Package de.julielab.jcore.ae.gnp

Class GNormPlusAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

de.julielab.jcore.ae.gnp.GNormPlusAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class GNormPlusAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Field Summary

Fields

Modifier and Type	Field	Description
static String	DESC_FOCUS_SPECIES
static String	DESC_GNP_SETUP_FILE
static String	DESC_INPUT_GENE_TYPE_NAME
static String	DESC_OUTPUT_DIR
static String	DESC_OUTPUT_GENE_TYPE_NAME
static String	DESC_USE_EXISTING_GENES
static String	PARAM_FOCUS_SPECIES
static String	PARAM_GNP_SETUP_FILE
static String	PARAM_INPUT_GENE_TYPE_NAME
static String	PARAM_OUTPUT_DIR
static String	PARAM_OUTPUT_GENE_TYPE_NAME
static String	PARAM_USE_EXISTING_GENE_ANNOTATIONS

Constructor Summary

Constructors

Constructor	Description
GNormPlusAnnotator()

Method Summary

Modifier and Type	Method	Description
void	initialize(org.apache.uima.UimaContext aContext)	This method is called a single time by the framework at component creation.
void	process(org.apache.uima.jcas.JCas aJCas)	This method is called for each document going through the component.

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Field Detail

PARAM_USE_EXISTING_GENE_ANNOTATIONS

public static final String PARAM_USE_EXISTING_GENE_ANNOTATIONS

See Also:

Constant Field Values

DESC_INPUT_GENE_TYPE_NAME

public static final String DESC_INPUT_GENE_TYPE_NAME

See Also:

Constant Field Values

DESC_OUTPUT_GENE_TYPE_NAME

public static final String DESC_OUTPUT_GENE_TYPE_NAME

See Also:

Constant Field Values

PARAM_INPUT_GENE_TYPE_NAME

public static final String PARAM_INPUT_GENE_TYPE_NAME

See Also:

Constant Field Values

PARAM_OUTPUT_GENE_TYPE_NAME

public static final String PARAM_OUTPUT_GENE_TYPE_NAME

See Also:

Constant Field Values

DESC_USE_EXISTING_GENES

public static final String DESC_USE_EXISTING_GENES

See Also:

Constant Field Values

PARAM_GNP_SETUP_FILE

public static final String PARAM_GNP_SETUP_FILE

See Also:

Constant Field Values

PARAM_FOCUS_SPECIES

public static final String PARAM_FOCUS_SPECIES

See Also:

Constant Field Values

PARAM_OUTPUT_DIR

public static final String PARAM_OUTPUT_DIR

See Also:

Constant Field Values

DESC_GNP_SETUP_FILE

public static final String DESC_GNP_SETUP_FILE

See Also:

Constant Field Values

DESC_FOCUS_SPECIES

public static final String DESC_FOCUS_SPECIES

See Also:

Constant Field Values

DESC_OUTPUT_DIR

public static final String DESC_OUTPUT_DIR

See Also:

Constant Field Values

Constructor Detail

GNormPlusAnnotator

public GNormPlusAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException

This method is called a single time by the framework at component creation. Here, descriptor parameters are read and initial setup is done.

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

process

public void process(org.apache.uima.jcas.JCas aJCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

This method is called for each document going through the component. This is where the actual work happens.

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException