org.molgenis.genetics.diag.genenetwork

Class GeneNetworkController

java.lang.Object

org.molgenis.ui.MolgenisPluginController

org.molgenis.genetics.diag.genenetwork.GeneNetworkController

@Controller
 @RequestMapping(value="/plugin/genenetwork")
public class GeneNetworkController
extends MolgenisPluginController

Field Summary

Fields

Modifier and Type	Field and Description
static int	BATCH_SIZE
static String	GN_APP
static String	URI

Fields inherited from class org.molgenis.ui.MolgenisPluginController

PLUGIN_URI_PREFIX

Constructor Summary

Constructors

Constructor and Description
GeneNetworkController(DataService dataService, GeneNetworkScoreFactory geneNetworkScoreFactory)

Method Summary

Modifier and Type	Method and Description
protected Map<String,String>	createEnsembleHugoMap(String geneMappingFilePath)
protected void	createEntities(List<String> hpoTerms, Map<String,String> geneMap, Scanner rowScanner, String gene, int i, List<Entity> entities)
protected List<String>	createHpoTermList(Scanner hpoScanner)
void	importScores(String geneNetworkFile, String geneMappingFile)
String	init(org.springframework.ui.Model model)
protected List<Entity>	processSingleInputLine(Scanner scanner, List<String> hpoTerms, Map<String,String> geneMap)

Methods inherited from class org.molgenis.ui.MolgenisPluginController

getId, getPluginSettings, getUri

Methods inherited from class java.lang.Object

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

Field Detail

GN_APP

public static final String GN_APP

See Also:

Constant Field Values

URI

public static final String URI

See Also:

Constant Field Values

BATCH_SIZE

public static final int BATCH_SIZE

See Also:

Constant Field Values

Constructor Detail

GeneNetworkController

@Autowired
public GeneNetworkController(DataService dataService,
                                        GeneNetworkScoreFactory geneNetworkScoreFactory)

Method Detail

init

@RequestMapping(method=GET)
public String init(org.springframework.ui.Model model)

importScores

@RequestMapping(value="/import",
                method=POST)
 @ResponseStatus(value=OK)
public void importScores(@RequestParam(value="genenetworkfile")
                                                                                                                  String geneNetworkFile,
                                                                                                                  @RequestParam(value="genemappingfile")
                                                                                                                  String geneMappingFile)
                                                                                                           throws IOException

Throws:

IOException

processSingleInputLine

protected List<Entity> processSingleInputLine(Scanner scanner,
                                              List<String> hpoTerms,
                                              Map<String,String> geneMap)

createHpoTermList

protected List<String> createHpoTermList(Scanner hpoScanner)

createEntities

protected void createEntities(List<String> hpoTerms,
                              Map<String,String> geneMap,
                              Scanner rowScanner,
                              String gene,
                              int i,
                              List<Entity> entities)

createEnsembleHugoMap

protected Map<String,String> createEnsembleHugoMap(String geneMappingFilePath)
                                            throws FileNotFoundException

Throws:

FileNotFoundException