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)

• setReturnType

  public void setReturnType​(HmmPfamOutputParser.ReturnType return_type)

• setVerbose

  public void setVerbose​(boolean verbose)