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

java.lang.Object
  extended by edu.uchsc.ccp.knowtator.textsource.TextSourceCollection
      extended by edu.uchsc.ccp.knowtator.textsource.filelines.FileLinesTextSourceCollection
          extended by 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)