Package com.compomics.util.experiment.io.identification

Class MzIdentMLIdfileSearchParametersConverter

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.io.identification.MzIdentMLIdfileSearchParametersConverter

All Implemented Interfaces:

Serializable

public class MzIdentMLIdfileSearchParametersConverter
extends ExperimentObject

Reads basic search parameters from mzIdentML result files.

Author:

Harald Barsnes

See Also:

• Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.personalization.ExperimentObject

NO_KEY

Constructor Summary

Constructors

Constructor	Description
MzIdentMLIdfileSearchParametersConverter(File mzIdentMLFile, SearchParameters searchParameters, String species, WaitingHandler waitingHandler)	Constructor.

Method Summary

Modifier and Type	Method	Description
String	getSearchParameters()	Updated the search parameters object and returns the search parameters as a string.

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, asLong, clearParametersMap, getId, getUrParam, getUrParams, removeUrParam, setId, setUrParams

Methods inherited from class java.lang.Object

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

Constructor Details

MzIdentMLIdfileSearchParametersConverter

public MzIdentMLIdfileSearchParametersConverter(File mzIdentMLFile,
 SearchParameters searchParameters,
 String species,
 WaitingHandler waitingHandler)
                                         throws IOException

Constructor.

Parameters:

mzIdentMLFile - the mzIdentML file

searchParameters - the search parameters

species - the species

waitingHandler - the waiting handler

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if an IOException occurs

Method Details

getSearchParameters

public String getSearchParameters()
                           throws FileNotFoundException,
IOException,
ClassNotFoundException,
org.xmlpull.v1.XmlPullParserException

Updated the search parameters object and returns the search parameters as a string.

Returns:

the search parameters as a string

Throws:

FileNotFoundException - if a FileNotFoundException occurs

IOException - if a IOException occurs

ClassNotFoundException - if a ClassNotFoundException occurs

org.xmlpull.v1.XmlPullParserException - if XmlPullParserException occurs