+ int filesRead = 0;
+ for (int clan = 0; clan < files; clan++)
+ {
+ System.out.println(clan);
+ String clanPath = "";
+ int numberOfFamilies = 0;
+ if (forClans)
+ {
+ clanPath = currentFolder + "/Clan" + clan;
+ if (!new File(clanPath).exists())
+ {
+ continue;
+ }
+ BufferedReader famCountReader = new BufferedReader(
+ new FileReader(clanPath + "/NumberOfFamilies.txt"));
+ numberOfFamilies = Integer.parseInt(famCountReader.readLine());
+ }
+ else
+ {
+ numberOfFamilies = 1;
+ }
+
+ for (int fam = 0; fam < numberOfFamilies; fam++)
+ {
+ if (forClans)
+ {
+ families = clanPath + "/Families/Fam" + fam + ".sto";
+ hmms = clanPath + "/HMMs/HMM" + fam + ".hmm";
+ }