_gl_dc";
+ // gain/loss counts:
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS = "_dollo_glc_d";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_BINARY_COMBINATIONS = "_dollo_glc_dc";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_DOMAINS = "_fitch_glc_d";
+ public final static String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS = "_fitch_glc_dc";
+ // tables:
+ public final static String PARSIMONY_OUTPUT_FITCH_GAINS_BC = "_fitch_gains_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC = "_fitch_gains_dc.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_BC = "_fitch_losses_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC = "_fitch_losses_dc.html";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_BC = "_fitch_present_dc";
+ public final static String PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC = "_fitch_present_dc.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_D = "_dollo_gains_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_GOID_D = "_dollo_gains_goid_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D = "_dollo_gains_d.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_D = "_dollo_losses_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D = "_dollo_losses_d.html";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_D = "_dollo_present_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_GOID_D = "_dollo_present_goid_d";
+ public final static String PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D = "_dollo_present_d.html";
+ public final static String DOMAINS_PRESENT_NEXUS = "_dom.nex";
+ public final static String BDC_PRESENT_NEXUS = "_dc.nex";
+ // ---
+ public final static String PRG_NAME = "surfacing";
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_d_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_d_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_dc_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH = "_dc_fitch"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String NEXUS_EXTERNAL_DOMAINS = "_dom.nex";
+ public static final String NEXUS_EXTERNAL_DOMAIN_COMBINATIONS = "_dc.nex";
+ public static final String NEXUS_SECONDARY_FEATURES = "_secondary_features.nex";
+ public static final String PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_gl_secondary_features";
+ public static final String PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES = "_dollo_glc_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES = "_dollo_gains_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES = "_dollo_losses_secondary_features";
+ public static final String PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES = "_dollo_present_secondary_features";
+ public static final String SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO = "_secondary_features_dollo"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_BIOLOGICAL_PROCESS = "_dollo_biol_proc_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_CELLULAR_COMPONENT = "_dollo_cell_comp_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_MOLECULAR_FUNCTION = "_dollo_mol_funct_goid_d";
+ public static final String PARSIMONY_OUTPUT_DOLLO_ALL_GOID_D_ALL_NAMESPACES = "_dollo_goid_d";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_BIOLOGICAL_PROCESS = "_fitch_biol_proc_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_CELLULAR_COMPONENT = "_fitch_cell_comp_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_MOLECULAR_FUNCTION = "_fitch_mol_funct_goid_dc";
+ public static final String PARSIMONY_OUTPUT_FITCH_ALL_GOID_BC_ALL_NAMESPACES = "_fitch_goid_dc";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String OUTPUT_DIR_OPTION = "out_dir";
+ final static private String SCORING_OPTION = "scoring";
+ private static final DomainSimilarityScoring SCORING_DEFAULT = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ final static private String SCORING_DOMAIN_COUNT_BASED = "domains";
+ final static private String SCORING_PROTEIN_COUNT_BASED = "proteins";
+ final static private String SCORING_COMBINATION_BASED = "combinations";
+ final static private String DETAILEDNESS_OPTION = "detail";
+ private final static Detailedness DETAILEDNESS_DEFAULT = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ final static private String SPECIES_MATRIX_OPTION = "smatrix";
+ final static private String DETAILEDNESS_BASIC = "basic";
+ final static private String DETAILEDNESS_LIST_IDS = "list_ids";
+ final static private String DETAILEDNESS_PUNCTILIOUS = "punctilious";
+ final static private String DOMAIN_SIMILARITY_SORT_OPTION = "sort";
+ private static final DomainSimilaritySortField DOMAIN_SORT_FILD_DEFAULT = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ final static private String DOMAIN_SIMILARITY_SORT_MIN = "min";
+ final static private String DOMAIN_SIMILARITY_SORT_MAX = "max";
+ final static private String DOMAIN_SIMILARITY_SORT_SD = "sd";
+ final static private String DOMAIN_SIMILARITY_SORT_MEAN = "mean";
+ final static private String DOMAIN_SIMILARITY_SORT_DIFF = "diff";
+ final static private String DOMAIN_SIMILARITY_SORT_COUNTS_DIFF = "count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF = "abs_count_diff";
+ final static private String DOMAIN_SIMILARITY_SORT_SPECIES_COUNT = "species";
+ final static private String DOMAIN_SIMILARITY_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION = "species_first";
+ final static private String DOMAIN_COUNT_SORT_OPTION = "dc_sort";
+ private static final GenomeWideCombinableDomainsSortOrder DOMAINS_SORT_ORDER_DEFAULT = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ final static private String DOMAIN_COUNT_SORT_ALPHA = "alpha";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT = "dom";
+ final static private String DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT = "prot";
+ final static private String DOMAIN_COUNT_SORT_COMBINATIONS_COUNT = "comb";
+ final static private String CUTOFF_SCORE_FILE_OPTION = "cos";
+ final static private String NOT_IGNORE_DUFS_OPTION = "dufs";
+ final static private String MAX_E_VALUE_OPTION = "e";
+ final static private String MAX_ALLOWED_OVERLAP_OPTION = "mo";
+ final static private String NO_ENGULFING_OVERLAP_OPTION = "no_eo";
+ final static private String IGNORE_COMBINATION_WITH_SAME_OPTION = "ignore_self_comb";
+ final static private String PAIRWISE_DOMAIN_COMPARISONS_PREFIX = "pwc_";
+ final static private String PAIRWISE_DOMAIN_COMPARISONS_OPTION = "pwc";
+ final static private String OUTPUT_FILE_OPTION = "o";
+ final static private String PFAM_TO_GO_FILE_USE_OPTION = "p2g";
+ final static private String GO_OBO_FILE_USE_OPTION = "obo";
+ final static private String GO_NAMESPACE_LIMIT_OPTION = "go_namespace";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION = "molecular_function";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS = "biological_process";
+ final static private String GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT = "cellular_component";
+ final static private String SECONDARY_FEATURES_PARSIMONY_MAP_FILE = "secondary";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED = "simple_tab";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML = "simple_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML = "detailed_html";
+ final static private String DOMAIN_SIMILARITY_PRINT_OPTION = "ds_output";
+ private static final PRINT_OPTION DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT = PrintableDomainSimilarity.PRINT_OPTION.HTML;
+ final static private String IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION = "ignore_singlet_domains";
+ final static private String IGNORE_VIRAL_IDS = "ignore_viral_ids";
+ final static private boolean IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT = false;
+ final static private String IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION = "ignore_species_specific_domains";
+ final static private boolean IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT = false;
+ final static private String MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score.pwd";
+ final static private String MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains.pwd";
+ final static private String MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations.pwd";
+ final static private String NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX = "_mean_score_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX = "_domains_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX = "_bin_combinations_NJ"
+ + ForesterConstants.PHYLO_XML_SUFFIX;
+ final static private String DISPLAY_M_HISTOGRAMS_OPTION = "mhisto";
+ // final static private boolean DISPLAY_M_HISTOGRAMS_OPTION_DEFAULT = false;
+ final static private String JACKNIFE_OPTION = "jack";
+ final static private String JACKNIFE_RANDOM_SEED_OPTION = "seed";
+ final static private String JACKNIFE_RATIO_OPTION = "jack_ratio";
+ private static final int JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT = 100;
+ final static private long JACKNIFE_RANDOM_SEED_DEFAULT = 19;
+ final static private double JACKNIFE_RATIO_DEFAULT = 0.5;
+ //final static private String INFER_SPECIES_TREES_OPTION = "species_tree_inference";
+ final static private String INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX = "_sd_nj.nh";
+ final static private String INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX = "_sbc_nj.nh";
+ final static private String FILTER_POSITIVE_OPTION = "pos_filter";
+ final static private String FILTER_NEGATIVE_OPTION = "neg_filter";
+ final static private String FILTER_NEGATIVE_DOMAINS_OPTION = "neg_dom_filter";
+ final static private String INPUT_FILES_FROM_FILE_OPTION = "input";
+ final static private String INPUT_SPECIES_TREE_OPTION = "species_tree";
+ final static private String SEQ_EXTRACT_OPTION = "prot_extract";
+ final static private char SEPARATOR_FOR_INPUT_VALUES = '#';
+ final static private String PRG_VERSION = "1.00";
+ final static private String PRG_DATE = "2009.07.06";
+ final static private String E_MAIL = "czmasek@burnham.org";
+ final static private String WWW = "www.phylosoft.org/forester/applications/surfacing";
+ final static private boolean IGNORE_DUFS_DEFAULT = true;
+ final static private boolean IGNORE_COMBINATION_WITH_SAME_DEFAULLT = false;
+ final static private double MAX_E_VALUE_DEFAULT = -1;
+ final static private int MAX_ALLOWED_OVERLAP_DEFAULT = -1;
+ final static private String DEFAULT_SEARCH_PARAMETER = "ls";
+ final private static boolean ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT = true;
+ final private static boolean VERBOSE_DEFAULT = true;
+ private static final String RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION = "random_seed";
+ private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS = "consider_bdc_direction";
+ private static final String CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY = "consider_bdc_adj";
+ private static final String SEQ_EXTRACT_SUFFIX = ".prot";
+ private static final String PLUS_MINUS_ANALYSIS_OPTION = "plus_minus";
+ private static final String PLUS_MINUS_DOM_SUFFIX = "_plus_minus_dom.txt";
+ private static final String PLUS_MINUS_DOM_SUFFIX_HTML = "_plus_minus_dom.html";
+ private static final String PLUS_MINUS_DC_SUFFIX_HTML = "_plus_minus_dc.html";
+ private static final int PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT = 0;
+ private static final double PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT = 1.0;
+ private static final String PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_all.txt";
+ private static final String PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX = "_plus_minus_go_ids_passing.txt";
+ private static final String OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS = "all_prot";
+ private static final boolean VERBOSE = false;
+ private static final String OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_gains_counts";
+ private static final String OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX = "_fitch_dc_losses_counts";
+ private static final String DOMAIN_LENGTHS_ANALYSIS_SUFFIX = "_domain_lengths_analysis";
+ private static final boolean PERFORM_DOMAIN_LENGTH_ANALYSIS = true;
+ public static final String ALL_PFAMS_ENCOUNTERED_SUFFIX = "_all_encountered_pfams";
+ public static final String ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX = "_all_encountered_pfams_with_go_annotation";
+ public static final String ENCOUNTERED_PFAMS_SUMMARY_SUFFIX = "_encountered_pfams_summary";
+ public static final String ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX = "_all_pfams_gained_as_domains";
+ public static final String ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX = "_all_pfams_lost_as_domains";
+ public static final String ALL_PFAMS_GAINED_AS_DC_SUFFIX = "_all_pfams_gained_as_dc";
+ public static final String ALL_PFAMS_LOST_AS_DC_SUFFIX = "_all_pfams_lost_as_dc";
+ public static final String BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES = "PER_NODE_EVENTS";
+ public static final String BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES = "PER_SUBTREE_EVENTS";
+ public static final String D_PROMISCUITY_FILE_SUFFIX = "_domain_promiscuities";
+
+ // final String error = ForesterUtil.isReadableFile( new File(
+ // input_file_properties[ i ][ 0 ] ) );
+ // if ( !ForesterUtil.isEmpty( error ) ) {
+ // ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+ // }
+ private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+ final String[][] input_file_properties,
+ final String automated_pairwise_comparison_suffix,
+ final File outdir ) {
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ for( int j = 0; j < i; ++j ) {
+ final String species_i = input_file_properties[ i ][ 1 ];
+ final String species_j = input_file_properties[ j ][ 1 ];
+ String pairwise_similarities_output_file_str = PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i + "_"
+ + species_j + automated_pairwise_comparison_suffix;
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+ pairwise_similarities_output_file_str += ".html";
+ }
+ break;
+ }
+ final String error = ForesterUtil
+ .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
+ + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, error );
+ }
+ }
+ }
+ }
+
+ private static StringBuilder createParametersAsString( final boolean ignore_dufs,
+ final double e_value_max,
+ final int max_allowed_overlap,
+ final boolean no_engulfing_overlaps,
+ final File cutoff_scores_file,
+ final BinaryDomainCombination.DomainCombinationType dc_type ) {
+ final StringBuilder parameters_sb = new StringBuilder();
+ parameters_sb.append( "E-value: " + e_value_max );
+ if ( cutoff_scores_file != null ) {
+ parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+ }
+ else {
+ parameters_sb.append( ", Cutoff-scores-file: not-set" );
+ }
+ if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
+ }
+ else {
+ parameters_sb.append( ", Max-overlap: not-set" );
+ }
+ if ( no_engulfing_overlaps ) {
+ parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
+ }
+ else {
+ parameters_sb.append( ", Engulfing-overlaps: allowed" );
+ }
+ if ( ignore_dufs ) {
+ parameters_sb.append( ", Ignore-dufs: true" );
+ }
+ else {
+ parameters_sb.append( ", Ignore-dufs: false" );
+ }
+ parameters_sb.append( ", DC type (if applicable): " + dc_type );
+ return parameters_sb;
+ }
+
+ /**
+ * Warning: This sideeffects 'all_bin_domain_combinations_encountered'!
