inprogress

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index f2019d4..ce716fe 100644 (file)
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -222,16 +222,14 @@ public class surfacing {
     private static final int                                  JACKNIFE_NUMBER_OF_RESAMPLINGS_DEFAULT                                        = 100;
     final static private long                                 JACKNIFE_RANDOM_SEED_DEFAULT                                                  = 19;
     final static private double                               JACKNIFE_RATIO_DEFAULT                                                        = 0.5;
-    //final static private String  INFER_SPECIES_TREES_OPTION                                             = "species_tree_inference";
     final static private String                               FILTER_POSITIVE_OPTION                                                        = "pos_filter";
     final static private String                               FILTER_NEGATIVE_OPTION                                                        = "neg_filter";
     final static private String                               FILTER_NEGATIVE_DOMAINS_OPTION                                                = "neg_dom_filter";
-    final static private String                               INPUT_FILES_FROM_FILE_OPTION                                                  = "input";
+    final static private String                               INPUT_GENOMES_FILE_OPTION                                                     = "genomes";
     final static private String                               INPUT_SPECIES_TREE_OPTION                                                     = "species_tree";
     final static private String                               SEQ_EXTRACT_OPTION                                                            = "prot_extract";
-    final static private char                                 SEPARATOR_FOR_INPUT_VALUES                                                    = '#';
-    final static private String                               PRG_VERSION                                                                   = "2.252";
-    final static private String                               PRG_DATE                                                                      = "2012.08.01";
+    final static private String                               PRG_VERSION                                                                   = "2.260";
+    final static private String                               PRG_DATE                                                                      = "130721";
     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;
@@ -283,7 +281,7 @@ public class surfacing {
     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 final boolean                              PERFORM_DC_REGAIN_PROTEINS_STATS                                              = true;
-    private static final boolean                              DA_ANALYSIS                                                                   = true;
+    private static final boolean                              DA_ANALYSIS                                                                   = false;
 
