java.lang.Object
- uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
- - psidev.psi.mi.jami.bridges.obo.AbstractOboLoader<T>

All Implemented Interfaces:

uk.ac.ebi.ols.loader.interfaces.Loader

Direct Known Subclasses:

CvOboLoader, OntologyOboLoader, SourceOboLoader
```
public abstract class AbstractOboLoader<T extends CvTerm>
extends uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
```
Abstract obo loader
Since:
```
17/07/13
```
Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields
Modifier and Type	Field	Description
`static String`	`ALIAS_IDENTIFIER`	Constant `ALIAS_IDENTIFIER="Alternate label curated by PSI-MI"`
`static String`	`COMMENT_KEY`	Constant `COMMENT_KEY="comment"`
`static String`	`EXACT_KEY`	Constant `EXACT_KEY="exact"`
`static String`	`GO`	Constant `GO="go"`
`static String`	`GO_MI_REF`	Constant `GO_MI_REF="MI:0448"`
`static String`	`HTTP_DEF`	Constant `HTTP_DEF="http"`
`static String`	`LINE_BREAK`	Constant `LINE_BREAK="\n"`
`static org.apache.commons.logging.Log`	`log`	Sets up a logger for that class.
`static String`	`META_XREF_SEPARATOR`	Constant `META_XREF_SEPARATOR=":"`
`static String`	`METHOD_REFERENCE`	Constant `METHOD_REFERENCE="method reference"`
`static String`	`METHOD_REFERENCE_MI_REF`	Constant `METHOD_REFERENCE_MI_REF="MI:0357"`
`static String`	`MOD_ALIAS_IDENTIFIER`	Constant `MOD_ALIAS_IDENTIFIER="Alternate name curated by PSI-MOD"`
`static String`	`MOD_SHORTLABEL_IDENTIFIER`	Constant `MOD_SHORTLABEL_IDENTIFIER="Short label curated by PSI-MOD"`
`static String`	`PMID`	Constant `PMID="PMID"`
`static String`	`PMID_APPLICATION`	Constant `PMID_APPLICATION="PMID for application instance"`
`static String`	`QUOTE`	Constant `QUOTE="""`
`static String`	`RESID`	Constant `RESID="resid"`
`static String`	`RESID_IDENTIFIER`	Constant `RESID_IDENTIFIER="Alternate name from RESID"`
`static String`	`RESID_MI_REF`	Constant `RESID_MI_REF="MI:0248"`
`static String`	`RESID_MISNOMER_IDENTIFIER`	Constant `RESID_MISNOMER_IDENTIFIER="Misnomer tagged alternate name from RES"{trunked}`
`static String`	`RESID_NAME_IDENTIFIER`	Constant `RESID_NAME_IDENTIFIER="Name from RESID"`
`static String`	`RESID_SYSTEMATIC_IDENTIFIER`	Constant `RESID_SYSTEMATIC_IDENTIFIER="Systematic name from RESID"`
`static String`	`SEARCH_URL`	Constant `SEARCH_URL="search-url"`
`static String`	`SEARCH_URL_MI_REF`	Constant `SEARCH_URL_MI_REF="MI:0615"`
`static String`	`SHORTLABEL_IDENTIFIER`	Constant `SHORTLABEL_IDENTIFIER="Unique short label curated by PSI-MI"`
`static String`	`SO`	Constant `SO="so"`
`static String`	`SO_MI_REF`	Constant `SO_MI_REF="MI:0601"`
`static String`	`UNIPROT_FEATURE_IDENTIFIER`	Constant `UNIPROT_FEATURE_IDENTIFIER="Protein feature description from UniPro"{trunked}`
`static int`	`XREF_TYPE`	Constant `XREF_TYPE=3`
`static String`	`XREF_VALIDATION_REGEXP`	Constant `XREF_VALIDATION_REGEXP="id-validation-regexp"`
`static String`	`XREF_VALIDATION_REGEXP_MI_REF`	Constant `XREF_VALIDATION_REGEXP_MI_REF="MI:0628"`

