org.forester.io.parsers
public final class HmmPfamOutputParser extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
static class |
HmmPfamOutputParser.FilterType |
static class |
HmmPfamOutputParser.ReturnType |
Constructor and 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.lang.String model_type,
java.util.Set<DomainId> filter,
HmmPfamOutputParser.FilterType filter_type) |
Modifier and Type | Method and 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<DomainId> |
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) |
public HmmPfamOutputParser(java.io.File input_file, java.lang.String species, java.lang.String model_type)
public HmmPfamOutputParser(java.io.File input_file, java.lang.String species, java.lang.String model_type, java.util.Set<DomainId> filter, HmmPfamOutputParser.FilterType filter_type)
public int getDomainsEncountered()
public int getDomainsIgnoredDueToDuf()
public int getDomainsIgnoredDueToEval()
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<DomainId> getDomainsStoredSet()
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 setAllowNonUniqueQuery(boolean allow_non_unique_query)
public void setDomainsIgnoredDueToEval(int domains_ignored_due_to_e_value)
public void setDomainsIgnoredDueToIndividualScoreCutoff(int domains_ignored_due_to_individual_score_cutoff)
public void setEValueMaximum(double 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 setIndividualDomainScoreCutoffs(java.util.Map<java.lang.String,java.lang.String> individual_domain_score_cutoffs)
individual_domain_score_cutoffs
- public void setMaxAllowedOverlap(int max_allowed_overlap)
public void setReturnType(HmmPfamOutputParser.ReturnType return_type)
public void setVerbose(boolean verbose)