+ *
+ *
+ * @param output_file
+ * @param all_bin_domain_combinations_changed
+ * @param sum_of_all_domains_encountered
+ * @param all_bin_domain_combinations_encountered
+ * @param is_gains_analysis
+ * @throws IOException
+ */
+ private static void executeFitchGainsAnalysis( final File output_file,
+ final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
+ final int sum_of_all_domains_encountered,
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
+ final boolean is_gains_analysis ) throws IOException {
+ SurfacingUtil.checkForOutputFileWriteability( output_file );
+ final Writer out = ForesterUtil.createBufferedWriter( output_file );
+ final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
+ .listToSortedCountsMap( all_bin_domain_combinations_changed );
+ final SortedSet<DomainId> all_domains_in_combination_changed_more_than_once = new TreeSet<DomainId>();
+ final SortedSet<DomainId> all_domains_in_combination_changed_only_once = new TreeSet<DomainId>();
+ int above_one = 0;
+ int one = 0;
+ for( final Object bdc_object : bdc_to_counts.keySet() ) {
+ final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
+ final int count = bdc_to_counts.get( bdc_object );
+ if ( count < 1 ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, "count < 1 " );
+ }
+ out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+ if ( count > 1 ) {
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
+ above_one++;
+ }
+ else if ( count == 1 ) {
+ all_domains_in_combination_changed_only_once.add( bdc.getId0() );
+ all_domains_in_combination_changed_only_once.add( bdc.getId1() );
+ one++;
+ }
+ }
+ final int all = all_bin_domain_combinations_encountered.size();
+ int never_lost = -1;
+ if ( !is_gains_analysis ) {
+ all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
+ never_lost = all_bin_domain_combinations_encountered.size();
+ for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
+ out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
+ }
+ }
+ if ( is_gains_analysis ) {
+ out.write( "Sum of all distinct domain combinations appearing once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations appearing more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations apppearing more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ else {
+ out.write( "Sum of all distinct domain combinations never lost : " + never_lost
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost once : " + one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domain combinations lost more than once : " + above_one
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost only once : "
+ + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
+ out.write( "Sum of all distinct domains in combinations lost more than once: "
+ + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+ }
+ out.write( "All binary combinations : " + all
+ + ForesterUtil.LINE_SEPARATOR );
+ out.write( "All domains : "
+ + sum_of_all_domains_encountered );
+ out.close();
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
+ + "\"" );
+ }
+
+ private static void executePlusMinusAnalysis( final File output_file,
+ final List<String> plus_minus_analysis_high_copy_base,
+ final List<String> plus_minus_analysis_high_copy_target,
+ final List<String> plus_minus_analysis_low_copy,
+ final List<GenomeWideCombinableDomains> gwcd_list,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map,
+ final List<Object> plus_minus_analysis_numbers ) {
+ final Set<String> all_spec = new HashSet<String>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_spec.add( gwcd.getSpecies().getSpeciesId() );
+ }
+ final File html_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX_HTML );
+ final File plain_out_dom = new File( output_file + PLUS_MINUS_DOM_SUFFIX );
+ final File html_out_dc = new File( output_file + PLUS_MINUS_DC_SUFFIX_HTML );
+ final File all_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
+ final File passing_domains_go_ids_out_dom = new File( output_file + PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
+ final File proteins_file_base = new File( output_file + "" );
+ final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
+ final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
+ try {
+ DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
+ protein_lists_per_species,
+ plus_minus_analysis_high_copy_base,
+ plus_minus_analysis_high_copy_target,
+ plus_minus_analysis_low_copy,
+ min_diff,
+ factor,
+ plain_out_dom,
+ html_out_dom,
+ html_out_dc,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ all_domains_go_ids_out_dom,
+ passing_domains_go_ids_out_dom,
+ proteins_file_base );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + html_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + plain_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis results to \""
+ + html_out_dc + "\"" );
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ "Wrote plus minus domain analysis based passing GO ids to \""
+ + passing_domains_go_ids_out_dom + "\"" );
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
+ + all_domains_go_ids_out_dom + "\"" );
+ }
+
+ private static Phylogeny[] getIntrees( final File[] intree_files,
+ final int number_of_genomes,
+ final String[][] input_file_properties ) {
+ final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
+ int i = 0;
+ for( final File intree_file : intree_files ) {
+ Phylogeny intree = null;
+ final String error = ForesterUtil.isReadableFile( intree_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
+ + error );
+ }
+ try {
+ final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
+ .create( intree_file, ForesterUtil.createParserDependingOnFileType( intree_file, true ) );
+ if ( p_array.length < 1 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "file [" + intree_file
+ + "] does not contain any phylogeny in phyloXML format" );
+ }
+ else if ( p_array.length > 1 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "file [" + intree_file
+ + "] contains more than one phylogeny in phyloXML format" );
+ }
+ intree = p_array[ 0 ];
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to read input tree from file [" + intree_file
+ + "]: " + error );
+ }
+ if ( ( intree == null ) || intree.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+ }
+ if ( !intree.isRooted() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+ }
+ if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "number of external nodes ["
+ + intree.getNumberOfExternalNodes() + "] of input tree [" + intree_file
+ + "] is smaller than the number of genomes the be analyzed [" + number_of_genomes + "]" );
+ }
+ final StringBuilder parent_names = new StringBuilder();
+ final int nodes_lacking_name = SurfacingUtil.getNumberOfNodesLackingName( intree, parent_names );
+ if ( nodes_lacking_name > 0 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "input tree [" + intree_file + "] has "
+ + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
+ }
+ preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
+ if ( !intree.isCompletelyBinary() ) {
+ ForesterUtil.printWarningMessage( surfacing_old.PRG_NAME, "input tree [" + intree_file
+ + "] is not completely binary" );
+ }
+ intrees[ i++ ] = intree;
+ }
+ return intrees;
+ }
+
+ private static List<Phylogeny> inferSpeciesTrees( final File outfile, final List<DistanceMatrix> distances_list ) {
+ final NeighborJoining nj = NeighborJoining.createInstance();
+ final List<Phylogeny> phylogenies = nj.execute( distances_list );
+ final PhylogenyWriter w = new PhylogenyWriter();
+ try {
+ w.toNewHampshire( phylogenies, true, true, outfile, ";" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "failed to write to outfile [" + outfile + "]: " + e.getMessage() );
+ }
+ return phylogenies;
+ }
+
+ public static void main( final String args[] ) {
+ final long start_time = new Date().getTime();
+ // final StringBuffer log = new StringBuffer();
+ final StringBuilder html_desc = new StringBuilder();
+ ForesterUtil.printProgramInformation( surfacing_old.PRG_NAME,
+ surfacing_old.PRG_VERSION,
+ surfacing_old.PRG_DATE,
+ surfacing_old.E_MAIL,
+ surfacing_old.WWW );
+ final String nl = ForesterUtil.LINE_SEPARATOR;
+ html_desc.append( "<table>" + nl );
+ html_desc.append( "<tr><td>Produced by:</td><td>" + surfacing_old.PRG_NAME + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Version:</td><td>" + surfacing_old.PRG_VERSION + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Release Date:</td><td>" + surfacing_old.PRG_DATE + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Contact:</td><td>" + surfacing_old.E_MAIL + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>WWW:</td><td>" + surfacing_old.WWW + "</td></tr>" + nl );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( surfacing_old.HELP_OPTION_1 ) || cla.isOptionSet( surfacing_old.HELP_OPTION_2 ) ) {
+ surfacing_old.printHelp();
+ System.exit( 0 );
+ }
+ if ( ( args.length < 1 ) ) {
+ surfacing_old.printHelp();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( surfacing_old.NOT_IGNORE_DUFS_OPTION );
+ allowed_options.add( surfacing_old.MAX_E_VALUE_OPTION );
+ allowed_options.add( surfacing_old.DETAILEDNESS_OPTION );
+ allowed_options.add( surfacing_old.OUTPUT_FILE_OPTION );
+ allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION );
+ allowed_options.add( surfacing_old.SPECIES_MATRIX_OPTION );
+ allowed_options.add( surfacing_old.SCORING_OPTION );
+ allowed_options.add( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION );
+ allowed_options.add( surfacing_old.NO_ENGULFING_OVERLAP_OPTION );
+ allowed_options.add( surfacing_old.DOMAIN_COUNT_SORT_OPTION );
+ allowed_options.add( surfacing_old.CUTOFF_SCORE_FILE_OPTION );
+ allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION );
+ allowed_options.add( surfacing_old.OUTPUT_DIR_OPTION );
+ allowed_options.add( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION );
+ allowed_options.add( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION );
+ allowed_options.add( surfacing_old.GO_OBO_FILE_USE_OPTION );
+ allowed_options.add( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION );
+ allowed_options.add( surfacing_old.GO_NAMESPACE_LIMIT_OPTION );
+ allowed_options.add( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
+ allowed_options.add( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION );
+ allowed_options.add( surfacing_old.DISPLAY_M_HISTOGRAMS_OPTION );
+ allowed_options.add( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS );
+ allowed_options.add( JACKNIFE_OPTION );
+ allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
+ allowed_options.add( JACKNIFE_RATIO_OPTION );
+ allowed_options.add( INPUT_SPECIES_TREE_OPTION );
+ //allowed_options.add( INFER_SPECIES_TREES_OPTION );
+ allowed_options.add( FILTER_POSITIVE_OPTION );
+ allowed_options.add( FILTER_NEGATIVE_OPTION );
+ allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
+ allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
+ allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
+ allowed_options.add( IGNORE_VIRAL_IDS );
+ allowed_options.add( SEQ_EXTRACT_OPTION );
+ allowed_options.add( SECONDARY_FEATURES_PARSIMONY_MAP_FILE );
+ allowed_options.add( PLUS_MINUS_ANALYSIS_OPTION );
+ allowed_options.add( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS );
+ allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS );
+ allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY );
+ boolean ignore_dufs = surfacing_old.IGNORE_DUFS_DEFAULT;
+ boolean ignore_combination_with_same = surfacing_old.IGNORE_COMBINATION_WITH_SAME_DEFAULLT;
+ double e_value_max = surfacing_old.MAX_E_VALUE_DEFAULT;
+ int max_allowed_overlap = surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT;
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ boolean output_binary_domain_combinationsfor_graph_analysis = false;
+ if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) {
+ output_binary_domain_combinationsfor_graph_analysis = true;
+ }
+ if ( cla.isOptionSet( surfacing_old.MAX_E_VALUE_OPTION ) ) {
+ try {
+ e_value_max = cla.getOptionValueAsDouble( surfacing_old.MAX_E_VALUE_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no acceptable value for E-value maximum" );
+ }
+ }
+ if ( cla.isOptionSet( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION ) ) {
+ try {
+ max_allowed_overlap = cla.getOptionValueAsInt( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "no acceptable value for maximal allowed domain overlap" );
+ }
+ }
+ boolean no_engulfing_overlaps = false;
+ if ( cla.isOptionSet( surfacing_old.NO_ENGULFING_OVERLAP_OPTION ) ) {
+ no_engulfing_overlaps = true;
+ }
+ boolean ignore_virus_like_ids = false;
+ if ( cla.isOptionSet( surfacing_old.IGNORE_VIRAL_IDS ) ) {
+ ignore_virus_like_ids = true;
+ }
+ if ( cla.isOptionSet( surfacing_old.NOT_IGNORE_DUFS_OPTION ) ) {
+ ignore_dufs = false;
+ }
+ if ( cla.isOptionSet( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION ) ) {
+ ignore_combination_with_same = true;
+ }
+ boolean ignore_domains_without_combs_in_all_spec = IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION ) ) {
+ ignore_domains_without_combs_in_all_spec = true;
+ }
+ boolean ignore_species_specific_domains = IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION ) ) {
+ ignore_species_specific_domains = true;
+ }
+ File output_file = null;
+ if ( cla.isOptionSet( surfacing_old.OUTPUT_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.OUTPUT_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "no value for domain combinations similarities output file: -"
+ + surfacing_old.OUTPUT_FILE_OPTION + "=<file>" );
+ }
+ output_file = new File( cla.getOptionValue( surfacing_old.OUTPUT_FILE_OPTION ) );
+ SurfacingUtil.checkForOutputFileWriteability( output_file );
+ }
+ File cutoff_scores_file = null;
+ Map<String, String> individual_domain_score_cutoffs = null;
+ if ( cla.isOptionSet( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for individual domain score cutoffs file: -"
+ + surfacing_old.CUTOFF_SCORE_FILE_OPTION + "=<file>" );
+ }
+ cutoff_scores_file = new File( cla.getOptionValue( surfacing_old.CUTOFF_SCORE_FILE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( cutoff_scores_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read individual domain score cutoffs file: "
+ + error );
+ }
+ try {
+ final BasicTable<String> scores_table = BasicTableParser.parse( cutoff_scores_file, " " );
+ individual_domain_score_cutoffs = scores_table.getColumnsAsMap( 0, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "cannot read from individual domain score cutoffs file: " + e );
+ }
+ }
+ BinaryDomainCombination.DomainCombinationType dc_type = BinaryDomainCombination.DomainCombinationType.BASIC;
+ if ( cla.isOptionSet( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS ) ) {
+ dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED;
+ }
+ if ( cla.isOptionSet( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ) ) {
+ dc_type = BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT;
+ }
+ File out_dir = null;
+ if ( cla.isOptionSet( surfacing_old.OUTPUT_DIR_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.OUTPUT_DIR_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for output directory: -"
+ + surfacing_old.OUTPUT_DIR_OPTION + "=<dir>" );
+ }
+ out_dir = new File( cla.getOptionValue( surfacing_old.OUTPUT_DIR_OPTION ) );
+ if ( out_dir.exists() && ( out_dir.listFiles().length > 0 ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "\"" + out_dir + "\" aready exists and is not empty" );
+ }
+ if ( !out_dir.exists() ) {
+ final boolean success = out_dir.mkdir();
+ if ( !success || !out_dir.exists() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to create \"" + out_dir + "\"" );
+ }
+ }
+ if ( !out_dir.canWrite() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot write to \"" + out_dir + "\"" );
+ }
+ }
+ File positive_filter_file = null;
+ File negative_filter_file = null;
+ File negative_domains_filter_file = null;
+ if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION )
+ && cla.isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) {
+ ForesterUtil
+ .fatalError( surfacing_old.PRG_NAME, "attempt to use both negative and positive protein filter" );
+ }
+ if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION )
+ && ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) || cla
+ .isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) ) {
+ ForesterUtil
+ .fatalError( surfacing_old.PRG_NAME,
+ "attempt to use both negative or positive protein filter together wirh a negative domains filter" );
+ }
+ if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.FILTER_NEGATIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for negative filter: -"
+ + surfacing_old.FILTER_NEGATIVE_OPTION + "=<file>" );
+ }
+ negative_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_NEGATIVE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( negative_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + negative_filter_file + "\": "
+ + msg );
+ }
+ }
+ else if ( cla.isOptionSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.FILTER_POSITIVE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for positive filter: -"
+ + surfacing_old.FILTER_POSITIVE_OPTION + "=<file>" );
+ }
+ positive_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_POSITIVE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( positive_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + positive_filter_file + "\": "
+ + msg );
+ }
+ }
+ else if ( cla.isOptionSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for negative domains filter: -"
+ + surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION + "=<file>" );
+ }
+ negative_domains_filter_file = new File( cla.getOptionValue( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( negative_domains_filter_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + negative_domains_filter_file
+ + "\": " + msg );
+ }
+ }
+ final List<String> plus_minus_analysis_high_copy_base_species = new ArrayList<String>();
+ final List<String> plus_minus_analysis_high_copy_target_species = new ArrayList<String>();
+ final List<String> plus_minus_analysis_high_low_copy_species = new ArrayList<String>();
+ final List<Object> plus_minus_analysis_numbers = new ArrayList<Object>();
+ processPlusMinusAnalysisOption( cla,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ plus_minus_analysis_numbers );
+ File input_files_file = null;
+ String[] input_file_names_from_file = null;
+ if ( cla.isOptionSet( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for input files file: -"
+ + surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ }
+ input_files_file = new File( cla.getOptionValue( surfacing_old.INPUT_FILES_FROM_FILE_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( input_files_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + input_files_file + "\": "
+ + msg );
+ }
+ try {
+ input_file_names_from_file = ForesterUtil.file2array( input_files_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "failed to read from \"" + input_files_file + "\": "
+ + e );
+ }
+ }
+ if ( ( cla.getNumberOfNames() < 1 )
+ && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "No hmmpfam output file indicated is input: use comand line directly or "
+ + surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+ }
+ DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.SCORING_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.SCORING_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "no value for scoring method for domain combinations similarity calculation: -"
+ + surfacing_old.SCORING_OPTION + "=<"
+ + surfacing_old.SCORING_DOMAIN_COUNT_BASED + "|"
+ + surfacing_old.SCORING_PROTEIN_COUNT_BASED + "|"
+ + surfacing_old.SCORING_COMBINATION_BASED + ">\"" );
+ }
+ final String scoring_str = cla.getOptionValue( surfacing_old.SCORING_OPTION );
+ if ( scoring_str.equals( surfacing_old.SCORING_DOMAIN_COUNT_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.DOMAINS;
+ }
+ else if ( scoring_str.equals( surfacing_old.SCORING_COMBINATION_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.COMBINATIONS;
+ }
+ else if ( scoring_str.equals( surfacing_old.SCORING_PROTEIN_COUNT_BASED ) ) {
+ scoring = DomainSimilarity.DomainSimilarityScoring.PROTEINS;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + scoring_str
+ + "\" for scoring method for domain combinations similarity calculation: \"-"
+ + surfacing_old.SCORING_OPTION + "=<" + surfacing_old.SCORING_DOMAIN_COUNT_BASED + "|"
+ + surfacing_old.SCORING_PROTEIN_COUNT_BASED + "|" + surfacing_old.SCORING_COMBINATION_BASED
+ + ">\"" );
+ }
+ }
+ boolean sort_by_species_count_first = false;
+ if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION ) ) {
+ sort_by_species_count_first = true;
+ }
+ boolean species_matrix = false;
+ if ( cla.isOptionSet( surfacing_old.SPECIES_MATRIX_OPTION ) ) {
+ species_matrix = true;
+ }
+ boolean output_protein_lists_for_all_domains = false;
+ if ( cla.isOptionSet( surfacing_old.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
+ output_protein_lists_for_all_domains = true;
+ }
+ Detailedness detailedness = DETAILEDNESS_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.DETAILEDNESS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.DETAILEDNESS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for -" + surfacing_old.DETAILEDNESS_OPTION
+ + "=<" + surfacing_old.DETAILEDNESS_BASIC + "|" + surfacing_old.DETAILEDNESS_LIST_IDS + "|"
+ + surfacing_old.DETAILEDNESS_PUNCTILIOUS + ">\"" );
+ }
+ final String detness = cla.getOptionValue( surfacing_old.DETAILEDNESS_OPTION ).toLowerCase();
+ if ( detness.equals( surfacing_old.DETAILEDNESS_BASIC ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.BASIC;
+ }
+ else if ( detness.equals( surfacing_old.DETAILEDNESS_LIST_IDS ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES;
+ }
+ else if ( detness.equals( surfacing_old.DETAILEDNESS_PUNCTILIOUS ) ) {
+ detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + detness
+ + "\" for detailedness: \"-" + surfacing_old.DETAILEDNESS_OPTION + "=<"
+ + surfacing_old.DETAILEDNESS_BASIC + "|" + surfacing_old.DETAILEDNESS_LIST_IDS + "|"
+ + surfacing_old.DETAILEDNESS_PUNCTILIOUS + ">\"" );
+ }
+ }
+ String automated_pairwise_comparison_suffix = null;
+ boolean perform_pwc = false;
+ boolean write_pwc_files = false;
+ if ( cla.isOptionSet( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
+ perform_pwc = true;
+ if ( !cla.isOptionValueSet( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION ) ) {
+ write_pwc_files = false;
+ }
+ else {
+ write_pwc_files = true;
+ automated_pairwise_comparison_suffix = "_"
+ + cla.getOptionValue( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION );
+ }
+ }
+ String query_domain_ids = null;
+ if ( cla.isOptionSet( surfacing_old.SEQ_EXTRACT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.SEQ_EXTRACT_OPTION ) ) {
+ ForesterUtil
+ .fatalError( surfacing_old.PRG_NAME,
+ "no domain ids given for sequences with given domains to be extracted : -"
+ + surfacing_old.SEQ_EXTRACT_OPTION
+ + "=<ordered domain sequences, domain ids separated by '~', sequences separated by '#'>" );
+ }
+ query_domain_ids = cla.getOptionValue( surfacing_old.SEQ_EXTRACT_OPTION );
+ }
+ DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field = DOMAIN_SORT_FILD_DEFAULT;
+ DomainSimilarity.DomainSimilaritySortField domain_similarity_sort_field_for_automated_pwc = DOMAIN_SORT_FILD_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "no value for domain combinations similarities sorting: -"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_MAX + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
+ }
+ final String sort_str = cla.getOptionValue( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION ).toLowerCase();
+ if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_MAX ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_MIN ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MIN;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MEAN;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MEAN;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SPECIES_COUNT;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_SD ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.SD;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.DOMAIN_ID;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_DIFFERENCE;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ }
+ else if ( sort_str.equals( surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
+ domain_similarity_sort_field_for_automated_pwc = DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort_str
+ + "\" for domain combinations similarities sorting: \"-"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + "=<"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_ALPHA + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_MAX
+ + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_MIN + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_MEAN + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_DIFF
+ + "|" + surfacing_old.DOMAIN_SIMILARITY_SORT_ABS_COUNTS_DIFF + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_COUNTS_DIFF + "|" + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_SPECIES_COUNT + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_SORT_SD + ">\"" );
+ }
+ }
+ PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option = DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for print option: -"
+ + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
+ }
+ final String sort = cla.getOptionValue( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION ).toLowerCase();
+ if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML ) ) {
+ domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
+ }
+ else if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
+ // domain_similarity_print_option =
+ // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "simple HTML output not implemented yet :(" );
+ }
+ else if ( sort.equals( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
+ domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.SIMPLE_TAB_DELIMITED;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort + "\" for print option: -"
+ + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_DETAILED_HTML + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML + "|"
+ + surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED + ">\"" );
+ }
+ }
+ GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order = DOMAINS_SORT_ORDER_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.DOMAIN_COUNT_SORT_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.DOMAIN_COUNT_SORT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for sorting of domain counts: -"
+ + surfacing_old.DOMAIN_COUNT_SORT_OPTION + "=<" + surfacing_old.DOMAIN_COUNT_SORT_ALPHA + "|"
+ + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ + surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
+ }
+ final String sort = cla.getOptionValue( surfacing_old.DOMAIN_COUNT_SORT_OPTION ).toLowerCase();
+ if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_ALPHA ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.ALPHABETICAL_KEY_ID;
+ }
+ else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_COUNT;
+ }
+ else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.KEY_DOMAIN_PROTEINS_COUNT;
+ }
+ else if ( sort.equals( surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT ) ) {
+ dc_sort_order = GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder.COMBINATIONS_COUNT;
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + sort
+ + "\" for sorting of domain counts: \"-" + surfacing_old.DOMAIN_COUNT_SORT_OPTION + "=<"
+ + surfacing_old.DOMAIN_COUNT_SORT_ALPHA + "|"
+ + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_COUNT + "|"
+ + surfacing_old.DOMAIN_COUNT_SORT_KEY_DOMAIN_PROTEINS_COUNT + "|"
+ + surfacing_old.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
+ }
+ }
+ String[][] input_file_properties = null;
+ if ( input_file_names_from_file != null ) {
+ input_file_properties = surfacing_old.processInputFileNames( input_file_names_from_file );
+ }
+ else {
+ input_file_properties = surfacing_old.processInputFileNames( cla.getNames() );
+ }
+ final int number_of_genomes = input_file_properties.length;
+ if ( number_of_genomes < 2 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot analyze less than two files" );
+ }
+ if ( ( number_of_genomes < 3 ) && perform_pwc ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use : -"
+ + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix> to turn on pairwise analyses with less than three input files" );
+ }
+ checkWriteabilityForPairwiseComparisons( domain_similarity_print_option,
+ input_file_properties,
+ automated_pairwise_comparison_suffix,
+ out_dir );
+ for( int i = 0; i < number_of_genomes; i++ ) {
+ File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
+ + surfacing_old.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+ if ( out_dir != null ) {
+ dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
+ }
+ SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
+ }
+ File pfam_to_go_file = null;
+ Map<DomainId, List<GoId>> domain_id_to_go_ids_map = null;
+ int domain_id_to_go_ids_count = 0;
+ if ( cla.isOptionSet( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for Pfam to GO mapping file: -"
+ + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
+ }
+ pfam_to_go_file = new File( cla.getOptionValue( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
