org.forester.io.parsers
Class HmmPfamOutputParser
java.lang.Object
org.forester.io.parsers.HmmPfamOutputParser
public final class HmmPfamOutputParser
- extends Object
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
HmmPfamOutputParser
public HmmPfamOutputParser(File input_file,
String species,
String model_type)
HmmPfamOutputParser
public HmmPfamOutputParser(File input_file,
String species,
String model_type,
Set<DomainId> filter,
HmmPfamOutputParser.FilterType filter_type)
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<DomainId> 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)