Class HmmPfamOutputParser

Method Details

• getDomainsEncountered

  public int getDomainsEncountered()

• getDomainsIgnoredDueToDuf

  public int getDomainsIgnoredDueToDuf()

• getDomainsIgnoredDueToEval

  public int getDomainsIgnoredDueToEval()

• 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()

• 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

• 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(Map<String,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)