import org.forester.protein.Protein;
import org.forester.species.Species;
import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
-import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
+import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
import org.forester.util.AsciiHistogram;
import org.forester.util.BasicDescriptiveStatistics;
import org.forester.util.BasicTable;
w.write( SurfacingConstants.NL );
w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
w.write( SurfacingConstants.NL );
+ //
+ w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.pl:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ //
+ w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ w.write( "a.ps:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; font-size: 7pt;}" );
+ w.write( SurfacingConstants.NL );
+ //
w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
w.write( SurfacingConstants.NL );
w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
}
public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
- final Detailedness detailedness,
- final GoAnnotationOutput go_annotation_output,
- final Map<GoId, GoTerm> go_id_to_term_map,
- final GoNameSpace go_namespace_limit ) {
- if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
- throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
- }
+ final Detailedness detailedness ) {
for( final DomainSimilarity domain_similarity : domain_similarities ) {
if ( domain_similarity instanceof PrintableDomainSimilarity ) {
final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
printable_domain_similarity.setDetailedness( detailedness );
- printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
- printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
- printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
}
}
}
out.write( species + "\t" );
}
out.write( ForesterUtil.LINE_SEPARATOR );
- // DescriptiveStatistics stats_for_domain = domain_lengths
- // .calculateMeanBasedStatistics();
- //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
- //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
}
}
out.write( ForesterUtil.LINE_SEPARATOR );
}
}
out.close();
- // final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
- // for( int i = 0; i < number_of_genomes; ++i ) {
- // final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
- // histogram_datas
- // .add( new HistogramData( species.toString(), domain_lengths_table
- // .calculateMeanBasedStatisticsForSpecies( species )
- // .getDataAsDoubleArray(), 5, 600, null, 60 ) );
- // }
- // final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
- // hf.setVisible( true );
System.gc();
}
}
}
- public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
- final StringBuilder html_title,
- final Writer single_writer,
- Map<Character, Writer> split_writers,
- final SortedSet<DomainSimilarity> similarities,
- final boolean treat_as_binary,
- final List<Species> species_order,
- final PrintableDomainSimilarity.PRINT_OPTION print_option,
- final DomainSimilarity.DomainSimilaritySortField sort_field,
- final DomainSimilarity.DomainSimilarityScoring scoring,
- final boolean verbose,
- final Map<String, Integer> tax_code_to_id_map )
+ public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
+ final StringBuilder html_title,
+ final Writer simple_tab_writer,
+ final Writer single_writer,
+ Map<Character, Writer> split_writers,
+ final SortedSet<DomainSimilarity> similarities,
+ final boolean treat_as_binary,
+ final List<Species> species_order,
+ final PrintableDomainSimilarity.PRINT_OPTION print_option,
+ final DomainSimilarity.DomainSimilarityScoring scoring,
+ final boolean verbose,
+ final Map<String, Integer> tax_code_to_id_map )
throws IOException {
- final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
- String histogram_title = null;
- switch ( sort_field ) {
- case ABS_MAX_COUNTS_DIFFERENCE:
- if ( treat_as_binary ) {
- histogram_title = "absolute counts difference:";
- }
- else {
- histogram_title = "absolute (maximal) counts difference:";
- }
- break;
- case MAX_COUNTS_DIFFERENCE:
- if ( treat_as_binary ) {
- histogram_title = "counts difference:";
- }
- else {
- histogram_title = "(maximal) counts difference:";
- }
- break;
- case DOMAIN_ID:
- histogram_title = "score mean:";
- break;
- case MIN:
- histogram_title = "score minimum:";
- break;
- case MAX:
- histogram_title = "score maximum:";
- break;
- case MAX_DIFFERENCE:
- if ( treat_as_binary ) {
- histogram_title = "difference:";
- }
- else {
- histogram_title = "(maximal) difference:";
- }
- break;
- case MEAN:
- histogram_title = "score mean:";
- break;
- case SD:
- histogram_title = "score standard deviation:";
- break;
- case SPECIES_COUNT:
- histogram_title = "species number:";
- break;
- default:
- throw new AssertionError( "Unknown sort field: " + sort_field );
- }
- for( final DomainSimilarity similarity : similarities ) {
- switch ( sort_field ) {
- case ABS_MAX_COUNTS_DIFFERENCE:
- stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
- break;
- case MAX_COUNTS_DIFFERENCE:
- stats.addValue( similarity.getMaximalDifferenceInCounts() );
- break;
- case DOMAIN_ID:
- stats.addValue( similarity.getMeanSimilarityScore() );
- break;
- case MIN:
- stats.addValue( similarity.getMinimalSimilarityScore() );
- break;
- case MAX:
- stats.addValue( similarity.getMaximalSimilarityScore() );
- break;
- case MAX_DIFFERENCE:
- stats.addValue( similarity.getMaximalDifference() );
- break;
- case MEAN:
