org.fhcrc.cpl.viewer.amt
Class AmtMatchedProtein

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

public class AmtMatchedProtein
extends java.lang.Object

Created by IntelliJ IDEA. User: dhmay Date: Jun 14, 2007 Time: 10:15:59 AM To change this template use File | Settings | File Templates.

Nested Class Summary

static class

AmtMatchedProtein.AmtMatchedPeptide

Field Summary

protected java.lang.String	header
protected java.lang.String	identifier
protected float	meanIntensity
protected int	numMatches
protected int	numUnique
java.util.Map<java.lang.String,AmtMatchedProtein.AmtMatchedPeptide>	peptideInfoMap

Constructor Summary

AmtMatchedProtein(Protein protein)

AmtMatchedProtein(java.lang.String identifier, int numMatches, int numUnique, float meanIntensity, java.lang.String header)

AmtMatchedProtein(java.lang.String identifier, java.lang.String header)

Method Summary

void	addMoreInfo(AmtMatchedProtein otherProteinInfo)
void	addPeptideInfo(AmtMatchedProtein.AmtMatchedPeptide newPeptideInfo)
static java.lang.String	getFileHeaderString()
java.lang.String	getHeader()
java.lang.String	getIdentifier()
float	getMeanIntensity()
int	getNumMatches()
int	getNumUniqueMatches()
AmtMatchedProtein.AmtMatchedPeptide	getPeptideInfo(java.lang.String sequence)
java.util.Map<java.lang.String,AmtMatchedProtein.AmtMatchedPeptide>	getPeptideInfoMap()
java.util.Set<java.lang.String>	getPeptideSequences()
static java.util.Map<java.lang.String,AmtMatchedProtein>	loadMatchedProteins(java.io.File file)
java.lang.String	oldToString()
void	recalculateMeanIntensity()
void	setHeader(java.lang.String header)
void	setIdentifier(java.lang.String identifier)
void	setMeanIntensity(float meanIntensity)
void	setNumMatches(int numMatches)
void	setNumUniqueMatches(int numUnique)
void	setPeptideInfoMap(java.util.Map<java.lang.String,AmtMatchedProtein.AmtMatchedPeptide> peptideInfoMap)
java.lang.String	toString()
java.lang.String	toString(java.lang.String prefixEachLine)

Methods inherited from class java.lang.Object

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

Field Detail

identifier

protected java.lang.String identifier

numMatches

protected int numMatches

numUnique

protected int numUnique

meanIntensity

protected float meanIntensity

header

protected java.lang.String header

peptideInfoMap

public java.util.Map<java.lang.String,AmtMatchedProtein.AmtMatchedPeptide> peptideInfoMap

Constructor Detail

AmtMatchedProtein

public AmtMatchedProtein(java.lang.String identifier,
                         java.lang.String header)

AmtMatchedProtein

public AmtMatchedProtein(Protein protein)

AmtMatchedProtein

public AmtMatchedProtein(java.lang.String identifier,
                         int numMatches,
                         int numUnique,
                         float meanIntensity,
                         java.lang.String header)

Method Detail

getFileHeaderString

public static java.lang.String getFileHeaderString()

addPeptideInfo

public void addPeptideInfo(AmtMatchedProtein.AmtMatchedPeptide newPeptideInfo)

getPeptideSequences

public java.util.Set<java.lang.String> getPeptideSequences()

getPeptideInfo

public AmtMatchedProtein.AmtMatchedPeptide getPeptideInfo(java.lang.String sequence)

addMoreInfo

public void addMoreInfo(AmtMatchedProtein otherProteinInfo)

recalculateMeanIntensity

public void recalculateMeanIntensity()

oldToString

public java.lang.String oldToString()

toString

public java.lang.String toString(java.lang.String prefixEachLine)

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getIdentifier

public java.lang.String getIdentifier()

setIdentifier

public void setIdentifier(java.lang.String identifier)

getNumMatches

public int getNumMatches()

setNumMatches

public void setNumMatches(int numMatches)

getNumUniqueMatches

public int getNumUniqueMatches()

setNumUniqueMatches

public void setNumUniqueMatches(int numUnique)

getMeanIntensity

public float getMeanIntensity()

setMeanIntensity

public void setMeanIntensity(float meanIntensity)

getHeader

public java.lang.String getHeader()

setHeader

public void setHeader(java.lang.String header)

getPeptideInfoMap

public java.util.Map<java.lang.String,AmtMatchedProtein.AmtMatchedPeptide> getPeptideInfoMap()

setPeptideInfoMap

public void setPeptideInfoMap(java.util.Map<java.lang.String,AmtMatchedProtein.AmtMatchedPeptide> peptideInfoMap)

loadMatchedProteins

public static java.util.Map<java.lang.String,AmtMatchedProtein> loadMatchedProteins(java.io.File file)
                                                                             throws java.io.IOException

Throws:

java.io.IOException