X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=preclustercommand.h;h=2b93328e64a038695a3abbd10cfe9be1165b783d;hp=e0767826ecde2fcf8056bbdebfb8d1bd8ce435c4;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=c85db0a4be3a1f8037a71a23ca73f9762184e28a diff --git a/preclustercommand.h b/preclustercommand.h index e076782..2b93328 100644 --- a/preclustercommand.h +++ b/preclustercommand.h @@ -254,56 +254,108 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){ int count = 0; - //think about running through twice... - for (int i = 0; i < numSeqs; i++) { - - //are you active - // itActive = active.find(alignSeqs[i].seq.getName()); - - if (alignSeqs[i].active) { //this sequence has not been merged yet - - string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n"; + if (pDataArray->topdown) { + //think about running through twice... + for (int i = 0; i < numSeqs; i++) { + + //are you active + // itActive = active.find(alignSeqs[i].seq.getName()); + + if (alignSeqs[i].active) { //this sequence has not been merged yet + + string chunk = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n"; - //try to merge it with all smaller seqs - for (int j = i+1; j < numSeqs; j++) { - - if (pDataArray->m->control_pressed) { delete parser; return 0; } - - if (alignSeqs[j].active) { //this sequence has not been merged yet - //are you within "diff" bases - //int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); - int mismatch = 0; - - for (int k = 0; k < alignSeqs[i].seq.getAligned().length(); k++) { - //do they match - if (alignSeqs[i].seq.getAligned()[k] != alignSeqs[j].seq.getAligned()[k]) { mismatch++; } - if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster - } - - if (mismatch <= pDataArray->diffs) { - //merge - alignSeqs[i].names += ',' + alignSeqs[j].names; - alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; - - alignSeqs[j].active = 0; - alignSeqs[j].numIdentical = 0; - alignSeqs[j].diffs = mismatch; - count++; - chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n"; - } - }//end if j active - }//end for loop j - - //remove from active list - alignSeqs[i].active = 0; - - out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl; - - }//end if active i - if(i % 100 == 0) { pDataArray->m->mothurOut(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); } - } - out.close(); - if(numSeqs % 100 != 0) { pDataArray->m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); } + //try to merge it with all smaller seqs + for (int j = i+1; j < numSeqs; j++) { + + if (pDataArray->m->control_pressed) { delete parser; return 0; } + + if (alignSeqs[j].active) { //this sequence has not been merged yet + //are you within "diff" bases + //int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); + int mismatch = 0; + + for (int k = 0; k < alignSeqs[i].seq.getAligned().length(); k++) { + //do they match + if (alignSeqs[i].seq.getAligned()[k] != alignSeqs[j].seq.getAligned()[k]) { mismatch++; } + if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster + } + + if (mismatch <= pDataArray->diffs) { + //merge + alignSeqs[i].names += ',' + alignSeqs[j].names; + alignSeqs[i].numIdentical += alignSeqs[j].numIdentical; + + alignSeqs[j].active = 0; + alignSeqs[j].numIdentical = 0; + alignSeqs[j].diffs = mismatch; + count++; + chunk += alignSeqs[j].seq.getName() + "\t" + toString(alignSeqs[j].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[j].seq.getAligned() + "\n"; + } + }//end if j active + }//end for loop j + + //remove from active list + alignSeqs[i].active = 0; + + out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << chunk << endl; + + }//end if active i + if(i % 100 == 0) { pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); } + } + + }else { + map mapFile; + map originalCount; + map::iterator itCount; + for (int i = 0; i < numSeqs; i++) { mapFile[i] = ""; originalCount[i] = alignSeqs[i].numIdentical; } + + //think about running through twice... + for (int i = 0; i < numSeqs; i++) { + + //try to merge it into larger seqs + for (int j = i+1; j < numSeqs; j++) { + + if (pDataArray->m->control_pressed) { out.close(); return 0; } + + if (originalCount[j] > originalCount[i]) { //this sequence is more abundant than I am + //are you within "diff" bases + //int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); + int mismatch = 0; + + for (int k = 0; k < alignSeqs[i].seq.getAligned().length(); k++) { + //do they match + if (alignSeqs[i].seq.getAligned()[k] != alignSeqs[j].seq.getAligned()[k]) { mismatch++; } + if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster + } + + if (mismatch <= pDataArray->diffs) { + //merge + alignSeqs[j].names += ',' + alignSeqs[i].names; + alignSeqs[j].numIdentical += alignSeqs[i].numIdentical; + + mapFile[j] = alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(mismatch) + "\t" + alignSeqs[i].seq.getAligned() + "\n" + mapFile[i]; + alignSeqs[i].numIdentical = 0; + originalCount.erase(i); + mapFile[i] = ""; + count++; + j+=numSeqs; //exit search, we merged this one in. + } + }//end abundance check + }//end for loop j + + if(i % 100 == 0) { pDataArray->m->mothurOutJustToScreen(toString(i) + "\t" + toString(numSeqs - count) + "\t" + toString(count)+"\n"); } + } + + for (int i = 0; i < numSeqs; i++) { + if (alignSeqs[i].numIdentical != 0) { + out << "ideal_seq_" << (i+1) << '\t' << alignSeqs[i].numIdentical << endl << alignSeqs[i].seq.getName() + "\t" + toString(alignSeqs[i].numIdentical) + "\t" + toString(0) + "\t" + alignSeqs[i].seq.getAligned() + "\n" << mapFile[i] << endl; + } + } + + } + out.close(); + if(numSeqs % 100 != 0) { pDataArray->m->mothurOut(toString(numSeqs) + "\t" + toString(numSeqs - count) + "\t" + toString(count)); pDataArray->m->mothurOutEndLine(); } //////////////////////////////////////////////////// if (pDataArray->m->control_pressed) { delete parser; return 0; }