- stats.addValue( similarity.getMeanSimilarityScore() );
- break;
- case SD:
- stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
- break;
- case SPECIES_COUNT:
- stats.addValue( similarity.getSpecies().size() );
- break;
- default:
- throw new AssertionError( "Unknown sort field: " + sort_field );
- }
- }
- AsciiHistogram histo = null;
- if ( stats.getMin() < stats.getMin() ) {
- histo = new AsciiHistogram( stats, histogram_title );
- }
- if ( verbose ) {
- if ( histo != null ) {
- System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
- }
- System.out.println();
- System.out.println( "N : " + stats.getN() );
- System.out.println( "Min : " + stats.getMin() );
- System.out.println( "Max : " + stats.getMax() );
- System.out.println( "Mean : " + stats.arithmeticMean() );
- if ( stats.getN() > 1 ) {
- System.out.println( "SD : " + stats.sampleStandardDeviation() );
- }
- else {
- System.out.println( "SD : n/a" );
- }
- System.out.println( "Median : " + stats.median() );
- if ( stats.getN() > 1 ) {
- System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
- }
- else {
- System.out.println( "Pearsonian skewness : n/a" );
- }
- }
if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
split_writers = new HashMap<Character, Writer>();
split_writers.put( '_', single_writer );
w.write( "<html>" );
w.write( SurfacingConstants.NL );
if ( key != '_' ) {
- addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
+ addHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
}
else {
- addHtmlHead( w, "DCs (" + html_title + ")" );
+ addHtmlHead( w, "DC analysis (" + html_title + ")" );
}
w.write( SurfacingConstants.NL );
w.write( "<body>" );
w.write( html_desc.toString() );
w.write( SurfacingConstants.NL );
w.write( "<hr>" );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tt><pre>" );
- w.write( SurfacingConstants.NL );
- if ( histo != null ) {
- w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
- w.write( SurfacingConstants.NL );
- }
- w.write( "</pre></tt>" );
- w.write( SurfacingConstants.NL );
- w.write( "<table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- if ( stats.getN() > 1 ) {
- w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
- }
- else {
- w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
- }
- w.write( SurfacingConstants.NL );
- w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
- w.write( SurfacingConstants.NL );
- if ( stats.getN() > 1 ) {
- w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
- }
- else {
- w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
- }
- w.write( SurfacingConstants.NL );
- w.write( "</table>" );
- w.write( SurfacingConstants.NL );
- w.write( "<br>" );
- w.write( SurfacingConstants.NL );
- w.write( "<hr>" );
w.write( SurfacingConstants.NL );
w.write( "<br>" );
w.write( SurfacingConstants.NL );
w.write( "<table>" );
w.write( SurfacingConstants.NL );
+ w.write( "<tr><td><b>Domains:</b></td></tr>" );
+ w.write( SurfacingConstants.NL );
}
break;
}
+ //
+ for( final DomainSimilarity similarity : similarities ) {
+ if ( ( species_order != null ) && !species_order.isEmpty() ) {
+ ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+ }
+ if ( single_writer != null ) {
+ single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ single_writer.write( SurfacingConstants.NL );
+ }
+ else {
+ Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+ .charAt( 0 ) );
+ if ( local_writer == null ) {
+ local_writer = split_writers.get( '0' );
+ }
+ local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+ + similarity.getDomainId() + "</a></b></td></tr>" );
+ local_writer.write( SurfacingConstants.NL );
+ }
+ }
for( final Writer w : split_writers.values() ) {
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<hr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
w.write( SurfacingConstants.NL );
}
+ //
for( final DomainSimilarity similarity : similarities ) {
if ( ( species_order != null ) && !species_order.isEmpty() ) {
( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
}
+ if ( simple_tab_writer != null ) {
+ simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
+ tax_code_to_id_map ).toString() );
+ }
if ( single_writer != null ) {
single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
single_writer.write( SurfacingConstants.NL );
local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
local_writer.write( SurfacingConstants.NL );
}
- // for( final Writer w : split_writers.values() ) {
- //w.write( SurfacingConstants.NL );
- // }
}
switch ( print_option ) {
case HTML:
for( final Writer w : split_writers.values() ) {
w.close();
}
- return stats;
+ }
+
+ private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
+ throws IOException {
+ w.write( "<hr>" );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tt><pre>" );
+ w.write( SurfacingConstants.NL );
+ if ( histo != null ) {
+ w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
+ w.write( SurfacingConstants.NL );
+ }
+ w.write( "</pre></tt>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
+ w.write( SurfacingConstants.NL );
+ if ( stats.getN() > 1 ) {
+ w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
+ }
+ else {
+ w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
+ }
+ w.write( SurfacingConstants.NL );
+ w.write( "</table>" );
+ w.write( SurfacingConstants.NL );
+ w.write( "<br>" );
+ w.write( SurfacingConstants.NL );
}
public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
git://source.jalview.org / jalview.git / blobdiff