org.proteios.io.mzdata
Class MzDataExpCommonAnnotation

java.lang.Object
  org.proteios.io.mzdata.MzDataExpCommon
      org.proteios.io.mzdata.MzDataExpCommonDc
          org.proteios.io.mzdata.MzDataExpCommonAnnotation

Direct Known Subclasses:

MzDataExpCommonPeakList, MzDataExpCommonPeakListSet

public class MzDataExpCommonAnnotation
extends MzDataExpCommonDc

This class supports export of mzData files from Proteios. An mzData file contains information on a mass spectrometry experiment. Given a Proteios peakListSet, MzDataExporter fetches stored data related to this peakListSet and stores it in an mzData file.

Version:

2.0

Author:

Olle

Last modified

$Date: 2006-10-31 11:05:43 +0100 (Tue, 31 Oct 2006) $

Field Summary

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

anna, dc, factory

Fields inherited from class org.proteios.io.mzdata.MzDataExpCommon

log

Constructor Summary

MzDataExpCommonAnnotation(SessionControl sc)
Default constructor.

Method Summary

AnnotationType	createAddedParamAnnotationType(String atName, Type atType, Item atItem, String addedParamType, String addedParamName, String addedParamValue) Creates added parameter annotation type for storing variable values as annotations.
AnnotationType	createAnnotationType(String atName, Type atType, Item atItem) Creates annotation type for storing variable values as annotations.
AnnotationType	createCvLookupAnnotationType(String atName, Type atType, Item atItem, String lookupFullName, String lookupVersion) Creates cvLookup annotation type for storing variable values as annotations.
AnnotationType	createCvParamAnnotationType(String atName, Type atType, Item atItem, String cvLabel, String accession) Creates cvParam annotation type for storing variable values as annotations.
AnnotationType	createUserParamAnnotationType(String atName, Type atType, Item atItem) Creates userParam annotation type for storing variable values as annotations.
AnnotationType	fetchAddedParamAnnotationType(String atName, Type atType, Item atItem, String addedParamType, String addedParamName, String addedParamValue) Fetches added parameter annotation type for storing variable values as annotations.
String	fetchAnnotation(AnnotationSet as, String atName, Type atType, DbControl argDc) Fetches annotation value from annotation for given annotation type.
CvLookup	fetchCvLookupAnnotation(AnnotationSet as, String atName, Type atType, DbControl argDc) Fetches annotation value from annotation for given cvLookup annotation type.
List<CvLookup>	fetchCvLookupAnnotationList(AnnotationSet as, Type atType, DbControl argDc) Fetches list of cvLookup type annotations.
AnnotationType	fetchCvLookupAnnotationType(String atName, Type atType, Item atItem, String lookupFullName, String lookupVersion) Fetches cvLookup annotation type for storing variable values as annotations.
CvParam	fetchCvParamAnnotation(AnnotationSet as, String atName, Type atType, DbControl argDc) Fetches annotation value from annotation for given cvParam annotation type.
List<CvParam>	fetchCvParamAnnotationList(AnnotationSet as, Type atType, DbControl argDc) Fetches list of cvParam type annotations.
UserParam	fetchUserParamAnnotation(AnnotationSet as, String atName, Type atType, DbControl argDc) Fetches annotation value from annotation for given userParam annotation type.
List<UserParam>	fetchUserParamAnnotationList(AnnotationSet as, Type atType, DbControl argDc) Fetches list of userParam type annotations.
AnnotationType	obtainAddedParamAnnotationType(String atName, Type atType, Item atItem, String addedParamType, String addedParamName, String addedParamValue) Obtains added parameter annotation type for storing variable values as annotations.
AnnotationType	obtainCvLookupAnnotationType(String atName, Type atType, Item atItem, String lookupFullName, String lookupVersion) Obtains cvLookup annotation type for storing variable values as annotations.
void	storeAnnotation(AnnotationSet as, String atName, Type atType, Item atItem, String value) Stores variable value as annotation.
void	storeCvLookupAnnotation(AnnotationSet as, String lookupCvLabel, Type atType, Item atItem, String lookupFullName, String lookupVersion, String lookupAddress) Stores variable values as cvLookup annotation.
void	storeCvParamAnnotation(AnnotationSet as, String atName, Type atType, Item atItem, String value, String cvLabel, String accession) Stores variable values as cvParam annotation.
void	storeUserParamAnnotation(AnnotationSet as, String atName, Type atType, Item atItem, String value) Stores variable values as userParam annotation.

