org.forester.io.parsers
Class HmmscanPerDomainTableParser

java.lang.Object
  org.forester.io.parsers.HmmscanPerDomainTableParser

public final class HmmscanPerDomainTableParser
extends java.lang.Object

Nested Class Summary

static class	HmmscanPerDomainTableParser.FilterType
static class	HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
static class	HmmscanPerDomainTableParser.ReturnType

Constructor Summary

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

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

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

Method Summary

int	getDomainsEncountered()
int	getDomainsIgnoredDueToDuf()
int	getDomainsIgnoredDueToEval()
int	getDomainsIgnoredDueToIndividualScoreCutoff()
int	getDomainsIgnoredDueToNegativeDomainFilter()
java.util.Map<java.lang.String,java.lang.Integer>	getDomainsIgnoredDueToNegativeDomainFilterCountsMap()
int	getDomainsIgnoredDueToOverlap()
java.util.Map<java.lang.String,java.lang.Integer>	getDomainsIgnoredDueToVirusLikeIdCountsMap()
int	getDomainsIgnoredDueToVirusLikeIds()
int	getDomainsStored()
java.util.SortedSet<DomainId>	getDomainsStoredSet()
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF	getIndividualCutoffAppliesTo()
int	getProteinsEncountered()
int	getProteinsIgnoredDueToFilter()
int	getProteinsStored()
long	getTime()
boolean	isAllowProteinsWithSameName()
java.util.List<Protein>	parse()
void	setEValueMaximum(double e_value_maximum)
void	setIgnoreDufs(boolean ignore_dufs)
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.
void	setIgnoreVirusLikeIds(boolean ignore_virus_like_ids)
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).
void	setMaxAllowedOverlap(int max_allowed_overlap)
void	setReturnType(HmmscanPerDomainTableParser.ReturnType return_type)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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<DomainId> 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<DomainId> 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()

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<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 java.util.List<Protein> parse()
                              throws java.io.IOException

Throws:

java.io.IOException

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(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)