private void makeClassFile(List<String> classStringList, SampleGroup[] sampleGroups) {
int totalSample = 0;
int totalGroup = 0;
int always = 1;
int base = 0;
String line1 = "";
StringBuffer line2 = new StringBuffer("#");
StringBuffer line3 = new StringBuffer();
for (SampleGroup sampleGroup : sampleGroups) {
totalSample = totalSample + sampleGroup.size();
totalGroup++;
line2.append("\t");
line2.append(sampleGroup.getGroupName());
makeLine3(line3, sampleGroup, base);
base++;
}
line1 =
Integer.toString(totalSample)
+ "\t"
+ Integer.toString(totalGroup)
+ "\t"
+ Integer.toString(always);
classStringList.add(line1);
classStringList.add(line2.toString());
classStringList.add(line3.toString());
}
private boolean isIdOverlap(SampleGroup[] sampleGroups) {
SampleGroup samples = new SampleGroup();
int total = 0;
for (SampleGroup sampleGroup : sampleGroups) {
total = total + sampleGroup.size();
samples.addAll(sampleGroup);
}
if (total > samples.size()) return true;
return false;
}
private void makeLine3(StringBuffer sb, SampleGroup sampleGroup, int base) {
int total = 0;
for (Iterator i = sampleGroup.iterator(); i.hasNext(); ) {
String id = (String) i.next();
// sb.append(DOUBLE_QUOTE+(String)i.next()+DOUBLE_QUOTE);
if (base == 0 && total == 0) {
sb.append(base);
} else {
sb.append("\t");
sb.append(base);
}
total++;
}
}