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##Cytoscape 3 Data Import UX

Scinario 1: Multiple Species Session

=====================

User Data

• n mouse network files
• m human network files

keiono

{
  "network" : {
    "selected" : {
      "type" : "boolean",
      "value" : true
    },
    "__Annotations" : [ ],
    "shared name" : {
      "type" : "string",
      "value" : "galFiltered.sif"

keiono

package org.cytoscape.io.internal.read;

/*
 * #%L
 * Cytoscape IO Impl (io-impl)
 * $Id:$
 * $HeadURL:$
 * %%
 * Copyright (C) 2006 - 2013 The Cytoscape Consortium
 * %%

keiono

// Handle locked values
		final Set<VisualPropertyDependency<?>> deps = vs.getAllVisualPropertyDependencies();

		for(VisualPropertyDependency<?> dep: deps) {
			if(dep.getIdString().equals("nodeSizeLocked")) {
				if(dep.isDependencyEnabled()) {
				  dep.setDependency(false);
				}
			}
			

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// Generate a complete graph

// Extract command-line arguments
var numberOfNodes = args[0];
if(numberOfNodes == null)
	numberOfNodes = 10;

// Create new network
var newNetwork = cyAppAdapter.getCyNetworkFactory().createNetwork();
newNetwork.getRow(newNetwork).set("name", "Complete Graph with " + numberOfNodes + " Nodes");

keiono

#
# Python Script to generate complete graph
#

NUM_NODES = 20

print "Creating complete graph with " + str(NUM_NODES) + " nodes..."

new_network = cyAppAdapter.getCyNetworkFactory().createNetwork()
new_network.getRow(new_network).set("name", "Complete Graph Created by Python Script")

keiono

; Node Names - sequence of integers.
(def nodenames (take 500 (range)))

; Create new network and register it to manager
(def newnet(. (. cyAppAdapter getCyNetworkFactory) createNetwork))
(.. newnet (getRow newnet) (set "name" "Random Network Created by Clojure Script"))
(.. cyAppAdapter (getCyNetworkManager) (addNetwork newnet))

; Create nodes
(doseq [nodename nodenames] 

keiono

from java.io import File

KEGG_DIR = "/Users/kono/kegg/"
pathways = ["hsa00010.xml", "hsa00020.xml", "hsa01100.xml"]

loadNetworkTF = cyAppAdapter.get_LoadNetworkFileTaskFactory()
taskManager = cyAppAdapter.getTaskManager()

allTasks = None
for pathway in pathways:

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public class KeggscapeFileFilter extends BasicCyFileFilter {

	private static final Logger logger = LoggerFactory.getLogger(KeggscapeFileFilter.class);

	private static final String KEGG_TAG = "www.kegg.jp/kegg";

	public KeggscapeFileFilter(Set<String> extensions, Set<String> contentTypes, String description,
			DataCategory category, StreamUtil streamUtil) {
		super(extensions, contentTypes, description, category, streamUtil);
	}

keiono

// VMM is VisualMappingManager
VisualStyle psiStyle = null;
for (VisualStyle style : vmm.getAllVisualStyles()) {
    if (style.getTitle().equals(PSIMI25VisualStyleBuilder.DEF_VS_NAME)) {
        psiStyle = style;
        break;
    }
}
if (psiStyle == null) {
    psiStyle = vsBuilder.getVisualStyle();