本文整理汇总了Java中org.cytoscape.model.subnetwork.CyRootNetwork类的典型用法代码示例。如果您正苦于以下问题:Java CyRootNetwork类的具体用法?Java CyRootNetwork怎么用?Java CyRootNetwork使用的例子?那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
CyRootNetwork类属于org.cytoscape.model.subnetwork包,在下文中一共展示了CyRootNetwork类的9个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Java代码示例。
示例1: collapse
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
private void collapse() {
if(!cluster.isCollapsed()) {
modelManager.ignore(VIEW_CHANGE, SELECTION).whileRunning(() -> {
CyNetwork network = cluster.getNetwork();
List<CyNode> nodes = new ArrayList<>(cluster.getNodes());
CyGroup group = groupFactory.createGroup(network, nodes, null, true);
CyRow groupRow = ((CySubNetwork)network).getRootNetwork().getRow(group.getGroupNode(), CyRootNetwork.SHARED_ATTRS);
groupRow.set(CyRootNetwork.SHARED_NAME, cluster.getLabel());
group.collapse(network);
if(overrideAttribute) {
maybeCreateAnotherAttributeForName(network, groupRow);
}
});
}
}
开发者ID:BaderLab,项目名称:AutoAnnotateApp,代码行数:20,代码来源:CollapseTask.java
示例2: SupervisedModel
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
/**
* Constructs model from the current network and a file with clusters for training.
*
* @param trainingNetwork CyNetwork with PPI data for analysis.
* @param trainingData Text file containing training clusters.
* @throws An exception from loading the training data file
*/
SupervisedModel(CyRootNetwork trainingNetwork, CyNetwork modelNetwork, CyNetwork outputBayesNet, InputTask userInput) throws Exception {
Set<String> featureDescs = null;
List<CySubNetwork> positiveExamples = null, negativeExamples = null;
rootNetwork = trainingNetwork;
this.complexPrior = userInput.clusterPrior;
this.userInput = userInput;
// Create the positive and negative bayes graphs
setup();
// Get the set of features from the template/model
for (Graph g: bayesGraphs) {
featureDescs = g.loadModelFrom(modelNetwork);
}
features = FeatureUtil.parse(featureDescs);
// Get positive training examples and generate negative training examples
positiveExamples = loadTrainingComplexes(userInput.trainingFile);
negativeExamples = generateNegativeExamples(userInput.negativeExamples, positiveExamples);
// Train
train(positiveExamples, negativeExamples);
saveGraphicalBayesianNetwork(outputBayesNet, features);
}
开发者ID:DataFusion4NetBio,项目名称:Paper16-SCODE,代码行数:32,代码来源:SupervisedModel.java
示例3: handleEvent
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
/**
* Update UI and network settings to match change in column name.
*/
@Override
public void handleEvent(final ColumnNameChangedEvent e) {
if (listenersEnabled.get()) {
System.out.println("Column name changed event: " + e.getOldColumnName() + ", source: " + e.getSource());
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
// get the root network first
CyRootNetwork rootNetwork = rootNetworkManager.getRootNetwork(networkManager.getNetwork(currentNetworkSUID));
// now for all subnetworks of this root network, update the
// column name
for (CyNetwork network : rootNetwork.getSubNetworkList()) {
if (networkSettings.containsKey(network.getSUID())) {
networkSettings.get(network.getSUID()).changeColumnName(e.getOldColumnName(), e.getNewColumnName());
}
}
updateUserInterface();
}
});
}
}
开发者ID:ls-cwi,项目名称:eXamine,代码行数:28,代码来源:ControlPanel.java
示例4: getTargetColumns
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
private ListSingleSelection<String> getTargetColumns()
{
final CyTable table = network.getTable(CyNode.class, CyNetwork.DEFAULT_ATTRS);
final List<String> colNames = new ArrayList<String>();
for (final CyColumn col : table.getColumns()) {
// Exclude list, numerical, boolean type columns
if (String.class.isAssignableFrom(col.getType())) {
colNames.add(col.getName());
}
}
ListSingleSelection<String> toReturn =
new ListSingleSelection<String>(colNames);
if(colNames.contains("UNIPROT"))
toReturn.setSelectedValue("UNIPROT");
else if(colNames.contains("GENE SYMBOL"))
toReturn.setSelectedValue("GENE SYMBOL");
else if(colNames.contains("URI"))
toReturn.setSelectedValue("URI");
else if(colNames.contains(CyRootNetwork.SHARED_NAME))
toReturn.setSelectedValue(CyRootNetwork.SHARED_NAME); //less desired
return toReturn;
}
开发者ID:PathwayCommons,项目名称:CyPath2,代码行数:27,代码来源:ExpandNetworkTask.java
示例5: createNewSession
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
