From: cmzmasek@gmail.com Date: Wed, 27 Nov 2013 18:10:08 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=612e51e63eb66025a04439fc380384a945a4a30f;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java index 40fc471..ebecc7a 100644 --- a/forester/java/src/org/forester/application/surfacing.java +++ b/forester/java/src/org/forester/application/surfacing.java @@ -87,6 +87,7 @@ public class surfacing { private static final int MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING = 1000; public final static String DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS = "graph_analysis_out"; + public final static String DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION = "dcc"; 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"; @@ -336,6 +337,7 @@ public class surfacing { 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( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ); allowed_options.add( OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ); allowed_options.add( CONSIDER_DOMAIN_COMBINATION_DIRECTEDNESS_AND_ADJACENCY ); allowed_options.add( WRITE_TO_NEXUS_OPTION ); @@ -376,6 +378,10 @@ public class surfacing { if ( cla.isOptionSet( DOMAIN_COMBINITONS_OUTPUT_OPTION_FOR_GRAPH_ANALYSIS ) ) { output_binary_domain_combinationsfor_graph_analysis = true; } + final boolean output_binary_domain_combinationsfor_counts = false; + if ( cla.isOptionSet( DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION ) ) { + output_binary_domain_combinationsfor_graph_analysis = true; + } if ( cla.isOptionSet( surfacing.MAX_FS_E_VALUE_OPTION ) ) { try { fs_e_value_max = cla.getOptionValueAsDouble( surfacing.MAX_FS_E_VALUE_OPTION ); @@ -1653,12 +1659,15 @@ public class surfacing { protein_length_stats_by_dc, domain_number_stats_by_dc ) ); 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_counts ) { + 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, @@ -2157,6 +2166,8 @@ public class surfacing { System.out.println( surfacing.SECONDARY_FEATURES_PARSIMONY_MAP_FILE + "=: to perfom parsimony analysis on secondary features" ); System.out.println( surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=: to presence/absence genome analysis" ); + System.out.println( surfacing.DOMAIN_COMBINITONS_COUNTS_OUTPUT_OPTION + + ": to output binary domain counts (as individual files)" ); 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" ); diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java index 9b5ae80..fabf400 100644 --- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java @@ -66,6 +66,9 @@ public class AdjactantDirectedBinaryDomainCombination extends BasicBinaryDomainC final AdjactantDirectedBinaryDomainCombination dc = new AdjactantDirectedBinaryDomainCombination( n_terminal, c_terminal ); ADDC_POOL.put( code, dc ); + if ( VERBOSE && ( ADDC_POOL.size() % 100 == 0 ) ) { + System.out.println( " addc pool size: " + ADDC_POOL.size() ); + } return dc; } } diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java index 47b4024..3d41e51 100644 --- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java @@ -35,6 +35,7 @@ import org.forester.util.ForesterUtil; public class BasicBinaryDomainCombination implements BinaryDomainCombination { + final static boolean VERBOSE = true; final private static Map DC_POOL = new HashMap(); final private static Map S_POOL = new HashMap(); short _id0; @@ -176,9 +177,6 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { else { final String s = getId0() + SEPARATOR + getId1(); S_POOL.put( code, s ); - if ( S_POOL.size() % 100 == 0 ) { - System.out.println( "ss=" + S_POOL.size() ); - } return s; } } @@ -208,8 +206,8 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination { else { final BasicBinaryDomainCombination dc = new BasicBinaryDomainCombination( id0, id1 ); DC_POOL.put( code, dc ); - if ( DC_POOL.size() % 100 == 0 ) { - System.out.println( "s=" + DC_POOL.size() ); + if ( VERBOSE && ( DC_POOL.size() % 100 == 0 ) ) { + System.out.println( " dc pool size: " + DC_POOL.size() ); } return dc; } diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java index 75abce7..a309603 100644 --- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java +++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java @@ -64,6 +64,9 @@ public class DirectedBinaryDomainCombination extends BasicBinaryDomainCombinatio else { final DirectedBinaryDomainCombination dc = new DirectedBinaryDomainCombination( n_terminal, c_terminal ); DDC_POOL.put( code, dc ); + if ( VERBOSE && ( DDC_POOL.size() % 100 == 0 ) ) { + System.out.println( " ddc pool size: " + DDC_POOL.size() ); + } return dc; } }