     private static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
                                                                  final String[][] input_file_properties,
@@ -610,10 +608,9 @@ public class surfacing {
         allowed_options.add( JACKNIFE_RANDOM_SEED_OPTION );
         allowed_options.add( JACKNIFE_RATIO_OPTION );
         allowed_options.add( INPUT_SPECIES_TREE_OPTION );
-        //allowed_options.add( INFER_SPECIES_TREES_OPTION );
         allowed_options.add( FILTER_POSITIVE_OPTION );
         allowed_options.add( FILTER_NEGATIVE_OPTION );
-        allowed_options.add( INPUT_FILES_FROM_FILE_OPTION );
+        allowed_options.add( INPUT_GENOMES_FILE_OPTION );
         allowed_options.add( RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION );
         allowed_options.add( FILTER_NEGATIVE_DOMAINS_OPTION );
         allowed_options.add( IGNORE_VIRAL_IDS );
@@ -790,30 +787,22 @@ public class surfacing {
                                         plus_minus_analysis_high_copy_target_species,
                                         plus_minus_analysis_high_low_copy_species,
                                         plus_minus_analysis_numbers );
-        File input_files_file = null;
-        String[] input_file_names_from_file = null;
-        if ( cla.isOptionSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
-            if ( !cla.isOptionValueSet( surfacing.INPUT_FILES_FROM_FILE_OPTION ) ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input files file: -"
-                        + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
-            }
-            input_files_file = new File( cla.getOptionValue( surfacing.INPUT_FILES_FROM_FILE_OPTION ) );
-            final String msg = ForesterUtil.isReadableFile( input_files_file );
+        File input_genomes_file = null;
+        if ( cla.isOptionSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
+            if ( !cla.isOptionValueSet( surfacing.INPUT_GENOMES_FILE_OPTION ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for input genomes file: -"
+                        + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
+            }
+            input_genomes_file = new File( cla.getOptionValue( surfacing.INPUT_GENOMES_FILE_OPTION ) );
+            final String msg = ForesterUtil.isReadableFile( input_genomes_file );
             if ( !ForesterUtil.isEmpty( msg ) ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + input_files_file + "\": " + msg );
-            }
-            try {
-                input_file_names_from_file = ForesterUtil.file2array( input_files_file );
-            }
-            catch ( final IOException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read from \"" + input_files_file + "\": " + e );
+                ForesterUtil
+                        .fatalError( surfacing.PRG_NAME, "can not read from \"" + input_genomes_file + "\": " + msg );
             }
         }
-        if ( ( cla.getNumberOfNames() < 1 )
-                && ( ( input_file_names_from_file == null ) || ( input_file_names_from_file.length < 1 ) ) ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME,
-                                     "No hmmpfam output file indicated is input: use comand line directly or "
-                                             + surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>" );
+        else {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "no input genomes file given: "
+                    + surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>" );
         }
         DomainSimilarity.DomainSimilarityScoring scoring = SCORING_DEFAULT;
         if ( cla.isOptionSet( surfacing.SCORING_OPTION ) ) {
@@ -854,7 +843,6 @@ public class surfacing {
         double output_list_of_all_proteins_per_domain_e_value_max = -1;
         if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_OPTIONS ) ) {
             output_protein_lists_for_all_domains = true;
-            //
             if ( cla.isOptionSet( surfacing.OUTPUT_LIST_OF_ALL_PROTEINS_PER_DOMAIN_E_VALUE_OPTION ) ) {
                 try {
                     output_list_of_all_proteins_per_domain_e_value_max = cla
@@ -864,7 +852,6 @@ public class surfacing {
                     ForesterUtil.fatalError( surfacing.PRG_NAME, "no acceptable value for per domain E-value maximum" );
                 }
             }
-            //
         }
         Detailedness detailedness = DETAILEDNESS_DEFAULT;
         if ( cla.isOptionSet( surfacing.DETAILEDNESS_OPTION ) ) {
@@ -989,8 +976,6 @@ public class surfacing {
                 domain_similarity_print_option = PrintableDomainSimilarity.PRINT_OPTION.HTML;
             }
             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_HTML ) ) {
-                // domain_similarity_print_option =
-                // DomainSimilarity.PRINT_OPTION.SIMPLE_HTML;
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "simple HTML output not implemented yet :(" );
             }
             else if ( sort.equals( surfacing.DOMAIN_SIMILARITY_PRINT_OPTION_SIMPLE_TAB_DELIMITED ) ) {
@@ -1033,12 +1018,12 @@ public class surfacing {
                         + surfacing.DOMAIN_COUNT_SORT_COMBINATIONS_COUNT + ">\"" );
             }
         }
-        String[][] input_file_properties = null;
-        if ( input_file_names_from_file != null ) {
-            input_file_properties = surfacing.processInputFileNames( input_file_names_from_file );
-        }
-        else {
-            input_file_properties = surfacing.processInputFileNames( cla.getNames() );
+        final String[][] input_file_properties = processInputGenomesFile( input_genomes_file );
+        for( final String[] input_file_propertie : input_file_properties ) {
+            for( int j = 0; j < input_file_propertie.length; j++ ) {
+                System.out.print( input_file_propertie[ j ] + " " );
+            }
+            System.out.println();
         }
         final int number_of_genomes = input_file_properties.length;
         if ( number_of_genomes < 2 ) {
@@ -1054,7 +1039,7 @@ public class surfacing {
                                                  automated_pairwise_comparison_suffix,
                                                  out_dir );
         for( int i = 0; i < number_of_genomes; i++ ) {
-            File dcc_outfile = new File( input_file_properties[ i ][ 0 ]
+            File dcc_outfile = new File( input_file_properties[ i ][ 1 ]
                     + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
             if ( out_dir != null ) {