Fields inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
ALT_ID, BATCH_MODE, BROAD, DEV_FROM_SET, DEVELOPS_FROM, EXACT, FULL_NAME, IS_A, IS_A_SET, logger, NARROW, ontBean, ONTOLOGY_DEFINITION, ontologyTerms, parser, PART_OF, PART_OF_SET, QUERY_URL, RELATED, SHORT_NAME, SOURCE_URL, SYNONYM, useGreedy

Fields inherited from interface uk.ac.ebi.ols.loader.interfaces.Loader
RELATION_TYPE, SYNONYM_TYPE

Constructor Summary

Constructors
Constructor	Description
`AbstractOboLoader(String databaseName)`	Constructor for AbstractOboLoader.
`AbstractOboLoader(CvTerm database)`	Constructor for AbstractOboLoader.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`buildOntology(Map<String,T> id2Terms, Map<String,T> name2Terms)`	buildOntology.
`protected void`	`configure(String filePath)`	configure.
`protected abstract void`	`createDefinitionFor(String def, T term)`	createDefinitionFor.
`protected T`	`createNewTerm(uk.ac.ebi.ols.model.interfaces.Term t)`	createNewTerm.
`protected CvTerm`	`getOntologyDatabase()`	Getter for the field `ontologyDatabase`.
`protected abstract T`	`instantiateNewTerm(String name, Xref identity)`	instantiateNewTerm.
`void`	`parseOboFile(File file, Map<String,T> id2Terms, Map<String,T> name2Terms)`	Parse the given OBO file and build a representation of the DAG into an Ontology.
`protected void`	`processAnnotations(uk.ac.ebi.ols.model.interfaces.Term term, T ontologyTerm)`	Process the annotations of a term
`protected void`	`processDefinition(String definition, T ontologyTerm)`	Process the definition String
`protected void`	`processDefinition(uk.ac.ebi.ols.model.interfaces.Term term, T ontologyTerm)`	Process the definition of a term
`protected void`	`processInfoInDescription(String definition, String otherInfoString, T ontologyTerm)`	Process the other information in the description
`protected void`	`processShortLabel(uk.ac.ebi.ols.model.interfaces.Term term, T ontologyTerm)`	processShortLabel.
`protected void`	`processSynonyms(uk.ac.ebi.ols.model.interfaces.Term term, T ontologyTerm)`	processSynonyms.
`protected void`	`processXref(String db, String accession, T ontologyTerm)`	processXref.
`protected String`	`processXrefDefinition(String xref, String database, String accession, String pubmedPrimary, T ontologyTerm)`	processXrefDefinition.
`protected void`	`processXrefs(uk.ac.ebi.ols.model.interfaces.Term term, T ontologyTerm)`	processXrefs.

Methods inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader
dumpOntology, dumpOntologyStats, dumpTerm, getOntology, getRootTerms, getUnknownRelationTermBean, initializeCommonObjects, initializeTermBean, load, process, processTerm, safeTrim, safeTrim, setParser, setUseGreedy, unload

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - SHORTLABEL_IDENTIFIER
```
public static final String SHORTLABEL_IDENTIFIER
```
    Constant SHORTLABEL_IDENTIFIER="Unique short label curated by PSI-MI"
    
    See Also:
    
    Constant Field Values
  - ALIAS_IDENTIFIER
```
public static final String ALIAS_IDENTIFIER
```
    Constant ALIAS_IDENTIFIER="Alternate label curated by PSI-MI"
    
    See Also:
    
    Constant Field Values
  - MOD_SHORTLABEL_IDENTIFIER
```
public static final String MOD_SHORTLABEL_IDENTIFIER
```
    Constant MOD_SHORTLABEL_IDENTIFIER="Short label curated by PSI-MOD"
    
