* The number of families to read before saving.
* @throws IOException
*/
- public void runToEnd(boolean keepRawData, boolean forClans)
+ public void runToEnd(int minCount, int maxCount, boolean keepRawData,
+ boolean forClans)
throws IOException
{
keepRaw = keepRawData;
readHMM(inputHMM);
int count = countValidResidues();
- processData(count);
+ if (count >= minCount && count < maxCount)
+ {
+ processData(count);
+ }
filesRead++;
System.out.println(filesRead);
endReached = atEnd(inputSTO);
{
char symbol;
int alignPos;
- alignPos = hmm.getNodeAlignmentColumn(length);
+ alignPos = hmm.getNodeMapPosition(length);
symbol = sequences.get(width).getCharAt(alignPos);
- if (ResidueProperties.aminoBackgroundFrequencies
+ if (ResidueProperties.backgroundFrequencies.get("amino")
.containsKey(symbol))
{
count++;
{
char symbol;
int alignPos;
- alignPos = hmm.getNodeAlignmentColumn(length);
+ alignPos = hmm.getNodeMapPosition(length);
symbol = sequences.get(width).getCharAt(alignPos);
- if (ResidueProperties.aminoBackgroundFrequencies
+ if (ResidueProperties.backgroundFrequencies.get("amino")
.containsKey(symbol))
{
Double prob;
Float bfreq;
Double llr;
prob = hmm.getMatchEmissionProbability(alignPos, symbol);
- bfreq = ResidueProperties.aminoBackgroundFrequencies.get(symbol);
+ bfreq = ResidueProperties.backgroundFrequencies.get("amino")
+ .get(symbol);
if (prob == 0 || bfreq == 0)
{
System.out.println("error");