                 dcc_outfile = new File( out_dir + ForesterUtil.FILE_SEPARATOR + dcc_outfile );
@@ -1206,17 +1191,6 @@ public class surfacing {
                 }
             }
         }
-        //        boolean infer_species_trees = false;
-        //        if ( cla.isOptionSet( surfacing.INFER_SPECIES_TREES_OPTION ) ) {
-        //            if ( ( output_file == null ) || ( number_of_genomes < 3 )
-        //                    || ForesterUtil.isEmpty( automated_pairwise_comparison_suffix ) ) {
-        //                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot infer species trees (-"
-        //                        + surfacing.INFER_SPECIES_TREES_OPTION + " without pairwise analyses ("
-        //                        + surfacing.PAIRWISE_DOMAIN_COMPARISONS_OPTION
-        //                        + "=<suffix for pairwise comparison output files>)" );
-        //            }
-        //            infer_species_trees = true;
-        //        }
         File[] intree_files = null;
         Phylogeny[] intrees = null;
         if ( cla.isOptionSet( surfacing.INPUT_SPECIES_TREE_OPTION ) ) {
@@ -1333,12 +1307,8 @@ public class surfacing {
                                              + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>)" );
         }
         System.out.println( "Output directory            : " + out_dir );
-        if ( input_file_names_from_file != null ) {
-            System.out.println( "Input files names from      : " + input_files_file + " ["
-                    + input_file_names_from_file.length + " input files]" );
-            html_desc.append( "<tr><td>Input files names from:</td><td>" + input_files_file + " ["
-                    + input_file_names_from_file.length + " input files]</td></tr>" + nl );
-        }
+        System.out.println( "Input genomes from          : " + input_genomes_file );
+        html_desc.append( "<tr><td>Input genomes from:</td><td>" + input_genomes_file + "</td></tr>" + nl );
         if ( positive_filter_file != null ) {
             final int filter_size = filter.size();
             System.out.println( "Positive protein filter     : " + positive_filter_file + " [" + filter_size
@@ -1613,10 +1583,6 @@ public class surfacing {
                 System.out.println( "    Ratio                   : " + ForesterUtil.round( jacknife_ratio, 2 ) );
                 System.out.println( "    Random number seed      : " + random_seed );
             }
-            //                if ( infer_species_trees ) {
-            //                    html_desc.append( "<tr><td>Infer species trees:</td><td>true</td></tr>" + nl );
-            //                    System.out.println( "  Infer species trees       : true" );
-            //                }
             if ( ( intrees != null ) && ( intrees.length > 0 ) ) {
                 for( final File intree_file : intree_files ) {
                     html_desc.append( "<tr><td>Intree for gain/loss parsimony analysis:</td><td>" + intree_file
@@ -1777,8 +1743,10 @@ public class surfacing {
             System.out.println();
             System.out.println( ( i + 1 ) + "/" + number_of_genomes );
             log( ( i + 1 ) + "/" + number_of_genomes, log_writer );
-            System.out.println( "Processing                                     : " + input_file_properties[ i ][ 0 ] );
-            log( "Genome                                         : " + input_file_properties[ i ][ 0 ], log_writer );
+            System.out.println( "Processing                                     : " + input_file_properties[ i ][ 1 ]
+                    + " [" + input_file_properties[ i ][ 0 ] + "]" );
+            log( "Genome                                         : " + input_file_properties[ i ][ 1 ] + " ["
+                    + input_file_properties[ i ][ 0 ] + "]", log_writer );
             HmmscanPerDomainTableParser parser = null;
             INDIVIDUAL_SCORE_CUTOFF ind_score_cutoff = INDIVIDUAL_SCORE_CUTOFF.NONE;
             if ( individual_score_cutoffs != null ) {
@@ -1924,10 +1892,6 @@ public class surfacing {
                         + parser.getProteinsIgnoredDueToFilter() );
             }
             html_desc.append( "</td></tr>" + nl );
-            // domain_partner_counts_array[ i ] =
-            // Methods.getDomainPartnerCounts( protein_domain_collections_array[
-            // i ],
-            // false, input_file_properties[ i ][ 1 ] );
             try {
                 int count = 0;
                 for( final Protein protein : protein_list ) {
@@ -2599,7 +2563,7 @@ public class surfacing {
                 + "=<file>: to filter out proteins containing at least one domain listed in <file>" );
         System.out.println( surfacing.FILTER_NEGATIVE_DOMAINS_OPTION
                 + "=<file>: to filter out (ignore) domains listed in <file>" );
-        System.out.println( surfacing.INPUT_FILES_FROM_FILE_OPTION + "=<file>: to read input files from <file>" );
+        System.out.println( surfacing.INPUT_GENOMES_FILE_OPTION + "=<file>: to read input files from <file>" );
         System.out
                 .println( surfacing.RANDOM_SEED_FOR_FITCH_PARSIMONY_OPTION
                         + "=<seed>: seed for random number generator for Fitch Parsimony analysis (type: long, default: no randomization - given a choice, prefer absence" );
@@ -2621,14 +2585,14 @@ public class surfacing {
         System.out.println();
         System.out.println( "Example 1: java -Xms128m -Xmx512m -cp path/to/forester.jar"
                 + " org.forester.application.surfacing p2g=pfam2go_2012_02_07.txt -dufs -cos=Pfam_260_NC1"
-                + " -no_eo -mo=0 -input=genomes_limited.txt -out_dir=out -o=o "
+                + " -no_eo -mo=0 -genomes=eukaryotes.txt -out_dir=out -o=o "
                 + " -species_tree=tol.xml -obo=gene_ontology_2012_02_07.obo -pos_filter=f.txt -all_prot" );
         System.out.println();
         System.out.println( "Example 2: java -Xms128m -Xmx512m -cp path/to/forester.jar"
                 + " org.forester.application.surfacing -detail=punctilious -o=TEST.html -pwc=TEST"
                 + " -cos=Pfam_ls_22_TC2 -p2g=pfam2go -obo=gene_ontology_edit.obo "
-                + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo "
-                + "-ds_output=detailed_html -scoring=domains -sort=alpha human mouse brafl strpu" );
+                + "-dc_sort=dom -ignore_with_self -no_singles -e=0.001 -mo=1 -no_eo -genomes=eukaryotes.txt "
+                + "-ds_output=detailed_html -scoring=domains -sort=alpha " );
         System.out.println();
     }
 
