Author: kono
Date: 2011-07-25 17:12:38 -0700 (Mon, 25 Jul 2011)
New Revision: 26264
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
Removed:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkWithoutGeneListTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderTask.java
Log:
fixes #300 Quick Start now have only one start panel.
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportNetworkFromPublicDataSetTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -15,7 +15,6 @@
import org.cytoscape.session.CyNetworkNaming;
import org.cytoscape.task.internal.loadnetwork.AbstractLoadNetworkTask;
import
org.cytoscape.task.internal.quickstart.datasource.InteractionFilePreprocessor;
-import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SearchRelatedGenesTask;
import org.cytoscape.view.model.CyNetworkViewManager;
import org.cytoscape.work.TaskMonitor;
import org.cytoscape.work.Tunable;
@@ -109,7 +108,6 @@
insertTasksAfterCurrentTask(new SetNetworkNameTask(reader,
selected));
taskMonitor.setStatusMessage("Loading network...");
loadNetwork(reader);
-
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/ImportTaskUtil.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -23,21 +23,21 @@
public class ImportTaskUtil {
- private CyNetworkReaderManager mgr;
- private CyNetworkManager netmgr;
- private final CyNetworkViewManager networkViewManager;
- private Properties props;
- private StreamUtil streamUtil;
+ protected CyNetworkReaderManager mgr;
+ protected CyNetworkManager netmgr;
+ protected final CyNetworkViewManager networkViewManager;
+ protected Properties props;
+ protected StreamUtil streamUtil;
- private CyNetworkNaming cyNetworkNaming;
+ protected CyNetworkNaming cyNetworkNaming;
- private final Set<InteractionFilePreprocessor> processors;
+ protected final Set<InteractionFilePreprocessor> processors;
- private CyTableManager tblMgr;
- private CyTableReaderManager tblReaderMgr;
+ protected CyTableManager tblMgr;
+ protected CyTableReaderManager tblReaderMgr;
- private final CyApplicationManager appManager;
- private CyProperty<Properties> cyProps;
+ protected final CyApplicationManager appManager;
+ protected CyProperty<Properties> cyProps;
public ImportTaskUtil(
CyNetworkReaderManager mgr,
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -43,6 +43,7 @@
import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderTask;
+// Currently not in use. StartTask is the actual Task.
public class QuickStartTask extends AbstractTask {
protected static final String LOAD_NETWORK = "Load a Network";
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/QuickStartTaskFactory2.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -12,7 +12,6 @@
}
public TaskIterator getTaskIterator() {
- return new TaskIterator(new
SimplifiedQuickStartTask(subnetworkUtil));
-// return new TaskIterator(new QuickStartTask2(new
QuickStartState(), util, networkManager, subnetworkUtil));
+ return new TaskIterator(new StartTask(new QuickStartState(),
util, networkManager, subnetworkUtil));
}
}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -30,9 +30,9 @@
final String selected = selection.getSelectedValue();
if(selected == SEARCH2_OPTION) {
- insertTasksAfterCurrentTask(new
SearchRelatedGenesTask(subnetworkUtil, new SubnetworkBuilderState()));
+ //insertTasksAfterCurrentTask(new
SearchRelatedGenesTask(subnetworkUtil, new SubnetworkBuilderState()));
} else if(selected == SEARCH1_OPTION) {
- insertTasksAfterCurrentTask(new
CreateSubnetworkWithoutGeneListTask(subnetworkUtil, new
SubnetworkBuilderState()));
+ //insertTasksAfterCurrentTask(new
CreateSubnetworkWithoutGeneListTask(subnetworkUtil, new
SubnetworkBuilderState()));
}
}
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SimplifiedQuickStartTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -1,21 +0,0 @@
-package org.cytoscape.task.internal.quickstart;
-
-import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
-import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.TaskMonitor;
-
-public class SimplifiedQuickStartTask extends AbstractTask {
-
- private final SubnetworkBuilderUtil subnetworkUtil;
-
- SimplifiedQuickStartTask(final SubnetworkBuilderUtil subnetworkUtil) {
- this.subnetworkUtil = subnetworkUtil;
- }
-
- @Override
- public void run(TaskMonitor taskMonitor) throws Exception {
- insertTasksAfterCurrentTask(new SelectNextTask(subnetworkUtil));
-
insertTasksAfterCurrentTask(subnetworkUtil.getWebServiceImportTask());
- }
-
-}
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/StartTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -0,0 +1,62 @@
