org.fhcrc.cpl.toolbox.proteomics.feature.filehandler
Class APMLFeatureFileHandler

java.lang.Object
  org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.BaseFeatureSetFileHandler
      org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.APMLFeatureFileHandler

All Implemented Interfaces:

FeatureSetFileHandler

public class APMLFeatureFileHandler
extends BaseFeatureSetFileHandler
implements FeatureSetFileHandler

File handler for native msInspect feature files

Field Summary

static java.lang.String	APML_CLUSTERS_DESCRIPTION_LABELED_QUANT
static java.lang.String	APML_QUALITY_SCORE_ACCMASS
static java.lang.String	APML_QUALITY_SCORE_NAME_KL
static java.lang.String	APML_QUALITY_SCORE_SUMSQUARESDIST
static java.lang.String	APML_SEARCH_SCORE_NAME_PEPTIDE_PROPHET
static java.lang.String	APML_SOFTWARE_PARAM_FEATURE_STRATEGY
static java.lang.String	APML_SOFTWARE_PARAM_QUANT_LABEL
protected static float	DUMMY_KL_SCORE
protected static int	DUMMY_NUM_PEAKS
static java.lang.String	FILE_TYPE_NAME
protected int	minFeaturesCount
protected static APMLFeatureFileHandler	singletonInstance

Fields inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.BaseFeatureSetFileHandler

dumpWindow

Constructor Summary

APMLFeatureFileHandler()

Method Summary

boolean	canHandleFile(java.io.File file) Can this type of file handler handle this specific file?
org.systemsbiology.apmlparser.v2.datatype.Feature	createAPMLFeature(Feature msInspectFeature) This method knows the mapping of fields from msInspect-style features to APML-style features
Feature	createMsInspectFeatureFromAPMLFeature(org.systemsbiology.apmlparser.v2.datatype.Feature apmlFeature) This method knows the mapping between APML feature fields and msInspect feature fields
static APMLFeatureFileHandler	getSingletonInstance()
FeatureSet	loadFeatureSet(java.io.File file) Load a FeatureSet
void	saveFeatureSet(FeatureSet featureSet, java.io.File outFile) Save a FeatureSet
void	saveFeatureSet(FeatureSet featureSet, java.io.PrintWriter out) Save a FeatureSet

Methods inherited from class org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.BaseFeatureSetFileHandler

getFileTypeName, isXMLFile, setDumpWindow

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.fhcrc.cpl.toolbox.proteomics.feature.filehandler.FeatureSetFileHandler

getFileTypeName, setDumpWindow

Field Detail

FILE_TYPE_NAME

public static final java.lang.String FILE_TYPE_NAME

See Also:

Constant Field Values

minFeaturesCount

protected int minFeaturesCount

DUMMY_KL_SCORE

protected static final float DUMMY_KL_SCORE

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Constant Field Values

DUMMY_NUM_PEAKS

protected static final int DUMMY_NUM_PEAKS

See Also:

Constant Field Values

APML_QUALITY_SCORE_NAME_KL

public static final java.lang.String APML_QUALITY_SCORE_NAME_KL

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Constant Field Values

APML_QUALITY_SCORE_ACCMASS

public static final java.lang.String APML_QUALITY_SCORE_ACCMASS

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Constant Field Values

APML_QUALITY_SCORE_SUMSQUARESDIST

public static final java.lang.String APML_QUALITY_SCORE_SUMSQUARESDIST

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Constant Field Values

APML_CLUSTERS_DESCRIPTION_LABELED_QUANT

public static final java.lang.String APML_CLUSTERS_DESCRIPTION_LABELED_QUANT

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Constant Field Values

APML_SOFTWARE_PARAM_FEATURE_STRATEGY

public static final java.lang.String APML_SOFTWARE_PARAM_FEATURE_STRATEGY

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Constant Field Values

APML_SOFTWARE_PARAM_QUANT_LABEL

public static final java.lang.String APML_SOFTWARE_PARAM_QUANT_LABEL

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Constant Field Values

APML_SEARCH_SCORE_NAME_PEPTIDE_PROPHET

public static final java.lang.String APML_SEARCH_SCORE_NAME_PEPTIDE_PROPHET

See Also:

Constant Field Values

singletonInstance

protected static APMLFeatureFileHandler singletonInstance

Constructor Detail

APMLFeatureFileHandler

public APMLFeatureFileHandler()

Method Detail

getSingletonInstance

public static APMLFeatureFileHandler getSingletonInstance()

loadFeatureSet

public FeatureSet loadFeatureSet(java.io.File file)
                          throws java.io.IOException

Load a FeatureSet

Specified by:

loadFeatureSet in interface FeatureSetFileHandler

Parameters:

file -

Returns:

Throws:

java.io.IOException

createMsInspectFeatureFromAPMLFeature

public Feature createMsInspectFeatureFromAPMLFeature(org.systemsbiology.apmlparser.v2.datatype.Feature apmlFeature)

This method knows the mapping between APML feature fields and msInspect feature fields

Parameters:

apmlFeature -

Returns:

saveFeatureSet

public void saveFeatureSet(FeatureSet featureSet,
                           java.io.File outFile)
                    throws java.io.IOException

Description copied from interface: FeatureSetFileHandler

Save a FeatureSet

Specified by:

saveFeatureSet in interface FeatureSetFileHandler

Throws:

java.io.IOException

createAPMLFeature

public org.systemsbiology.apmlparser.v2.datatype.Feature createAPMLFeature(Feature msInspectFeature)

This method knows the mapping of fields from msInspect-style features to APML-style features

Parameters:

msInspectFeature -

Returns:

saveFeatureSet

public void saveFeatureSet(FeatureSet featureSet,
                           java.io.PrintWriter out)

Save a FeatureSet

Specified by:

saveFeatureSet in interface FeatureSetFileHandler

Parameters:

featureSet -

out -

canHandleFile

public boolean canHandleFile(java.io.File file)
                      throws java.io.IOException

Can this type of file handler handle this specific file?

Specified by:

canHandleFile in interface FeatureSetFileHandler

Parameters:

file -

Returns:

Throws:

java.io.IOException