@@ -2653,24 +2617,17 @@ public class surfacing {
         }
     }
 
-    private static String[][] processInputFileNames( final String[] names ) {
-        final String[][] input_file_properties = new String[ names.length ][];
-        for( int i = 0; i < names.length; ++i ) {
-            if ( names[ i ].indexOf( SEPARATOR_FOR_INPUT_VALUES ) < 0 ) {
-                input_file_properties[ i ] = new String[ 2 ];
-                input_file_properties[ i ][ 0 ] = names[ i ];
-                input_file_properties[ i ][ 1 ] = names[ i ];
-            }
-            else {
-                input_file_properties[ i ] = names[ i ].split( surfacing.SEPARATOR_FOR_INPUT_VALUES + "" );
-                if ( input_file_properties[ i ].length != 3 ) {
-                    ForesterUtil
-                            .fatalError( surfacing.PRG_NAME,
-                                         "properties for the input files (hmmpfam output) are expected "
-                                                 + "to be in the following format \"<hmmpfam output file>#<species>\" (or just one word, which is both the filename and the species id), instead received \""
-                                                 + names[ i ] + "\"" );
-                }
-            }
+    private static String[][] processInputGenomesFile( final File input_genomes ) {
+        String[][] input_file_properties = null;
+        try {
+            input_file_properties = ForesterUtil.file22dArray( input_genomes );
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                     "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
+                                             + e.getLocalizedMessage() );
+        }
+        for( int i = 0; i < input_file_properties.length; ++i ) {
             final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
             if ( !ForesterUtil.isEmpty( error ) ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, error );

diff --git a/forester/java/src/org/forester/go/BasicGoSubset.java b/forester/java/src/org/forester/go/BasicGoSubset.java
index f1658d7..420f01b 100644 (file)
--- a/forester/java/src/org/forester/go/BasicGoSubset.java
+++ b/forester/java/src/org/forester/go/BasicGoSubset.java
@@ -58,17 +58,8 @@ public class BasicGoSubset implements GoSubset {
         else if ( my_s.equals( GOSLIM_POMBE_STR ) ) {
             _type = Type.GOSLIM_POMBE;
         }
-        else if ( my_s.equals( HIGH_LEVEL_ANNOTATION_QC_STR ) ) {
-            _type = Type.HIGH_LEVEL_ANNOTATION_QC;
-        }
-        else if ( my_s.equals( UNVETTED_STR ) ) {
-            _type = Type.UNVETTED;
-        }
-        else if ( my_s.equals( MF_NEEDS_REVIEW_STR ) ) {
-            _type = Type.MF_NEEDS_REVIEW;
-        }
         else {
-            throw new IllegalArgumentException( "unknown GO subset type: " + my_s );
+            _type = Type.OTHER;
         }
     }
 
