public final class HmmscanPerDomainTableParser
extends java.lang.Object
Modifier and Type | Class | Description |
---|---|---|
static class |
HmmscanPerDomainTableParser.FilterType |
|
static class |
HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF |
|
static class |
HmmscanPerDomainTableParser.ReturnType |
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) |
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) |
public HmmscanPerDomainTableParser(java.io.File input_file, java.lang.String species, HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to)
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)
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)
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)
public boolean isAllowProteinsWithSameName()
public int getDomainsEncountered()
public int getDomainsIgnoredDueToDuf()
public int getDomainsIgnoredDueToIEval()
public int getDomainsIgnoredDueToFsEval()
public int getDomainsIgnoredDueToIndividualScoreCutoff()
public int getDomainsIgnoredDueToNegativeDomainFilter()
public java.util.Map<java.lang.String,java.lang.Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap()
public int getDomainsIgnoredDueToOverlap()
public java.util.Map<java.lang.String,java.lang.Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap()
public int getDomainsIgnoredDueToVirusLikeIds()
public int getDomainsStored()
public java.util.SortedSet<java.lang.String> getDomainsStoredSet()
public HmmscanPerDomainTableParser.INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo()
public int getProteinsEncountered()
public int getProteinsIgnoredDueToFilter()
public int getProteinsStored()
public long getTime()
public java.util.List<Protein> parse() throws java.io.IOException
java.io.IOException
public void setFsEValueMaximum(double fs_e_value_maximum)
public void setIEValueMaximum(double i_e_value_maximum)
public void setIgnoreDufs(boolean ignore_dufs)
public void setIgnoreEngulfedDomains(boolean ignore_engulfed_domains)
ignored_engulfed_domains
- public void setIgnoreVirusLikeIds(boolean ignore_virus_like_ids)
public void setIndividualScoreCutoffs(java.util.Map<java.lang.String,java.lang.Double> individual_score_cutoffs)
individual_score_cutoffs
- public void setMaxAllowedOverlap(int max_allowed_overlap)
public void setReturnType(HmmscanPerDomainTableParser.ReturnType return_type)