public class CytoscapeHelperImpl extends java.lang.Object implements CytoscapeHelper
Modifier and Type | Field and Description |
---|---|
protected ClassifierEvaluationDao |
classifierEvaluationDao |
protected ConceptDao |
conceptDao |
protected UMLSDao |
umlsDao |
Constructor and Description |
---|
CytoscapeHelperImpl() |
Modifier and Type | Method and Description |
---|---|
private void |
addConcepts(ConceptGraph cg,
java.lang.String conceptId,
java.util.Set<java.lang.String> nodesToInclude,
java.util.Set<java.lang.String> leaves) |
private void |
addSubtree(java.util.Set<java.lang.String> nodes,
ConcRel cr) |
private void |
exportEdges(ConceptGraph cg,
java.io.BufferedWriter network) |
void |
exportNetwork(ConceptGraph cg,
java.lang.String corpusName,
java.lang.String conceptGraphName,
java.lang.String conceptSetName,
int leafChildrenDepth,
java.io.BufferedWriter networkData,
java.io.BufferedWriter nodeData) |
void |
exportNetwork(java.lang.String filePrefix,
java.util.Properties props) |
private void |
exportNodes(java.util.List<java.lang.String> subList,
java.io.BufferedWriter nodeData,
java.util.Map<java.lang.String,java.lang.Double> ic) |
private void |
exportNodes(java.util.Set<java.lang.String> exportedNodes,
java.io.BufferedWriter nodeData,
java.util.Map<java.lang.String,java.lang.Double> ic) |
void |
exportSubtree(java.lang.String conceptID,
java.util.Properties props) |
ClassifierEvaluationDao |
getClassifierEvaluationDao() |
ConceptDao |
getConceptDao() |
UMLSDao |
getUmlsDao() |
static void |
main(java.lang.String[] args) |
private static void |
printHelp(Options options) |
void |
setClassifierEvaluationDao(ClassifierEvaluationDao classifierEvaluationDao) |
void |
setConceptDao(ConceptDao conceptDao) |
void |
setUmlsDao(UMLSDao umlsDao) |
boolean |
validateProps(java.util.Properties props) |
protected ClassifierEvaluationDao classifierEvaluationDao
protected ConceptDao conceptDao
protected UMLSDao umlsDao
public static void main(java.lang.String[] args) throws ParseException, java.io.IOException
args
- ParseException
java.io.IOException
private static void printHelp(Options options)
private void addConcepts(ConceptGraph cg, java.lang.String conceptId, java.util.Set<java.lang.String> nodesToInclude, java.util.Set<java.lang.String> leaves)
private void addSubtree(java.util.Set<java.lang.String> nodes, ConcRel cr)
private void exportEdges(ConceptGraph cg, java.io.BufferedWriter network) throws java.io.IOException
java.io.IOException
public void exportNetwork(ConceptGraph cg, java.lang.String corpusName, java.lang.String conceptGraphName, java.lang.String conceptSetName, int leafChildrenDepth, java.io.BufferedWriter networkData, java.io.BufferedWriter nodeData) throws java.io.IOException
exportNetwork
in interface CytoscapeHelper
java.io.IOException
public void exportNetwork(java.lang.String filePrefix, java.util.Properties props) throws java.io.IOException
exportNetwork
in interface CytoscapeHelper
java.io.IOException
private void exportNodes(java.util.List<java.lang.String> subList, java.io.BufferedWriter nodeData, java.util.Map<java.lang.String,java.lang.Double> ic) throws java.io.IOException
java.io.IOException
private void exportNodes(java.util.Set<java.lang.String> exportedNodes, java.io.BufferedWriter nodeData, java.util.Map<java.lang.String,java.lang.Double> ic) throws java.io.IOException
java.io.IOException
public void exportSubtree(java.lang.String conceptID, java.util.Properties props) throws java.io.IOException
exportSubtree
in interface CytoscapeHelper
java.io.IOException
public ClassifierEvaluationDao getClassifierEvaluationDao()
public ConceptDao getConceptDao()
public UMLSDao getUmlsDao()
public void setClassifierEvaluationDao(ClassifierEvaluationDao classifierEvaluationDao)
public void setConceptDao(ConceptDao conceptDao)
public void setUmlsDao(UMLSDao umlsDao)
public boolean validateProps(java.util.Properties props)
validateProps
in interface CytoscapeHelper