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommonDc

enableAnnotator, enableDbControl, enableDbControl, getDbControl, getSessionControl, setDbControl

Methods inherited from class org.proteios.io.mzdata.MzDataExpCommon

getBlockTagName, setBlockTagName, write, writeAttribute, writeEndTag, writeNamespace, writeSimpleElementPair, writeSimpleElementPair, writeSingleElementEnd, writeStartElement, writeStartElementEnd, writeStartListTag, writeStartTag, zeroPad, zeroPad, zeroPad

Methods inherited from class java.lang.Object

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

Constructor Detail

MzDataExpCommonAnnotation

public MzDataExpCommonAnnotation(SessionControl sc)

Default constructor.

Method Detail

createAnnotationType

public AnnotationType createAnnotationType(String atName,
                                           Type atType,
                                           Item atItem)

Creates annotation type for storing variable values as annotations.

Parameters:

atName - String the name of annotationType

atType - Type the type of the annotationType

atItem - Item the Item the annotationType should be enabled for

Returns:

at AnnotationType the created annotationType

createAddedParamAnnotationType

public AnnotationType createAddedParamAnnotationType(String atName,
                                                     Type atType,
                                                     Item atItem,
                                                     String addedParamType,
                                                     String addedParamName,
                                                     String addedParamValue)

Creates added parameter annotation type for storing variable values as annotations. An added parameter annotation is an annotation, tagged by having annotationtype AddedParameterType set to addedParamType, and where data for addedParamName and addedParamValue are stored as String attributes in the annotationType for the annotation.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

addedParamType - String the annotation added parameter type as a String

addedParamName - String the annotation added parameter name as a String

addedParamValue - String the annotation added parameter value as a String

Returns:

at AnnotationType the created AnnotationType

fetchAddedParamAnnotationType

public AnnotationType fetchAddedParamAnnotationType(String atName,
                                                    Type atType,
                                                    Item atItem,
                                                    String addedParamType,
                                                    String addedParamName,
                                                    String addedParamValue)

Fetches added parameter annotation type for storing variable values as annotations. This method tries to find an existing added parameter AnnotationType with the desired specifications in the database. If one is found, it is returned, otherwise null. An added parameter annotation is an annotation, tagged by having annotationtype AddedParameterType set to addedParamType, and where data for addedParamName and addedParamValue are stored as String attributes in the annotationType for the annotation.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

addedParamType - String the annotation added parameter type as a String

addedParamName - String the annotation added parameter name as a String

addedParamValue - String the annotation added parameter value as a String

Returns:

at AnnotationType the fetched annotationType, or null if none is found.

obtainAddedParamAnnotationType

public AnnotationType obtainAddedParamAnnotationType(String atName,
                                                     Type atType,
                                                     Item atItem,
                                                     String addedParamType,
                                                     String addedParamName,
                                                     String addedParamValue)

Obtains added parameter annotation type for storing variable values as annotations. This method tries to find an existing added parameter AnnotationType with the desired specifications in the database. If one is found, it is returned, otherwise one is created. An added parameter annotation is an annotation, tagged by having annotationtype AddedParameterType set to addedParamType, and where data for addedParamName and addedParamValue are stored as String attributes in the annotationType for the annotation.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

addedParamType - String the annotation added parameter type as a String

addedParamName - String the annotation added parameter name as a String

addedParamValue - String the annotation added parameter value as a String

Returns:

at AnnotationType the obtained AnnotationType

storeAnnotation

public void storeAnnotation(AnnotationSet as,
                            String atName,
                            Type atType,
                            Item atItem,
                            String value)

Stores variable value as annotation.