@@ -134,17 +125,9 @@ public class BasicGoSubset implements GoSubset {
             case GOSLIM_POMBE:
                 sb.append( GOSLIM_POMBE_STR );
                 break;
-            case MF_NEEDS_REVIEW:
-                sb.append( MF_NEEDS_REVIEW_STR );
-                break;
-            case HIGH_LEVEL_ANNOTATION_QC:
-                sb.append( HIGH_LEVEL_ANNOTATION_QC_STR );
-                break;
-            case UNVETTED:
-                sb.append( UNVETTED_STR );
+            case OTHER:
+                sb.append( "other" );
                 break;
-            default:
-                new AssertionError( "unknown type: " + getType() );
         }
         return sb.toString();
     }

diff --git a/forester/java/src/org/forester/go/BasicGoXRef.java b/forester/java/src/org/forester/go/BasicGoXRef.java
index c523102..548a7a6 100644 (file)
--- a/forester/java/src/org/forester/go/BasicGoXRef.java
+++ b/forester/java/src/org/forester/go/BasicGoXRef.java
@@ -100,7 +100,7 @@ public class BasicGoXRef implements GoXRef {
             _type = Type.SABIO_RK;
         }
         else {
-            throw new IllegalArgumentException( "unknown GO xref type: " + type );
+            _type = Type.OTHER;
         }
         _xref = sa[ 1 ].trim();
     }
@@ -192,6 +192,9 @@ public class BasicGoXRef implements GoXRef {
             case WIKIPEDIA:
                 sb.append( WIKIPEDIA_STR );
                 break;
+            case OTHER:
+                sb.append( "other" );
+                break;
             default:
                 new AssertionError( "unknown type: " + getType() );
         }

diff --git a/forester/java/src/org/forester/go/GoSubset.java b/forester/java/src/org/forester/go/GoSubset.java
index 02a2f03..2b7d2b5 100644 (file)
--- a/forester/java/src/org/forester/go/GoSubset.java
+++ b/forester/java/src/org/forester/go/GoSubset.java
@@ -27,18 +27,15 @@ package org.forester.go;
 
 public interface GoSubset extends Comparable<GoSubset> {
 
-    public static final String GOSLIM_GENERIC_STR           = "goslim_generic";
-    public static final String GOSLIM_GOA_STR               = "goslim_goa";
-    public static final String GOSLIM_PIR_STR               = "goslim_pir";
-    public static final String GOSUBSET_PROK_STR            = "gosubset_prok";
-    public static final String GOSLIM_CANDIDA_STR           = "goslim_candida";
-    public static final String GOSLIM_ASPERGILLUS_STR       = "goslim_aspergillus";
-    public static final String GOSLIM_PLANT_STR             = "goslim_plant";
-    public static final String GOSLIM_YEAST_STR             = "goslim_yeast";
-    public static final String GOSLIM_POMBE_STR             = "goslim_pombe";
-    public static final String HIGH_LEVEL_ANNOTATION_QC_STR = "high_level_annotation_qc";
-    public static final String UNVETTED_STR                 = "unvetted";
-    public static final String MF_NEEDS_REVIEW_STR          = "mf_needs_review";
+    public static final String GOSLIM_GENERIC_STR     = "goslim_generic";
+    public static final String GOSLIM_GOA_STR         = "goslim_goa";
+    public static final String GOSLIM_PIR_STR         = "goslim_pir";
+    public static final String GOSUBSET_PROK_STR      = "gosubset_prok";
+    public static final String GOSLIM_CANDIDA_STR     = "goslim_candida";
+    public static final String GOSLIM_ASPERGILLUS_STR = "goslim_aspergillus";
+    public static final String GOSLIM_PLANT_STR       = "goslim_plant";
+    public static final String GOSLIM_YEAST_STR       = "goslim_yeast";
+    public static final String GOSLIM_POMBE_STR       = "goslim_pombe";
 
     public Type getType();
 
