Author: ruschein
Date: 2011-08-24 14:55:01 -0700 (Wed, 24 Aug 2011)
New Revision: 26632
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
Log:
Fixed various spelling errors and general cleanup.
Modified:
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
===================================================================
---
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
2011-08-24 21:43:13 UTC (rev 26631)
+++
core3/impl/trunk/core-task-impl/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
2011-08-24 21:55:01 UTC (rev 26632)
@@ -1,5 +1,6 @@
package org.cytoscape.task.internal.quickstart;
+
import org.cytoscape.model.CyNetworkManager;
import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.CreateSubnetworkWithoutGeneListTask;
import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SearchRelatedGenesTask;
@@ -11,33 +12,36 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+
public class StartTask extends ImportNetworkFromPublicDataSetTask {
-
private static final Logger logger =
LoggerFactory.getLogger(StartTask.class);
@Tunable(description = "Gene Ontology (Optional)")
public String go;
- @Tunable(description = "Disease/Phynotype (Optional)")
- public String phynotype;
+ @Tunable(description = "Disease/Phenotype (Optional)")
+ public String phenotype;
- @Tunable(description = "List of genes you are interested in (Optional.
Separated by space)")
+ @Tunable(description = "List of genes you are interested in (Optional.
Separated by spaces)")
public String queryGenes;
@Tunable(description = "Gene ID Type (Optional)")
- public ListSingleSelection<IDType> selection = new
ListSingleSelection<IDType>(IDType.GENE_SYMBOL, IDType.ENSEMBL,
- IDType.ENTREZ_GENE, IDType.UNIPROT);
+ public ListSingleSelection<IDType> selection =
+ new ListSingleSelection<IDType>(IDType.GENE_SYMBOL,
IDType.ENSEMBL,
+ IDType.ENTREZ_GENE,
IDType.UNIPROT);
protected final QuickStartState state;
protected final ImportTaskUtil importTaskUtil;
-
protected final CyNetworkManager networkManager;
protected final SubnetworkBuilderUtil subnetworkUtil;
public StartTask(final QuickStartState state, final ImportTaskUtil
importTaskUtil,
- final CyNetworkManager networkManager, final
SubnetworkBuilderUtil subnetworkUtil) {
- super(importTaskUtil.processors, importTaskUtil.mgr,
networkManager, importTaskUtil.networkViewManager,
- importTaskUtil.props,
importTaskUtil.cyNetworkNaming, importTaskUtil.streamUtil);
+ final CyNetworkManager networkManager,
+ final SubnetworkBuilderUtil subnetworkUtil)
+ {
+ super(importTaskUtil.processors, importTaskUtil.mgr,
networkManager,
+ importTaskUtil.networkViewManager, importTaskUtil.props,
+ importTaskUtil.cyNetworkNaming,
importTaskUtil.streamUtil);
this.state = state;
this.importTaskUtil = importTaskUtil;
this.networkManager = networkManager;
@@ -45,16 +49,24 @@
}
public void run(TaskMonitor tm) throws Exception {
- if((go != null && go.trim().length() != 0)|| (phynotype != null
&& phynotype.trim().length() !=0)) {
+ if (go != null && go.trim().length() != 0
+ || phenotype != null && phenotype.trim().length() != 0)
+ {
logger.info("GO = " + go);
- logger.info("Phynotype = " + phynotype);
- insertTasksAfterCurrentTask(new
SearchRelatedGenesTask(subnetworkUtil, new SubnetworkBuilderState(), go,
phynotype));
+ logger.info("Phenotype = " + phenotype);
+ insertTasksAfterCurrentTask(
+ new SearchRelatedGenesTask(subnetworkUtil,
+ new
SubnetworkBuilderState(), go,
+ phenotype));
}
- if(queryGenes != null && queryGenes.trim().length() != 0) {
+ if (queryGenes != null && queryGenes.trim().length() != 0) {
logger.info("Query Genes: " + queryGenes);
final IDType selectedType =
selection.getSelectedValue();
- insertTasksAfterCurrentTask(new
CreateSubnetworkWithoutGeneListTask(subnetworkUtil, new
SubnetworkBuilderState(), queryGenes, selectedType));
+ insertTasksAfterCurrentTask(
+ new
CreateSubnetworkWithoutGeneListTask(subnetworkUtil,
+ new
SubnetworkBuilderState(),
+
queryGenes, selectedType));
}
super.run(tm);
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