org.forester.io.parsers

Class HmmPfamOutputParser

java.lang.Object

org.forester.io.parsers.HmmPfamOutputParser

public final class HmmPfamOutputParser
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	HmmPfamOutputParser.FilterType
static class	HmmPfamOutputParser.ReturnType

Constructor Summary

Constructors

Constructor and Description
HmmPfamOutputParser(File input_file, String species, Set<String> filter, HmmPfamOutputParser.FilterType filter_type)
HmmPfamOutputParser(File input_file, String species, String model_type)

Method Summary

Modifier and Type	Method and Description
int	getDomainsEncountered()
int	getDomainsIgnoredDueToDuf()
int	getDomainsIgnoredDueToEval()
int	getDomainsIgnoredDueToIndividualScoreCutoff()
int	getDomainsIgnoredDueToNegativeDomainFilter()
Map<String,Integer>	getDomainsIgnoredDueToNegativeDomainFilterCountsMap()
int	getDomainsIgnoredDueToOverlap()
Map<String,Integer>	getDomainsIgnoredDueToVirusLikeIdCountsMap()
int	getDomainsIgnoredDueToVirusLikeIds()
int	getDomainsStored()
SortedSet<String>	getDomainsStoredSet()
int	getProteinsEncountered()
int	getProteinsIgnoredDueToFilter()
int	getProteinsStored()
long	getTime()
List<Protein>	parse()
void	setAllowNonUniqueQuery(boolean allow_non_unique_query)
void	setDomainsIgnoredDueToEval(int domains_ignored_due_to_e_value)
void	setDomainsIgnoredDueToIndividualScoreCutoff(int domains_ignored_due_to_individual_score_cutoff)
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	setIndividualDomainScoreCutoffs(Map<String,String> individual_domain_score_cutoffs) Sets the individual domain score cutoff values (for example, gathering thresholds from Pfam).
void	setMaxAllowedOverlap(int max_allowed_overlap)
void	setReturnType(HmmPfamOutputParser.ReturnType return_type)
void	setVerbose(boolean verbose)

Methods inherited from class java.lang.Object

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

Constructor Detail

HmmPfamOutputParser

public HmmPfamOutputParser(File input_file,
                           String species,
                           String model_type)

HmmPfamOutputParser

public HmmPfamOutputParser(File input_file,
                           String species,
                           Set<String> filter,
                           HmmPfamOutputParser.FilterType filter_type)

Method Detail

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)