+ }
+ try {
+ final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
+ final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+ domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
+ if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME,
+ "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
+ }
+ domain_id_to_go_ids_count = parser.getMappingCount();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+ }
+ }
+ File go_obo_file = null;
+ List<GoTerm> go_terms = null;
+ if ( cla.isOptionSet( surfacing_old.GO_OBO_FILE_USE_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.GO_OBO_FILE_USE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for GO OBO file: -"
+ + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>" );
+ }
+ if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use GO OBO file (-"
+ + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
+ + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
+ }
+ go_obo_file = new File( cla.getOptionValue( surfacing_old.GO_OBO_FILE_USE_OPTION ) );
+ final String error = ForesterUtil.isReadableFile( go_obo_file );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read GO OBO file: " + error );
+ }
+ try {
+ final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
+ go_terms = parser.parse();
+ if ( parser.getGoTermCount() != go_terms.size() ) {
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME,
+ "parser.getGoTermCount() != go_terms.size()" );
+ }
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read from GO OBO file: "
+ + e.getLocalizedMessage() );
+ }
+ }
+ Map<GoId, GoTerm> go_id_to_term_map = null;
+ if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
+ && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
+ go_id_to_term_map = GoUtils.createGoIdToGoTermMap( go_terms );
+ }
+ GoNameSpace go_namespace_limit = null;
+ if ( cla.isOptionSet( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ) ) {
+ if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use GO namespace limit (-"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<namespace>) without Pfam to GO mapping file ("
+ + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>) and GO OBO file (-"
+ + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>)" );
+ }
+ if ( !cla.isOptionValueSet( surfacing_old.GO_NAMESPACE_LIMIT_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for GO namespace limit: \"-"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
+ }
+ final String go_namespace_limit_str = cla.getOptionValue( surfacing_old.GO_NAMESPACE_LIMIT_OPTION )
+ .toLowerCase();
+ if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION ) ) {
+ go_namespace_limit = GoNameSpace.createMolecularFunction();
+ }
+ else if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS ) ) {
+ go_namespace_limit = GoNameSpace.createBiologicalProcess();
+ }
+ else if ( go_namespace_limit_str.equals( surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT ) ) {
+ go_namespace_limit = GoNameSpace.createCellularComponent();
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "unknown value \"" + go_namespace_limit_str
+ + "\" for GO namespace limit: \"-" + surfacing_old.GO_NAMESPACE_LIMIT_OPTION + "=<"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_MOLECULAR_FUNCTION + "|"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_BIOLOGICAL_PROCESS + "|"
+ + surfacing_old.GO_NAMESPACE_LIMIT_OPTION_CELLULAR_COMPONENT + ">\"" );
+ }
+ }
+ if ( ( domain_similarity_sort_field == DomainSimilarity.DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE )
+ && ( number_of_genomes > 2 ) ) {
+ domain_similarity_sort_field = DomainSimilarity.DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE;
+ }
+ boolean jacknifed_distances = false;
+ int jacknife_resamplings = JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT;
+ double jacknife_ratio = JACKNIFE_RATIO_DEFAULT;
+ long random_seed = JACKNIFE_RANDOM_SEED_DEFAULT;
+ if ( cla.isOptionSet( surfacing_old.JACKNIFE_OPTION ) ) {
+ if ( ( number_of_genomes < 3 ) || !perform_pwc ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot use jacknife resampling analysis (-"
+ + surfacing_old.JACKNIFE_OPTION + "[=<number of resamplings>]) without pairwise analyses ("
+ + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix for pairwise comparison output files>)" );
+ }
+ jacknifed_distances = true;
+ if ( cla.isOptionHasAValue( surfacing_old.JACKNIFE_OPTION ) ) {
+ try {
+ jacknife_resamplings = cla.getOptionValueAsInt( surfacing_old.JACKNIFE_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for number of resamplings" );
+ }
+ if ( jacknife_resamplings < 2 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "attempt to use less than 2 resamplings" );
+ }
+ }
+ if ( cla.isOptionSet( surfacing_old.JACKNIFE_RATIO_OPTION )
+ && cla.isOptionHasAValue( surfacing_old.JACKNIFE_RATIO_OPTION ) ) {
+ try {
+ jacknife_ratio = cla.getOptionValueAsDouble( surfacing_old.JACKNIFE_RATIO_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for jacknife ratio" );
+ }
+ if ( ( jacknife_ratio <= 0.0 ) || ( jacknife_ratio >= 1.0 ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "attempt to use illegal value for jacknife ratio: " + jacknife_ratio );
+ }
+ }
+ if ( cla.isOptionSet( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION )
+ && cla.isOptionHasAValue( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION ) ) {
+ try {
+ random_seed = cla.getOptionValueAsLong( surfacing_old.JACKNIFE_RANDOM_SEED_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "illegal format for random generator seed" );
+ }
+ }
+ }
+ // boolean infer_species_trees = false;
+ // if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
+ // if ( ( output_file == null ) || ( number_of_genomes < 3 )
+ // || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
+ // ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
+ // + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
+ // + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ // + "=<suffix for pairwise comparison output files>)" );
+ // }
+ // infer_species_trees = true;
+ // }
+ File[] intree_files = null;
+ Phylogeny[] intrees = null;
+ if ( cla.isOptionSet( surfacing_old.INPUT_SPECIES_TREE_OPTION ) ) {
+ // TODO FIXME if jacknife.... maybe not
+ if ( number_of_genomes < 3 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "cannot infer gains and losses on input species trees (-"
+ + surfacing_old.INPUT_SPECIES_TREE_OPTION
+ + " without pairwise analyses ("
+ + surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "=<suffix for pairwise comparison output files>)" );
+ }
+ if ( !cla.isOptionValueSet( surfacing_old.INPUT_SPECIES_TREE_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for input tree: -"
+ + surfacing_old.INPUT_SPECIES_TREE_OPTION + "=<tree file in phyloXML format>" );
+ }
+ final String intrees_str = cla.getOptionValue( surfacing_old.INPUT_SPECIES_TREE_OPTION );
+ if ( intrees_str.indexOf( "#" ) > 0 ) {
+ final String[] intrees_strs = intrees_str.split( "#" );
+ intree_files = new File[ intrees_strs.length ];
+ int i = 0;
+ for( final String s : intrees_strs ) {
+ intree_files[ i++ ] = new File( s.trim() );
+ }
+ }
+ else {
+ intree_files = new File[ 1 ];
+ intree_files[ 0 ] = new File( intrees_str );
+ }
+ intrees = getIntrees( intree_files, number_of_genomes, input_file_properties );
+ }
+ long random_number_seed_for_fitch_parsimony = 0l;
+ boolean radomize_fitch_parsimony = false;
+ if ( cla.isOptionSet( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for random number seed: -"
+ + surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION + "=<seed>" );
+ }
+ try {
+ random_number_seed_for_fitch_parsimony = cla
+ .getOptionValueAsLong( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ }
+ radomize_fitch_parsimony = true;
+ }
+ SortedSet<DomainId> filter = null;
+ if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
+ || ( negative_domains_filter_file != null ) ) {
+ filter = new TreeSet<DomainId>();
+ if ( positive_filter_file != null ) {
+ processFilter( positive_filter_file, filter );
+ }
+ else if ( negative_filter_file != null ) {
+ processFilter( negative_filter_file, filter );
+ }
+ else if ( negative_domains_filter_file != null ) {
+ processFilter( negative_domains_filter_file, filter );
+ }
+ }
+ Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps = null;
+ File[] secondary_features_map_files = null;
+ final File domain_lengths_analysis_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file
+ + DOMAIN_LENGTHS_ANALYSIS_SUFFIX );
+ if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
+ SurfacingUtil.checkForOutputFileWriteability( domain_lengths_analysis_outfile );
+ }
+ if ( cla.isOptionSet( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for secondary features map file: -"
+ + surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=<file>" );
+ }
+ final String[] secondary_features_map_files_strs = cla
+ .getOptionValue( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE ).split( "#" );
+ secondary_features_map_files = new File[ secondary_features_map_files_strs.length ];
+ domain_id_to_secondary_features_maps = new Map[ secondary_features_map_files_strs.length ];
+ int i = 0;
+ for( final String secondary_features_map_files_str : secondary_features_map_files_strs ) {
+ secondary_features_map_files[ i ] = new File( secondary_features_map_files_str );
+ final String error = ForesterUtil.isReadableFile( secondary_features_map_files[ i ] );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read secondary features map file: "
+ + error );
+ }
+ try {
+ domain_id_to_secondary_features_maps[ i ] = SurfacingUtil
+ .createDomainIdToSecondaryFeaturesMap( secondary_features_map_files[ i ] );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "cannot read secondary features map file: "
+ + e.getMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "problem with contents of features map file ["
+ + secondary_features_map_files[ i ] + "]: " + e.getMessage() );
+ }
+ i++;
+ }
+ }
+ if ( out_dir == null ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no output directory indicated (-"
+ + surfacing_old.OUTPUT_DIR_OPTION + "=<dir>)" );
+ }
+ if ( output_file == null ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no name for (main) output file indicated (-"
+ + surfacing_old.OUTPUT_FILE_OPTION + "=<file>)" );
+ }
+ if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "no (acceptable) Pfam to GO id mapping file provided ('pfam2go file') (-"
+ + surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
+ }
+ if ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "no (acceptable) go id to term mapping file provided ('GO OBO file') (-"
+ + surfacing_old.GO_OBO_FILE_USE_OPTION + "=<file>)" );
+ }
+ boolean display_histograms = false;
+ if ( cla.isOptionSet( surfacing_old.DISPLAY_M_HISTOGRAMS_OPTION ) ) {
+ display_histograms = true;
+ }
+ System.out.println( "Output directory : " + out_dir );
+ if ( input_file_names_from_file != null ) {
+ System.out.println( "Input files names from : " + input_files_file + " ["
+ + input_file_names_from_file.length + " input files]" );
+ html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
+ + input_file_names_from_file.length + " input files]</td></tr>" + nl );
+ }
+ if ( positive_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Positive protein filter : " + positive_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Positive protein filter:</td><td>" + positive_filter_file + " [" + filter_size
+ + " domain ids]</td></tr>" + nl );
+ }
+ if ( negative_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Negative protein filter : " + negative_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Negative protein filter:</td><td>" + negative_filter_file + " [" + filter_size
+ + " domain ids]</td></tr>" + nl );
+ }
+ if ( negative_domains_filter_file != null ) {
+ final int filter_size = filter.size();
+ System.out.println( "Negative domain filter : " + negative_domains_filter_file + " [" + filter_size
+ + " domain ids]" );
+ html_desc.append( "<tr><td>Negative domain filter:</td><td>" + negative_domains_filter_file + " ["
+ + filter_size + " domain ids]</td></tr>" + nl );
+ }
+ if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
+ String plus0 = "";
+ for( final String s : plus_minus_analysis_high_copy_base_species ) {
+ plus0 += "+" + s + " ";
+ }
+ String plus1 = "";
+ for( final String s : plus_minus_analysis_high_copy_target_species ) {
+ plus1 += "*" + s + " ";
+ }
+ String minus = "";
+ for( final String s : plus_minus_analysis_high_low_copy_species ) {
+ minus += "-" + s + " ";
+ }
+ System.out.println( "Plus-minus analysis : " + plus1 + "&& " + plus0 + "&& " + minus );
+ html_desc.append( "<tr><td>Plus-minus analysis:</td><td>" + plus1 + "&& " + plus0 + "&& " + minus
+ + "</td></tr>" + nl );
+ }
+ if ( cutoff_scores_file != null ) {
+ System.out.println( "Cutoff scores file : " + cutoff_scores_file );
+ html_desc.append( "<tr><td>Cutoff scores file:</td><td>" + cutoff_scores_file + "</td></tr>" + nl );
+ }
+ if ( e_value_max >= 0.0 ) {
+ System.out.println( "E-value maximum (inclusive) : " + e_value_max );
+ html_desc.append( "<tr><td>E-value maximum (inclusive):</td><td>" + e_value_max + "</td></tr>" + nl );
+ }
+ System.out.println( "Ignore DUFs : " + ignore_dufs );
+ if ( ignore_virus_like_ids ) {
+ System.out.println( "Ignore virus like ids : " + ignore_virus_like_ids );
+ html_desc.append( "<tr><td>Ignore virus, phage, transposition related ids:</td><td>"
+ + ignore_virus_like_ids + "</td></tr>" + nl );
+ }
+ html_desc.append( "<tr><td>Ignore DUFs:</td><td>" + ignore_dufs + "</td></tr>" + nl );
+ if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ System.out.println( "Max allowed domain overlap : " + max_allowed_overlap );
+ html_desc.append( "<tr><td>Max allowed domain overlap:</td><td>" + max_allowed_overlap + "</td></tr>" + nl );
+ }
+ if ( no_engulfing_overlaps ) {
+ System.out.println( "Ignore engulfed domains : " + no_engulfing_overlaps );
+ html_desc.append( "<tr><td>Ignore (lower confidence) engulfed domains:</td><td>" + no_engulfing_overlaps
+ + "</td></tr>" + nl );
+ }
+ System.out.println( "Ignore singlet domains : " + ignore_domains_without_combs_in_all_spec );
+ html_desc
+ .append( "<tr><td>Ignore singlet domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
+ + ignore_domains_without_combs_in_all_spec + "</td></tr>" + nl );
+ System.out.println( "Ignore species specific doms: " + ignore_species_specific_domains );
+ html_desc
+ .append( "<tr><td>Ignore species specific domains for domain combination similarity analyses (not for parsimony analyses):</td><td>"
+ + ignore_species_specific_domains + "</td></tr>" + nl );
