Author: kono
Date: 2011-06-24 17:06:38 -0700 (Fri, 24 Jun 2011)
New Revision: 25936
Added:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkFromSearchTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkWithoutGeneListTask.java
Removed:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
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/subnetworkbuilder/SearchRelatedGenesTask.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderState.java
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/VisualStyleBuilder.java
Log:
Simplified version of Quick Start had been implemented.
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
2011-06-24 23:10:26 UTC (rev 25935)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/SelectNextTask.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -1,5 +1,7 @@
package org.cytoscape.task.internal.quickstart;
+import
org.cytoscape.task.internal.quickstart.subnetworkbuilder.CreateSubnetworkFromSearchTask;
+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;
@@ -10,11 +12,12 @@
public class SelectNextTask extends AbstractTask {
- private static final String SEARCH_OPTION = "Search this network and
create subnetwork";
+ private static final String SEARCH1_OPTION = "Create subnetwork from
gene list";
+ private static final String SEARCH2_OPTION = "Create subnetwork related
to phynotypes/diseases";
private static final String FINISH_OPTION = "Finished";
@Tunable(description = "What would you like to do next?")
- public ListSingleSelection<String> selection = new
ListSingleSelection<String>(SEARCH_OPTION, FINISH_OPTION);
+ public ListSingleSelection<String> selection = new
ListSingleSelection<String>(SEARCH1_OPTION, SEARCH2_OPTION, FINISH_OPTION);
private final SubnetworkBuilderUtil subnetworkUtil;
@@ -26,8 +29,11 @@
public void run(TaskMonitor taskMonitor) throws Exception {
final String selected = selection.getSelectedValue();
- if(selected == SEARCH_OPTION)
+ if(selected == SEARCH2_OPTION) {
insertTasksAfterCurrentTask(new
SearchRelatedGenesTask(subnetworkUtil, new SubnetworkBuilderState()));
+ } else if(selected == SEARCH1_OPTION) {
+ insertTasksAfterCurrentTask(new
CreateSubnetworkWithoutGeneListTask(subnetworkUtil, new
SubnetworkBuilderState()));
+ }
}
}
Copied:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkFromSearchTask.java
(from rev 25922,
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java)
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkFromSearchTask.java
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkFromSearchTask.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -0,0 +1,91 @@
+package org.cytoscape.task.internal.quickstart.subnetworkbuilder;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyTable;
+import org.cytoscape.model.CyTableEntry;
+import org.cytoscape.task.internal.select.SelectFirstNeighborsTask;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.Task;
+import org.cytoscape.work.TaskMonitor;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+public class CreateSubnetworkFromSearchTask extends AbstractTask {
+
+ private static final Logger logger =
LoggerFactory.getLogger(CreateSubnetworkFromSearchTask.class);
+
+ static final String QUERY_GENE_ATTR_NAME = "Gene Type";
+ static final String SEARCH_GENE_ATTR_NAME = "Search Term";
+
+ private final SubnetworkBuilderUtil util;
+ private final SubnetworkBuilderState state;
+
+ public CreateSubnetworkFromSearchTask(final SubnetworkBuilderUtil util,
final SubnetworkBuilderState state) {
+ this.util = util;
+ this.state = state;
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ taskMonitor.setStatusMessage("Searching related genes in parent
network...");
+ taskMonitor.setProgress(-1);
+
+ selectGenes(new ArrayList<String>());
+
+ taskMonitor.setProgress(1.0);
+
+ }
+
+ protected void selectGenes(final List<String> geneList) {
+ final CyNetwork target = util.appManager.getCurrentNetwork();
+ final CyTable nodeTable = target.getDefaultNodeTable();
+
+ if (nodeTable.getColumn(QUERY_GENE_ATTR_NAME) == null)
+ nodeTable.createColumn(QUERY_GENE_ATTR_NAME,
String.class, false);
+ if (nodeTable.getColumn(SEARCH_GENE_ATTR_NAME) == null)
+ nodeTable.createColumn(SEARCH_GENE_ATTR_NAME,
String.class, false);
+
+ boolean found = false;
+
+
+ List<CyNode> nodeList = target.getNodeList();
+ for (final CyNode node : nodeList) {
+ final String nodeName =