@@ -52,8 +49,6 @@ public interface GoSubset extends Comparable<GoSubset> {
         GOSLIM_PLANT,
         GOSLIM_YEAST,
         GOSLIM_POMBE,
-        HIGH_LEVEL_ANNOTATION_QC,
-        UNVETTED,
-        MF_NEEDS_REVIEW;
+        OTHER;
     }
 }

diff --git a/forester/java/src/org/forester/go/GoXRef.java b/forester/java/src/org/forester/go/GoXRef.java
index e0a4ca8..794a5be 100644 (file)
--- a/forester/java/src/org/forester/go/GoXRef.java
+++ b/forester/java/src/org/forester/go/GoXRef.java
@@ -74,6 +74,7 @@ public interface GoXRef extends Comparable<GoXRef> {
         CORUM,
         UNIPATHWAY,
         PO,
-        SABIO_RK;
+        SABIO_RK,
+        OTHER;
     }
 }

diff --git a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
index 9d9a441..81cdf08 100644 (file)
--- a/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/AdjactantDirectedBinaryDomainCombination.java
@@ -36,13 +36,15 @@ public class AdjactantDirectedBinaryDomainCombination extends BasicBinaryDomainC
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        //   _id_0 = n_terminal.getId();
-        //  _id_1 = c_terminal.getId();
         _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId();
     }
 
     public AdjactantDirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {
-        this( new DomainId( n_terminal ), new DomainId( c_terminal ) );
+        super();
+        if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
+            throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
+        }
+        _data = n_terminal + BinaryDomainCombination.SEPARATOR + c_terminal;
     }
 
     public static AdjactantDirectedBinaryDomainCombination createInstance( final String ids ) {

diff --git a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
index 39c7450..da009b5 100644 (file)
--- a/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/BasicBinaryDomainCombination.java
@@ -34,13 +34,7 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     String _data;
 
-    //String _id_0;
-    // String _id_1;
-    //DomainId _id_0;
-    //DomainId _id_1;
     BasicBinaryDomainCombination() {
-        //_id_0 = null;
-        // _id_1 = null;
         _data = null;
     }
 
@@ -48,17 +42,11 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
         if ( ( id_0 == null ) || ( id_1 == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        final String my_id_0 = id_0.trim();
-        final String my_id_1 = id_1.trim();
-        if ( my_id_0.toLowerCase().compareTo( my_id_1.toLowerCase() ) < 0 ) {
-            //_id_0 = my_id_0;
-            //_id_1 = my_id_1;
-            _data = my_id_0 + BinaryDomainCombination.SEPARATOR + my_id_1;
+        if ( id_0.toLowerCase().compareTo( id_1.toLowerCase() ) < 0 ) {
+            _data = id_0 + BinaryDomainCombination.SEPARATOR + id_1;
         }
         else {
-            //_id_0 = my_id_1;
-            // _id_1 = my_id_0;
-            _data = my_id_1 + BinaryDomainCombination.SEPARATOR + my_id_0;
+            _data = id_1 + BinaryDomainCombination.SEPARATOR + id_0;
         }
     }
 
@@ -109,14 +97,11 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
 
     @Override
     public DomainId getId1() {
-        // return new DomainId( _id_1 );
         return new DomainId( _data.split( BinaryDomainCombination.SEPARATOR )[ 1 ] );
     }
 
     @Override
     public int hashCode() {
-        // return getId0().hashCode() + ( 19 * getId1().hashCode() );
-        // return ( _id_0 + _id_1 ).hashCode();
         return _data.hashCode();
     }
 
@@ -167,11 +152,6 @@ public class BasicBinaryDomainCombination implements BinaryDomainCombination {
     @Override
     public String toString() {
         return _data;
-        //        final StringBuffer sb = new StringBuffer();
-        //        sb.append( _id_0 );
-        //        sb.append( BinaryDomainCombination.SEPARATOR );
-        //        sb.append( _id_1 );
-        //        return sb.toString();
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {

diff --git a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
index 2e5d797..bfd7b2e 100644 (file)
--- a/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
+++ b/forester/java/src/org/forester/surfacing/DirectedBinaryDomainCombination.java
@@ -36,13 +36,15 @@ public class DirectedBinaryDomainCombination extends BasicBinaryDomainCombinatio
         if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
             throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
         }
-        //_id_0 = n_terminal.getId();
-        //_id_1 = c_terminal.getId();
         _data = n_terminal.getId() + BinaryDomainCombination.SEPARATOR + c_terminal.getId();
     }
 
