Constructor Detail

• HmmscanPerDomainTableParser

  public HmmscanPerDomainTableParser​(java.io.File input_file,
                                     java.lang.String species,
                                     HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)

• HmmscanPerDomainTableParser

  public HmmscanPerDomainTableParser​(java.io.File input_file,
                                     java.lang.String species,
                                     HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
                                     boolean allow_proteins_with_same_name)

• HmmscanPerDomainTableParser

  public HmmscanPerDomainTableParser​(java.io.File input_file,
                                     java.lang.String species,
                                     java.util.Set<java.lang.String> filter,
                                     HmmscanPerDomainTableParser.FilterType filter_type,
                                     HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)

• HmmscanPerDomainTableParser

  public HmmscanPerDomainTableParser​(java.io.File input_file,
                                     java.lang.String species,
                                     java.util.Set<java.lang.String> filter,
                                     HmmscanPerDomainTableParser.FilterType filter_type,
                                     HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
                                     boolean allow_proteins_with_same_name)

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()

• 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 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)

• setReturnType

  public void setReturnType​(HmmscanPerDomainTableParser.ReturnType return_type)