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Merge branch 'develop' into features/mchmmer
[jalview.git]
/
src
/
jalview
/
util
/
HMMProbabilityDistributionAnalyser.java
diff --git
a/src/jalview/util/HMMProbabilityDistributionAnalyser.java
b/src/jalview/util/HMMProbabilityDistributionAnalyser.java
index
24b3bc3
..
66ae552
100644
(file)
--- a/
src/jalview/util/HMMProbabilityDistributionAnalyser.java
+++ b/
src/jalview/util/HMMProbabilityDistributionAnalyser.java
@@
-185,7
+185,8
@@
public class HMMProbabilityDistributionAnalyser
* The number of families to read before saving.
* @throws IOException
*/
* 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;
throws IOException
{
keepRaw = keepRawData;
@@
-241,7
+242,10
@@
public class HMMProbabilityDistributionAnalyser
readHMM(inputHMM);
int count = countValidResidues();
readHMM(inputHMM);
int count = countValidResidues();
- processData(count);
+ if (count >= minCount && count < maxCount)
+ {
+ processData(count);
+ }
filesRead++;
System.out.println(filesRead);
endReached = atEnd(inputSTO);
filesRead++;
System.out.println(filesRead);
endReached = atEnd(inputSTO);
@@
-369,10
+373,10
@@
public class HMMProbabilityDistributionAnalyser
{
char symbol;
int alignPos;
{
char symbol;
int alignPos;
- alignPos = hmm.getNodeAlignmentColumn(length);
+ alignPos = hmm.getNodeMapPosition(length);
symbol = sequences.get(width).getCharAt(alignPos);
symbol = sequences.get(width).getCharAt(alignPos);
- if (ResidueProperties.aminoBackgroundFrequencies
+ if (ResidueProperties.backgroundFrequencies.get("amino")
.containsKey(symbol))
{
count++;
.containsKey(symbol))
{
count++;
@@
-403,17
+407,18
@@
public class HMMProbabilityDistributionAnalyser
{
char symbol;
int alignPos;
{
char symbol;
int alignPos;
- alignPos = hmm.getNodeAlignmentColumn(length);
+ alignPos = hmm.getNodeMapPosition(length);
symbol = sequences.get(width).getCharAt(alignPos);
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);
.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");
if (prob == 0 || bfreq == 0)
{
System.out.println("error");