SafeSession createNewSession(CyNetworkView view) {
SafeSession session = new SafeSession();
session.setNetworkView(view);
session.setNameColumn(CyRootNetwork.SHARED_NAME);
session.setIdColumn(CyRootNetwork.SHARED_NAME);
session.setDistanceThreshold(0.5);
session.setForceUndirectedEdges(true);
session.setMinimumLandscapeSize(10);
session.setSimilarityThreshold(0.75);
session.setRestrictionMethod(new RadiusBasedRestrictionMethod(0, 0));
session.setGroupingMethod(new ClusterBasedGroupingMethod(0, new JaccardDistanceMethod(d -> d != 0)));
return session;
}
开发者ID:baryshnikova-lab,项目名称:safe-java,代码行数:14,代码来源:SafeController.java
示例6: createCyNetwork
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
public CyNetwork createCyNetwork(String networkName, CyRootNetwork rootNetwork) {
CyNetwork network = (rootNetwork == null)
? networkFactory.createNetwork()
: rootNetwork.addSubNetwork();
// First, create nodes for all Entity class objects
createEntityNodes(network);
// create edges
createInteractionEdges(network);
createComplexEdges(network);
// TODO create pathwayComponent edges (requires pathway nodes)?
// create PE->memberPE edges!
createMemberEdges(network);
// Finally, set network attributes:
// name
AttributeUtil.set(network, network, CyNetwork.NAME, networkName, String.class);
// default Quick Find Index
AttributeUtil.set(network, network, "quickfind.default_index", CyNetwork.NAME, String.class);
return network;
}
开发者ID:cytoscape,项目名称:biopax,代码行数:28,代码来源:BioPaxMapper.java
示例7: createCyNetwork
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
public CyNetwork createCyNetwork(String networkName, CyRootNetwork rootNetwork) {
CyNetwork network = (rootNetwork == null)
? networkFactory.createNetwork()
: rootNetwork.addSubNetwork();
// First, create nodes for all Entity class objects
createEntityNodes(network);
// create edges
createInteractionEdges(network);
createComplexEdges(network);
// TODO create pathwayComponent edges (requires pathway nodes)?
// create PE->memberPE edges!
createMemberEdges(network);
// Finally, set network attributes:
// name
Attributes.set(network, network, CyNetwork.NAME, networkName, String.class);
// default Quick Find Index
Attributes.set(network, network, "quickfind.default_index", CyNetwork.NAME, String.class);
return network;
}
开发者ID:PathwayCommons,项目名称:CyPath2,代码行数:28,代码来源:BioPaxMapper.java
示例8: BioPaxReaderTask
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
/**
* Constructor
*
* @param stream input biopax stream
* @param inputName a file or pathway name (can be later updated using actual data)
* @param cyServices api services
* @param visualStyleUtil biopax/sif visual style utilities
*/
public BioPaxReaderTask(InputStream stream, String inputName,
CyServices cyServices, VisualStyleUtil visualStyleUtil)
{
this.networks = new HashSet<CyNetwork>();
this.stream = stream;
this.inputName = inputName;
this.cyServices = cyServices;
this.visualStyleUtil = visualStyleUtil;
// initialize the root networks Collection
nameToRootNetworkMap = new HashMap<String, CyRootNetwork>();
for (CyNetwork net : cyServices.networkManager.getNetworkSet()) {
final CyRootNetwork rootNet = cyServices.rootNetworkManager.getRootNetwork(net);
if (!nameToRootNetworkMap.containsValue(rootNet))
nameToRootNetworkMap.put(rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class), rootNet);
}
List<String> rootNames = new ArrayList<String>();
rootNames.add(CREATE_NEW_COLLECTION);
rootNames.addAll(nameToRootNetworkMap.keySet());
rootNetworkSelection = new ListSingleSelection<String>(rootNames);
rootNetworkSelection.setSelectedValue(CREATE_NEW_COLLECTION);
// initialize the list of data processing modes
readerMode = new ListSingleSelection<>(ReaderMode.values());
readerMode.setSelectedValue(ReaderMode.DEFAULT);
// init the SIF rules/patterns list
sifSelection = new ListMultipleSelection<SIFType>(SIFEnum.values());
sifSelection.setSelectedValues(sifSelection.getPossibleValues());
//TODO init SBGN options
sbgnSelection = new ListSingleSelection<String>();
// initialize renderer list
final List<NetworkViewRenderer> renderers = new ArrayList<>();
final Set<NetworkViewRenderer> rendererSet = cyServices.applicationManager.getNetworkViewRendererSet();
// If there is only one registered renderer, we don't want to add it to the List Selection,
// so the combo-box does not appear to the user, since there is nothing to select anyway.
