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