X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=nast.cpp;h=50d3b2440f3a2523257d20faabba51098b345cd4;hb=2a07f8664a7fd1ef0d572b88e8b5bede24cc0b3c;hp=4aed5903aec4985f92d5668d39301cabe3d779e6;hpb=3abb236c602eb168ee112f080b563ebe2c705029;p=mothur.git diff --git a/nast.cpp b/nast.cpp index 4aed590..50d3b24 100644 --- a/nast.cpp +++ b/nast.cpp @@ -23,16 +23,15 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method), candidateSeq(cand), templateSeq(temp) { 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) { - errorOut(e, "Nast", "Nast"); + m->errorOut(e, "Nast", "Nast"); exit(1); } - } /**************************************************************************************************/ @@ -40,12 +39,12 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment methods to align our unaligned candidate // and template sequences try { - + alignment->align(candidateSeq->getUnaligned(), templateSeq->getUnaligned()); - + string candAln = alignment->getSeqAAln(); string tempAln = alignment->getSeqBAln(); - + if(candAln == ""){ candidateSeq->setPairwise(""); @@ -53,7 +52,6 @@ void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment me } else{ - if(tempAln[0] == '-'){ int pairwiseAlignmentLength = tempAln.length(); // we need to make sure that the candidate sequence alignment for(int i=0;i=0; i--){// ends where the template sequence alignment ends, if it runs @@ -80,10 +77,9 @@ void Nast::pairwiseAlignSeqs(){ // Here we call one of the pairwise alignment me candidateSeq->setPairwise(candAln); // set the pairwise sequences in the Sequence objects for templateSeq->setPairwise(tempAln); // the candidate and template sequences - } catch(exception& e) { - errorOut(e, "Nast", "pairwiseAlignSeqs"); + m->errorOut(e, "Nast", "pairwiseAlignSeqs"); exit(1); } } @@ -96,7 +92,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl try { int longAlignmentLength = newTemplateAlign.length(); - + for(int i=0; i0;leftIndex--){ // then we've got problems... + for(leftIndex=i-1;leftIndex>0;leftIndex--){ // then we've got problems... if(!isalpha(candAln[leftIndex])){ leftRoom = 1; //count how far it is to the nearest gap on the LEFT side of the anomaly while(leftIndex-leftRoom>=0 && !isalpha(candAln[leftIndex-leftRoom])) { leftRoom++; } break; } } - - + for(rightIndex=i+1;rightIndex maxInsertLength){ maxInsertLength = insertLength; } - + if((leftRoom + rightRoom) >= insertLength){ // Parts D & E from Fig. 2 of DeSantis et al. 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 - string leftTemplateString = newTemplateAlign.substr(0,i); string rightTemplateString = newTemplateAlign.substr(i+insertLength); newTemplateAlign = leftTemplateString + rightTemplateString; @@ -159,7 +153,6 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl } else{ // the right gap is closer - > move stuff right there's if(rightRoom >= insertLength){ // enough room to the right to move - string leftTemplateString = newTemplateAlign.substr(0,i); string rightTemplateString = newTemplateAlign.substr(i+insertLength); newTemplateAlign = leftTemplateString + rightTemplateString; @@ -170,7 +163,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl candAln = leftCandidateString + rightCandidateString; } - else{ // not enough room to the right, have to steal some + else{ // not enough room to the right, have to steal some // space to the left lets move left and then right... string leftTemplateString = newTemplateAlign.substr(0,i); string rightTemplateString = newTemplateAlign.substr(i+insertLength); @@ -184,10 +177,13 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl } } + i -= insertLength; + } else{ - // there could be a case where there isn't enough room in - string leftTemplateString = newTemplateAlign.substr(0,i); // either direction to move stuff + // there could be a case where there isn't enough room in either direction to move stuff + + string leftTemplateString = newTemplateAlign.substr(0,i); string rightTemplateString = newTemplateAlign.substr(i+leftRoom+rightRoom); newTemplateAlign = leftTemplateString + rightTemplateString; longAlignmentLength = newTemplateAlign.length(); @@ -196,18 +192,18 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl string insertString = candAln.substr(leftIndex+1,rightIndex-leftIndex-1); string rightCandidateString = candAln.substr(rightIndex+rightRoom); candAln = leftCandidateString + insertString + rightCandidateString; - + + i -= (leftRoom + rightRoom); } - - i -= insertLength; + +// i -= insertLength; } } } catch(exception& e) { - errorOut(e, "Nast", "removeExtraGaps"); + m->errorOut(e, "Nast", "removeExtraGaps"); exit(1); } - } /**************************************************************************************************/ @@ -229,7 +225,7 @@ void Nast::regapSequences(){ //This is essentially part B in Fig 2. of DeSantis candidateSeq->setAligned(candAln); return; } - + int fullAlignIndex = 0; int pairwiseAlignIndex = 0; string newTemplateAlign = ""; // this is going to be messy so we want a temporary template @@ -239,7 +235,7 @@ void Nast::regapSequences(){ //This is essentially part B in Fig 2. of DeSantis newTemplateAlign += tempAln[fullAlignIndex];// pairwise sequences fullAlignIndex++; } - + string lastLoop = ""; while(pairwiseAlignIndexmothurOut("We're into D " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); m->mothurOutEndLine(); pairwiseAlignIndex++; } else{ // everything has a gap - not possible // not tested yet - mothurOut("We're into F " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); mothurOutEndLine(); + m->mothurOut("We're into F " + toString(fullAlignIndex) + " " + toString(pairwiseAlignIndex)); m->mothurOutEndLine(); pairwiseAlignIndex++; fullAlignIndex++; } @@ -326,7 +322,9 @@ void Nast::regapSequences(){ //This is essentially part B in Fig 2. of DeSantis newTemplateAlign += tempAln[i];// } - int start, end; + int start = 0; + int end = candAln.length()-1; + for(int i=0;isetAligned(candAln); } catch(exception& e) { - errorOut(e, "Nast", "regapSequences"); + m->errorOut(e, "Nast", "regapSequences"); exit(1); } } @@ -385,7 +382,7 @@ float Nast::getSimilarityScore(){ } catch(exception& e) { - errorOut(e, "Nast", "getSimilarityScore"); + m->errorOut(e, "Nast", "getSimilarityScore"); exit(1); } }