Class HmmPfamOutputParser


  • public final class HmmPfamOutputParser
    extends java.lang.Object
    • Constructor Detail

      • HmmPfamOutputParser

        public HmmPfamOutputParser​(java.io.File input_file,
                                   java.lang.String species,
                                   java.lang.String model_type)
      • HmmPfamOutputParser

        public HmmPfamOutputParser​(java.io.File input_file,
                                   java.lang.String species,
                                   java.util.Set<java.lang.String> filter,
                                   HmmPfamOutputParser.FilterType filter_type)
    • Method Detail

      • getDomainsEncountered

        public int getDomainsEncountered()
      • getDomainsIgnoredDueToDuf

        public int getDomainsIgnoredDueToDuf()
      • getDomainsIgnoredDueToEval

        public int getDomainsIgnoredDueToEval()
      • getDomainsIgnoredDueToIndividualScoreCutoff

        public int getDomainsIgnoredDueToIndividualScoreCutoff()
      • getDomainsIgnoredDueToNegativeDomainFilter

        public int getDomainsIgnoredDueToNegativeDomainFilter()
      • getDomainsIgnoredDueToNegativeDomainFilterCountsMap

        public java.util.Map<java.lang.String,​java.lang.Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap()
      • getDomainsIgnoredDueToOverlap

        public int getDomainsIgnoredDueToOverlap()
      • getDomainsIgnoredDueToVirusLikeIdCountsMap

        public java.util.Map<java.lang.String,​java.lang.Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap()
      • getDomainsIgnoredDueToVirusLikeIds

        public int getDomainsIgnoredDueToVirusLikeIds()
      • getDomainsStored

        public int getDomainsStored()
      • getDomainsStoredSet

        public java.util.SortedSet<java.lang.String> getDomainsStoredSet()
      • getProteinsEncountered

        public int getProteinsEncountered()
      • getProteinsIgnoredDueToFilter

        public int getProteinsIgnoredDueToFilter()
      • getProteinsStored

        public int getProteinsStored()
      • getTime

        public long getTime()
      • parse

        public java.util.List<Protein> parse()
                                      throws java.io.IOException
        Throws:
        java.io.IOException
      • setAllowNonUniqueQuery

        public void setAllowNonUniqueQuery​(boolean allow_non_unique_query)
      • setDomainsIgnoredDueToEval

        public void setDomainsIgnoredDueToEval​(int domains_ignored_due_to_e_value)
      • setDomainsIgnoredDueToIndividualScoreCutoff

        public void setDomainsIgnoredDueToIndividualScoreCutoff​(int domains_ignored_due_to_individual_score_cutoff)
      • setEValueMaximum

        public void setEValueMaximum​(double e_value_maximum)
      • setIgnoreDufs

        public void setIgnoreDufs​(boolean ignore_dufs)
      • setIgnoreEngulfedDomains

        public void setIgnoreEngulfedDomains​(boolean ignore_engulfed_domains)
        To ignore domains which are completely engulfed by domains (individual ones or stretches of overlapping ones) with better support values.
        Parameters:
        ignored_engulfed_domains -
      • setIgnoreVirusLikeIds

        public void setIgnoreVirusLikeIds​(boolean ignore_virus_like_ids)
      • setIndividualDomainScoreCutoffs

        public void setIndividualDomainScoreCutoffs​(java.util.Map<java.lang.String,​java.lang.String> individual_domain_score_cutoffs)
        Sets the individual domain score cutoff values (for example, gathering thresholds from Pfam). Domain ids are the keys, cutoffs the values.
        Parameters:
        individual_domain_score_cutoffs -
      • setMaxAllowedOverlap

        public void setMaxAllowedOverlap​(int max_allowed_overlap)
      • setVerbose

        public void setVerbose​(boolean verbose)