+ System.out.println( "Ignore combination with self: " + ignore_combination_with_same );
+ html_desc.append( "<tr><td>Ignore combination with self for domain combination similarity analyses:</td><td>"
+ + ignore_combination_with_same + "</td></tr>" + nl );
+ ;
+ System.out.println( "Consider directedness : "
+ + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) );
+ html_desc.append( "<tr><td>Consider directedness of binary domain combinations:</td><td>"
+ + ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) + "</td></tr>" + nl );
+ if ( dc_type != BinaryDomainCombination.DomainCombinationType.BASIC ) {
+ System.out.println( "Consider adjacency : "
+ + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) );
+ html_desc.append( "<tr><td>Consider djacency of binary domain combinations:</td><td>"
+ + ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) + "</td></tr>"
+ + nl );
+ }
+ System.out.print( "Domain counts sort order : " );
+ switch ( dc_sort_order ) {
+ case ALPHABETICAL_KEY_ID:
+ System.out.println( "alphabetical" );
+ break;
+ case KEY_DOMAIN_COUNT:
+ System.out.println( "domain count" );
+ break;
+ case KEY_DOMAIN_PROTEINS_COUNT:
+ System.out.println( "domain proteins count" );
+ break;
+ case COMBINATIONS_COUNT:
+ System.out.println( "domain combinations count" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for dc sort order" );
+ }
+ if ( domain_id_to_go_ids_map != null ) {
+ System.out.println( "Pfam to GO mappings from : " + pfam_to_go_file + " [" + domain_id_to_go_ids_count
+ + " mappings]" );
+ html_desc.append( "<tr><td>Pfam to GO mappings from:</td><td>" + pfam_to_go_file + " ["
+ + domain_id_to_go_ids_count + " mappings]" + "</td></tr>" + nl );
+ }
+ if ( go_terms != null ) {
+ System.out.println( "GO terms from : " + go_obo_file + " [" + go_terms.size() + " terms]" );
+ html_desc.append( "<tr><td>GO terms from:</td><td>" + go_obo_file + " [" + go_terms.size() + " terms]"
+ + "</td></tr>" + nl );
+ }
+ if ( go_namespace_limit != null ) {
+ System.out.println( "Limit GO terms to : " + go_namespace_limit.toString() );
+ html_desc.append( "<tr><td>Limit GO terms to</td><td>" + go_namespace_limit + "</td></tr>" + nl );
+ }
+ if ( perform_pwc ) {
+ System.out.println( "Suffix for PWC files : " + automated_pairwise_comparison_suffix );
+ html_desc.append( "<tr><td>Suffix for PWC files</td><td>" + automated_pairwise_comparison_suffix
+ + "</td></tr>" + nl );
+ }
+ if ( out_dir != null ) {
+ System.out.println( "Output directory : " + out_dir );
+ }
+ if ( query_domain_ids != null ) {
+ System.out.println( "Query domains (ordered) : " + query_domain_ids );
+ html_desc.append( "<tr><td></td><td>" + query_domain_ids + "</td></tr>" + nl );
+ }
+ System.out.println( "Write similarities to : " + output_file );
+ System.out.print( " Scoring method : " );
+ html_desc.append( "<tr><td>Scoring method:</td><td>" );
+ switch ( scoring ) {
+ case COMBINATIONS:
+ System.out.println( "domain combinations based" );
+ html_desc.append( "domain combinations based" + "</td></tr>" + nl );
+ break;
+ case DOMAINS:
+ System.out.println( "domain counts based" );
+ html_desc.append( "domain counts based" + "</td></tr>" + nl );
+ break;
+ case PROTEINS:
+ System.out.println( "domain proteins counts based" );
+ html_desc.append( "domain proteins counts based" + "</td></tr>" + nl );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for scoring" );
+ }
+ System.out.print( " Sort by : " );
+ html_desc.append( "<tr><td>Sort by:</td><td>" );
+ switch ( domain_similarity_sort_field ) {
+ case MIN:
+ System.out.print( "score minimum" );
+ html_desc.append( "score minimum" );
+ break;
+ case MAX:
+ System.out.print( "score maximum" );
+ html_desc.append( "score maximum" );
+ break;
+ case MEAN:
+ System.out.print( "score mean" );
+ html_desc.append( "score mean" );
+ break;
+ case SD:
+ System.out.print( "score standard deviation" );
+ html_desc.append( "score standard deviation" );
+ break;
+ case SPECIES_COUNT:
+ System.out.print( "species number" );
+ html_desc.append( "species number" );
+ break;
+ case DOMAIN_ID:
+ System.out.print( "alphabetical domain identifier" );
+ html_desc.append( "alphabetical domain identifier" );
+ break;
+ case MAX_DIFFERENCE:
+ System.out.print( "(maximal) difference" );
+ html_desc.append( "(maximal) difference" );
+ break;
+ case ABS_MAX_COUNTS_DIFFERENCE:
+ System.out.print( "absolute (maximal) counts difference" );
+ html_desc.append( "absolute (maximal) counts difference" );
+ break;
+ case MAX_COUNTS_DIFFERENCE:
+ System.out.print( "(maximal) counts difference" );
+ html_desc.append( "(maximal) counts difference" );
+ break;
+ default:
+ ForesterUtil
+ .unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for similarities" );
+ }
+ if ( sort_by_species_count_first ) {
+ System.out.println( " (sort by species count first)" );
+ html_desc.append( " (sort by species count first)" );
+ }
+ else {
+ System.out.println();
+ }
+ html_desc.append( "</td></tr>" + nl );
+ System.out.print( " Detailedness : " );
+ switch ( detailedness ) {
+ case BASIC:
+ System.out.println( "basic" );
+ break;
+ case LIST_COMBINING_DOMAIN_FOR_EACH_SPECIES:
+ System.out.println( "list combining domains for each species" );
+ break;
+ case PUNCTILIOUS:
+ System.out.println( "punctilious" );
+ break;
+ default:
+ ForesterUtil
+ .unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for detailedness" );
+ }
+ System.out.print( " Print option : " );
+ switch ( domain_similarity_print_option ) {
+ case HTML:
+ System.out.println( "HTML" );
+ break;
+ case SIMPLE_TAB_DELIMITED:
+ System.out.println( "simple tab delimited" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for print option" );
+ }
+ System.out.print( " Species matrix : " + species_matrix );
+ System.out.println();
+ if ( perform_pwc ) {
+ System.out.println( "Pairwise comparisons: " );
+ html_desc.append( "<tr><td>Pairwise comparisons:</td><td></td></tr>" );
+ System.out.print( " Sort by : " );
+ html_desc.append( "<tr><td>Sort by:</td><td>" );
+ switch ( domain_similarity_sort_field_for_automated_pwc ) {
+ case MEAN:
+ System.out.print( "score mean" );
+ html_desc.append( "score mean" );
+ break;
+ case DOMAIN_ID:
+ System.out.print( "alphabetical domain identifier" );
+ html_desc.append( "alphabetical domain identifier" );
+ break;
+ case MAX_DIFFERENCE:
+ System.out.print( "difference" );
+ html_desc.append( "difference" );
+ break;
+ case ABS_MAX_COUNTS_DIFFERENCE:
+ System.out.print( "absolute counts difference" );
+ html_desc.append( "absolute counts difference" );
+ break;
+ case MAX_COUNTS_DIFFERENCE:
+ System.out.print( "counts difference" );
+ html_desc.append( "counts difference" );
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME,
+ "unknown value for sorting for similarities" );
+ }
+ System.out.println();
+ html_desc.append( "</td></tr>" + nl );
+ if ( jacknifed_distances ) {
+ html_desc.append( "<tr><td>Jacknife:</td><td>" + jacknife_resamplings + " resamplings</td></tr>" + nl );
+ html_desc.append( "<tr><td>Jacknife ratio:</td><td>" + ForesterUtil.round( jacknife_ratio, 2 )
+ + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Jacknife random number seed:</td><td>" + random_seed + "</td></tr>" + nl );
+ System.out.println( " Jacknife : " + jacknife_resamplings + " resamplings" );
+ System.out.println( " Ratio : " + ForesterUtil.round( jacknife_ratio, 2 ) );
+ System.out.println( " Random number seed : " + random_seed );
+ }
+ // if ( infer_species_trees ) {
+ // html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
+ // System.out.println( " Infer species trees : true" );
+ // }
+ if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
+ for( final File intree_file : intree_files ) {
+ html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
+ + "</td></tr>" + nl );
+ System.out.println( " Intree for gain/loss pars.: " + intree_file );
+ }
+ }
+ if ( radomize_fitch_parsimony ) {
+ html_desc.append( "<tr><td> Random number seed for Fitch parsimony analysis:</td><td>"
+ + random_number_seed_for_fitch_parsimony + "</td></tr>" + nl );
+ System.out.println( " Random number seed : " + random_number_seed_for_fitch_parsimony );
+ }
+ if ( ( domain_id_to_secondary_features_maps != null ) && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
+ for( int i = 0; i < secondary_features_map_files.length; i++ ) {
+ html_desc.append( "<tr><td>Secondary features map file:</td><td>"
+ + secondary_features_map_files[ i ] + "</td></tr>" + nl );
+ System.out.println( "Secondary features map file : " + secondary_features_map_files[ i ]
+ + " [mappings for " + domain_id_to_secondary_features_maps[ i ].size() + " domain ids]" );
+ if ( VERBOSE ) {
+ System.out.println();
+ System.out.println( "Domain ids to secondary features map:" );
+ for( final DomainId domain_id : domain_id_to_secondary_features_maps[ i ].keySet() ) {
+ System.out.print( domain_id.getId() );
+ System.out.print( " => " );
+ for( final String sec : domain_id_to_secondary_features_maps[ i ].get( domain_id ) ) {
+ System.out.print( sec );
+ System.out.print( " " );
+ }
+ System.out.println();
+ }
+ }
+ }
+ }
+ } // if ( perform_pwc ) {
+ System.out.println();
+ html_desc.append( "<tr><td>Command line:</td><td>" + cla.getCommandLineArgsAsString() + "</td></tr>" + nl );
+ System.out.println( "Command line : " + cla.getCommandLineArgsAsString() );
+ BufferedWriter[] query_domains_writer_ary = null;
+ List<DomainId>[] query_domain_ids_array = null;
+ if ( query_domain_ids != null ) {
+ final String[] query_domain_ids_str_array = query_domain_ids.split( "#" );
+ query_domain_ids_array = new ArrayList[ query_domain_ids_str_array.length ];
+ query_domains_writer_ary = new BufferedWriter[ query_domain_ids_str_array.length ];
+ for( int i = 0; i < query_domain_ids_str_array.length; i++ ) {
+ String query_domain_ids_str = query_domain_ids_str_array[ i ];
+ final String[] query_domain_ids_str_ary = query_domain_ids_str.split( "~" );
+ final List<DomainId> query = new ArrayList<DomainId>();
+ for( final String element : query_domain_ids_str_ary ) {
+ query.add( new DomainId( element ) );
+ }
+ query_domain_ids_array[ i ] = query;
+ query_domain_ids_str = query_domain_ids_str.replace( '~', '_' );
+ String protein_names_writer_str = query_domain_ids_str + surfacing_old.SEQ_EXTRACT_SUFFIX;
+ if ( out_dir != null ) {
+ protein_names_writer_str = out_dir + ForesterUtil.FILE_SEPARATOR + protein_names_writer_str;
+ }
+ try {
+ query_domains_writer_ary[ i ] = new BufferedWriter( new FileWriter( protein_names_writer_str ) );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "Could not open [" + protein_names_writer_str
+ + "]: " + e.getLocalizedMessage() );
+ }
+ }
+ }
+ SortedMap<Species, List<Protein>> protein_lists_per_species = null; //This will only be created if neede.
+ boolean need_protein_lists_per_species = false;
+ if ( ( plus_minus_analysis_high_copy_base_species.size() > 0 ) || output_protein_lists_for_all_domains ) {
+ need_protein_lists_per_species = true;
+ }
+ if ( need_protein_lists_per_species ) {
+ protein_lists_per_species = new TreeMap<Species, List<Protein>>();
+ }
+ final List<GenomeWideCombinableDomains> gwcd_list = new ArrayList<GenomeWideCombinableDomains>( number_of_genomes );
+ final SortedSet<DomainId> all_domains_encountered = new TreeSet<DomainId>();
+ final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered = new TreeSet<BinaryDomainCombination>();
+ List<BinaryDomainCombination> all_bin_domain_combinations_gained_fitch = null;
+ List<BinaryDomainCombination> all_bin_domain_combinations_lost_fitch = null;
+ if ( ( intrees != null ) && ( intrees.length == 1 ) ) {
+ all_bin_domain_combinations_gained_fitch = new ArrayList<BinaryDomainCombination>();
+ all_bin_domain_combinations_lost_fitch = new ArrayList<BinaryDomainCombination>();
+ }
+ final DomainLengthsTable domain_lengths_table = new DomainLengthsTable();
+ final File per_genome_domain_promiscuity_statistics_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR
+ + output_file + D_PROMISCUITY_FILE_SUFFIX );
+ BufferedWriter per_genome_domain_promiscuity_statistics_writer = null;
+ try {
+ per_genome_domain_promiscuity_statistics_writer = new BufferedWriter( new FileWriter( per_genome_domain_promiscuity_statistics_file ) );
+ per_genome_domain_promiscuity_statistics_writer.write( "Species:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Mean:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "SD:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Median:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Min:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Max:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "N:\t" );
+ per_genome_domain_promiscuity_statistics_writer.write( "Max Promiscuous Domains:"
+ + ForesterUtil.LINE_SEPARATOR );
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e2.getMessage() );
+ }
+ for( int i = 0; i < number_of_genomes; ++i ) {
+ System.out.println();
+ System.out.println( ( i + 1 ) + "/" + number_of_genomes );
+ System.out.println( "Processing : " + input_file_properties[ i ][ 0 ] );
+ HmmPfamOutputParser parser = null;
+ if ( ( positive_filter_file != null ) || ( negative_filter_file != null )
+ || ( negative_domains_filter_file != null ) ) {
+ HmmPfamOutputParser.FilterType filter_type = HmmPfamOutputParser.FilterType.NONE;
+ if ( positive_filter_file != null ) {
+ filter_type = HmmPfamOutputParser.FilterType.POSITIVE_PROTEIN;
+ }
+ else if ( negative_filter_file != null ) {
+ filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_PROTEIN;
+ }
+ else if ( negative_domains_filter_file != null ) {
+ filter_type = HmmPfamOutputParser.FilterType.NEGATIVE_DOMAIN;
+ }
+ parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
+ input_file_properties[ i ][ 1 ],
+ input_file_properties[ i ][ 2 ],
+ filter,
+ filter_type );
+ }
+ else {
+ parser = new HmmPfamOutputParser( new File( input_file_properties[ i ][ 0 ] ),
+ input_file_properties[ i ][ 1 ],
+ input_file_properties[ i ][ 2 ] );
+ }
+ if ( e_value_max >= 0.0 ) {
+ parser.setEValueMaximum( e_value_max );
+ }
+ parser.setIgnoreDufs( ignore_dufs );
+ parser.setIgnoreVirusLikeIds( ignore_virus_like_ids );
+ parser.setIgnoreEngulfedDomains( no_engulfing_overlaps );
+ if ( max_allowed_overlap != surfacing_old.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+ parser.setMaxAllowedOverlap( max_allowed_overlap );
+ }
+ parser.setReturnType( HmmPfamOutputParser.ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN );
+ if ( individual_domain_score_cutoffs != null ) {
+ parser.setIndividualDomainScoreCutoffs( individual_domain_score_cutoffs );
+ }
+ parser.setAllowNonUniqueQuery( ALLOW_NON_UNIQUE_QUERY_IN_HMMPFAM_OUTPUT_DEFAULT );
+ parser.setVerbose( VERBOSE_DEFAULT );
+ List<Protein> protein_list = null;
+ try {
