try {
m = MothurOut::getInstance();
maxInsertLength = 0;
+
pairwiseAlignSeqs(); // This is part A in Fig. 2 of DeSantis et al.
regapSequences(); // This is parts B-F in Fig. 2 of DeSantis et al.
+
}
catch(exception& e) {
m->errorOut(e, "Nast", "Nast");
void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment methods to align our unaligned candidate
// and template sequences
- try {
-
+ try {
alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned());
string candAln = alignment->getSeqAAln();
candidateSeq->setPairwise(candAln); // set the pairwise sequences in the Sequence objects for
templateSeq->setPairwise(tempAln); // the candidate and template sequences
+
}
catch(exception& e) {
m->errorOut(e, "Nast", "pairwiseAlignSeqs");
// here we do steps C-F of Fig. 2 from DeSantis et al.
try {
-
+
int longAlignmentLength = newTemplateAlign.length();
for(int i=0; i<longAlignmentLength; i++){ // use the long alignment as the standard
int rightIndex, rightRoom, leftIndex, leftRoom;
-
+
// Part C of Fig. 2 from DeSantis et al.
if((isalpha(newTemplateAlign[i]) != isalpha(tempAln[i]))){ //if there is a discrepancy between the regapped
if((i-leftIndex) <= (rightIndex-i)){ // the left gap is closer - > move stuff left there's
if(leftRoom >= insertLength){ // enough room to the left to move
+ //cout << "lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
- string leftCandidateString = candAln.substr(0,leftIndex-insertLength+1);
- string rightCandidateString = candAln.substr(leftIndex+1);
+ //cout << "lr candAln = " << candAln.length() << '\t' << leftIndex << '\t' << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-insertLength+1));
+ string rightCandidateString = candAln.substr((leftIndex+1));
candAln = leftCandidateString + rightCandidateString;
-
- }
- else{ // not enough room to the left, have to steal some space to
- string leftTemplateString = newTemplateAlign.substr(0,i); // the right
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+
+ }else{ // not enough room to the left, have to steal some space to the right
+
+ //cout << "in else lr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << insertLength << endl;
+ string leftTemplateString = newTemplateAlign.substr(0,i);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
- string leftCandidateString = candAln.substr(0,leftIndex-leftRoom+1);
- string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
- string rightCandidateString = candAln.substr(rightIndex+(insertLength-leftRoom));
+ //cout << " in else lr candAln = " << candAln.length() << '\t' << " leftIndex = " << leftIndex << " leftroom = " << leftRoom << " rightIndex = " << rightIndex << '\t' << " rightroom = " << rightRoom << '\t' << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+(insertLength-leftRoom)));
candAln = leftCandidateString + insertString + rightCandidateString;
}
- }
- else{ // the right gap is closer - > move stuff right there's
+ }else{ // the right gap is closer - > move stuff right there's
if(rightRoom >= insertLength){ // enough room to the right to move
+ //cout << "rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
+ //cout << "rr candAln = " << candAln.length() << '\t' << i << '\t' << rightIndex << '\t' << rightIndex+insertLength << endl;
string leftCandidateString = candAln.substr(0,rightIndex);
- string rightCandidateString = candAln.substr(rightIndex+insertLength);
+ string rightCandidateString = candAln.substr((rightIndex+insertLength));
candAln = leftCandidateString + rightCandidateString;
}
else{ // not enough room to the right, have to steal some
// space to the left lets move left and then right...
+ //cout << "in else rr newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << i+insertLength << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+insertLength);
+ string rightTemplateString = newTemplateAlign.substr((i+insertLength));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
-
- string leftCandidateString = candAln.substr(0,leftIndex-(insertLength-rightRoom)+1);
- string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
- string rightCandidateString = candAln.substr(rightIndex+rightRoom);
+ //cout << "in else rr candAln = " << candAln.length() << '\t' << '\t' << (leftIndex-(insertLength-rightRoom)+1) << '\t' << (leftIndex+1,rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-(insertLength-rightRoom)+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+rightRoom));
candAln = leftCandidateString + insertString + rightCandidateString;
}
}
- i -= insertLength;
+
+ if ((i - insertLength) < 0) { i = 0; }
+ else { i -= insertLength; }
}
else{
// there could be a case where there isn't enough room in either direction to move stuff
-
+//cout << "in else else newTemplateAlign = " << newTemplateAlign.length() << '\t' << i << '\t' << (i+leftRoom+rightRoom) << endl;
string leftTemplateString = newTemplateAlign.substr(0,i);
- string rightTemplateString = newTemplateAlign.substr(i+leftRoom+rightRoom);
+ string rightTemplateString = newTemplateAlign.substr((i+leftRoom+rightRoom));
newTemplateAlign = leftTemplateString + rightTemplateString;
longAlignmentLength = newTemplateAlign.length();
- string leftCandidateString = candAln.substr(0,leftIndex-leftRoom+1);
- string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1);
- string rightCandidateString = candAln.substr(rightIndex+rightRoom);
+ //cout << "in else else newTemplateAlign = " << candAln.length() << '\t' << (leftIndex-leftRoom+1) << '\t' << (leftIndex+1) << '\t' << (rightIndex-leftIndex-1) << '\t' << (rightIndex+rightRoom) << endl;
+ string leftCandidateString = candAln.substr(0,(leftIndex-leftRoom+1));
+ string insertString = candAln.substr((leftIndex+1),(rightIndex-leftIndex-1));
+ string rightCandidateString = candAln.substr((rightIndex+rightRoom));
candAln = leftCandidateString + insertString + rightCandidateString;
i -= (leftRoom + rightRoom);
}
// i -= insertLength;
+
+ //if i is negative, we want to remove the extra gaps to the right
+ if (i < 0) { m->mothurOut("i is negative"); m->mothurOutEndLine(); }
}
}
}
void Nast::regapSequences(){ //This is essentially part B in Fig 2. of DeSantis et al.
try {
-
+ //cout << candidateSeq->getName() << endl;
string candPair = candidateSeq->getPairwise();
string candAln = "";
string lastLoop = "";
while(pairwiseAlignIndex<pairwiseLength){
+ //cout << pairwiseAlignIndex << '\t' << fullAlignIndex << '\t' << pairwiseLength << endl;
if(isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
&& isalpha(candPair[pairwiseAlignIndex])){
// the template and candidate pairwise and template aligned have characters
} // 2 of Desantis et al.
candidateSeq->setAligned(candAln);
+ //cout << "here" << endl;
}
catch(exception& e) {
m->errorOut(e, "Nast", "regapSequences");
projects / mothur.git / blobdiff