+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;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderState;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.SubnetworkBuilderUtil;
+import org.cytoscape.work.TaskMonitor;
+import org.cytoscape.work.Tunable;
+import org.cytoscape.work.util.ListSingleSelection;
+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 = "Enter list of genes you are interested in
(should be separated by space)")
+ public String queryGenes;
+
+ @Tunable(description = "Select ID Type")
+ 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);
+ this.state = state;
+ this.importTaskUtil = importTaskUtil;
+ this.networkManager = networkManager;
+ this.subnetworkUtil = subnetworkUtil;
+ }
+
+ public void run(TaskMonitor tm) throws Exception {
+ if((go != null && go.trim().length() != 0)|| (phynotype != null
&& phynotype.trim().length() !=0)) {
+ logger.info("GO = " + go);
+ logger.info("Phynotype = " + phynotype);
+ insertTasksAfterCurrentTask(new
SearchRelatedGenesTask(subnetworkUtil, new SubnetworkBuilderState(), go,
phynotype));
+ }
+
+ 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));
+ }
+
+ super.run(tm);
+ }
+}
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkWithoutGeneListTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkWithoutGeneListTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkWithoutGeneListTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -8,25 +8,20 @@
import org.cytoscape.task.internal.quickstart.IDType;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
-import org.cytoscape.work.util.ListSingleSelection;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class CreateSubnetworkWithoutGeneListTask extends
CreateSubnetworkFromSearchTask {
private static final Logger logger =
LoggerFactory.getLogger(CreateSubnetworkWithoutGeneListTask.class);
-
- @Tunable(description = "Enter list of genes you are interested in
(should be separated by space)")
- public String queryGenes;
+ private final String queryGenes;
+ private final IDType idType;
- @Tunable(description = "Select ID Type")
- public ListSingleSelection<IDType> selection = new
ListSingleSelection<IDType>(IDType.GENE_SYMBOL, IDType.ENSEMBL,
- IDType.ENTREZ_GENE, IDType.UNIPROT);
-
- public CreateSubnetworkWithoutGeneListTask(SubnetworkBuilderUtil util,
SubnetworkBuilderState state) {
+ public CreateSubnetworkWithoutGeneListTask(SubnetworkBuilderUtil util,
SubnetworkBuilderState state, final String queryGenes, final IDType idType) {
super(util, state);
+ this.idType = idType;
+ this.queryGenes = queryGenes;
}
@Override
@@ -34,16 +29,14 @@
taskMonitor.setStatusMessage("Searching related genes in parent
network...");
taskMonitor.setProgress(-1);
- final IDType selected = selection.getSelectedValue();
-
final List<String> geneList;
- if (selected == IDType.ENTREZ_GENE) {
+ if (idType == IDType.ENTREZ_GENE) {
final String[] genes = queryGenes.split("\\s+");
logger.debug("Got gene list: " + genes.length);
geneList = Arrays.asList(genes);
} else {
- geneList = new ArrayList<String>(convert(selected));
+ geneList = new ArrayList<String>(convert(idType));
}
for (final String gene : geneList)
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -4,7 +4,6 @@
import org.cytoscape.work.AbstractTask;
import org.cytoscape.work.TaskMonitor;
-import org.cytoscape.work.Tunable;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -12,18 +11,17 @@
private static final Logger logger =
LoggerFactory.getLogger(SearchRelatedGenesTask.class);
- @Tunable(description = "Gene Ontology")
- public String go;
+ private final String go;
+ private final String phynotype;
- @Tunable(description = "Disease/Phynotype")
- public String phynotype;
-
private final SubnetworkBuilderState state;
private final SubnetworkBuilderUtil util;
- public SearchRelatedGenesTask(final SubnetworkBuilderUtil util, final
SubnetworkBuilderState state) {
+ public SearchRelatedGenesTask(final SubnetworkBuilderUtil util, final
SubnetworkBuilderState state, final String go, final String phynotype) {
this.state = state;
this.util = util;
+ this.go = go;
+ this.phynotype = phynotype;
}
@Override
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderTask.java
2011-07-25 21:11:24 UTC (rev 26263)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderTask.java
2011-07-26 00:12:38 UTC (rev 26264)
@@ -39,7 +39,7 @@
final String selected = selection.getSelectedValue();
- insertTasksAfterCurrentTask(new SearchRelatedGenesTask(util,
state));
+ //insertTasksAfterCurrentTask(new SearchRelatedGenesTask(util,
state));
if (selected == LOAD_NEW_NETWORK) {
insertTasksAfterCurrentTask(util.getWebServiceImportTask());
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