    See Also:
    
    Constant Field Values
  - EXACT_KEY
```
public static final String EXACT_KEY
```
    Constant EXACT_KEY="exact"
    
    See Also:
    
    Constant Field Values
  - MOD_ALIAS_IDENTIFIER
```
public static final String MOD_ALIAS_IDENTIFIER
```
    Constant MOD_ALIAS_IDENTIFIER="Alternate name curated by PSI-MOD"
    
    See Also:
    
    Constant Field Values
  - RESID_IDENTIFIER
```
public static final String RESID_IDENTIFIER
```
    Constant RESID_IDENTIFIER="Alternate name from RESID"
    
    See Also:
    
    Constant Field Values
  - RESID_MISNOMER_IDENTIFIER
```
public static final String RESID_MISNOMER_IDENTIFIER
```
    Constant RESID_MISNOMER_IDENTIFIER="Misnomer tagged alternate name from RES"{trunked}
    
    See Also:
    
    Constant Field Values
  - RESID_NAME_IDENTIFIER
```
public static final String RESID_NAME_IDENTIFIER
```
    Constant RESID_NAME_IDENTIFIER="Name from RESID"
    
    See Also:
    
    Constant Field Values
  - RESID_SYSTEMATIC_IDENTIFIER
```
public static final String RESID_SYSTEMATIC_IDENTIFIER
```
    Constant RESID_SYSTEMATIC_IDENTIFIER="Systematic name from RESID"
    
    See Also:
    
    Constant Field Values
  - UNIPROT_FEATURE_IDENTIFIER
```
public static final String UNIPROT_FEATURE_IDENTIFIER
```
    Constant UNIPROT_FEATURE_IDENTIFIER="Protein feature description from UniPro"{trunked}
    
    See Also:
    
    Constant Field Values
  - XREF_TYPE
```
public static final int XREF_TYPE
```
    Constant XREF_TYPE=3
    
    See Also:
    
    Constant Field Values
  - PMID_APPLICATION
```
public static final String PMID_APPLICATION
```
    Constant PMID_APPLICATION="PMID for application instance"
    
    See Also:
    
    Constant Field Values
  - SO
```
public static final String SO
```
    Constant SO="so"
    
    See Also:
    
    Constant Field Values
  - SO_MI_REF
```
public static final String SO_MI_REF
```
    Constant SO_MI_REF="MI:0601"
    
    See Also:
    
    Constant Field Values
  - HTTP_DEF
```
public static final String HTTP_DEF
```
    Constant HTTP_DEF="http"
    
    See Also:
    
    Constant Field Values
  - XREF_VALIDATION_REGEXP
```
public static final String XREF_VALIDATION_REGEXP
```
    Constant XREF_VALIDATION_REGEXP="id-validation-regexp"
    
    See Also:
    
    Constant Field Values
  - XREF_VALIDATION_REGEXP_MI_REF
```
public static final String XREF_VALIDATION_REGEXP_MI_REF
```
    Constant XREF_VALIDATION_REGEXP_MI_REF="MI:0628"
    
    See Also:
    
    Constant Field Values
  - SEARCH_URL
```
public static final String SEARCH_URL
```
    Constant SEARCH_URL="search-url"
    
    See Also:
    
    Constant Field Values
  - SEARCH_URL_MI_REF
```
public static final String SEARCH_URL_MI_REF
```
    Constant SEARCH_URL_MI_REF="MI:0615"
    
    See Also:
    
    Constant Field Values
  - QUOTE
```
public static final String QUOTE
```
    Constant QUOTE="""
    
    See Also:
    
    Constant Field Values
  - META_XREF_SEPARATOR
```
public static final String META_XREF_SEPARATOR
```
    Constant META_XREF_SEPARATOR=":"
    
    See Also:
    
    Constant Field Values
  - LINE_BREAK
```
public static final String LINE_BREAK
```
    Constant LINE_BREAK="\n"
    
