org.fhcrc.cpl.viewer.amt
Class AmtRunEntry

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

public class AmtRunEntry
extends java.lang.Object

Encapsulates everything we need to retrieve from / store into an AMT database related to a run.

Field Summary

protected java.lang.String	mLSID
protected double	mMinPeptideProphet
protected java.lang.String	mMzXmlFilename
protected java.lang.String	mPepXmlFilename
protected java.util.Date	mTimeAdded
protected java.util.Date	mTimeAnalyzed
protected double[]	mTimeHydMapCoefficients

Constructor Summary

AmtRunEntry(double[] timeHydMapCoefficients, MS2Modification[] modifications)
Created a new run entry dated right now

AmtRunEntry(double[] timeHydMapCoefficients, MS2Modification[] modifications, java.util.Date timeAdded)

Method Summary

double	convertTimeToHydrophobicity(double time) convert time to hydrophobicity for this run
java.lang.String	getLSID()
double	getMinPeptideProphet()
MS2Modification[]	getModifications()
java.lang.String	getMzXmlFilename()
java.lang.String	getPepXmlFilename()
MS2Modification	getStaticMod(java.lang.String residue)
MS2Modification[]	getStaticModifications()
java.util.Date	getTimeAdded()
java.util.Date	getTimeAnalyzed()
double[]	getTimeHydMapCoefficients()
MS2Modification[]	getVariableModifications()
java.util.Map<MS2Modification,MS2Modification>	overrideDuplicateModifications(AmtDatabase amtDB) when a run is folded into a new database, that database's mods take precedence.
double	recoverTimeForHydrophobicity(double hydrophobicity) Recover the time, within this run, that something with a given hydrophobicity value must have occurred.
void	setLSID(java.lang.String lsid)
void	setMinPeptideProphet(double minPeptideProphet)
void	setModifications(MS2Modification[] modifications)
void	setMzXmlFilename(java.lang.String mMzXmlFilename)
void	setPepXmlFilename(java.lang.String mPepXmlFilename)
void	setTimeAdded(java.util.Date mTimeAdded)
void	setTimeAnalyzed(java.util.Date mTimeAnalyzed)
void	setTimeHydMapCoefficients(double[] timeHydMapCoefficients)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

mTimeAdded

protected java.util.Date mTimeAdded

mTimeHydMapCoefficients

protected double[] mTimeHydMapCoefficients

mTimeAnalyzed

protected java.util.Date mTimeAnalyzed

mPepXmlFilename

protected java.lang.String mPepXmlFilename

mMzXmlFilename

protected java.lang.String mMzXmlFilename

mLSID

protected java.lang.String mLSID

mMinPeptideProphet

protected double mMinPeptideProphet

Constructor Detail

AmtRunEntry

public AmtRunEntry(double[] timeHydMapCoefficients,
                   MS2Modification[] modifications)

Created a new run entry dated right now

AmtRunEntry

public AmtRunEntry(double[] timeHydMapCoefficients,
                   MS2Modification[] modifications,
                   java.util.Date timeAdded)

Method Detail

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

recoverTimeForHydrophobicity

public double recoverTimeForHydrophobicity(double hydrophobicity)

Recover the time, within this run, that something with a given hydrophobicity value must have occurred. Work the regression line backward. Can ONLY do this for linear mapping

Parameters:

hydrophobicity -

Returns:

convertTimeToHydrophobicity

public double convertTimeToHydrophobicity(double time)

convert time to hydrophobicity for this run

Parameters:

time -

Returns:

getTimeAdded

public java.util.Date getTimeAdded()

setTimeAdded

public void setTimeAdded(java.util.Date mTimeAdded)

getTimeAnalyzed

public java.util.Date getTimeAnalyzed()

setTimeAnalyzed

public void setTimeAnalyzed(java.util.Date mTimeAnalyzed)

getPepXmlFilename

public java.lang.String getPepXmlFilename()

setPepXmlFilename

public void setPepXmlFilename(java.lang.String mPepXmlFilename)

getMzXmlFilename

public java.lang.String getMzXmlFilename()

setMzXmlFilename

public void setMzXmlFilename(java.lang.String mMzXmlFilename)

getTimeHydMapCoefficients

public double[] getTimeHydMapCoefficients()

setTimeHydMapCoefficients

public void setTimeHydMapCoefficients(double[] timeHydMapCoefficients)

getLSID

public java.lang.String getLSID()

setLSID

public void setLSID(java.lang.String lsid)

getMinPeptideProphet

public double getMinPeptideProphet()

setMinPeptideProphet

public void setMinPeptideProphet(double minPeptideProphet)

getModifications

public MS2Modification[] getModifications()

getStaticModifications

public MS2Modification[] getStaticModifications()

getVariableModifications

public MS2Modification[] getVariableModifications()

setModifications

public void setModifications(MS2Modification[] modifications)

getStaticMod

public MS2Modification getStaticMod(java.lang.String residue)

overrideDuplicateModifications

public java.util.Map<MS2Modification,MS2Modification> overrideDuplicateModifications(AmtDatabase amtDB)

when a run is folded into a new database, that database's mods take precedence. They're equivalent, but this makes the pointers point in the right places.

Parameters:

amtDB -