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of the annotationType

atType - Type the type of the annotationType

atItem - Item the Item the annotationType should be enabled for

value - String the annotation value as a String

fetchAnnotation

public String fetchAnnotation(AnnotationSet as,
                              String atName,
                              Type atType,
                              DbControl argDc)

Fetches annotation value from annotation for given annotation type.

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of annotationType

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

String the annotation value as a String

createCvLookupAnnotationType

public AnnotationType createCvLookupAnnotationType(String atName,
                                                   Type atType,
                                                   Item atItem,
                                                   String lookupFullName,
                                                   String lookupVersion)

Creates cvLookup annotation type for storing variable values as annotations. A cvLookup annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvLookup", and where data for fullName and version are stored as String attributes in the annotationType for the annotation. Data for cvLabel and address are used as name and value for the annotation, as this information is viewable by the user.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

lookupFullName - String the annotation added parameter name as a String

lookupVersion - String the annotation added parameter value as a String

Returns:

at AnnotationType the created AnnotationType

fetchCvLookupAnnotationType

public AnnotationType fetchCvLookupAnnotationType(String atName,
                                                  Type atType,
                                                  Item atItem,
                                                  String lookupFullName,
                                                  String lookupVersion)

Fetches cvLookup annotation type for storing variable values as annotations. A cvLookup annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvLookup", and where data for fullName and version are stored as String attributes in the annotationType for the annotation. Data for cvLabel and address are used as name and value for the annotation, as this information is viewable by the user.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

lookupFullName - String the annotation added parameter name as a String

lookupVersion - String the annotation added parameter value as a String

Returns:

at AnnotationType the fetched AnnotationType

obtainCvLookupAnnotationType

public AnnotationType obtainCvLookupAnnotationType(String atName,
                                                   Type atType,
                                                   Item atItem,
                                                   String lookupFullName,
                                                   String lookupVersion)

Obtains cvLookup annotation type for storing variable values as annotations. A cvLookup annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvLookup", and where data for fullName and version are stored as String attributes in the annotationType for the annotation. Data for cvLabel and address are used as name and value for the annotation, as this information is viewable by the user.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

lookupFullName - String the annotation added parameter name as a String

lookupVersion - String the annotation added parameter value as a String

Returns:

at AnnotationType the obtained AnnotationType

storeCvLookupAnnotation

public void storeCvLookupAnnotation(AnnotationSet as,
                                    String lookupCvLabel,
                                    Type atType,
                                    Item atItem,
                                    String lookupFullName,
                                    String lookupVersion,
                                    String lookupAddress)

Stores variable values as cvLookup annotation. A cvLookup annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvLookup", and where data for fullName and version are stored as String attributes in the annotationType for the annotation. Data for cvLabel and address are used as name and value for the annotation, as this information is viewable by the user.

Parameters:

as - AnnotationSet the AnnotationSet to use

lookupCvLabel - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

lookupFullName - String the annotation added parameter name as a String

lookupVersion - String the annotation added parameter value as a String

lookupAddress - String the annotation value as a String

fetchCvLookupAnnotation

public CvLookup fetchCvLookupAnnotation(AnnotationSet as,
                                        String atName,
                                        Type atType,
                                        DbControl argDc)

Fetches annotation value from annotation for given cvLookup annotation type. A cvLookup annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvLookup", and where data for fullName and version are stored as String attributes in the annotationType for the annotation. Data for cvLabel and address are used as name and value for the annotation, as this information is viewable by the user.

