X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2FHmmPfamOutputParser.java;h=2fae940976f7dea67003871466e22540295a2ac8;hb=a648fae3c8d0402dbdafa379ff3d42bbea96633d;hp=4c9914eccc1a1af774086ccd3a8772282af685bd;hpb=07d2b6864846c6c95ec1d4f1b083c248ffbcc591;p=jalview.git

diff --git a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
index 4c9914e..2fae940 100644
--- a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
@@ -22,7 +22,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.io.parsers;
 
@@ -43,7 +43,6 @@ import java.util.TreeSet;
 import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
@@ -62,7 +61,7 @@ public final class HmmPfamOutputParser {
     private static final ReturnType RETURN_TYPE_DEFAULT         = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
     private static final boolean    IGNORE_DUFS_DEFAULT         = false;
     private static final int        MAX_ALLOWED_OVERLAP_DEFAULT = -1;
-    private final Set<DomainId>     _filter;
+    private final Set<String>       _filter;
     private final FilterType        _filter_type;
     private final File              _input_file;
     private final String            _species;
@@ -85,7 +84,7 @@ public final class HmmPfamOutputParser {
     private int                     _domains_ignored_due_to_e_value;
     private int                     _domains_ignored_due_to_individual_score_cutoff;
     private int                     _domains_stored;
-    private SortedSet<DomainId>     _domains_stored_set;
+    private SortedSet<String>       _domains_stored_set;
     private long                    _time;
     private int                     _domains_ignored_due_to_negative_domain_filter;
     private Map<String, Integer>    _domains_ignored_due_to_negative_domain_filter_counts_map;
@@ -104,7 +103,7 @@ public final class HmmPfamOutputParser {
     public HmmPfamOutputParser( final File input_file,
                                 final String species,
                                 final String model_type,
-                                final Set<DomainId> filter,
+                                final Set<String> filter,
                                 final FilterType filter_type ) {
         _input_file = input_file;
         _species = species;
@@ -125,7 +124,7 @@ public final class HmmPfamOutputParser {
 
     private void addProtein( final List<Protein> proteins, final Protein current_protein ) {
         if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
-            final Set<DomainId> domain_ids_in_protein = new HashSet<DomainId>();
+            final Set<String> domain_ids_in_protein = new HashSet<String>();
             for( final Domain d : current_protein.getProteinDomains() ) {
                 domain_ids_in_protein.add( d.getDomainId() );
             }
@@ -192,7 +191,7 @@ public final class HmmPfamOutputParser {
         return _domains_stored;
     }
 
-    public SortedSet<DomainId> getDomainsStoredSet() {
+    public SortedSet<String> getDomainsStoredSet() {
         return _domains_stored_set;
     }
 
@@ -200,7 +199,7 @@ public final class HmmPfamOutputParser {
         return _e_value_maximum;
     }
 
-    private Set<DomainId> getFilter() {
+    private Set<String> getFilter() {
         return _filter;
     }
 
@@ -262,7 +261,7 @@ public final class HmmPfamOutputParser {
     }
 
     private void intitCounts() {
-        setDomainsStoredSet( new TreeSet<DomainId>() );
+        setDomainsStoredSet( new TreeSet<String>() );
         setDomainsEncountered( 0 );
         setProteinsEncountered( 0 );
         setProteinsIgnoredDueToFilter( 0 );
@@ -539,8 +538,7 @@ public final class HmmPfamOutputParser {
                     ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), id );
                     ++_domains_ignored_due_to_virus_like_id;
                 }
-                else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN )
-                        && getFilter().contains( new DomainId( id ) ) ) {
+                else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN ) && getFilter().contains( id ) ) {
                     ++_domains_ignored_due_to_negative_domain_filter;
                     ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), id );
                 }
@@ -608,7 +606,7 @@ public final class HmmPfamOutputParser {
         _domains_stored = domains_stored;
     }
 
-    private void setDomainsStoredSet( final SortedSet<DomainId> _storeddomains_stored ) {
+    private void setDomainsStoredSet( final SortedSet<String> _storeddomains_stored ) {
         _domains_stored_set = _storeddomains_stored;
     }