    See Also:
    
    Constant Field Values
  - COMMENT_KEY
```
public static final String COMMENT_KEY
```
    Constant COMMENT_KEY="comment"
    
    See Also:
    
    Constant Field Values
  - PMID
```
public static final String PMID
```
    Constant PMID="PMID"
    
    See Also:
    
    Constant Field Values
  - METHOD_REFERENCE
```
public static final String METHOD_REFERENCE
```
    Constant METHOD_REFERENCE="method reference"
    
    See Also:
    
    Constant Field Values
  - METHOD_REFERENCE_MI_REF
```
public static final String METHOD_REFERENCE_MI_REF
```
    Constant METHOD_REFERENCE_MI_REF="MI:0357"
    
    See Also:
    
    Constant Field Values
  - GO
```
public static final String GO
```
    Constant GO="go"
    
    See Also:
    
    Constant Field Values
  - GO_MI_REF
```
public static final String GO_MI_REF
```
    Constant GO_MI_REF="MI:0448"
    
    See Also:
    
    Constant Field Values
  - RESID
```
public static final String RESID
```
    Constant RESID="resid"
    
    See Also:
    
    Constant Field Values
  - RESID_MI_REF
```
public static final String RESID_MI_REF
```
    Constant RESID_MI_REF="MI:0248"
    
    See Also:
    
    Constant Field Values
  - log
```
public static final org.apache.commons.logging.Log log
```
    Sets up a logger for that class.
- Constructor Detail
  - AbstractOboLoader
```
public AbstractOboLoader(CvTerm database)
```
    Constructor for AbstractOboLoader.
    
    Parameters:
    
    database - a CvTerm object.
  - AbstractOboLoader
```
public AbstractOboLoader(String databaseName)
```
    Constructor for AbstractOboLoader.
    
    Parameters:
    
    databaseName - a String object.
- Method Detail
  - getOntologyDatabase
```
protected CvTerm getOntologyDatabase()
```
    Getter for the field ontologyDatabase.
    
    Returns:
    
    a CvTerm object.
  - configure
```
protected void configure(String filePath)
```
    configure.
    
    Parameters:
    
    filePath - a String object.
  - buildOntology
```
public void buildOntology(Map<String,T> id2Terms,
                          Map<String,T> name2Terms)
```
    buildOntology.
    
    Parameters:
    
    id2Terms - a Map object.
    
    name2Terms - a Map object.
  - createNewTerm
```
protected T createNewTerm(uk.ac.ebi.ols.model.interfaces.Term t)
```
    createNewTerm.
    
    Parameters:
    
    t - a Term object.
    
    Returns:
    
    a T object.
  - processAnnotations
```
protected void processAnnotations(uk.ac.ebi.ols.model.interfaces.Term term,
                                  T ontologyTerm)
```
    Process the annotations of a term
    
    Parameters:
    
    term - a Term object.
    
    ontologyTerm - a T object.
  - processXrefs
```
protected void processXrefs(uk.ac.ebi.ols.model.interfaces.Term term,
                            T ontologyTerm)
```
    processXrefs.
    
    Parameters:
    
    term - a Term object.
    
    ontologyTerm - a T object.
  - processXrefDefinition
```
protected String processXrefDefinition(String xref,
                                       String database,
                                       String accession,
                                       String pubmedPrimary,
                                       T ontologyTerm)
```
    processXrefDefinition.
    
    Parameters:
    
    xref - a String object.
    
    database - a String object.
    
    accession - a String object.
    
    pubmedPrimary - a String object.
    
    ontologyTerm - a T object.
    
    Returns:
    
    a String object.
  - processXref
```
protected void processXref(String db,
                           String accession,
                           T ontologyTerm)
```
    processXref.
    
