public static HashMap<String, Double> getOneWayAnovaPValues(ENode root) throws Exception {
HashMap<String, Double> returnMap = new HashMap<String, Double>();
HashMap<Float, List<ENode>> map = ReadCluster.getMapByLevel(root);
System.out.println(map.size());
for (Float f : map.keySet()) {
File outFile =
new File(
ConfigReader.getETreeTestDir()
+ File.separator
+ "Mel74ColumnsAsTaxaFor"
+ f
+ ".txt");
System.out.println(outFile.getAbsolutePath());
PivotOut.pivotOut(map.get(f), outFile.getAbsolutePath());
OtuWrapper wrapper = new OtuWrapper(outFile);
List<List<Double>> list = wrapper.getDataPointsNormalizedThenLogged();
for (int x = 0; x < wrapper.getOtuNames().size(); x++) {
double pValue = 1;
if (!wrapper.getOtuNames().get(x).equals(ETree.ROOT_NAME)) {
List<Number> data = new ArrayList<Number>();
List<String> factors = new ArrayList<String>();
for (int y = 0; y < wrapper.getSampleNames().size(); y++) {
if (!wrapper.getSampleNames().get(y).equals(ETree.ROOT_NAME)) {
data.add(list.get(y).get(x));
factors.add("" + stripSuffix(wrapper.getSampleNames().get(y)));
}
}
OneWayAnova owa = new OneWayAnova(data, factors);
if (map.containsKey(wrapper.getOtuNames().get(x))) throw new Exception("Duplicate");
pValue = owa.getPValue();
}
returnMap.put(wrapper.getOtuNames().get(x), pValue);
}
}
return returnMap;
}
