org.fhcrc.cpl.viewer.amt
Class AMTFileRestrictor

java.lang.Object
  org.fhcrc.cpl.viewer.amt.AMTFileRestrictor

public class AMTFileRestrictor
extends java.lang.Object

Field Summary

static float

DEFAULT_MIN_PROTEIN_PROPHET_FOR_RESTRICTION

Constructor Summary

AMTFileRestrictor()

Method Summary

static java.util.ArrayList<Feature>	identifyCorrespondingProteinFeaturesInProtXml(Feature[] inputFeatures, java.util.List<Protein> proteinList, java.io.File protXmlFile) identify all features that match peptides that were used to support a given list of proteins in a protxml file
static java.util.ArrayList<Feature>	removeFeaturesWithProteinsFromProtXml(Feature[] inputFeatures, java.util.List<Protein> proteinList, java.io.File protXmlFile) remove all features that match features that were used to support a given list of proteins in a protxml file
static java.util.ArrayList<Protein>	restrictProteinListWithProtXml(java.util.List<Protein> fullProteinList, java.io.File protXmlFile, float minProbability, int minPeptidesPerProtein) Load all proteins with a minimum protein prophet score from a protxml file

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

DEFAULT_MIN_PROTEIN_PROPHET_FOR_RESTRICTION

public static float DEFAULT_MIN_PROTEIN_PROPHET_FOR_RESTRICTION

Constructor Detail

AMTFileRestrictor

public AMTFileRestrictor()

Method Detail

restrictProteinListWithProtXml

public static java.util.ArrayList<Protein> restrictProteinListWithProtXml(java.util.List<Protein> fullProteinList,
                                                                          java.io.File protXmlFile,
                                                                          float minProbability,
                                                                          int minPeptidesPerProtein)

Load all proteins with a minimum protein prophet score from a protxml file

Returns:

removeFeaturesWithProteinsFromProtXml

public static java.util.ArrayList<Feature> removeFeaturesWithProteinsFromProtXml(Feature[] inputFeatures,
                                                                                 java.util.List<Protein> proteinList,
                                                                                 java.io.File protXmlFile)

remove all features that match features that were used to support a given list of proteins in a protxml file

Returns:

identifyCorrespondingProteinFeaturesInProtXml

public static java.util.ArrayList<Feature> identifyCorrespondingProteinFeaturesInProtXml(Feature[] inputFeatures,
                                                                                         java.util.List<Protein> proteinList,
                                                                                         java.io.File protXmlFile)

identify all features that match peptides that were used to support a given list of proteins in a protxml file

Returns: