*/
public final class DomainCountsDifferenceUtil {
- private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES = COPY_CALCULATION_MODE.MIN;
private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_BASE_SPECIES = COPY_CALCULATION_MODE.MIN;
+ private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_HIGH_COPY_TARGET_SPECIES = COPY_CALCULATION_MODE.MIN;
private static final COPY_CALCULATION_MODE COPY_CALC_MODE_FOR_LOW_COPY_SPECIES = COPY_CALCULATION_MODE.MAX;
private static final String PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX = ".prot";
- //FIXME really needs to be tested!
- private static void addCounts( final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
- final BinaryDomainCombination dc,
- final GenomeWideCombinableDomains genome,
- final Set<BinaryDomainCombination> bdc ) {
- if ( !copy_counts.containsKey( dc ) ) {
- copy_counts.put( dc, new ArrayList<Integer>() );
- }
- if ( bdc.contains( dc )
- && ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
- final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains()
- .get( dc.getId1() );
- copy_counts.get( dc ).add( count );
- }
- else {
- copy_counts.get( dc ).add( 0 );
- }
- }
-
- private static void addCounts( final SortedMap<String, List<Integer>> copy_counts,
- final String domain,
- final GenomeWideCombinableDomains genome ) {
- if ( !copy_counts.containsKey( domain ) ) {
- copy_counts.put( domain, new ArrayList<Integer>() );
- }
- if ( genome.contains( domain ) ) {
- copy_counts.get( domain ).add( genome.get( domain ).getKeyDomainProteinsCount() );
- }
- else {
- copy_counts.get( domain ).add( 0 );
- }
- }
-
- private static StringBuilder addGoInformation( final String d,
- final Map<String, List<GoId>> domain_id_to_go_ids_map,
- final Map<GoId, GoTerm> go_id_to_term_map ) {
- final StringBuilder sb = new StringBuilder();
- if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty()
- || !domain_id_to_go_ids_map.containsKey( d ) ) {
- return sb;
- }
- final List<GoId> go_ids = domain_id_to_go_ids_map.get( d );
- for( int i = 0; i < go_ids.size(); ++i ) {
- final GoId go_id = go_ids.get( i );
- if ( go_id_to_term_map.containsKey( go_id ) ) {
- appendGoTerm( sb, go_id_to_term_map.get( go_id ) );
- sb.append( "<br>" );
- }
- else {
- sb.append( "go id \"" + go_id + "\" not found [" + d + "]" );
- }
- }
- return sb;
- }
-
- private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) {
- final GoId go_id = go_term.getGoId();
- sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
- + "</a>" );
- sb.append( ":" );
- sb.append( go_term.getName() );
- sb.append( " [" );
- sb.append( go_term.getGoNameSpace().toShortString() );
- sb.append( "]" );
- }
-
public static void calculateCopyNumberDifferences( final List<GenomeWideCombinableDomains> genomes,
final SortedMap<Species, List<Protein>> protein_lists_per_species,
final List<String> high_copy_base_species,
if ( high_copy_base_species.contains( high_copy_target_species )
|| low_copy_species.contains( high_copy_target_species ) ) {
throw new IllegalArgumentException( "species [" + high_copy_target_species
- + "] appears in other list as well" );
+ + "] appears in other list as well" );
}
if ( min_diff < 0 ) {
throw new IllegalArgumentException( "attempt to use negative addition [" + min_diff + "]" );
writeGoIdsToFile( passing_gos_writer, go_ids_of_passing_domains );
}
+ //FIXME really needs to be tested!
+ private static void addCounts( final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
+ final BinaryDomainCombination dc,
+ final GenomeWideCombinableDomains genome,
+ final Set<BinaryDomainCombination> bdc ) {
+ if ( !copy_counts.containsKey( dc ) ) {
+ copy_counts.put( dc, new ArrayList<Integer>() );
+ }
+ if ( bdc.contains( dc )
+ && ( ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains().get( dc.getId1() ) != null ) ) {
+ final int count = ( ( BasicCombinableDomains ) genome.get( dc.getId0() ) ).getCombiningDomains()
+ .get( dc.getId1() );
+ copy_counts.get( dc ).add( count );
+ }
+ else {
+ copy_counts.get( dc ).add( 0 );
+ }
+ }
+
+ private static void addCounts( final SortedMap<String, List<Integer>> copy_counts,
+ final String domain,
+ final GenomeWideCombinableDomains genome ) {
+ if ( !copy_counts.containsKey( domain ) ) {
+ copy_counts.put( domain, new ArrayList<Integer>() );
+ }
+ if ( genome.contains( domain ) ) {
+ copy_counts.get( domain ).add( genome.get( domain ).getKeyDomainProteinsCount() );
+ }
+ else {
+ copy_counts.get( domain ).add( 0 );
+ }
+ }
+
+ private static StringBuilder addGoInformation( final String d,
+ final Map<String, List<GoId>> domain_id_to_go_ids_map,
+ final Map<GoId, GoTerm> go_id_to_term_map ) {
+ final StringBuilder sb = new StringBuilder();
+ if ( ( domain_id_to_go_ids_map == null ) || domain_id_to_go_ids_map.isEmpty()