+ protein_list = parser.parse();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, e.getMessage(), e );
+ }
+ if ( VERBOSE ) {
+ System.out.println( "Domains ignored due to negative domain filter: " );
+ ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToNegativeDomainFilterCountsMap() );
+ System.out.println( "Domains ignored due to virus like id: " );
+ ForesterUtil.printCountingMap( parser.getDomainsIgnoredDueToVirusLikeIdCountsMap() );
+ }
+ System.out.println( "Number of proteins encountered : " + parser.getProteinsEncountered() );
+ System.out.println( "Number of proteins stored : " + protein_list.size() );
+ System.out.println( "Domains encountered : " + parser.getDomainsEncountered() );
+ System.out.println( "Domains stored : " + parser.getDomainsStored() );
+ System.out.println( "Distinct domains stored : "
+ + parser.getDomainsStoredSet().size() );
+ System.out.println( "Domains ignored due to individual score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff() );
+ System.out.println( "Domains ignored due to E-value : "
+ + parser.getDomainsIgnoredDueToEval() );
+ System.out.println( "Domains ignored due to DUF designation : "
+ + parser.getDomainsIgnoredDueToDuf() );
+ if ( ignore_virus_like_ids ) {
+ System.out.println( "Domains ignored due virus like ids : "
+ + parser.getDomainsIgnoredDueToVirusLikeIds() );
+ }
+ System.out.println( "Domains ignored due negative domain filter : "
+ + parser.getDomainsIgnoredDueToNegativeDomainFilter() );
+ System.out.println( "Domains ignored due to overlap : "
+ + parser.getDomainsIgnoredDueToOverlap() );
+ if ( negative_filter_file != null ) {
+ System.out.println( "Proteins ignored due to negative filter : "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ if ( positive_filter_file != null ) {
+ System.out.println( "Proteins ignored due to positive filter : "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ System.out.println( "Time for processing : " + parser.getTime() + "ms" );
+ html_desc.append( "<tr><td>" + input_file_properties[ i ][ 0 ] + " [species: "
+ + input_file_properties[ i ][ 1 ] + "]" + ":</td><td>domains analyzed: "
+ + parser.getDomainsStored() + "; domains ignored: [ind score cutoffs: "
+ + parser.getDomainsIgnoredDueToIndividualScoreCutoff() + "] [E-value cutoff: "
+ + parser.getDomainsIgnoredDueToEval() + "] [DUF: " + parser.getDomainsIgnoredDueToDuf()
+ + "] [virus like ids: " + parser.getDomainsIgnoredDueToVirusLikeIds()
+ + "] [negative domain filter: " + parser.getDomainsIgnoredDueToNegativeDomainFilter()
+ + "] [overlap: " + parser.getDomainsIgnoredDueToOverlap() + "]" );
+ if ( negative_filter_file != null ) {
+ html_desc.append( "; proteins ignored due to negative filter: "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ if ( positive_filter_file != null ) {
+ html_desc.append( "; proteins ignored due to positive filter: "
+ + parser.getProteinsIgnoredDueToFilter() );
+ }
+ html_desc.append( "</td></tr>" + nl );
+ // domain_partner_counts_array[ i ] =
+ // Methods.getDomainPartnerCounts( protein_domain_collections_array[
+ // i ],
+ // false, input_file_properties[ i ][ 1 ] );
+ gwcd_list.add( BasicGenomeWideCombinableDomains
+ .createInstance( protein_list,
+ ignore_combination_with_same,
+ new BasicSpecies( input_file_properties[ i ][ 1 ] ),
+ domain_id_to_go_ids_map,
+ dc_type ) );
+ domain_lengths_table.addLengths( protein_list );
+ if ( gwcd_list.get( i ).getSize() > 0 ) {
+ SurfacingUtil.writeDomainCombinationsCountsFile( input_file_properties,
+ out_dir,
+ per_genome_domain_promiscuity_statistics_writer,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ if ( output_binary_domain_combinationsfor_graph_analysis ) {
+ SurfacingUtil.writeBinaryDomainCombinationsFileForGraphAnalysis( input_file_properties,
+ out_dir,
+ gwcd_list.get( i ),
+ i,
+ dc_sort_order );
+ }
+ SurfacingUtil.addAllDomainIdsToSet( gwcd_list.get( i ), all_domains_encountered );
+ SurfacingUtil.addAllBinaryDomainCombinationToSet( gwcd_list.get( i ),
+ all_bin_domain_combinations_encountered );
+ }
+ if ( query_domains_writer_ary != null ) {
+ for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ try {
+ SurfacingUtil.extractProteinNames( protein_list,
+ query_domain_ids_array[ j ],
+ query_domains_writer_ary[ j ],
+ "\t" );
+ query_domains_writer_ary[ j ].flush();
+ }
+ catch ( final IOException e ) {
+ e.printStackTrace();
+ }
+ }
+ }
+ if ( need_protein_lists_per_species ) {
+ protein_lists_per_species.put( new BasicSpecies( input_file_properties[ i ][ 1 ] ), protein_list );
+ }
+ System.gc();
+ } // for( int i = 0; i < number_of_hmmpfam_files_to_analyze; ++i ) {
+ try {
+ per_genome_domain_promiscuity_statistics_writer.flush();
+ per_genome_domain_promiscuity_statistics_writer.close();
+ }
+ catch ( final IOException e2 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e2.toString() );
+ }
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain promiscuities to: "
+ + per_genome_domain_promiscuity_statistics_file );
+ if ( query_domains_writer_ary != null ) {
+ for( int j = 0; j < query_domain_ids_array.length; j++ ) {
+ try {
+ query_domains_writer_ary[ j ].close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.toString() );
+ }
+ }
+ }
+ if ( PERFORM_DOMAIN_LENGTH_ANALYSIS ) {
+ try {
+ SurfacingUtil.executeDomainLengthAnalysis( input_file_properties,
+ number_of_genomes,
+ domain_lengths_table,
+ domain_lengths_analysis_outfile );
+ }
+ catch ( final IOException e1 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e1.toString() );
+ }
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "Wrote domain length data to: " + domain_lengths_analysis_outfile );
+ System.out.println();
+ }
+ final long analysis_start_time = new Date().getTime();
+ PairwiseDomainSimilarityCalculator pw_calc = null;
+ // double[] values_for_all_scores_histogram = null;
+ final DomainSimilarityCalculator calc = new BasicDomainSimilarityCalculator( domain_similarity_sort_field,
+ sort_by_species_count_first,
+ number_of_genomes == 2 );
+ switch ( scoring ) {
+ case COMBINATIONS:
+ pw_calc = new CombinationsBasedPairwiseDomainSimilarityCalculator();
+ break;
+ case DOMAINS:
+ pw_calc = new DomainCountsBasedPairwiseSimilarityCalculator();
+ break;
+ case PROTEINS:
+ pw_calc = new ProteinCountsBasedPairwiseDomainSimilarityCalculator();
+ break;
+ default:
+ ForesterUtil.unexpectedFatalError( surfacing_old.PRG_NAME, "unknown value for sorting for scoring" );
+ }
+ DomainSimilarityCalculator.GoAnnotationOutput go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.NONE;
+ if ( domain_id_to_go_ids_map != null ) {
+ go_annotation_output = DomainSimilarityCalculator.GoAnnotationOutput.ALL;
+ }
+ final SortedSet<DomainSimilarity> similarities = calc
+ .calculateSimilarities( pw_calc,
+ gwcd_list,
+ ignore_domains_without_combs_in_all_spec,
+ ignore_species_specific_domains );
+ SurfacingUtil.decoratePrintableDomainSimilarities( similarities,
+ detailedness,
+ go_annotation_output,
+ go_id_to_term_map,
+ go_namespace_limit );
+ DescriptiveStatistics pw_stats = null;
+ try {
+ String my_outfile = output_file.toString();
+ if ( !my_outfile.endsWith( ".html" ) ) {
+ my_outfile += ".html";
+ }
+ final Writer writer = new BufferedWriter( new FileWriter( out_dir == null ? my_outfile : out_dir
+ + ForesterUtil.FILE_SEPARATOR + my_outfile ) );
+ List<Species> species_order = null;
+ if ( species_matrix ) {
+ species_order = new ArrayList<Species>();
+ for( int i = 0; i < number_of_genomes; i++ ) {
+ species_order.add( new BasicSpecies( input_file_properties[ i ][ 1 ] ) );
+ }
+ }
+ html_desc.append( "<tr><td>Sum of all distinct binary combinations:</td><td>"
+ + all_bin_domain_combinations_encountered.size() + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Sum of all distinct domains:</td><td>" + all_domains_encountered.size()
+ + "</td></tr>" + nl );
+ html_desc.append( "<tr><td>Analysis date/time:</td><td>"
+ + new java.text.SimpleDateFormat( "yyyy.MM.dd HH:mm:ss" ).format( new java.util.Date() )
+ + "</td></tr>" + nl );
+ html_desc.append( "</table>" + nl );
+ pw_stats = SurfacingUtil
+ .writeDomainSimilaritiesToFile( html_desc,
+ new StringBuilder( number_of_genomes + " genomes" ),
+ writer,
+ similarities,
+ number_of_genomes == 2,
+ species_order,
+ domain_similarity_print_option,
+ domain_similarity_sort_field,
+ scoring,
+ true );
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME,
+ "Wrote main output (includes domain similarities) to: \""
+ + ( out_dir == null ? my_outfile : out_dir
+ + ForesterUtil.FILE_SEPARATOR + my_outfile ) + "\"" );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "Failed to write similarites to: \"" + output_file
+ + "\" [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ // values_for_all_scores_histogram = pw_stats.getDataAsDoubleArray();
+ final Species[] species = new Species[ number_of_genomes ];
+ for( int i = 0; i < number_of_genomes; ++i ) {
+ species[ i ] = new BasicSpecies( input_file_properties[ i ][ 1 ] );
+ }
+ List<Phylogeny> inferred_trees = null;
+ if ( ( number_of_genomes > 2 ) && perform_pwc ) {
+ final PairwiseGenomeComparator pwgc = new PairwiseGenomeComparator();
+ pwgc.performPairwiseComparisons( html_desc,
+ sort_by_species_count_first,
+ detailedness,
+ ignore_domains_without_combs_in_all_spec,
+ ignore_species_specific_domains,
+ domain_similarity_sort_field_for_automated_pwc,
+ domain_similarity_print_option,
+ scoring,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ species,
+ number_of_genomes,
+ gwcd_list,
+ pw_calc,
+ automated_pairwise_comparison_suffix,
+ true,
+ surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_PREFIX,
+ surfacing_old.PRG_NAME,
+ display_histograms,
+ out_dir,
+ write_pwc_files );
+ String matrix_output_file = new String( output_file.toString() );
+ if ( matrix_output_file.indexOf( '.' ) > 1 ) {
+ matrix_output_file = matrix_output_file.substring( 0, matrix_output_file.indexOf( '.' ) );
+ }
+ if ( out_dir != null ) {
+ matrix_output_file = out_dir + ForesterUtil.FILE_SEPARATOR + matrix_output_file;
+ output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
+ }
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing_old.MATRIX_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getDomainDistanceScoresMeans() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing_old.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file
+ + surfacing_old.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances() );
+ final Phylogeny nj_gd = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing_old.NJ_TREE_MEAN_SCORE_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getDomainDistanceScoresMeans().get( 0 ) );
+ final Phylogeny nj_bc = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing_old.NJ_TREE_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances().get( 0 ) );
+ final Phylogeny nj_d = SurfacingUtil.createNjTreeBasedOnMatrixToFile( new File( matrix_output_file
+ + surfacing_old.NJ_TREE_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances().get( 0 ) );
+ inferred_trees = new ArrayList<Phylogeny>();
+ inferred_trees.add( nj_gd );
+ inferred_trees.add( nj_bc );
+ inferred_trees.add( nj_d );
+ // final List<HistogramData> histogram_datas = pwgc.getHistogramDatas();
+ // if ( infer_species_trees ) {
+ // inferred_trees = new ArrayList<Phylogeny>();
+ // final List<Phylogeny> inferred_trees_bc = inferSpeciesTrees( new File( output_file + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedBinaryCombinationsBasedDistances() );
+ // final List<Phylogeny> inferred_trees_d = inferSpeciesTrees( new File( output_file + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedDomainsBasedDistances() );
+ // inferred_trees.addAll( inferred_trees_bc );
+ // inferred_trees.addAll( inferred_trees_d );
+ // }
+ if ( jacknifed_distances ) {
+ pwgc.performPairwiseComparisonsJacknifed( species,
+ number_of_genomes,
+ gwcd_list,
+ true,
+ jacknife_resamplings,
+ jacknife_ratio,
+ random_seed );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ + surfacing_old.MATRIX_SHARED_BIN_COMBINATIONS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedBinaryCombinationsBasedDistances() );
+ SurfacingUtil.writeMatrixToFile( new File( matrix_output_file + "_"
+ + ForesterUtil.round( jacknife_ratio, 2 ) + "_" + jacknife_resamplings
+ + surfacing_old.MATRIX_SHARED_DOMAINS_BASED_GENOME_DISTANCE_SUFFIX ), pwgc
+ .getSharedDomainsBasedDistances() );
+ // if ( infer_species_trees ) {
+ // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
+ // + INFERRED_SBC_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc
+ // .getSharedBinaryCombinationsBasedDistances() );
+ // inferSpeciesTrees( new File( output_file + "_" + jacknife_resamplings
+ // + INFERRED_SD_BASED_NJ_SPECIES_TREE_SUFFIX ), pwgc.getSharedDomainsBasedDistances() );
+ // }
+ }
+ if ( display_histograms ) {
+ // final List<HistogramData> histogram_datas_all = new ArrayList<HistogramData>();
+ // histogram_datas_all.add( new HistogramData( "all",
+ // values_for_all_scores_histogram,
+ // null,
+ // 20 ) );
+ // final HistogramsFrame hf_all = new HistogramsFrame( histogram_datas_all );
+ // final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
+ // hf_all.setVisible( true );
+ // hf.setVisible( true );
+ }
+ } // if ( ( output_file != null ) && ( number_of_genomes > 2 ) && !isEmpty( automated_pairwise_comparison_suffix ) )
+ if ( ( out_dir != null ) && ( !perform_pwc ) ) {
+ output_file = new File( out_dir + ForesterUtil.FILE_SEPARATOR + output_file );
+ }
+ writePresentToNexus( output_file, positive_filter_file, filter, gwcd_list );
+ if ( ( ( intrees != null ) && ( intrees.length > 0 ) ) && ( number_of_genomes > 2 ) ) {
+ final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ e_value_max,
+ max_allowed_overlap,
+ no_engulfing_overlaps,
+ cutoff_scores_file,
+ dc_type );
+ String s = "_";
+ if ( radomize_fitch_parsimony ) {
+ s += random_number_seed_for_fitch_parsimony + "_";
+ }
+ int i = 0;
+ for( final Phylogeny intree : intrees ) {
+ final String outfile_name = ForesterUtil.removeSuffix( output_file.toString() ) + s
+ + ForesterUtil.removeSuffix( intree_files[ i ].toString() );
+ final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator.createInstance( intree,
+ gwcd_list );
+ SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
+ radomize_fitch_parsimony,
+ outfile_name,
+ domain_parsimony,
+ intree,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ go_namespace_limit,
+ parameters_sb.toString(),
+ domain_id_to_secondary_features_maps,
+ positive_filter_file == null ? null : filter,
+ output_binary_domain_combinationsfor_graph_analysis,
+ all_bin_domain_combinations_gained_fitch,
+ all_bin_domain_combinations_lost_fitch,
+ dc_type );
+ // Listing of all domain combinations gained is only done if only one input tree is used.