node.getCyRow().get(CyTableEntry.NAME, String.class);
+
+ if (geneList.contains(nodeName) &&
state.getDiseaseGenes().contains(nodeName)) {
+ node.getCyRow().set(CyNetwork.SELECTED,
true);
+
node.getCyRow().set(QUERY_GENE_ATTR_NAME, "query and disease");
+
node.getCyRow().set(SEARCH_GENE_ATTR_NAME, state.getSearchTerms());
+ found = true;
+ } else if (geneList.contains(nodeName)) {
+ node.getCyRow().set(CyNetwork.SELECTED,
true);
+
node.getCyRow().set(QUERY_GENE_ATTR_NAME, "query");
+ found = true;
+ } else if
(state.getDiseaseGenes().contains(nodeName)) {
+ node.getCyRow().set(CyNetwork.SELECTED,
true);
+
node.getCyRow().set(QUERY_GENE_ATTR_NAME, "disease");
+
node.getCyRow().set(SEARCH_GENE_ATTR_NAME, state.getSearchTerms());
+ }
+ }
+
+ if (!found) {
+ logger.error("Query genes were not found in the
interactome.");
+ return;
+ }
+
+ this.insertTasksAfterCurrentTask(new
BuildVisualStyleTask(util));
+
+ this.insertTasksAfterCurrentTask(util.getApplLayoutTask());
+
+ Task createNetworkTask =
util.getNewNetworkSelectedNodesOnlyTask(target);
+ this.insertTasksAfterCurrentTask(createNetworkTask);
+
+ SelectFirstNeighborsTask nextTask = new
SelectFirstNeighborsTask(target, util.networkViewManager,
+ util.eventHelper);
+ this.insertTasksAfterCurrentTask(nextTask);
+ }
+}
Deleted:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
2011-06-24 23:10:26 UTC (rev 25935)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkTask.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -1,133 +0,0 @@
-package org.cytoscape.task.internal.quickstart.subnetworkbuilder;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Set;
-
-import org.cytoscape.model.CyNetwork;
-import org.cytoscape.model.CyNode;
-import org.cytoscape.model.CyTable;
-import org.cytoscape.model.CyTableEntry;
-import org.cytoscape.task.internal.quickstart.IDType;
-import org.cytoscape.task.internal.select.SelectFirstNeighborsTask;
-import org.cytoscape.work.AbstractTask;
-import org.cytoscape.work.Task;
-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 CreateSubnetworkTask extends AbstractTask {
-
- private static final Logger logger =
LoggerFactory.getLogger(CreateSubnetworkTask.class);
-
- static final String QUERY_GENE_ATTR_NAME = "Gene Type";
- static final String SEARCH_GENE_ATTR_NAME = "Search Term";
-
- @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);
-
- private final SubnetworkBuilderUtil util;
- private final SubnetworkBuilderState state;
-
- CreateSubnetworkTask(final SubnetworkBuilderUtil util, final
SubnetworkBuilderState state) {
- this.util = util;
- this.state = state;
- }
-
- @Override
- public void run(TaskMonitor taskMonitor) throws Exception {
- 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) {
- final String[] genes = queryGenes.split("\\s+");
- logger.debug("Got gene list: " + genes.length);
- for (final String gene : genes) {
- logger.debug("Gene: " + gene);
- }
- geneList = Arrays.asList(genes);
- } else {
- geneList = new ArrayList<String>(convert(selected));
- }
-
-
- selectGenes(geneList);
-
- taskMonitor.setProgress(1.0);
-
- }
-
- private Set<String> convert(IDType selected) throws IOException {
- final boolean isGeneSymbol;
-
- if (selected == IDType.GENE_SYMBOL)
- isGeneSymbol = true;
- else
- isGeneSymbol = false;
-
- final NCBISearchClient client = new NCBISearchClient();
-
- return client.convert(queryGenes, isGeneSymbol);
- }
-
- private void selectGenes(final List<String> geneList) {
- final CyNetwork target = util.appManager.getCurrentNetwork();
- final CyTable nodeTable = target.getDefaultNodeTable();
-
- if (nodeTable.getColumn(QUERY_GENE_ATTR_NAME) == null)
- nodeTable.createColumn(QUERY_GENE_ATTR_NAME,
String.class, false);
- if (nodeTable.getColumn(SEARCH_GENE_ATTR_NAME) == null)
- nodeTable.createColumn(SEARCH_GENE_ATTR_NAME,
String.class, false);
-
- boolean found = false;
-
-
- List<CyNode> nodeList = target.getNodeList();
- for (final CyNode node : nodeList) {
- final String nodeName =
node.getCyRow().get(CyTableEntry.NAME, String.class);
-
- if (geneList.contains(nodeName) &&
state.getDiseaseGenes().contains(nodeName)) {
- node.getCyRow().set(CyNetwork.SELECTED,
true);
-
node.getCyRow().set(QUERY_GENE_ATTR_NAME, "query and disease");
-
node.getCyRow().set(SEARCH_GENE_ATTR_NAME, state.getSearchTerms());
- found = true;
- } else if (geneList.contains(nodeName)) {
