org.forester.io.parsers
Class HmmPfamOutputParser

java.lang.Object
  extended by org.forester.io.parsers.HmmPfamOutputParser

public final class HmmPfamOutputParser
extends Object


Nested Class Summary
static class HmmPfamOutputParser.FilterType
           
static class HmmPfamOutputParser.ReturnType
           
 
Constructor Summary
HmmPfamOutputParser(File input_file, String species, String model_type)
           
HmmPfamOutputParser(File input_file, String species, String model_type, Set<DomainId> filter, HmmPfamOutputParser.FilterType filter_type)
           
 
Method Summary
 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<DomainId> 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,
                           String model_type,
                           Set<DomainId> 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<DomainId> 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)