@Override
public boolean isMissingParameters(NucleotidSequences sequences, int pos1, int pos2) {
int[] positions = correctPositions(pos1, pos2, sequences.getDuplexLength());
pos1 = positions[0];
pos2 = positions[1];
NucleotidSequences newSequences = sequences.getEquivalentSequences("rna");
String sequence =
NucleotidSequences.convertToPyr_Pur(sequences.getSequenceContainig("-", pos1, pos2));
String complementary =
NucleotidSequences.convertToPyr_Pur(
sequences.getComplementaryTo(
sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2));
if (sequence.charAt(0) == '-') {
if (complementary.charAt(1) == 'Y'
|| (complementary.charAt(1) != 'Y' && complementary.charAt(2) == 'Y')) {
complementary = complementary.substring(1, 3);
}
} else {
if (complementary.charAt(1) == 'Y'
|| (complementary.charAt(1) != 'Y' && complementary.charAt(0) == 'Y')) {
complementary = complementary.substring(0, 2);
}
}
if (sequences
.getSequenceSens(sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2)
.equals("5'3'")) {
if (this.collector.getDanglingValue(sequence, complementary) == null) {
OptionManagement.logWarning(
"\n The thermodymamic parameters for "
+ sequence
+ "/"
+ complementary
+ " are missing. Check the second dangling ends parameters.");
return true;
}
} else {
if (this.collector.getDanglingValue(complementary, sequence) == null) {
OptionManagement.logWarning(
"\n The thermodymamic parameters for "
+ complementary
+ "/"
+ sequence
+ " are missing. Check the second dangling ends parameters.");
return true;
}
}
return super.isMissingParameters(newSequences, pos1, pos2);
}
@Override
public ThermoResult computeThermodynamics(
NucleotidSequences sequences, int pos1, int pos2, ThermoResult result) {
int[] positions = super.correctPositions(pos1, pos2, sequences.getDuplexLength());
pos1 = positions[0];
pos2 = positions[1];
NucleotidSequences newSequences = sequences.getEquivalentSequences("rna");
OptionManagement.logMessage("\n The nearest neighbor model for double" + " dangling end is");
OptionManagement.logMethodName(methodName);
OptionManagement.logFileName(this.fileName);
result = super.computeThermodynamics(newSequences, pos1, pos2, result);
double enthalpy = result.getEnthalpy();
double entropy = result.getEntropy();
String sequence =
NucleotidSequences.convertToPyr_Pur(sequences.getSequenceContainig("-", pos1, pos2));
String complementary =
NucleotidSequences.convertToPyr_Pur(
sequences.getComplementaryTo(
sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2));
Thermodynamics doubleDanglingValue;
if (sequence.charAt(0) == '-') {
if (complementary.charAt(1) == 'Y'
|| (complementary.charAt(1) != 'Y' && complementary.charAt(2) == 'Y')) {
complementary = complementary.substring(1, 3);
}
} else {
if (complementary.charAt(1) == 'Y'
|| (complementary.charAt(1) != 'Y' && complementary.charAt(0) == 'Y')) {
complementary = complementary.substring(0, 2);
}
}
if (sequences
.getSequenceSens(sequences.getSequenceContainig("-", pos1, pos2), pos1, pos2)
.equals("5'3'")) {
doubleDanglingValue = this.collector.getDanglingValue(sequence, complementary);
} else {
doubleDanglingValue = this.collector.getDanglingValue(complementary, sequence);
}
OptionManagement.logMessage(
"\n"
+ sequences.getSequence(pos1, pos2)
+ "/"
+ sequences.getComplementary(pos1, pos2)
+ ": incremented enthalpy = "
+ doubleDanglingValue.getEnthalpy()
+ " incremented entropy = "
+ doubleDanglingValue.getEntropy());
enthalpy += doubleDanglingValue.getEnthalpy();
entropy += doubleDanglingValue.getEntropy();
result.setEnthalpy(enthalpy);
result.setEntropy(entropy);
return result;
}