    Parameters:
    
    db - a String object.
    
    accession - a String object.
    
    ontologyTerm - a T object.
  - processDefinition
```
protected void processDefinition(uk.ac.ebi.ols.model.interfaces.Term term,
                                 T ontologyTerm)
```
    Process the definition of a term
    
    Parameters:
    
    term - a Term object.
    
    ontologyTerm - a T object.
  - processDefinition
```
protected void processDefinition(String definition,
                                 T ontologyTerm)
```
    Process the definition String
    
    Parameters:
    
    definition - a String object.
    
    ontologyTerm - a T object.
  - processInfoInDescription
```
protected void processInfoInDescription(String definition,
                                        String otherInfoString,
                                        T ontologyTerm)
```
    Process the other information in the description
    
    Parameters:
    
    definition - a String object.
    
    otherInfoString - a String object.
    
    ontologyTerm - a T object.
  - processSynonyms
```
protected void processSynonyms(uk.ac.ebi.ols.model.interfaces.Term term,
                               T ontologyTerm)
```
    processSynonyms.
    
    Parameters:
    
    term - a Term object.
    
    ontologyTerm - a T object.
  - processShortLabel
```
protected void processShortLabel(uk.ac.ebi.ols.model.interfaces.Term term,
                                 T ontologyTerm)
```
    processShortLabel.
    
    Parameters:
    
    term - a Term object.
    
    ontologyTerm - a T object.
  - instantiateNewTerm
```
protected abstract T instantiateNewTerm(String name,
                                        Xref identity)
```
    instantiateNewTerm.
    
    Parameters:
    
    name - a String object.
    
    identity - a Xref object.
    
    Returns:
    
    a T object.
  - createDefinitionFor
```
protected abstract void createDefinitionFor(String def,
                                            T term)
```
    createDefinitionFor.
    
    Parameters:
    
    def - a String object.
    
    term - a T object.
  - parseOboFile
```
public void parseOboFile(File file,
                         Map<String,T> id2Terms,
                         Map<String,T> name2Terms)
```
    Parse the given OBO file and build a representation of the DAG into an Ontology.
    
    Parameters:
    
    file - the input file. It has to exist and to be readable, otherwise it will break.
    
    id2Terms - : the map id2Term to populate
    
    name2Terms - : the map name2Term to populate

Class AbstractOboLoader<T extends CvTerm>

Field Summary

Fields inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

Fields inherited from interface uk.ac.ebi.ols.loader.interfaces.Loader

Constructor Summary

Method Summary

Methods inherited from class uk.ac.ebi.ols.loader.impl.BaseOBO2AbstractLoader

Methods inherited from class java.lang.Object

Field Detail

SHORTLABEL_IDENTIFIER

ALIAS_IDENTIFIER

MOD_SHORTLABEL_IDENTIFIER

EXACT_KEY

MOD_ALIAS_IDENTIFIER

RESID_IDENTIFIER

RESID_MISNOMER_IDENTIFIER

RESID_NAME_IDENTIFIER

RESID_SYSTEMATIC_IDENTIFIER

UNIPROT_FEATURE_IDENTIFIER

XREF_TYPE

PMID_APPLICATION

SO

SO_MI_REF

HTTP_DEF

XREF_VALIDATION_REGEXP

XREF_VALIDATION_REGEXP_MI_REF

SEARCH_URL

SEARCH_URL_MI_REF

QUOTE

META_XREF_SEPARATOR

LINE_BREAK

COMMENT_KEY

PMID

METHOD_REFERENCE

METHOD_REFERENCE_MI_REF

GO

GO_MI_REF

RESID

RESID_MI_REF

log

Constructor Detail

AbstractOboLoader

AbstractOboLoader

Method Detail

getOntologyDatabase

configure

buildOntology

createNewTerm

processAnnotations

processXrefs

processXrefDefinition

processXref

processDefinition

processDefinition

processInfoInDescription

processSynonyms

processShortLabel

instantiateNewTerm

createDefinitionFor

parseOboFile