+ if ( ( domain_id_to_secondary_features_maps != null )
+ && ( domain_id_to_secondary_features_maps.length > 0 ) ) {
+ int j = 0;
+ for( final Map<DomainId, Set<String>> domain_id_to_secondary_features_map : domain_id_to_secondary_features_maps ) {
+ final Map<Species, MappingResults> mapping_results_map = new TreeMap<Species, MappingResults>();
+ final DomainParsimonyCalculator secondary_features_parsimony = DomainParsimonyCalculator
+ .createInstance( intree, gwcd_list, domain_id_to_secondary_features_map );
+ SurfacingUtil
+ .executeParsimonyAnalysisForSecondaryFeatures( outfile_name
+ + "_"
+ + secondary_features_map_files[ j++ ],
+ secondary_features_parsimony,
+ intree,
+ parameters_sb.toString(),
+ mapping_results_map );
+ if ( i == 0 ) {
+ System.out.println();
+ System.out.println( "Mapping to secondary features:" );
+ for( final Species spec : mapping_results_map.keySet() ) {
+ final MappingResults mapping_results = mapping_results_map.get( spec );
+ final int total_domains = mapping_results.getSumOfFailures()
+ + mapping_results.getSumOfSuccesses();
+ System.out.print( spec + ":" );
+ System.out.print( " mapped domains = " + mapping_results.getSumOfSuccesses() );
+ System.out.print( ", not mapped domains = " + mapping_results.getSumOfFailures() );
+ if ( total_domains > 0 ) {
+ System.out.println( ", mapped ratio = "
+ + ( 100 * mapping_results.getSumOfSuccesses() / total_domains ) + "%" );
+ }
+ else {
+ System.out.println( ", mapped ratio = n/a (total domains = 0 )" );
+ }
+ }
+ }
+ }
+ }
+ i++;
+ } // for( final Phylogeny intree : intrees ) {
+ }
+ if ( plus_minus_analysis_high_copy_base_species.size() > 0 ) {
+ executePlusMinusAnalysis( output_file,
+ plus_minus_analysis_high_copy_base_species,
+ plus_minus_analysis_high_copy_target_species,
+ plus_minus_analysis_high_low_copy_species,
+ gwcd_list,
+ protein_lists_per_species,
+ domain_id_to_go_ids_map,
+ go_id_to_term_map,
+ plus_minus_analysis_numbers );
+ }
+ if ( output_protein_lists_for_all_domains ) {
+ writeProteinListsForAllSpecies( out_dir, protein_lists_per_species, gwcd_list );
+ }
+ // if ( ( intrees != null ) && ( intrees.length > 0 ) && ( inferred_trees != null ) && ( inferred_trees.size() > 0 ) ) {
+ // final StringBuilder parameters_sb = createParametersAsString( ignore_dufs,
+ // e_value_max,
+ // max_allowed_overlap,
+ // no_engulfing_overlaps,
+ // cutoff_scores_file );
+ // String s = "_";
+ // if ( radomize_fitch_parsimony ) {
+ // s += random_number_seed_for_fitch_parsimony + "_";
+ // }
+ // int i = 0;
+ // for( final Phylogeny inferred_tree : inferred_trees ) {
+ // if ( !inferred_tree.isRooted() ) {
+ // intrees[ 0 ].getRoot().getName();
+ // inferred_tree.r
+ // }
+ // final String outfile_name = ForesterUtil.removeSuffix( inferred_tree.getName() ) + s;
+ // final DomainParsimonyCalculator domain_parsimony = DomainParsimonyCalculator
+ // .createInstance( inferred_tree, gwcd_list );
+ // SurfacingUtil.executeParsimonyAnalysis( random_number_seed_for_fitch_parsimony,
+ // radomize_fitch_parsimony,
+ // outfile_name,
+ // domain_parsimony,
+ // inferred_tree,
+ // domain_id_to_go_ids_map,
+ // go_id_to_term_map,
+ // go_namespace_limit,
+ // parameters_sb.toString() );
+ // i++;
+ // }
+ // }
+ if ( all_bin_domain_combinations_gained_fitch != null ) {
+ try {
+ executeFitchGainsAnalysis( new File( output_file
+ + surfacing_old.OUTPUT_DOMAIN_COMBINATIONS_GAINED_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_gained_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ true );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ if ( all_bin_domain_combinations_lost_fitch != null ) {
+ try {
+ executeFitchGainsAnalysis( new File( output_file
+ + surfacing_old.OUTPUT_DOMAIN_COMBINATIONS_LOST_MORE_THAN_ONCE_ANALYSIS_SUFFIX ),
+ all_bin_domain_combinations_lost_fitch,
+ all_domains_encountered.size(),
+ all_bin_domain_combinations_encountered,
+ false );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+ final Runtime rt = java.lang.Runtime.getRuntime();
+ final long free_memory = rt.freeMemory() / 1000000;
+ final long total_memory = rt.totalMemory() / 1000000;
+ System.out.println();
+ System.out.println( "Time for analysis : " + ( new Date().getTime() - analysis_start_time ) + "ms" );
+ System.out.println( "Total running time: " + ( new Date().getTime() - start_time ) + "ms " );
+ System.out.println( "Free memory : " + free_memory + "MB, total memory: " + total_memory + "MB" );
+ System.out.println();
+ System.out.println( "If this application is useful to you, please cite:" );
+ System.out.println( surfacing_old.WWW );
+ System.out.println();
+ ForesterUtil.programMessage( PRG_NAME, "OK" );
+ System.out.println();
+ }
+
+ private static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
+ final String[][] input_file_properties ) {
+ final String[] genomes = new String[ input_file_properties.length ];
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] is not unique in input tree " + intree.getName() );
+ }
+ genomes[ i ] = input_file_properties[ i ][ 1 ];
+ }
+ PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
+ for( int i = 0; i < input_file_properties.length; ++i ) {
+ try {
+ intree.getNode( input_file_properties[ i ][ 1 ] );
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+ + "] not present/not unique in input tree" );
+ }
+ }
+ }
+
+ // public static StringBuffer stringCombinableDomainsMapToStringBuffer(
+ // final SortedMap<String, CombinableDomains> map ) {
+ // final StringBuffer sb = new StringBuffer();
+ // for( final Iterator<String> iter = map.keySet().iterator();
+ // iter.hasNext(); ) {
+ // final Object key = iter.next();
+ // sb.append( ForesterUtil.pad( new StringBuffer( key.toString() ), 18, ' ',
+ // false ) );
+ // final CombinableDomains domain_combination = map.get( key );
+ // sb.append( ForesterUtil.pad( new StringBuffer( "" +
+ // domain_combination.getNumberOfCombiningDomains() ), 8,
+ // ' ', false ) );
+ // sb.append( domain_combination.toStringBuffer() );
+ // sb.append( ForesterUtil.getLineSeparator() );
+ // }
+ // return sb;
+ // }
+ private static void printHelp() {
+ System.out.println();
+ System.out.println( "Usage:" );
+ System.out.println();
+ System.out.println( "% java -Xms256m -Xmx512m -cp forester.jar org.forester.applications."
+ + surfacing_old.PRG_NAME
+ + " [options] <phylogen(y|ies) infile> [external node name 1] [name 2] ... [name n]" );
+ System.out.println();
+ System.out.println( " Note: This software might need a significant amount of memory (heap space);" );
+ System.out
+ .println( " hence use \"-Xms128m -Xmx512m\" (or more) to prevent a \"java.lang.OutOfMemoryError\"." );
+ System.out.println();
+ System.out.println( " Options: " );
+ System.out.println( surfacing_old.DETAILEDNESS_OPTION
+ + ": level of detail for similarities output file (default:" + DETAILEDNESS_DEFAULT + ")" );
+ System.out.println( surfacing_old.IGNORE_COMBINATION_WITH_SAME_OPTION
+ + ": to ignore combinations with self (default: not to ignore)" );
+ System.out
+ .println( surfacing_old.IGNORE_DOMAINS_WITHOUT_COMBINATIONS_IN_ALL_SPECIES_OPTION
+ + ": to ignore domains without combinations in any species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
+ System.out
+ .println( surfacing_old.IGNORE_DOMAINS_SPECIFIC_TO_ONE_SPECIES_OPTION
+ + ": to ignore domains specific to one species (for similarity calc purposes, not for parsimony analyses) (default: not to ignore)" );
+ System.out.println( surfacing_old.NOT_IGNORE_DUFS_OPTION
+ + ": to _not_ ignore DUFs (domains with unknown function) (default: ignore DUFs)" );
+ System.out
+ .println( surfacing_old.IGNORE_VIRAL_IDS
+ + ": to ignore domains with ids containing 'vir', 'retro', 'transpos', 'phage', or starting with 'rv' or 'gag_'" );
+ System.out.println( surfacing_old.DOMAIN_SIMILARITY_SORT_OPTION + ": sorting for similarities (default: "
+ + DOMAIN_SORT_FILD_DEFAULT + ")" );
+ System.out.println( surfacing_old.OUTPUT_FILE_OPTION + ": name for (main) output file (mandatory)" );
+ System.out.println( surfacing_old.MAX_E_VALUE_OPTION + ": max (inclusive) E-value" );
+ System.out.println( surfacing_old.MAX_ALLOWED_OVERLAP_OPTION + ": maximal allowed domain overlap" );
+ System.out
+ .println( surfacing_old.NO_ENGULFING_OVERLAP_OPTION + ": to ignore engulfed lower confidence domains" );
+ System.out.println( surfacing_old.SPECIES_MATRIX_OPTION + ": species matrix" );
+ System.out.println( surfacing_old.SCORING_OPTION + ": scoring (default:" + SCORING_DEFAULT + ")" );
+ System.out.println( surfacing_old.DOMAIN_COUNT_SORT_OPTION + ": sorting for domain counts (default:"
+ + DOMAINS_SORT_ORDER_DEFAULT + ")" );
+ System.out.println( surfacing_old.DOMAIN_SIMILARITY_PRINT_OPTION + ": domain similarity print option (default:"
+ + DOMAIN_SIMILARITY_PRINT_OPTION_DEFAULT + ")" );
+ System.out.println( surfacing_old.CUTOFF_SCORE_FILE_OPTION + ": cutoff score file" );
+ System.out.println( surfacing_old.DOMAIN_SIMILARITY_SORT_BY_SPECIES_COUNT_FIRST_OPTION
+ + ": sort by species count first" );
+ System.out.println( surfacing_old.OUTPUT_DIR_OPTION + ": output directory" );
+ System.out.println( surfacing_old.PFAM_TO_GO_FILE_USE_OPTION + ": Pfam to GO mapping file" );
+ System.out.println( surfacing_old.GO_OBO_FILE_USE_OPTION + ": GO terms file (OBO format)" );
+ System.out.println( surfacing_old.GO_NAMESPACE_LIMIT_OPTION + ": limit GO term to one GO namespace" );
+ System.out.println( surfacing_old.PAIRWISE_DOMAIN_COMPARISONS_OPTION
+ + "[=<suffix for pairwise comparison output files>]: to perform pairwise comparison based analyses" );
+ System.out.println( surfacing_old.INPUT_SPECIES_TREE_OPTION
+ + ": species tree, to perform (Dollo, Fitch) parismony analyses" );
+ System.out.println( surfacing_old.DISPLAY_M_HISTOGRAMS_OPTION
+ + ": to display multiple histograms (using fluorite)" );
+ System.out
+ .println( JACKNIFE_OPTION
+ + ": perform jacknife resampling for domain and binary domain combination based distance matrices [default resamplings: "
+ + JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT + "]" );
+ System.out.println( JACKNIFE_RATIO_OPTION + ": ratio for jacknife resampling [default: "
+ + JACKNIFE_RATIO_DEFAULT + "]" );
+ System.out.println( JACKNIFE_RANDOM_SEED_OPTION
+ + ": seed for random number generator for jacknife resampling [default: "
+ + JACKNIFE_RANDOM_SEED_DEFAULT + "]" );
+ // System.out.println( surfacing.INFER_SPECIES_TREES_OPTION
+ // + ": to infer NJ species trees based on shared domains/binary domain combinations" );
+ System.out
+ .println( surfacing_old.INPUT_SPECIES_TREE_OPTION
+ + "=<treefiles in phyloXML format, separated by #>: to infer domain/binary domain combination gains/losses on given species trees" );
+ System.out.println( surfacing_old.FILTER_POSITIVE_OPTION
+ + "=<file>: to filter out proteins not containing at least one domain listed in <file>" );
+ System.out.println( surfacing_old.FILTER_NEGATIVE_OPTION
+ + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
+ System.out.println( surfacing_old.FILTER_NEGATIVE_DOMAINS_OPTION
+ + "=<file>: to filter out (ignore) domains listed in <file>" );
+ System.out.println( surfacing_old.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
+ System.out
+ .println( surfacing_old.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
+ + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
+ System.out.println( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS
+ + ": to consider directedness in binary combinations: e.g. A-B != B-A" );
+ System.out.println( surfacing_old.CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY
+ + ": to consider directedness and adjacency in binary combinations" );
+ System.out
+ .println( surfacing_old.SEQ_EXTRACT_OPTION
+ + "=<domain ids (Pfam names)>: to extract sequence names of sequences containing matching domains and/or domain-sequences (order N to C) (domain separator: '~', domain sequences speparator: '#', e.g. 'NACHT#BIR~CARD')" );
+ System.out.println( surfacing_old.SECONDARY_FEATURES_PARSIMONY_MAP_FILE
+ + "=<file>: to perfom parsimony analysis on secondary features" );
+ System.out.println( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION + "=<file>: to presence/absence genome analysis" );
+ System.out.println( surfacing_old.DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS
+ + ": to output binary domain combinations for (downstream) graph analysis" );
+ System.out.println( surfacing_old.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS + ": to output all proteins per domain" );
+ System.out.println();
+ System.out.println();
+ System.out.println( "Example: java -Xms128m -Xmx512m -cp path/to/forester.jar"
+ + "org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
+ + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
+ + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
+ + "-ds_output=detailed_html -scoring=domains -sort=alpha -" + JACKNIFE_OPTION
+ + "=50 human mouse brafl strpu" );
+ System.out.println();
+ }
+
+ private static void processFilter( final File filter_file, final SortedSet<DomainId> filter ) {
+ SortedSet<String> filter_str = null;
+ try {
+ filter_str = ForesterUtil.file2set( filter_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ }
+ if ( filter_str != null ) {
+ for( final String string : filter_str ) {
+ filter.add( new DomainId( string ) );
+ }
+ }
+ if ( VERBOSE ) {
+ System.out.println( "Filter:" );
+ for( final DomainId domainId : filter ) {
+ System.out.println( domainId.getId() );
+ }
+ }
+ }
+
+ private static String[][] processInputFileNames( final String[] names ) {
+ final String[][] input_file_properties = new String[ names.length ][];
+ for( int i = 0; i < names.length; ++i ) {
+ if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
+ input_file_properties[ i ] = new String[ 3 ];
+ input_file_properties[ i ][ 0 ] = names[ i ];
+ input_file_properties[ i ][ 1 ] = names[ i ];
+ input_file_properties[ i ][ 2 ] = DEFAULT_SEARCH_PARAMETER;
+ }
+ else {
+ input_file_properties[ i ] = names[ i ].split( surfacing_old.SEPARATOR_FOR_INPUT_VALUES + "" );
+ if ( input_file_properties[ i ].length != 3 ) {
+ ForesterUtil
+ .fatalError( surfacing_old.PRG_NAME,
+ "properties for the input files (hmmpfam output) are expected "
+ + "to be in the following format \"<hmmpfam output file>#<species>#<search"
+ + " parameter>\" (or just one word, which is both the filename and the species id), instead received \""
+ + names[ i ] + "\"" );
+ }
+ }
+ final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
+ if ( !ForesterUtil.isEmpty( error ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, error );
+ }
+ }
+ return input_file_properties;
+ }
+
+ private static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ if ( cla.isOptionSet( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ if ( !cla.isOptionValueSet( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "no value for 'plus-minus' file: -"
+ + surfacing_old.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
+ }
+ final File plus_minus_file = new File( cla.getOptionValue( surfacing_old.PLUS_MINUS_ANALYSIS_OPTION ) );
+ final String msg = ForesterUtil.isReadableFile( plus_minus_file );
+ if ( !ForesterUtil.isEmpty( msg ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "can not read from \"" + plus_minus_file + "\": "
+ + msg );
+ }
+ processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
+ }
+ }
+
+ // First numbers is minimal difference, second is factor.