+ || !domain_id_to_go_ids_map.containsKey( d ) ) {
+ return sb;
+ }
+ final List<GoId> go_ids = domain_id_to_go_ids_map.get( d );
+ for( int i = 0; i < go_ids.size(); ++i ) {
+ final GoId go_id = go_ids.get( i );
+ if ( go_id_to_term_map.containsKey( go_id ) ) {
+ appendGoTerm( sb, go_id_to_term_map.get( go_id ) );
+ sb.append( "<br>" );
+ }
+ else {
+ sb.append( "go id \"" + go_id + "\" not found [" + d + "]" );
+ }
+ }
+ return sb;
+ }
+
+ private static void appendGoTerm( final StringBuilder sb, final GoTerm go_term ) {
+ final GoId go_id = go_term.getGoId();
+ sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
+ + "</a>" );
+ sb.append( ":" );
+ sb.append( go_term.getName() );
+ sb.append( " [" );
+ sb.append( go_term.getGoNameSpace().toShortString() );
+ sb.append( "]" );
+ }
+
private static void calculateDomainCountsBasedValue( final SortedMap<BinaryDomainCombination, Double> copy_values,
final SortedMap<BinaryDomainCombination, List<Integer>> copy_counts,
final BinaryDomainCombination bdc,
final SortedMap<BinaryDomainCombination, Double> low_copy_values,
final SortedSet<BinaryDomainCombination> all_bdcs,
final Map<String, Set<BinaryDomainCombination>> bdcs_per_genome )
- throws IOException {
+ throws IOException {
int counter = 0;
int total_absense_counter = 0;
int not_total_absense_counter = 0;
- SurfacingUtil.addHtmlHead( html_writer, "Binary Domain Combination Copy Differences" );
+ SurfacingUtil.writeHtmlHead( html_writer, "Binary Domain Combination Copy Differences" );
html_writer.write( "<body><table>" );
for( final BinaryDomainCombination bdc : all_bdcs ) {
if ( ( high_copy_base_values.get( bdc ) > 0 ) && ( high_copy_target_values.get( bdc ) > 0 )
}
++counter;
html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + bdc.getId0()
- + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
- + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
+ + "\">" + bdc.getId0() + "</a> = <a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK
+ + bdc.getId1() + "\">" + bdc.getId1() + "</a>" );
html_writer.write( "</td><td>" );
html_writer.write( "<table>" );
for( final GenomeWideCombinableDomains genome : genomes ) {
bdcs_per_genome,
species,
html_writer,
- "#0000FF" );
+ "#0000FF" );
html_writer.write( "</tr>" );
}
else if ( low_copy_species.contains( species ) ) {
bdcs_per_genome,
species,
html_writer,
- "#A0A0A0" );
+ "#A0A0A0" );
html_writer.write( "</tr>" );
}
else if ( high_copy_base_species.contains( species ) ) {
bdcs_per_genome,
species,
html_writer,
- "#404040" );
+ "#404040" );
html_writer.write( "</tr>" );
}
}
final SortedSet<String> all_domains,
final SortedSet<GoId> go_ids_of_passing_domains,
final SortedMap<Species, List<Protein>> protein_lists_per_species )
- throws IOException {
+ throws IOException {
int counter = 0;
int total_absense_counter = 0;
int not_total_absense_counter = 0;
- SurfacingUtil.addHtmlHead( html_writer, "Domain Copy Differences" );
+ SurfacingUtil.writeHtmlHead( html_writer, "Domain Copy Differences" );
html_writer.write( "<body><table>" );
for( final String domain_id : all_domains ) {
if ( ( high_copy_base_values.get( domain_id ) > 0 ) && ( high_copy_target_values.get( domain_id ) > 0 )
plain_writer.write( domain_id );
plain_writer.write( SurfacingConstants.NL );
html_writer.write( "<tr><td><a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_id
- + "\">" + domain_id + "</a></td><td>" );
+ + "\">" + domain_id + "</a></td><td>" );
html_writer.write( addGoInformation( domain_id, domain_id_to_go_ids_map, go_id_to_term_map )
- .toString() );
+ .toString() );
html_writer.write( "</td><td>" );
html_writer.write( "<table>" );
for( final GenomeWideCombinableDomains genome : genomes ) {
species,
plain_writer,
html_writer,
- "#0000FF" );
+ "#0000FF" );
html_writer.write( "</tr>" );
}
else if ( low_copy_species.contains( species ) ) {
species,
plain_writer,
html_writer,
- "#A0A0A0" );
+ "#A0A0A0" );
html_writer.write( "</tr>" );
}
else if ( high_copy_base_species.contains( species ) ) {
species,
plain_writer,
html_writer,
- "#404040" );
+ "#404040" );
html_writer.write( "</tr>" );
}
}
final SortedMap<Species, List<Protein>> protein_lists_per_species,
final String domain_id ) throws IOException {
final File my_proteins_file = new File( proteins_file_base.getParentFile() + ForesterUtil.FILE_SEPARATOR
- + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
+ + domain_id + PLUS_MINUS_PROTEINS_FILE_DOM_SUFFIX );
SurfacingUtil.checkForOutputFileWriteability( my_proteins_file );
final Writer proteins_file_writer = new BufferedWriter( new FileWriter( my_proteins_file ) );
SurfacingUtil.extractProteinNames( protein_lists_per_species,
}
public static enum COPY_CALCULATION_MODE {
- MEAN, MEDIAN, MAX, MIN
+ MAX, MEAN, MEDIAN, MIN
}
}
git://source.jalview.org / jalview.git / blobdiff