in progress

[jalview.git] / forester / java / src / org / forester / io / parsers / HmmscanPerDomainTableParser.java

diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
index 4495009..f595349 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -45,7 +45,6 @@ import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
 import org.forester.protein.Protein;
-import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
 
 public final class HmmscanPerDomainTableParser {
@@ -64,6 +63,7 @@ public final class HmmscanPerDomainTableParser {
     private static final boolean          IGNORE_DUFS_DEFAULT         = false;
     private static final int              MAX_ALLOWED_OVERLAP_DEFAULT = -1;
     private static final boolean          IGNORE_REPLACED_RRMS        = false;
+    private static final boolean          IGNORE_hGDE_amylase         = true;                                                      //TODO eventually remove me, added 10/22/13
     private final Set<String>             _filter;
     private final FilterType              _filter_type;
     private final File                    _input_file;
@@ -164,9 +164,9 @@ public final class HmmscanPerDomainTableParser {
         if ( ( getMaxAllowedOverlap() != HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT )
                 || isIgnoreEngulfedDomains() ) {
             final int domains_count = current_protein.getNumberOfProteinDomains();
-            current_protein = SurfacingUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
-                                                                      isIgnoreEngulfedDomains(),
-                                                                      current_protein );
+            current_protein = ForesterUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
+                                                                     isIgnoreEngulfedDomains(),
+                                                                     current_protein );
             final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
             _domains_stored -= domains_removed;
             _domains_ignored_due_to_overlap += domains_removed;
@@ -451,6 +451,8 @@ public final class HmmscanPerDomainTableParser {
                     && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id
                             .contains( "RRM_6" ) ) ) {
             }
+            else if ( IGNORE_hGDE_amylase && ( uc_id.equals( "hGDE_amylase" ) ) ) {
+            }
             else if ( isIgnoreVirusLikeIds()
                     && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
                             || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )