X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fapplication%2Fsurfacing.java;h=141db17d78e239612bc29e8e7e63a93e5f5a4fcb;hb=7a194f3da2c3a659ecc67bff021d9f64c845e923;hp=a3e9524a69baed5c8c4430ca33490fd8da428eb1;hpb=c24204e229d63d29d2d1d79f6914c3ba1faeaaa1;p=jalview.git

diff --git a/forester/java/src/org/forester/application/surfacing.java b/forester/java/src/org/forester/application/surfacing.java
index a3e9524..141db17 100644
--- a/forester/java/src/org/forester/application/surfacing.java
+++ b/forester/java/src/org/forester/application/surfacing.java
@@ -806,62 +806,56 @@ public class surfacing {
             }
             SurfacingUtil.checkForOutputFileWriteability( dcc_outfile );
         }
-        File pfam_to_go_file = null;
-        Map<String, List<GoId>> domain_id_to_go_ids_map = null;
-        int domain_id_to_go_ids_count = 0;
+        File pfam_to_go_file = new File( "pfam2go.txt" );
         if ( cla.isOptionSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
             if ( !cla.isOptionValueSet( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for Pfam to GO mapping file: -"
                         + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>" );
             }
             pfam_to_go_file = new File( cla.getOptionValue( surfacing.PFAM_TO_GO_FILE_USE_OPTION ) );
-            final String error = ForesterUtil.isReadableFile( pfam_to_go_file );
-            if ( !ForesterUtil.isEmpty( error ) ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error );
-            }
-            try {
-                final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
-                final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
-                domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
-                if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
-                    ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
-                                                       "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
-                }
-                domain_id_to_go_ids_count = parser.getMappingCount();
-            }
-            catch ( final IOException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+        }
+        final String error1 = ForesterUtil.isReadableFile( pfam_to_go_file );
+        if ( !ForesterUtil.isEmpty( error1 ) ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read Pfam to GO mapping file: " + error1 );
+        }
+        Map<String, List<GoId>> domain_id_to_go_ids_map = null;
+        int domain_id_to_go_ids_count = 0;
+        try {
+            final PfamToGoParser parser = new PfamToGoParser( pfam_to_go_file );
+            final List<PfamToGoMapping> pfam_to_go_mappings = parser.parse();
+            domain_id_to_go_ids_map = SurfacingUtil.createDomainIdToGoIdMap( pfam_to_go_mappings );
+            if ( parser.getMappingCount() < domain_id_to_go_ids_map.size() ) {
+                ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME,
+                                                   "parser.getMappingCount() < domain_id_to_go_ids_map.size()" );
             }
+            domain_id_to_go_ids_count = parser.getMappingCount();
         }
-        File go_obo_file = null;
-        List<GoTerm> go_terms = null;
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from Pfam to GO mapping file: " + e );
+        }
+        File go_obo_file = new File( "go.obo" );
         if ( cla.isOptionSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
             if ( !cla.isOptionValueSet( surfacing.GO_OBO_FILE_USE_OPTION ) ) {
                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for GO OBO file: -"
                         + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>" );
             }
-            if ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot use GO OBO file (-"
-                        + surfacing.GO_OBO_FILE_USE_OPTION + "=<file>) without Pfam to GO mapping file ("
-                        + surfacing.PFAM_TO_GO_FILE_USE_OPTION + "=<file>)" );
-            }
             go_obo_file = new File( cla.getOptionValue( surfacing.GO_OBO_FILE_USE_OPTION ) );
-            final String error = ForesterUtil.isReadableFile( go_obo_file );
-            if ( !ForesterUtil.isEmpty( error ) ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error );
-            }
-            try {
-                final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
-                go_terms = parser.parse();
-                if ( parser.getGoTermCount() != go_terms.size() ) {
-                    ForesterUtil
-                            .unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
-                }
-            }
-            catch ( final IOException e ) {
-                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
+        }
+        final String error2 = ForesterUtil.isReadableFile( go_obo_file );
+        if ( !ForesterUtil.isEmpty( error2 ) ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read GO OBO file: " + error2 );
+        }
+        List<GoTerm> go_terms = null;
+        try {
+            final OBOparser parser = new OBOparser( go_obo_file, OBOparser.ReturnType.BASIC_GO_TERM );
+            go_terms = parser.parse();
+            if ( parser.getGoTermCount() != go_terms.size() ) {
+                ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "parser.getGoTermCount() != go_terms.size()" );
             }
         }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read from GO OBO file: " + e );
+        }
         Map<GoId, GoTerm> go_id_to_term_map = null;
         if ( ( ( domain_id_to_go_ids_map != null ) && ( domain_id_to_go_ids_map.size() > 0 ) )
                 && ( ( go_terms != null ) && ( go_terms.size() > 0 ) ) ) {
@@ -2198,7 +2192,10 @@ public class surfacing {
         System.out.println();
         System.out.println();
         System.out
-                .println( "Example: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -detail=punctilious -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" );
+                .println( "Example 1: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -no_eo -ie=0.01 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -out_dir=_tf1 -o=tf1" );
+        System.out.println();
+        System.out
+                .println( "Example 2: surfacing -p2g=pfam2go.txt -obo=go.obo -species_tree=tol_156.xml -last -ignore_viral_ids -no_eo -ie=0.1 -dufs -genomes=genomes_all.txt -pos_filter=tf_1.txt -all_prot -all_prot_e=0.1 -out_dir=_tf1_e01_ape01 -o=tf1_e01_ape01" );
         System.out.println();
     }
 }