@Test
public void testReadMultiWordProteinsFileWithErrantSpaces() throws Exception {
List<CyNetworkView> views = getViews("multiWordProteinsFileTrailingSpaces.sif");
CyNetwork net = checkSingleNetwork(views, 28, 31);
findInteraction(
net, "26S ubiquitin dependent proteasome", "I-kappa-B-alpha", "interactsWith", 1);
findInteraction(net, "TRAF6", "RIP2", "interactsWith", 13);
findInteraction(net, "TRAF6", "ABCDE oopah", "interactsWith", 13);
findInteraction(net, "TRAF6", "HJKOL coltrane", "interactsWith", 13);
}
/** 'typical' means that all lines have the form "node1 pd node2 [node3 node4 ...] */
@Test
public void testReadFromTypicalFile() throws Exception {
List<CyNetworkView> views = getViews("sample.sif");
for (CyNetworkView view : views) {
for (CyNode n : view.getModel().getNodeList()) {
System.out.println(
"sample.sif: NODE " + view.getModel().getRow(n).get("name", String.class));
}
for (CyEdge e : view.getModel().getEdgeList()) {
System.out.println(
"sample.sif: EDGE " + view.getModel().getRow(e).get("name", String.class));
}
}
CyNetwork net = checkSingleNetwork(views, 31, 27);
findInteraction(net, "YNL312W", "YPL111W", "pd", 1);
}