edu.uchsc.ccp.knowtator.textsource.generif
Class GeneRIFTextSourceCollection

java.lang.Object
  edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
      edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
          edu.uchsc.ccp.knowtator.textsource.generif.GeneRIFTextSourceCollection

public class GeneRIFTextSourceCollection
extends FileLinesTextSourceCollection

This TextSourceCollection implementation is useful for GeneRIFs stored in in a single file line-by-line. The format of the file should be:
id|gene_name|gene_symbol|text
Where id is some local identifier (not provided by entrez) assigned to the geneRIF.

Field Summary

static String	CLS_NAME
static String	DISPLAY_NAME
static String	PROJECT_SETTING_RECENT_FILE

Fields inherited from class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection

namesToTextSource, textSourceToIndex

Constructor Summary

GeneRIFTextSourceCollection(File file)

GeneRIFTextSourceCollection(String fileName)

Method Summary

static void	createCls(KnowledgeBase kb)
protected TextSource	createTextSource(String fileLine)
static TextSourceCollection	open(Project project)
static TextSourceCollection	open(Project project, Component parent)
void	save(Project project) This method saves information about this text source collection to the Protege project.

Methods inherited from class edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection

find, get, get, getFile, getIndex, getName, iterator, select, size

Methods inherited from class java.lang.Object

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

Field Detail

DISPLAY_NAME

public static final String DISPLAY_NAME

See Also:

Constant Field Values

CLS_NAME

public static final String CLS_NAME

See Also:

Constant Field Values

PROJECT_SETTING_RECENT_FILE

public static final String PROJECT_SETTING_RECENT_FILE

Constructor Detail

GeneRIFTextSourceCollection

public GeneRIFTextSourceCollection(String fileName)
                            throws IOException

Throws:

IOException

GeneRIFTextSourceCollection

public GeneRIFTextSourceCollection(File file)
                            throws IOException

Throws:

IOException

Method Detail

createTextSource

protected TextSource createTextSource(String fileLine)

Overrides:

createTextSource in class FileLinesTextSourceCollection

open

public static TextSourceCollection open(Project project,
                                        Component parent)

save

public void save(Project project)

Description copied from class: TextSourceCollection

This method saves information about this text source collection to the Protege project. The information saved should be sufficient to reinstantiate this text source collection the next time Protege is started.

Overrides:

save in class FileLinesTextSourceCollection

open

public static TextSourceCollection open(Project project)

createCls

public static void createCls(KnowledgeBase kb)