Package org.forester.io.parsers
Class HmmscanPerDomainTableParser
- java.lang.Object
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- org.forester.io.parsers.HmmscanPerDomainTableParser
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public final class HmmscanPerDomainTableParser extends java.lang.Object
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
HmmscanPerDomainTableParser.FilterType
static class
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
static class
HmmscanPerDomainTableParser.ReturnType
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Constructor Summary
Constructors Constructor Description HmmscanPerDomainTableParser(java.io.File input_file, java.lang.String species, java.util.Set<java.lang.String> 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<java.lang.String> filter, HmmscanPerDomainTableParser.FilterType filter_type, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to, boolean allow_proteins_with_same_name)
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)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getDomainsEncountered()
int
getDomainsIgnoredDueToDuf()
int
getDomainsIgnoredDueToFsEval()
int
getDomainsIgnoredDueToIEval()
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()
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF
getIndividualCutoffAppliesTo()
int
getProteinsEncountered()
int
getProteinsIgnoredDueToFilter()
int
getProteinsStored()
long
getTime()
boolean
isAllowProteinsWithSameName()
java.util.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(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)
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Constructor Detail
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HmmscanPerDomainTableParser
public HmmscanPerDomainTableParser(java.io.File input_file, java.lang.String species, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)
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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)
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HmmscanPerDomainTableParser
public HmmscanPerDomainTableParser(java.io.File input_file, java.lang.String species, java.util.Set<java.lang.String> filter, HmmscanPerDomainTableParser.FilterType filter_type, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)
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HmmscanPerDomainTableParser
public HmmscanPerDomainTableParser(java.io.File input_file, java.lang.String species, java.util.Set<java.lang.String> filter, HmmscanPerDomainTableParser.FilterType filter_type, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to, boolean allow_proteins_with_same_name)
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Method Detail
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isAllowProteinsWithSameName
public boolean isAllowProteinsWithSameName()
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getDomainsEncountered
public int getDomainsEncountered()
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getDomainsIgnoredDueToDuf
public int getDomainsIgnoredDueToDuf()
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getDomainsIgnoredDueToIEval
public int getDomainsIgnoredDueToIEval()
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getDomainsIgnoredDueToFsEval
public int getDomainsIgnoredDueToFsEval()
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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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getIndividualCutoffAppliesTo
public HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo()
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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
- Throws:
java.io.IOException
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setFsEValueMaximum
public void setFsEValueMaximum(double fs_e_value_maximum)
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setIEValueMaximum
public void setIEValueMaximum(double i_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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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
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setMaxAllowedOverlap
public void setMaxAllowedOverlap(int max_allowed_overlap)
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setReturnType
public void setReturnType(HmmscanPerDomainTableParser.ReturnType return_type)
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