/**
* Returns a set of GO term nodes which provides 100% coverage of the associated genes (if
* possible). If a user gene set has been imported, than the gene set considered for coverage is
* the user gene set. Otherwise, the returned set of nodes covers the complete gene set.
*
* @param selectedGONodes the set of GO term nodes which have already been selected
* @return the set of GO term nodes which provide a covering set for the associated genes
*/
public Set<Node> getCoveringSet(Set<Node> selectedGONodes) {
Set<Node> coveringSet = new HashSet<Node>(selectedGONodes);
// Determine the gene set for which the covering set should be determined
Set<String> geneIds = null;
boolean userGenesImported = session.isUserGeneSetImported();
if (userGenesImported) { // user gene set was imported, so use user gene set
geneIds = new HashSet<String>(session.getUserGeneSet());
} else { // no user gene set, use all genes
geneIds = session.getGaru().getGeneIds();
}
// Loop until all the genes are covered, or there is no other node that can increase the current
// gene coverage.
Node nextBestNode = getNextBestTerm(coveringSet, geneIds, userGenesImported);
while (nextBestNode != null) {
coveringSet.add(nextBestNode);
nextBestNode = getNextBestTerm(coveringSet, geneIds, userGenesImported);
}
return coveringSet;
}
/**
* Returns an array of strings representing the GO terms with the best direct coverage of the
* remaining uncovered genes. Each string in the array is in the format <GOTerm name> (<GOTerm
* id>): <Number of remaining genes covered>. If a user gene set has been imported, than the gene
* set considered for coverage is the user gene set. Otherwise, the returned strings represent the
* nodes with the best coverage of the complete gene set.
*
* @param selectedGONodes the set of GO term nodes which have already been selected
* @param numTerms the number of terms to return in the array
* @return an array of strings representing the GO terms with the best direct coverage of the
* remaining uncovered genes. The size of the array will be the minimum of numTerms and the
* number of GOTerms with a gene coverage greater than 0.
*/
public String[] getTopTermsStringsDirect(Set<Node> selectedGONodes, int numTerms) {
CyNetwork network = Cytoscape.getCurrentNetwork();
Set<String> geneIds = null;
// Determine the gene set for which coverage of Go terms should be determined
boolean userGenesImported = session.isUserGeneSetImported();
if (userGenesImported) { // user gene set was imported, so use user gene set
geneIds = new HashSet<String>(session.getUserGeneSet());
} else { // no user gene set, use all genes
geneIds = session.getGaru().getGeneIds();
}
ArrayList<GOSetTerm> goTermList = new ArrayList<GOSetTerm>();
// Get list of covered genes
Set<String> coveredGenes = new HashSet<String>();
for (Node node : selectedGONodes) {
coveredGenes.addAll(
GOSlimmerUtil.listToSet(
GOSlimmerUtil.getGenesCoveredByGoNode(node, false, userGenesImported)));
}
// Get list of uncovered genes from covered genes and all genes
Set<String> uncoveredGenes = new HashSet<String>();
for (String gene : geneIds) {
if (!coveredGenes.contains(gene)) {
uncoveredGenes.add(gene);
}
}
int numUncoveredGenes = uncoveredGenes.size();
// Sort nodes by coverage for remaining genes.
// Iterate through all nodes in network, and determine the coverage of the remaining uncovered
// genes.
Iterator nodes_i = network.nodesIterator();
while (nodes_i.hasNext()) {
Node node = (Node) nodes_i.next();
if (!selectedGONodes.contains(node)) {
Set<String> nodeCoveredGenes =
new HashSet<String>(
GOSlimmerUtil.getGenesCoveredByGoNode(node, false, userGenesImported));
Set<String> newCoveredGenes = new HashSet<String>();
// Select set to iterate through depending on size to cut down on execution time
if (nodeCoveredGenes.size() < numUncoveredGenes) {
for (String gene : nodeCoveredGenes) {
if (uncoveredGenes.contains(gene)) {
newCoveredGenes.add(gene);
}
}
} else {
for (String gene : uncoveredGenes) {
if (nodeCoveredGenes.contains(gene)) {
newCoveredGenes.add(gene);
}
}
}
// Create GOSetTerm and add to list if it covers at least one gene
if (newCoveredGenes.size() > 0) {
GOSetTerm goSetTerm = new GOSetTerm(node, newCoveredGenes.size());
goTermList.add(goSetTerm);
}
}
}
// Sort list based on number of remaining genes covered
Collections.sort(goTermList);
// Build string array to return
int numSortedTerms = goTermList.size();
int actualNumTerms = Math.min(numTerms, numSortedTerms);
String[] goTermsStr = new String[actualNumTerms];
for (int i = 0; i < actualNumTerms; i++) {
goTermsStr[i] = (goTermList.get(numSortedTerms - 1 - i)).getDescriptiveString();
}
return goTermsStr;
}