Package org.forester.io.parsers
Class HmmPfamOutputParser
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- org.forester.io.parsers.HmmPfamOutputParser
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public final class HmmPfamOutputParser extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
HmmPfamOutputParser.FilterType
static class
HmmPfamOutputParser.ReturnType
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Constructor Summary
Constructors Constructor Description HmmPfamOutputParser(java.io.File input_file, java.lang.String species, java.lang.String model_type)
HmmPfamOutputParser(java.io.File input_file, java.lang.String species, java.util.Set<java.lang.String> filter, HmmPfamOutputParser.FilterType filter_type)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description 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<java.lang.String>
getDomainsStoredSet()
int
getProteinsEncountered()
int
getProteinsIgnoredDueToFilter()
int
getProteinsStored()
long
getTime()
java.util.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(java.util.Map<java.lang.String,java.lang.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)
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Constructor Detail
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HmmPfamOutputParser
public HmmPfamOutputParser(java.io.File input_file, java.lang.String species, java.lang.String model_type)
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HmmPfamOutputParser
public HmmPfamOutputParser(java.io.File input_file, java.lang.String species, java.util.Set<java.lang.String> filter, HmmPfamOutputParser.FilterType filter_type)
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Method Detail
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getDomainsEncountered
public int getDomainsEncountered()
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getDomainsIgnoredDueToDuf
public int getDomainsIgnoredDueToDuf()
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getDomainsIgnoredDueToEval
public int getDomainsIgnoredDueToEval()
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getDomainsIgnoredDueToIndividualScoreCutoff
public int getDomainsIgnoredDueToIndividualScoreCutoff()
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getDomainsIgnoredDueToNegativeDomainFilter
public int getDomainsIgnoredDueToNegativeDomainFilter()
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getDomainsIgnoredDueToNegativeDomainFilterCountsMap
public java.util.Map<java.lang.String,java.lang.Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap()
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getDomainsIgnoredDueToOverlap
public int getDomainsIgnoredDueToOverlap()
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getDomainsIgnoredDueToVirusLikeIdCountsMap
public java.util.Map<java.lang.String,java.lang.Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap()
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getDomainsIgnoredDueToVirusLikeIds
public int getDomainsIgnoredDueToVirusLikeIds()
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getDomainsStored
public int getDomainsStored()
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getDomainsStoredSet
public java.util.SortedSet<java.lang.String> getDomainsStoredSet()
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getProteinsEncountered
public int getProteinsEncountered()
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getProteinsIgnoredDueToFilter
public int getProteinsIgnoredDueToFilter()
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getProteinsStored
public int getProteinsStored()
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getTime
public long getTime()
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parse
public java.util.List<Protein> parse() throws java.io.IOException
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java.io.IOException
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setAllowNonUniqueQuery
public void setAllowNonUniqueQuery(boolean allow_non_unique_query)
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setDomainsIgnoredDueToEval
public void setDomainsIgnoredDueToEval(int domains_ignored_due_to_e_value)
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setDomainsIgnoredDueToIndividualScoreCutoff
public void setDomainsIgnoredDueToIndividualScoreCutoff(int domains_ignored_due_to_individual_score_cutoff)
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setEValueMaximum
public void setEValueMaximum(double e_value_maximum)
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setIgnoreDufs
public void setIgnoreDufs(boolean ignore_dufs)
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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
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setIgnoreVirusLikeIds
public void setIgnoreVirusLikeIds(boolean ignore_virus_like_ids)
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setIndividualDomainScoreCutoffs
public void setIndividualDomainScoreCutoffs(java.util.Map<java.lang.String,java.lang.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
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setMaxAllowedOverlap
public void setMaxAllowedOverlap(int max_allowed_overlap)
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setReturnType
public void setReturnType(HmmPfamOutputParser.ReturnType return_type)
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setVerbose
public void setVerbose(boolean verbose)
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