     public DirectedBinaryDomainCombination( final String n_terminal, final String c_terminal ) {
-        this( new DomainId( n_terminal ), new DomainId( c_terminal ) );
+        super();
+        if ( ( n_terminal == null ) || ( c_terminal == null ) ) {
+            throw new IllegalArgumentException( "attempt to create binary domain combination using null" );
+        }
+        _data = n_terminal + BinaryDomainCombination.SEPARATOR + c_terminal;
     }
 
     public static BinaryDomainCombination createInstance( final String ids ) {

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index abcd31f..9497ea9 100644 (file)
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -1748,7 +1748,7 @@ public final class SurfacingUtil {
                                                                           final GenomeWideCombinableDomains gwcd,
                                                                           final int i,
                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
-        File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
+        File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
         if ( output_dir != null ) {
             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
@@ -2046,7 +2046,7 @@ public final class SurfacingUtil {
                                                           final GenomeWideCombinableDomains gwcd,
                                                           final int i,
                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
-        File dc_outfile = new File( input_file_properties[ i ][ 0 ]
+        File dc_outfile = new File( input_file_properties[ i ][ 1 ]
                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
         if ( output_dir != null ) {
             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
@@ -2062,7 +2062,7 @@ public final class SurfacingUtil {
         }
         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
         try {
-            per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
+            per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
             if ( stats.getN() < 2 ) {
                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );

diff --git a/forester/java/src/org/forester/surfacing/TestSurfacing.java b/forester/java/src/org/forester/surfacing/TestSurfacing.java
index bb4a722..3efaccb 100644 (file)
--- a/forester/java/src/org/forester/surfacing/TestSurfacing.java
+++ b/forester/java/src/org/forester/surfacing/TestSurfacing.java
@@ -1245,7 +1245,7 @@ public class TestSurfacing {
             final BasicBinaryDomainCombination s6 = new BasicBinaryDomainCombination( "b", "c" );
             final BasicBinaryDomainCombination s7 = new BasicBinaryDomainCombination( "d", "a" );
             final BasicBinaryDomainCombination s8 = new BasicBinaryDomainCombination( "b", "d" );
-            final BinaryDomainCombination s9 = BasicBinaryDomainCombination.createInstance( " z-z=a-aa " );
+            final BinaryDomainCombination s9 = BasicBinaryDomainCombination.createInstance( "z-z=a-aa" );
             if ( !s9.toString().equals( "a-aa=z-z" ) ) {
                 System.out.println( s9.toString() );
                 return false;

diff --git a/forester/java/src/org/forester/util/ForesterUtil.java b/forester/java/src/org/forester/util/ForesterUtil.java
index c98edc0..47e6aa7 100644 (file)
--- a/forester/java/src/org/forester/util/ForesterUtil.java
+++ b/forester/java/src/org/forester/util/ForesterUtil.java
@@ -477,6 +477,34 @@ public final class ForesterUtil {
         return ary;
     }
 
+    public static String[][] file22dArray( final File file ) throws IOException {
+        final List<String> list = new ArrayList<String>();
+        final BufferedReader in = new BufferedReader( new FileReader( file ) );
+        String str;
+        while ( ( str = in.readLine() ) != null ) {
+            str = str.trim();
+            if ( ( str.length() > 0 ) && !str.startsWith( "#" ) ) {
+                list.add( str );
+            }
+        }
+        in.close();
+        final String[][] ary = new String[ list.size() ][ 2 ];
+        final Pattern pa = Pattern.compile( "(\\S+)\\s+(\\S+)" );
+        int i = 0;
+        for( final String s : list ) {
+            final Matcher m = pa.matcher( s );
+            if ( m.matches() ) {
+                ary[ i ][ 0 ] = m.group( 1 );
+                ary[ i ][ 1 ] = m.group( 2 );
+                ++i;
+            }
+            else {
+                throw new IOException( "unexpcted format: " + s );
+            }
+        }
+        return ary;
+    }
+
     final public static List<String> file2list( final File file ) throws IOException {
         final List<String> list = new ArrayList<String>();
         final BufferedReader in = new BufferedReader( new FileReader( file ) );