public LinkedHashMap<String, ArrayList<Integer>> uniqueGeneMap(
OntGeneAssociations assoc, String[] geneNames) {
LinkedHashMap<String, ArrayList<Integer>> geneCounts =
new LinkedHashMap<String, ArrayList<Integer>>();
int i = 0;
ArrayList<Integer> geneList = null;
OntGene gene = null;
for (i = 0; i < geneNames.length; i++) {
gene = assoc.getGene(geneNames[i]);
if (!geneCounts.containsKey(gene.REFSEQ)) {
geneList = new ArrayList<Integer>();
geneList.add(i);
geneCounts.put(gene.REFSEQ, geneList);
} else {
geneList = geneCounts.get(gene.REFSEQ);
geneList.add(i);
}
}
return geneCounts;
}
public OntGeneAssociations readFile(OntDAG DAG, HashSet<String> useGenes) throws IOException {
BufferedReader is = new BufferedReader(new FileReader(fName));
String line = "";
String s = "";
line = is.readLine();
int i = 0;
String[] colNames = new String[15];
String[] cols = null;
String[] cols2 = null;
while (!line.contentEquals("!platform_table_begin")) {
line = is.readLine();
}
line = is.readLine();
colNames = line.split("\t");
line = is.readLine();
OntGene gene = null;
OntGeneAssociations assoc = new OntGeneAssociations();
ArrayList<String> GoIDs = null;
int numGenes = 0;
boolean useGene = false;
while (!line.contentEquals("!platform_table_end")) {
cols = line.split("\t");
cols2 = new String[15];
for (i = 0; i < cols.length; i++) {
cols2[i] = "";
}
for (i = 0; i < cols.length; i++) {
cols2[i] = cols[i];
}
cols = cols2;
gene = new OntGene();
if (!useREFSEQ) {
gene.ID = cols[0];
} else {
if (cols[3] != null) {
gene.ID = cols[3];
} else {
gene.ID = cols[0];
}
}
// see if the gene is in the filter list
useGene = true;
if (useGenes != null) {
useGene = useGenes.contains(gene.ID);
}
if (!assoc.checkGene(gene) && useGene) {
gene.Description = cols[7];
gene.Name = cols[8];
gene.REFSEQ = cols[3];
GoIDs = parseGoLine(cols[12]);
addGoTerms(gene, GoIDs, DAG);
GoIDs = parseGoLine(cols[13]);
addGoTerms(gene, GoIDs, DAG);
GoIDs = parseGoLine(cols[14]);
addGoTerms(gene, GoIDs, DAG);
assoc.addGene(gene);
numGenes++;
}
line = is.readLine();
}
is.close();
DAG.propagateGeneCounts();
return assoc;
}