Package org.forester.io.parsers

Class HmmscanPerDomainTableParser

java.lang.Object
org.forester.io.parsers.HmmscanPerDomainTableParser
public final class HmmscanPerDomainTableParser extends Object

  • Constructor Details

  • Method Details

    • 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 Map<String,Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap()

    • getDomainsIgnoredDueToOverlap

      public int getDomainsIgnoredDueToOverlap()

    • getDomainsIgnoredDueToVirusLikeIdCountsMap

      public Map<String,Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap()

    • getDomainsIgnoredDueToVirusLikeIds

      public int getDomainsIgnoredDueToVirusLikeIds()

    • getDomainsStored

      public int getDomainsStored()

    • getDomainsStoredSet

      public SortedSet<String> getDomainsStoredSet()

    • getIndividualCutoffAppliesTo

      public HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo()

    • getProteinsEncountered

      public int getProteinsEncountered()

    • getProteinsIgnoredDueToFilter

      public int getProteinsIgnoredDueToFilter()

    • getProteinsStored

      public int getProteinsStored()

    • getTime

      public long getTime()

    • parse

      public List<Protein> parse() throws IOException
      Throws:
      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(Map<String,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)

    • setReturnType

      public void setReturnType(HmmscanPerDomainTableParser.ReturnType return_type)