in progress

[jalview.git] / forester / java / src / org / forester / application / surfacing.java

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index aafd989..62c6981 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -99,6 +99,7 @@ import org.forester.util.ForesterUtil;
 
 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_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";
@@ -234,7 +235,7 @@ public class surfacing {
     final static private String                               SEQ_EXTRACT_OPTION                                                     = "prot_extract";
     final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                             = '#';
     final static private String                               PRG_VERSION                                                            = "2.210";
-    final static private String                               PRG_DATE                                                               = "2011.12.08";
+    final static private String                               PRG_DATE                                                               = "2012.02.21";
     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;
@@ -277,6 +278,13 @@ public class surfacing {
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX                       = "_indep_dc_gains_fitch_lists.txt";
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX        = "_indep_dc_gains_fitch_lists_for_go_mapping.txt";
     public static final String                                INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique.txt";
+    public static final String                                LIMIT_SPEC_FOR_PROT_EX                                                 = null;                                                                                                                                                                                       // e.g. "HUMAN"; set to null for not using this feature (default).
+    public static final String BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED  = "_dc_MAPPED_secondary_features_fitch"
+        + ForesterConstants.PHYLO_XML_SUFFIX;
+    public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX =  "_indep_dc_gains_fitch_counts_MAPPED.txt";
+    public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX =  "_indep_dc_gains_fitch_lists_MAPPED.txt";
+    public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_MAPPED.txt";
+    public static final String INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX = "_indep_dc_gains_fitch_lists_for_go_mapping_unique_MAPPED.txt";
 
     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                                                  final String[][] input_file_properties,
@@ -1945,7 +1953,8 @@ public class surfacing {
                         SurfacingUtil.extractProteinNames( protein_list,
                                                            query_domain_ids_array[ j ],
                                                            query_domains_writer_ary[ j ],
-                                                           "\t" );
+                                                           "\t",
+                                                           LIMIT_SPEC_FOR_PROT_EX );
                         query_domains_writer_ary[ j ].flush();
                     }
                     catch ( final IOException e ) {
@@ -2076,7 +2085,7 @@ public class surfacing {
             String my_outfile = output_file.toString();
             Map<Character, Writer> split_writers = null;
             Writer writer = null;
-            if ( similarities.size() > 1000 ) {
+            if ( similarities.size() > MINIMAL_NUMBER_OF_SIMILARITIES_FOR_SPLITTING ) {
                 if ( my_outfile.endsWith( ".html" ) ) {
                     my_outfile = my_outfile.substring( 0, my_outfile.length() - 5 );
                 }
@@ -2373,8 +2382,9 @@ public class surfacing {
         System.out.println();
     }
 
-    private static void createSplitWriters( File out_dir, String my_outfile, Map<Character, Writer> split_writers )
-            throws IOException {
+    private static void createSplitWriters( final File out_dir,
+                                            final String my_outfile,
+                                            final Map<Character, Writer> split_writers ) throws IOException {
         split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
                 + "_domains_A.html" ) ) );
         split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
@@ -2428,7 +2438,7 @@ public class surfacing {
         split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
                 + "_domains_Z.html" ) ) );
         split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
-                + "_09.html" ) ) );
+                + "_domains_0.html" ) ) );
     }
 
     private static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
@@ -2786,7 +2796,11 @@ public class surfacing {
             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" );
+                SurfacingUtil.extractProteinNames( protein_lists_per_species,
+                                                   domain,
+                                                   proteins_file_writer,
+                                                   "\t",
+                                                   LIMIT_SPEC_FOR_PROT_EX );
                 proteins_file_writer.close();
             }
             catch ( final IOException e ) {