Class HmmscanPerDomainTableParser


  • public final class HmmscanPerDomainTableParser
    extends java.lang.Object
    • Method Detail

      • isAllowProteinsWithSameName

        public boolean isAllowProteinsWithSameName()
      • getDomainsEncountered

        public int getDomainsEncountered()
      • getDomainsIgnoredDueToDuf

        public int getDomainsIgnoredDueToDuf()
      • getDomainsIgnoredDueToIEval

        public int getDomainsIgnoredDueToIEval()
      • getDomainsIgnoredDueToFsEval

        public int getDomainsIgnoredDueToFsEval()
      • 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
      • setFsEValueMaximum

        public void setFsEValueMaximum​(double fs_e_value_maximum)
      • setIEValueMaximum

        public void setIEValueMaximum​(double i_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)
      • setIndividualScoreCutoffs

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

        public void setMaxAllowedOverlap​(int max_allowed_overlap)