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

diff --git a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
index 2fae940..96729a4 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmPfamOutputParser.java
@@ -44,7 +44,6 @@ 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 HmmPfamOutputParser {
@@ -65,7 +64,6 @@ public final class HmmPfamOutputParser {
     private final FilterType        _filter_type;
     private final File              _input_file;
     private final String            _species;
-    private final String            _model_type;
     private double                  _e_value_maximum;
     private Map<String, String>     _individual_domain_score_cutoffs;
     private boolean                 _ignore_dufs;
@@ -94,7 +92,6 @@ public final class HmmPfamOutputParser {
     public HmmPfamOutputParser( final File input_file, final String species, final String model_type ) {
         _input_file = input_file;
         _species = species;
-        _model_type = model_type;
         _filter = null;
         _filter_type = FilterType.NONE;
         init();
@@ -102,12 +99,10 @@ public final class HmmPfamOutputParser {
 
     public HmmPfamOutputParser( final File input_file,
                                 final String species,
-                                final String model_type,
                                 final Set<String> filter,
                                 final FilterType filter_type ) {
         _input_file = input_file;
         _species = species;
-        _model_type = model_type;
         _filter = filter;
         _filter_type = filter_type;
         init();
@@ -219,10 +214,6 @@ public final class HmmPfamOutputParser {
         return _max_allowed_overlap;
     }
 
-    private String getModelType() {
-        return _model_type;
-    }
-
     public int getProteinsEncountered() {
         return _proteins_encountered;
     }
@@ -342,8 +333,8 @@ public final class HmmPfamOutputParser {
                     }
                     else if ( isVerbose() ) {
                         ForesterUtil.printWarningMessage( getClass().getName(), "query \"" + query
-                                + "\" is not unique [line " + line_number + "] in ["
-                                + getInputFile().getCanonicalPath() + "]" );
+                                                          + "\" is not unique [line " + line_number + "] in ["
+                                                          + getInputFile().getCanonicalPath() + "]" );
                     }
                 }
                 else {
@@ -408,9 +399,9 @@ public final class HmmPfamOutputParser {
                     if ( ( getMaxAllowedOverlap() != HmmPfamOutputParser.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;
@@ -437,38 +428,36 @@ public final class HmmPfamOutputParser {
                 int to = -1;
                 double e_value = -1;
                 double score = -1;
-                boolean is_complete_hmm_match = false;
-                boolean is_complete_query_match = false;
                 try {
                     from = Integer.valueOf( from_str ).intValue();
                 }
                 catch ( final NumberFormatException e ) {
                     throw new IOException( "could not parse seq-f from \"" + line + "\" [line " + line_number
-                            + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                           + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 try {
                     to = Integer.valueOf( to_str ).intValue();
                 }
                 catch ( final NumberFormatException e ) {
                     throw new IOException( "could not parse seq-t from \"" + line + "\" [line " + line_number
-                            + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                           + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 try {
                     score = Double.valueOf( score_str ).doubleValue();
                 }
                 catch ( final NumberFormatException e ) {
                     throw new IOException( "could not parse score from \"" + line + "\" [line " + line_number
-                            + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                           + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 try {
                     e_value = Double.valueOf( e_value_str ).doubleValue();
                 }
                 catch ( final NumberFormatException e ) {
                     throw new IOException( "could not parse E-value from \"" + line + "\" [line " + line_number
-                            + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                           + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 if ( hmm_match_str.equals( "[]" ) ) {
-                    is_complete_hmm_match = true;
+                    //is_complete_hmm_match = true;
                 }
                 else if ( !( hmm_match_str.equals( ".]" ) || hmm_match_str.equals( "[." ) || hmm_match_str
                         .equals( ".." ) ) ) {
@@ -476,7 +465,7 @@ public final class HmmPfamOutputParser {
                             + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 if ( query_match_str.equals( ".." ) ) {
-                    is_complete_query_match = true;
+                    // is_complete_query_match = true;
                 }
                 else if ( !( query_match_str.equals( ".]" ) || query_match_str.equals( "[." ) || query_match_str
                         .equals( "[]" ) ) ) {
@@ -497,14 +486,14 @@ public final class HmmPfamOutputParser {
                 }
                 catch ( final NumberFormatException e ) {
                     throw new IOException( "could not parse domain number from \"" + line + "\" [line " + line_number
-                            + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                           + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 try {
                     total = Integer.valueOf( ( total_str ) ).intValue();
                 }
                 catch ( final NumberFormatException e ) {
                     throw new IOException( "could not parse domain count from \"" + line + "\" [line " + line_number
-                            + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                           + "] in [" + getInputFile().getCanonicalPath() + "]" );
                 }
                 ++_domains_encountered;
                 boolean failed_cutoff = false;
@@ -517,7 +506,7 @@ public final class HmmPfamOutputParser {
                     }
                     else {
                         throw new IOException( "could not find a score cutoff value for domain id \"" + id
-                                + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
+                                               + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
                     }
                 }
                 final String uc_id = id.toUpperCase();
@@ -624,8 +613,8 @@ public final class HmmPfamOutputParser {
     /**
      * To ignore domains which are completely engulfed by domains (individual
      * ones or stretches of overlapping ones) with better support values.
-     * 
-     * 
+     *
+     *
      * @param ignored_engulfed_domains
      */
     public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) {
@@ -639,7 +628,7 @@ public final class HmmPfamOutputParser {
     /**
      * Sets the individual domain score cutoff values (for example, gathering
      * thresholds from Pfam). Domain ids are the keys, cutoffs the values.
-     * 
+     *
      * @param individual_domain_score_cutoffs
      */
     public void setIndividualDomainScoreCutoffs( final Map<String, String> individual_domain_score_cutoffs ) {