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of annotationType

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

CvLookup A CvLookup object with annotation values, or null if not found

fetchCvLookupAnnotationList

public List<CvLookup> fetchCvLookupAnnotationList(AnnotationSet as,
                                                  Type atType,
                                                  DbControl argDc)

Fetches list of cvLookup type annotations. A cvLookup annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvLookup", and where data for fullName and version are stored as String attributes in the annotationType for the annotation. Data for cvLabel and address are used as name and value for the annotation, as this information is viewable by the user.

Parameters:

as - AnnotationSet the AnnotationSet to use

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

List A list of CvLookup objects with annotation values.

createCvParamAnnotationType

public AnnotationType createCvParamAnnotationType(String atName,
                                                  Type atType,
                                                  Item atItem,
                                                  String cvLabel,
                                                  String accession)

Creates cvParam annotation type for storing variable values as annotations. A cvParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvParam", and where data for cvLabel and accession are stored as String attributes in the annotationType for the annotation.

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

cvLabel - String the annotation cvLabel as a String

accession - String the annotation accession as a String

Returns:

at AnnotationType the created AnnotationType

storeCvParamAnnotation

public void storeCvParamAnnotation(AnnotationSet as,
                                   String atName,
                                   Type atType,
                                   Item atItem,
                                   String value,
                                   String cvLabel,
                                   String accession)

Stores variable values as cvParam annotation. A cvParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvParam", and where data for cvLabel and accession are stored as String attributes in the annotationType for the annotation.

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

value - String the annotation value as a String

cvLabel - String the annotation cvLabel as a String

accession - String the annotation accession as a String

fetchCvParamAnnotation

public CvParam fetchCvParamAnnotation(AnnotationSet as,
                                      String atName,
                                      Type atType,
                                      DbControl argDc)

Fetches annotation value from annotation for given cvParam annotation type. A cvParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvParam", and where data for cvLabel and accession are stored as String attributes in the annotationType for the annotation.

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of annotationType

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

CvParam A CvParam object with annotation values, or null if not found

fetchCvParamAnnotationList

public List<CvParam> fetchCvParamAnnotationList(AnnotationSet as,
                                                Type atType,
                                                DbControl argDc)

Fetches list of cvParam type annotations. A cvParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "cvParam", and where data for cvLabel and accession are stored as String attributes in the annotationType for the annotation.

Parameters:

as - AnnotationSet the AnnotationSet to use

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

List A list of CvParam objects with annotation values.

createUserParamAnnotationType

public AnnotationType createUserParamAnnotationType(String atName,
                                                    Type atType,
                                                    Item atItem)

Creates userParam annotation type for storing variable values as annotations. A userParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "userParam".

Parameters:

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

Returns:

at AnnotationType the created AnnotationType

storeUserParamAnnotation

public void storeUserParamAnnotation(AnnotationSet as,
                                     String atName,
                                     Type atType,
                                     Item atItem,
                                     String value)

Stores variable values as userParam annotation. A userParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "userParam".

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of the AnnotationType

atType - Type the type of the AnnotationType

atItem - Item the Item the AnnotationType should be enabled for

value - String the annotation value as a String

fetchUserParamAnnotation

public UserParam fetchUserParamAnnotation(AnnotationSet as,
                                          String atName,
                                          Type atType,
                                          DbControl argDc)

Fetches annotation value from annotation for given userParam annotation type. A userParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "userParam".

Parameters:

as - AnnotationSet the AnnotationSet to use

atName - String the name of annotationType

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

UserParam A UserParam object with annotation values, or null if not found

fetchUserParamAnnotationList

public List<UserParam> fetchUserParamAnnotationList(AnnotationSet as,
                                                    Type atType,
                                                    DbControl argDc)

Fetches list of userParam type annotations. A userParam annotation is an annotation, tagged by having annotationtype AddedParameterType set to "userParam".

Parameters:

as - AnnotationSet the AnnotationSet to use

atType - Type the type of the annotationType

argDc - DbControl the DbControl object to use

Returns:

List A list of UserParam objects with annotation values.