if (rendererSet.size() > 1) {
renderers.addAll(rendererSet);
Collections.sort(renderers, new Comparator<NetworkViewRenderer>() {
@Override
public int compare(NetworkViewRenderer r1, NetworkViewRenderer r2) {
return r1.toString().compareToIgnoreCase(r2.toString());
}
});
}
rendererList = new ListSingleSelection<>(renderers);
}
开发者ID:cytoscape,项目名称:biopax,代码行数:58,代码来源:BioPaxReaderTask.java
示例9: BioPaxReaderTask
import org.cytoscape.model.subnetwork.CyRootNetwork; //导入依赖的package包/类
/**
* Constructor
* @param stream input biopax stream
* @param inputName a file or pathway name (can be later updated using actual data)
*/
public BioPaxReaderTask(InputStream stream, String inputName)
{
this.networks = new HashSet<CyNetwork>();
this.stream = stream;
this.inputName = inputName;
// initialize the root networks Collection
nameToRootNetworkMap = new HashMap<String, CyRootNetwork>();
for (CyNetwork net : App.cyServices.networkManager.getNetworkSet()) {
final CyRootNetwork rootNet = App.cyServices.rootNetworkManager.getRootNetwork(net);
if (!nameToRootNetworkMap.containsValue(rootNet))
nameToRootNetworkMap.put(rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class), rootNet);
}
List<String> rootNames = new ArrayList<String>();
rootNames.add(CREATE_NEW_COLLECTION);
rootNames.addAll(nameToRootNetworkMap.keySet());
rootNetworkSelection = new ListSingleSelection<String>(rootNames);
rootNetworkSelection.setSelectedValue(CREATE_NEW_COLLECTION);
// initialize the list of data processing modes
readerMode = new ListSingleSelection<>(ReaderMode.values());
readerMode.setSelectedValue(ReaderMode.DEFAULT);
// init the SIF rules/patterns list
sifSelection = new ListMultipleSelection<SIFType>(SIFEnum.values());
List<SIFType> values = sifSelection.getPossibleValues();
//remove sif rules/types/patterns that we don't want to apply by default
for(SIFType item : sifSelection.getPossibleValues()) {
if(item == SIFEnum.NEIGHBOR_OF // excl. this ubiquitous but confusing type (not useful)
|| item == SIFEnum.INTERACTS_WITH //excl. PPIs (mostly PSI-MI data)
// || item == SIFEnum.REACTS_WITH
)
{
values.remove(item);
}
}
sifSelection.setSelectedValues(values);
// initialize renderer list
final List<NetworkViewRenderer> renderers = new ArrayList<>();
final Set<NetworkViewRenderer> rendererSet = App.cyServices.applicationManager.getNetworkViewRendererSet();
// If there is only one registered renderer, we don't want to add it to the List Selection,
// so the combo-box does not appear to the user, since there is nothing to select anyway.
if (rendererSet.size() > 1) {
renderers.addAll(rendererSet);
Collections.sort(renderers, new Comparator<NetworkViewRenderer>() {
@Override
public int compare(NetworkViewRenderer r1, NetworkViewRenderer r2) {
return r1.toString().compareToIgnoreCase(r2.toString());
}
});
}
rendererList = new ListSingleSelection<>(renderers);
}
开发者ID:PathwayCommons,项目名称:CyPath2,代码行数:60,代码来源:BioPaxReaderTask.java
注:本文中的org.cytoscape.model.subnetwork.CyRootNetwork类示例整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。 |
请发表评论