org.forester.io.parsers

Class HmmscanPerDomainTableParser

java.lang.Object

org.forester.io.parsers.HmmscanPerDomainTableParser

public final class HmmscanPerDomainTableParser
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	HmmscanPerDomainTableParser.FilterType
static class	HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
static class	HmmscanPerDomainTableParser.ReturnType

Constructor Summary

Constructors

Constructor and Description
HmmscanPerDomainTableParser(File input_file, String species, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)
HmmscanPerDomainTableParser(File input_file, String species, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to, boolean allow_proteins_with_same_name)
HmmscanPerDomainTableParser(File input_file, String species, Set<String> filter, HmmscanPerDomainTableParser.FilterType filter_type, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)
HmmscanPerDomainTableParser(File input_file, String species, Set<String> filter, HmmscanPerDomainTableParser.FilterType filter_type, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to, boolean allow_proteins_with_same_name)

Method Summary

Modifier and Type	Method and Description
int	getDomainsEncountered()
int	getDomainsIgnoredDueToDuf()
int	getDomainsIgnoredDueToFsEval()
int	getDomainsIgnoredDueToIEval()
int	getDomainsIgnoredDueToIndividualScoreCutoff()
int	getDomainsIgnoredDueToNegativeDomainFilter()
Map<String,Integer>	getDomainsIgnoredDueToNegativeDomainFilterCountsMap()
int	getDomainsIgnoredDueToOverlap()
Map<String,Integer>	getDomainsIgnoredDueToVirusLikeIdCountsMap()
int	getDomainsIgnoredDueToVirusLikeIds()
int	getDomainsStored()
SortedSet<String>	getDomainsStoredSet()
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF	getIndividualCutoffAppliesTo()
int	getProteinsEncountered()
int	getProteinsIgnoredDueToFilter()
int	getProteinsStored()
long	getTime()
boolean	isAllowProteinsWithSameName()
List<Protein>	parse()
void	setFsEValueMaximum(double fs_e_value_maximum)
void	setIEValueMaximum(double i_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(Map<String,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(File input_file,
                                   String species,
                                   HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)

HmmscanPerDomainTableParser

public HmmscanPerDomainTableParser(File input_file,
                                   String species,
                                   HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
                                   boolean allow_proteins_with_same_name)

HmmscanPerDomainTableParser

public HmmscanPerDomainTableParser(File input_file,
                                   String species,
                                   Set<String> filter,
                                   HmmscanPerDomainTableParser.FilterType filter_type,
                                   HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)

HmmscanPerDomainTableParser

public HmmscanPerDomainTableParser(File input_file,
                                   String species,
                                   Set<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 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()

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

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(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)