- public static void writeBinaryStatesMatrixToListORIGIG( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final GoNameSpace go_namespace_limit,
- final boolean domain_combinations,
- final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
- final CharacterStateMatrix.GainLossStates state,
- final String filename,
- final String indentifier_characters_separator,
- final String character_separator,
- final String title_for_html,
- final String prefix_for_html,
- final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
- final SortedSet<String> all_pfams_encountered,
- final SortedSet<String> pfams_gained_or_lost,
- final String suffix_for_per_node_events_file ) {
- if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
- throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
- }
- else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
- throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
- }
- else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
- throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
- }
- final File outfile = new File( filename );
- checkForOutputFileWriteability( outfile );
- final SortedSet<String> sorted_ids = new TreeSet<String>();
- for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
- sorted_ids.add( matrix.getIdentifier( i ) );
- }
- try {
- final Writer out = new BufferedWriter( new FileWriter( outfile ) );
- final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
- domain_combinations,
- state,
- filename );
- Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
- File per_node_go_mapped_domain_gain_loss_outfile = null;
- int per_node_counter = 0;
- out.write( "<html>" );
- out.write( SurfacingConstants.NL );
- addHtmlHead( out, title_for_html );
- out.write( SurfacingConstants.NL );
- out.write( "<body>" );
- out.write( SurfacingConstants.NL );
- out.write( "<h1>" );
- out.write( SurfacingConstants.NL );
- out.write( title_for_html );
- out.write( SurfacingConstants.NL );
- out.write( "</h1>" );
- out.write( SurfacingConstants.NL );
- out.write( "<table>" );
- out.write( SurfacingConstants.NL );
- for( final String id : sorted_ids ) {
- out.write( "<tr>" );
- out.write( "<td>" );
- out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
- writeTaxonomyLinks( out, id );
- out.write( "</td>" );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- }
- out.write( "</table>" );
- out.write( SurfacingConstants.NL );
- for( final String id : sorted_ids ) {
- out.write( SurfacingConstants.NL );
- out.write( "<h2>" );
- out.write( "<a name=\"" + id + "\">" + id + "</a>" );
- writeTaxonomyLinks( out, id );
- out.write( "</h2>" );
- out.write( SurfacingConstants.NL );
- out.write( "<table>" );
- out.write( SurfacingConstants.NL );
- out.write( "<tr>" );
- out.write( "<td><b>" );
- out.write( "Pfam domain(s)" );
- out.write( "</b></td><td><b>" );
- out.write( "GO term acc" );
- out.write( "</b></td><td><b>" );
- out.write( "GO term" );
- out.write( "</b></td><td><b>" );
- out.write( "Penultimate GO term" );
- out.write( "</b></td><td><b>" );
- out.write( "GO namespace" );
- out.write( "</b></td>" );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- out.write( "</tr>" );
- out.write( SurfacingConstants.NL );
- per_node_counter = 0;
- if ( matrix.getNumberOfCharacters() > 0 ) {
- per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
- + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
- SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
- per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
- .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
- }
- else {
- per_node_go_mapped_domain_gain_loss_outfile = null;
- per_node_go_mapped_domain_gain_loss_outfile_writer = null;
- }
- for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
- // Not nice:
- // using null to indicate either UNCHANGED_PRESENT or GAIN.
- if ( ( matrix.getState( id, c ) == state )
- || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
- .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
- final String character = matrix.getCharacter( c );
- String domain_0 = "";
- String domain_1 = "";
- if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
- final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
- if ( s.length != 2 ) {
- throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
- + character + "]" );
- }
- domain_0 = s[ 0 ];
- domain_1 = s[ 1 ];
- }
- else {
- domain_0 = character;
- }
- writeDomainData( domain_id_to_go_ids_map,
- go_id_to_term_map,
- go_namespace_limit,
- out,
- domain_0,
- domain_1,
- prefix_for_html,
- character_separator,
- domain_id_to_secondary_features_maps,
- null );
- all_pfams_encountered.add( domain_0 );
- if ( pfams_gained_or_lost != null ) {
- pfams_gained_or_lost.add( domain_0 );
- }
- if ( !ForesterUtil.isEmpty( domain_1 ) ) {
- all_pfams_encountered.add( domain_1 );
- if ( pfams_gained_or_lost != null ) {
- pfams_gained_or_lost.add( domain_1 );
- }
- }
- if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
- writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
- domain_0,
- domain_1 );
- per_node_counter++;
- }
- }
- }
- if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
- per_node_go_mapped_domain_gain_loss_outfile_writer.close();
- if ( per_node_counter < 1 ) {
- per_node_go_mapped_domain_gain_loss_outfile.delete();
- }
- per_node_counter = 0;
- }
- out.write( "</table>" );
- out.write( SurfacingConstants.NL );
- out.write( "<hr>" );
- out.write( SurfacingConstants.NL );
- } // for( final String id : sorted_ids ) {
- out.write( "</body>" );
- out.write( SurfacingConstants.NL );
- out.write( "</html>" );
- out.write( SurfacingConstants.NL );
- out.flush();
- out.close();
- }
- catch ( final IOException e ) {
- ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
- }
- ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
- }
-