private void saveCluster(File file, Experiment experiment, IData data, int[] rows)
throws Exception {
PrintWriter out = new PrintWriter(new FileOutputStream(file));
String[] fieldNames = data.getFieldNames();
out.print("Original row");
out.print("\t");
for (int i = 0; i < fieldNames.length; i++) {
out.print(fieldNames[i]);
// if (i < fieldNames.length - 1) {
out.print("\t");
// }
}
for (int i = 0; i < geneGroupMeans[0].length; i++) {
out.print("Group" + (i + 1) + " mean\t");
out.print("Group" + (i + 1) + " std.dev.\t");
}
// out.print("\t");
out.print("F ratio");
out.print("\t");
out.print("SS(Groups)\t");
out.print("SS(Error)\t");
out.print("df (Groups)\t");
out.print("df (Error)\t");
out.print("raw p value\t");
out.print("adj p value");
// out.print("UniqueID\tName");
for (int i = 0; i < experiment.getNumberOfSamples(); i++) {
out.print("\t");
out.print(data.getFullSampleName(experiment.getSampleIndex(i)));
}
out.print("\n");
for (int i = 0; i < rows.length; i++) {
out.print(Integer.toString(experiment.getGeneIndexMappedToData(rows[i]) + 1));
// out.print(data.getUniqueId(rows[i]));
out.print("\t");
// out.print(data.getGeneName(rows[i]));
for (int k = 0; k < fieldNames.length; k++) {
out.print(data.getElementAttribute(experiment.getGeneIndexMappedToData(rows[i]), k));
// if (k < fieldNames.length - 1) {
out.print("\t");
// }
}
for (int j = 0; j < geneGroupMeans[rows[i]].length; j++) {
out.print(geneGroupMeans[rows[i]][j] + "\t");
out.print(geneGroupSDs[rows[i]][j] + "\t");
}
// out.print("\t");
out.print("" + ((Float) fValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) ssGroups.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) ssError.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) dfNumValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) dfDenomValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) rawPValues.get(rows[i])).floatValue());
out.print("\t");
out.print("" + ((Float) adjPValues.get(rows[i])).floatValue());
for (int j = 0; j < experiment.getNumberOfSamples(); j++) {
out.print("\t");
out.print(Float.toString(experiment.get(rows[i], j)));
}
out.print("\n");
}
out.flush();
out.close();
}
