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Support for hidden nodes. Requires cytoscape 3.4.
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159
AutoAnnotate/src/main/java/org/baderlab/autoannotate/internal/task/CreateSubnetworkTask.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,159 @@ | ||
| package org.baderlab.autoannotate.internal.task; | ||
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| import java.util.ArrayList; | ||
| import java.util.Collection; | ||
| import java.util.HashSet; | ||
| import java.util.List; | ||
| import java.util.Set; | ||
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| import org.cytoscape.model.CyColumn; | ||
| import org.cytoscape.model.CyEdge; | ||
| import org.cytoscape.model.CyNetwork; | ||
| import org.cytoscape.model.CyNode; | ||
| import org.cytoscape.model.CyRow; | ||
| import org.cytoscape.model.CyTable; | ||
| import org.cytoscape.model.VirtualColumnInfo; | ||
| import org.cytoscape.model.subnetwork.CyRootNetworkManager; | ||
| import org.cytoscape.model.subnetwork.CySubNetwork; | ||
| import org.cytoscape.work.AbstractTask; | ||
| import org.cytoscape.work.ObservableTask; | ||
| import org.cytoscape.work.TaskMonitor; | ||
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| import com.google.inject.Inject; | ||
| import com.google.inject.assistedinject.Assisted; | ||
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| public class CreateSubnetworkTask extends AbstractTask implements ObservableTask { | ||
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| @Inject private CyRootNetworkManager rootNetMgr; | ||
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| private final CyNetwork parentNetwork; | ||
| private final Collection<CyNode> nodes; | ||
| private CySubNetwork resultNetwork; | ||
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| public interface Factory { | ||
| CreateSubnetworkTask create(CyNetwork parentNetwork, Collection<CyNode> nodes); | ||
| } | ||
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| @Inject | ||
| public CreateSubnetworkTask(@Assisted CyNetwork parentNetwork, @Assisted Collection<CyNode> nodes) { | ||
| this.parentNetwork = parentNetwork; | ||
| this.nodes = nodes; | ||
| } | ||
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| @Override | ||
| public void run(TaskMonitor tm) { | ||
| if (parentNetwork == null) { | ||
| tm.showMessage(TaskMonitor.Level.ERROR, "Source network must be specified."); | ||
| return; | ||
| } | ||
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| tm.setProgress(0.2); | ||
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| // create subnetwork and add selected nodes and appropriate edges | ||
| final CySubNetwork newNet = rootNetMgr.getRootNetwork(parentNetwork).addSubNetwork(); | ||
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| //We need to cpy the columns to local tables, since copying them to default table will duplicate the virtual columns. | ||
| addColumns(parentNetwork.getTable(CyNode.class, CyNetwork.LOCAL_ATTRS), newNet.getTable(CyNode.class, CyNetwork.LOCAL_ATTRS)); | ||
| addColumns(parentNetwork.getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS), newNet.getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS) ); | ||
| addColumns(parentNetwork.getTable(CyNetwork.class, CyNetwork.LOCAL_ATTRS), newNet.getTable(CyNetwork.class, CyNetwork.LOCAL_ATTRS)); | ||
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| tm.setProgress(0.3); | ||
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| for(CyNode node : nodes) { | ||
| newNet.addNode(node); | ||
| cloneRow(parentNetwork.getRow(node), newNet.getRow(node)); | ||
| //Set rows and edges to not selected state to avoid conflicts with table browser | ||
| newNet.getRow(node).set(CyNetwork.SELECTED, false); | ||
| } | ||
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| tm.setProgress(0.4); | ||
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| for (final CyEdge edge : getEdges(parentNetwork, nodes)) { | ||
| newNet.addEdge(edge); | ||
| cloneRow(parentNetwork.getRow(edge), newNet.getRow(edge)); | ||
| //Set rows and edges to not selected state to avoid conflicts with table browser | ||
| newNet.getRow(edge).set(CyNetwork.SELECTED, false); | ||
| } | ||
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| tm.setProgress(0.5); | ||
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| newNet.getRow(newNet).set(CyNetwork.NAME, getNetworkName()); | ||
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| resultNetwork = newNet; | ||
| tm.setProgress(1.0); | ||
| } | ||
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| private void addColumns(CyTable parentTable, CyTable subTable) { | ||
| List<CyColumn> colsToAdd = new ArrayList<CyColumn>(); | ||
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| for (CyColumn col: parentTable.getColumns()) | ||
| if (subTable.getColumn(col.getName()) == null) | ||
| colsToAdd.add( col ); | ||
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| for (CyColumn col: colsToAdd) { | ||
| VirtualColumnInfo colInfo = col.getVirtualColumnInfo(); | ||
| if (colInfo.isVirtual()) | ||
| addVirtualColumn(col, subTable); | ||
| else | ||
| copyColumn(col, subTable); | ||
| } | ||
| } | ||
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| private void addVirtualColumn (CyColumn col, CyTable subTable){ | ||
| VirtualColumnInfo colInfo = col.getVirtualColumnInfo(); | ||
| CyColumn checkCol= subTable.getColumn(col.getName()); | ||
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| if (checkCol == null) | ||
| subTable.addVirtualColumn(col.getName(), colInfo.getSourceColumn(), colInfo.getSourceTable(), | ||
| colInfo.getTargetJoinKey(), col.isImmutable()); | ||
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| else | ||
| if (!checkCol.getVirtualColumnInfo().isVirtual() || | ||
| !checkCol.getVirtualColumnInfo().getSourceTable().equals(colInfo.getSourceTable()) || | ||
| !checkCol.getVirtualColumnInfo().getSourceColumn().equals(colInfo.getSourceColumn())) | ||
| subTable.addVirtualColumn(col.getName(), colInfo.getSourceColumn(), colInfo.getSourceTable(), | ||
| colInfo.getTargetJoinKey(), col.isImmutable()); | ||
| } | ||
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| private void copyColumn(CyColumn col, CyTable subTable) { | ||
| if (List.class.isAssignableFrom(col.getType())) | ||
| subTable.createListColumn(col.getName(), col.getListElementType(), false); | ||
| else | ||
| subTable.createColumn(col.getName(), col.getType(), false); | ||
| } | ||
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| private void cloneRow(final CyRow from, final CyRow to) { | ||
| for (final CyColumn column : from.getTable().getColumns()){ | ||
| if (!column.getVirtualColumnInfo().isVirtual()) | ||
| to.set(column.getName(), from.getRaw(column.getName())); | ||
| } | ||
| } | ||
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| private String getNetworkName() { | ||
| return "AutoAnnotate_Temp"; | ||
| } | ||
|
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| /** | ||
| * Returns all edges that connect the selected nodes. | ||
| */ | ||
| private static Set<CyEdge> getEdges(CyNetwork net, Collection<CyNode> nodes) { | ||
| Set<CyEdge> edges = new HashSet<CyEdge>(); | ||
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| for (final CyNode n1 : nodes) { | ||
| for (final CyNode n2 : nodes) | ||
| edges.addAll(net.getConnectingEdgeList(n1, n2, CyEdge.Type.ANY)); | ||
| } | ||
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| return edges; | ||
| } | ||
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| @Override | ||
| public <R> R getResults(Class<? extends R> type) { | ||
| if(CyNetwork.class.equals(type)) { | ||
| return type.cast(resultNetwork); | ||
| } | ||
| return null; | ||
| } | ||
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| } |
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