- node.getCyRow().set(CyNetwork.SELECTED,
true);
-
node.getCyRow().set(QUERY_GENE_ATTR_NAME, "query");
- found = true;
- } else if
(state.getDiseaseGenes().contains(nodeName)) {
- node.getCyRow().set(CyNetwork.SELECTED,
true);
-
node.getCyRow().set(QUERY_GENE_ATTR_NAME, "disease");
-
node.getCyRow().set(SEARCH_GENE_ATTR_NAME, state.getSearchTerms());
- }
- }
-
- if (!found) {
- logger.error("Query genes were not found in the
interactome.");
- return;
- }
-
- this.insertTasksAfterCurrentTask(new
BuildVisualStyleTask(util));
-
- this.insertTasksAfterCurrentTask(util.getApplLayoutTask());
-
- Task createNetworkTask =
util.getNewNetworkSelectedNodesOnlyTask(target);
- this.insertTasksAfterCurrentTask(createNetworkTask);
-
- SelectFirstNeighborsTask nextTask = new
SelectFirstNeighborsTask(target, util.networkViewManager,
- util.eventHelper);
- this.insertTasksAfterCurrentTask(nextTask);
- }
-}
Added:
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
(rev 0)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/CreateSubnetworkWithoutGeneListTask.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -0,0 +1,71 @@
+package org.cytoscape.task.internal.quickstart.subnetworkbuilder;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Set;
+
+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;
+
+ @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) {
+ super(util, state);
+ }
+
+ @Override
+ public void run(TaskMonitor taskMonitor) throws Exception {
+ 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) {
+ final String[] genes = queryGenes.split("\\s+");
+ logger.debug("Got gene list: " + genes.length);
+ geneList = Arrays.asList(genes);
+ } else {
+ geneList = new ArrayList<String>(convert(selected));
+ }
+
+ for (final String gene : geneList)
+ logger.debug("Gene Found: " + gene);
+
+ selectGenes(geneList);
+
+ taskMonitor.setProgress(1.0);
+
+ }
+
+ private Set<String> convert(IDType selected) throws IOException {
+ final boolean isGeneSymbol;
+
+ if (selected == IDType.GENE_SYMBOL)
+ isGeneSymbol = true;
+ else
+ isGeneSymbol = false;
+
+ final NCBISearchClient client = new NCBISearchClient();
+
+ return client.convert(queryGenes, isGeneSymbol);
+ }
+
+}
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
2011-06-24 23:10:26 UTC (rev 25935)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SearchRelatedGenesTask.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -32,7 +32,7 @@
tm.setProgress(0.0);
- insertTasksAfterCurrentTask(new CreateSubnetworkTask(util,
state));
+ insertTasksAfterCurrentTask(new
CreateSubnetworkFromSearchTask(util, state));
final NCBISearchClient client = new NCBISearchClient();
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderState.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderState.java
2011-06-24 23:10:26 UTC (rev 25935)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/SubnetworkBuilderState.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -1,5 +1,6 @@
package org.cytoscape.task.internal.quickstart.subnetworkbuilder;
+import java.util.HashSet;
import java.util.Set;
public class SubnetworkBuilderState {
@@ -18,11 +19,17 @@
}
Set<String> getQueryGenes() {
- return this.queryGenes;
+ if(queryGenes != null)
+ return this.queryGenes;
+ else
+ return new HashSet<String>();
}
Set<String> getDiseaseGenes() {
- return this.diseaseGenes;
+ if(diseaseGenes != null)
+ return this.diseaseGenes;
+ else
+ return new HashSet<String>();
}
void setSearchTerms(final String searchTerms) {
Modified:
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/VisualStyleBuilder.java
===================================================================
---
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/VisualStyleBuilder.java
2011-06-24 23:10:26 UTC (rev 25935)
+++
core3/core-task-impl/trunk/src/main/java/org/cytoscape/task/internal/quickstart/subnetworkbuilder/VisualStyleBuilder.java
2011-06-25 00:06:38 UTC (rev 25936)
@@ -13,7 +13,7 @@
import org.cytoscape.view.vizmap.VisualStyleFactory;
import org.cytoscape.view.vizmap.mappings.DiscreteMapping;
-import static
org.cytoscape.task.internal.quickstart.subnetworkbuilder.CreateSubnetworkTask.*;
+import static
org.cytoscape.task.internal.quickstart.subnetworkbuilder.CreateSubnetworkFromSearchTask.*;
/**
* Builder for Visual Style
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