org.gcube.dataanalysis.executor.nodes.transducers.bionym

Class CometMatcherManager

java.lang.Object

org.gcube.dataanalysis.executor.nodes.transducers.bionym.CometMatcherManager

public class CometMatcherManager
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CometMatcherManager.Parsers
static class	CometMatcherManager.Reference
static class	CometMatcherManager.Weights

Constructor Summary

Constructors

Constructor and Description
CometMatcherManager()

Method Summary

Methods

Modifier and Type	Method and Description
static void	cometMatch(String pathToComet, String parser, String reference, String outFile, String inFile, float sxnw, int maxresults)
static void	cometParse(String pathToComet, String parser, String outFile, String inFile)
static void	dumpCometInput(String inputFile, List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> rawNames)
List<String>	getMatches()
List<String>	getScores()
List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>>	match(String parser, String reference, String sandboxFolder, List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> inputNamesList, float soundexweightF, int maxResults)
List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>>	parseCometOutput(String parserOutput)
static List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>>	parseCometParserOutput(String parserOutput)

Methods inherited from class java.lang.Object

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

Constructor Detail

CometMatcherManager

public CometMatcherManager()

Method Detail

cometParse

public static void cometParse(String pathToComet,
              String parser,
              String outFile,
              String inFile)
                       throws Exception

Throws:

Exception

cometMatch

public static void cometMatch(String pathToComet,
              String parser,
              String reference,
              String outFile,
              String inFile,
              float sxnw,
              int maxresults)
                       throws Exception

Throws:

Exception

parseCometParserOutput

public static List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> parseCometParserOutput(String parserOutput)
                                                                                         throws Exception

Throws:

Exception

getScores

public List<String> getScores()

getMatches

public List<String> getMatches()

parseCometOutput

public List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> parseCometOutput(String parserOutput)
                                                                            throws Exception

Throws:

Exception

dumpCometInput

public static void dumpCometInput(String inputFile,
                  List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> rawNames)
                           throws Exception

Throws:

Exception

match

public List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> match(String parser,
                                                               String reference,
                                                               String sandboxFolder,
                                                               List<org.gcube.dataanalysis.ecoengine.utils.Tuple<String>> inputNamesList,
                                                               float soundexweightF,
                                                               int maxResults)
                                                                 throws Exception

Throws:

Exception