+ private static void processPlusMinusFile( final File plus_minus_file,
+ final List<String> high_copy_base,
+ final List<String> high_copy_target,
+ final List<String> low_copy,
+ final List<Object> numbers ) {
+ Set<String> species_set = null;
+ int min_diff = PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
+ double factor = PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
+ try {
+ species_set = ForesterUtil.file2set( plus_minus_file );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getMessage() );
+ }
+ if ( species_set != null ) {
+ for( final String species : species_set ) {
+ final String species_trimmed = species.substring( 1 );
+ if ( species.startsWith( "+" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_base.add( species_trimmed );
+ }
+ else if ( species.startsWith( "*" ) ) {
+ if ( low_copy.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ high_copy_target.add( species_trimmed );
+ }
+ else if ( species.startsWith( "-" ) ) {
+ if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+ + species_trimmed + "\"" );
+ }
+ low_copy.add( species_trimmed );
+ }
+ else if ( species.startsWith( "$D" ) ) {
+ try {
+ min_diff = Integer.parseInt( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "could not parse integer value for minimal difference from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "$F" ) ) {
+ try {
+ factor = Double.parseDouble( species.substring( 3 ) );
+ }
+ catch ( final NumberFormatException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME,
+ "could not parse double value for factor from: \""
+ + species.substring( 3 ) + "\"" );
+ }
+ }
+ else if ( species.startsWith( "#" ) ) {
+ // Comment, ignore.
+ }
+ else {
+ ForesterUtil
+ .fatalError( surfacing_old.PRG_NAME,
+ "species/genome names in 'plus minus' file must begin with '*' (high copy target genome), '+' (high copy base genomes), '-' (low copy genomes), '$D=<integer>' minimal Difference (default is 1), '$F=<double>' factor (default is 1.0), double), or '#' (ignore) suffix, encountered: \""
+ + species + "\"" );
+ }
+ numbers.add( new Integer( min_diff + "" ) );
+ numbers.add( new Double( factor + "" ) );
+ }
+ }
+ else {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, "'plus minus' file [" + plus_minus_file
+ + "] appears empty" );
+ }
+ }
+
+ private static void writePresentToNexus( final File output_file,
+ final File positive_filter_file,
+ final SortedSet<DomainId> filter,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ try {
+ SurfacingUtil
+ .writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfDomainPresenceOrAbsence( gwcd_list, positive_filter_file == null ? null
+ : filter ), output_file + DOMAINS_PRESENT_NEXUS, Format.NEXUS_BINARY );
+ SurfacingUtil.writeMatrixToFile( DomainParsimonyCalculator
+ .createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ), output_file
+ + BDC_PRESENT_NEXUS, Format.NEXUS_BINARY );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ }
+ }
+
+ private static void writeProteinListsForAllSpecies( final File output_dir,
+ final SortedMap<Species, List<Protein>> protein_lists_per_species,
+ final List<GenomeWideCombinableDomains> gwcd_list ) {
+ final SortedSet<DomainId> all_domains = new TreeSet<DomainId>();
+ for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+ all_domains.addAll( gwcd.getAllDomainIds() );
+ }
+ for( final DomainId domain : all_domains ) {
+ final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + SEQ_EXTRACT_SUFFIX );
+ SurfacingUtil.checkForOutputFileWriteability( out );
+ try {
+ final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+ SurfacingUtil.extractProteinNames( protein_lists_per_species, domain, proteins_file_writer, "\t" );
+ proteins_file_writer.close();
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( surfacing_old.PRG_NAME, e.getLocalizedMessage() );
+ }
+ ForesterUtil.programMessage( surfacing_old.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+ }
+ }
+}
--- /dev/null
+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// 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.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.forester.io.parsers.PhylogenyParser;
+import org.forester.io.writers.PhylogenyWriter;
+import org.forester.phylogeny.Phylogeny;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
+import org.forester.phylogeny.factories.PhylogenyFactory;
+import org.forester.sdi.GSDI;
+import org.forester.sdi.SDI;
+import org.forester.sdi.SDIse;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public class ta {
+
+ final static private String STRIP_OPTION = "s";
+ final static private String SDISE_OPTION = "b";
+ final static private String MOST_PARSIMONIOUS_OPTION = "m";
+ final static private String HELP_OPTION_1 = "help";
+ final static private String HELP_OPTION_2 = "h";
+ final static private String DEFAULT_OUTFILE = "sdi_out.xml";
+ final static private String PRG_NAME = "sdi";
+ final static private String PRG_VERSION = "alpha 0.3";
+ final static private String PRG_DATE = "2008.03.04";
+
+ public static void main( final String args[] ) {
+ ForesterUtil.printProgramInformation( PRG_NAME, PRG_VERSION, PRG_DATE );
+ CommandLineArguments cla = null;
+ try {
+ cla = new CommandLineArguments( args );
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.fatalError( PRG_NAME, e.getMessage() );
+ }
+ if ( cla.isOptionSet( HELP_OPTION_1 ) || cla.isOptionSet( HELP_OPTION_2 ) ) {
+ System.out.println();
+ print_help();
+ System.exit( 0 );
+ }
+ else if ( ( args.length < 2 ) || ( cla.getNumberOfNames() < 2 ) || ( cla.getNumberOfNames() > 3 ) ) {
+ System.out.println();
+ System.out.println( "Wrong number of arguments." );
+ System.out.println();
+ print_help();
+ System.exit( -1 );
+ }
+ final List<String> allowed_options = new ArrayList<String>();
+ allowed_options.add( STRIP_OPTION );
+ allowed_options.add( SDISE_OPTION );
+ allowed_options.add( MOST_PARSIMONIOUS_OPTION );
+ final String dissallowed_options = cla.validateAllowedOptionsAsString( allowed_options );
+ if ( dissallowed_options.length() > 0 ) {
+ ForesterUtil.fatalError( PRG_NAME, "unknown option(s): " + dissallowed_options );
+ }
+ boolean use_sdise = false;
+ boolean strip = false;
+ boolean most_parsimonous_duplication_model = false;
+ if ( cla.isOptionSet( STRIP_OPTION ) ) {
+ strip = true;
+ }
+ if ( cla.isOptionSet( SDISE_OPTION ) ) {
+ use_sdise = true;
+ }
+ if ( cla.isOptionSet( MOST_PARSIMONIOUS_OPTION ) ) {
+ if ( use_sdise ) {
+ ForesterUtil.fatalError( PRG_NAME, "Can only use most parsimonious duplication mode with GSDI" );
+ }
+ most_parsimonous_duplication_model = true;
+ }
+ Phylogeny species_tree = null;
+ Phylogeny gene_tree = null;
+ File gene_tree_file = null;
+ File species_tree_file = null;
+ File out_file = null;
+ try {
+ gene_tree_file = cla.getFile( 0 );
+ species_tree_file = cla.getFile( 1 );
+ if ( cla.getNumberOfNames() == 3 ) {
+ out_file = cla.getFile( 2 );
+ }
+ else {
+ out_file = new File( DEFAULT_OUTFILE );
+ }
+ }
+ catch ( final IllegalArgumentException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "error in command line: " + e.getMessage() );
+ }
+ if ( ForesterUtil.isReadableFile( gene_tree_file ) != null ) {
+ ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isReadableFile( gene_tree_file ) );
+ }
+ if ( ForesterUtil.isReadableFile( species_tree_file ) != null ) {
+ ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isReadableFile( species_tree_file ) );
+ }
+ if ( ForesterUtil.isWritableFile( out_file ) != null ) {
+ ForesterUtil.fatalError( PRG_NAME, ForesterUtil.isWritableFile( out_file ) );
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( species_tree_file, true );
+ species_tree = factory.create( species_tree_file, pp )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "Failed to read species tree from \"" + gene_tree_file + "\" ["
+ + e.getMessage() + "]" );
+ }
+ try {
+ final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+ final PhylogenyParser pp = ForesterUtil.createParserDependingOnFileType( gene_tree_file, true );
+ gene_tree = factory.create( gene_tree_file, pp )[ 0 ];
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "Failed to read gene tree from \"" + gene_tree_file + "\" ["
+ + e.getMessage() + "]" );
+ }
+ gene_tree.setRooted( true );
+ species_tree.setRooted( true );
+ if ( !gene_tree.isCompletelyBinary() ) {
+ ForesterUtil.fatalError( PRG_NAME, "gene tree is not completely binary." );
+ }
+ if ( use_sdise ) {
+ if ( !species_tree.isCompletelyBinary() ) {
+ ForesterUtil.fatalError( PRG_NAME, "species tree is not completely binary." );
+ }
+ }
+ // For timing.
+ // gene_tree = Helper.createBalancedTree( 10 );
+ // species_tree = Helper.createBalancedTree( 13 );
+ // species_tree = Helper.createUnbalancedTree( 1024 );
+ // gene_tree = Helper.createUnbalancedTree( 8192 );
+ // species_tree = gene_tree.copyTree();
+ // gene_tree = species_tree.copyTree();
+ // Helper.numberSpeciesInOrder( species_tree );
+ // Helper.numberSpeciesInOrder( gene_tree );
+ // Helper.randomizeSpecies( 1, 8192, gene_tree );
+ // Helper.intervalNumberSpecies( gene_tree, 4096 );
+ // Helper.numberSpeciesInDescOrder( gene_tree );
+ System.out.println();
+ System.out.println( "Strip species tree: " + strip );
+ SDI sdi = null;
+ final long start_time = new Date().getTime();
+ try {
+ if ( use_sdise ) {
+ System.out.println();
+ System.out.println( "Using SDIse algorithm." );
+ sdi = new SDIse( gene_tree, species_tree );
+ }
+ else {
+ System.out.println();
+ System.out.println( "Using GSDI algorithm." );
+ System.out.println();
+ System.out.println( "Use most parsimonous duplication model: " + most_parsimonous_duplication_model );
+ sdi = new GSDI( gene_tree, species_tree, most_parsimonous_duplication_model );
+ }
+ }
+ catch ( final Exception e ) {
+ ForesterUtil.unexpectedFatalError( PRG_NAME, e );
+ }
+ System.out.println();
+ System.out.println( "Running time (excluding I/O): " + ( new Date().getTime() - start_time ) + "ms" );
+ try {
+ final PhylogenyWriter writer = new PhylogenyWriter();
+ writer.toPhyloXML( out_file, gene_tree, 1 );
+ }
+ catch ( final IOException e ) {
+ ForesterUtil.fatalError( PRG_NAME, "Failed to write to \"" + out_file + "\" [" + e.getMessage() + "]" );
+ }
+ System.out.println();
+ System.out.println( "Successfully wrote resulting gene tree to: " + out_file );
+ System.out.println();
+ // if ( use_sdise ) {
+ // computeMappingCostL();
+ // System.out.println( "Mapping cost : " + computeMappingCostL() );
+ // }
+ // System.out.println( "Number of duplications : " + getDuplicationsSum() );
+ if ( !use_sdise && !most_parsimonous_duplication_model ) {
+ System.out.println( "Number of potential duplications: "
+ + ( ( GSDI ) sdi ).getSpeciationOrDuplicationEventsSum() );
+ }
+ if ( !use_sdise ) {
+ System.out.println( "Number speciations : " + ( ( GSDI ) sdi ).getSpeciationsSum() );
+ }
+ System.out.println();
+ } // main( final String args[] )
+
+ private static void print_help() {
+ System.out.println( "Usage: \"" + PRG_NAME
+ + " [-options] <gene tree file name> <species tree file name> [outfile name]\"" );
+ System.out.println();
+ System.out.println( "Options:" );
+ System.out.println( " -" + STRIP_OPTION + ": to strip the species tree prior to duplication inference" );
+ System.out.println( " -" + SDISE_OPTION
+ + ": to use SDIse algorithm instead of GSDI algorithm (for binary trees only, faster)" );
+ System.out.println( " -" + MOST_PARSIMONIOUS_OPTION + ": use most parimonious duplication model for GSDI: " );
+ System.out.println( " assign nodes as speciations which would otherwise be assiged" );
+ System.out.println( " as unknown because of polytomies in the species tree" );
+ System.out.println();
+ System.out.println( "Species tree file" );
+ System.out.println( " In NHX format, with species names in species name fields unless -n option" );
+ System.out.println( " is used." );
+ System.out.println();
+ System.out.println( "Gene tree file" );
+ System.out.println( " In NHX format, with species names in species name fields and sequence names" );
+ System.out.println( " in sequence name fields." );
+ System.out.println();
+ System.out.println( "!! WARNING: GSDI algorithm is under development, please use SDIse (-b) instead !!" );
+ System.out.println();
+ } // print_help()
+}
git://source.jalview.org / jalview.git / commitdiff