out << "For full window mapping info refer to " << mapInfo << endl << endl;
}
//***************************************************************************************************************
-void Ccode::print(ostream& out) {
+int Ccode::print(ostream& out, ostream& outAcc) {
try {
- mothurOutEndLine();
-
ofstream out2;
openOutputFileAppend(mapInfo, out2);
out << endl;
if (results) {
- mothurOut(querySeq->getName() + " was found have at least one chimeric window."); mothurOutEndLine();
+ m->mothurOut(querySeq->getName() + " was found have at least one chimeric window."); m->mothurOutEndLine();
+ outAcc << querySeq->getName() << endl;
}
//free memory
for (int i = 0; i < closest.size(); i++) { delete closest[i].seq; }
-
+ return 0;
}
catch(exception& e) {
- errorOut(e, "Ccode", "print");
+ m->errorOut(e, "Ccode", "print");
exit(1);
}
}
//find closest matches to query
closest = findClosest(query, numWanted);
+ if (m->control_pressed) { return 0; }
+
//initialize spotMap
for (int i = 0; i < query->getAligned().length(); i++) { spotMap[i] = i; }
createFilter(temp, 0.5);
- for (int i = 0; i < temp.size(); i++) { runFilter(temp[i]); }
+ for (int i = 0; i < temp.size(); i++) {
+ if (m->control_pressed) { return 0; }
+ runFilter(temp[i]);
+ }
//update spotMap
map<int, int> newMap;
//trim sequences - this follows ccodes remove_extra_gaps
trimSequences(query);
-
+ if (m->control_pressed) { return 0; }
//windows are equivalent to words - ccode paper recommends windows are between 5% and 20% on alignment length().
//Our default will be 10% and we will warn if user tries to use a window above or below these recommendations
windows = findWindows();
-
+ if (m->control_pressed) { return 0; }
//remove sequences that are more than 20% different and less than 0.5% different - may want to allow user to specify this later
removeBadReferenceSeqs(closest);
-
+ if (m->control_pressed) { return 0; }
//find the averages for each querys references
getAverageRef(closest); //fills sumRef, averageRef, sumSquaredRef and refCombo.
getAverageQuery(closest, query); //fills sumQuery, averageQuery, sumSquaredQuery.
-
+ if (m->control_pressed) { return 0; }
//find the averages for each querys references
findVarianceRef(); //fills varRef and sdRef also sets minimum error rate to 0.001 to avoid divide by 0.
-
+ if (m->control_pressed) { return 0; }
//find the averages for the query
findVarianceQuery(); //fills varQuery and sdQuery also sets minimum error rate to 0.001 to avoid divide by 0.
+ if (m->control_pressed) { return 0; }
determineChimeras(); //fills anova, isChimericConfidence, isChimericTStudent and isChimericANOVA.
+ if (m->control_pressed) { return 0; }
return 0;
}
catch(exception& e) {
- errorOut(e, "Ccode", "getChimeras");
+ m->errorOut(e, "Ccode", "getChimeras");
exit(1);
}
}
//check to make sure that is not whole seq
- if ((rearPos - frontPos - 1) <= 0) { mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); mothurOutEndLine(); exit(1); }
+ if ((rearPos - frontPos - 1) <= 0) { m->mothurOut("Error, when I trim your sequences, the entire sequence is trimmed."); m->mothurOutEndLine(); exit(1); }
map<int, int> tempTrim;
tempTrim[frontPos] = rearPos;
spotMap = newMap;
}
catch(exception& e) {
- errorOut(e, "Ccode", "trimSequences");
+ m->errorOut(e, "Ccode", "trimSequences");
exit(1);
}
}
//default is wanted = 10% of total length
if (windowSizes > length) {
- mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
+ m->mothurOut("You have slected a window larger than your sequence length after all filters, masks and trims have been done. I will use the default 10% of sequence length.");
windowSizes = length / 10;
}else if (windowSizes == 0) { windowSizes = length / 10; }
else if (windowSizes > (length * 0.20)) {
- mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine();
+ m->mothurOut("You have selected a window that is larger than 20% of your sequence length. This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
}else if (windowSizes < (length * 0.05)) {
- mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); mothurOutEndLine();
+ m->mothurOut("You have selected a window that is smaller than 5% of your sequence length. This is not recommended, but I will continue anyway."); m->mothurOutEndLine();
}
//save starting points of each window
return win;
}
catch(exception& e) {
- errorOut(e, "Ccode", "findWindows");
+ m->errorOut(e, "Ccode", "findWindows");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "getDiff");
+ m->errorOut(e, "Ccode", "getDiff");
exit(1);
}
}
seqs = goodSeqs;
}else { //warn, but dont remove any
- mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check."); mothurOutEndLine();
+ m->mothurOut(querySeq->getName() + " does not have an adaquate number of reference sequences that are within 20% and 0.5% similarity. I will continue, but please check."); m->mothurOutEndLine();
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "removeBadReferenceSeqs");
+ m->errorOut(e, "Ccode", "removeBadReferenceSeqs");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "findClosestSides");
+ m->errorOut(e, "Ccode", "findClosestSides");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "getAverageRef");
+ m->errorOut(e, "Ccode", "getAverageRef");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "getAverageQuery");
+ m->errorOut(e, "Ccode", "getAverageQuery");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "findVarianceRef");
+ m->errorOut(e, "Ccode", "findVarianceRef");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "findVarianceQuery");
+ m->errorOut(e, "Ccode", "findVarianceQuery");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "Ccode", "determineChimeras");
+ m->errorOut(e, "Ccode", "determineChimeras");
exit(1);
}
}
else if (numseq > 2) tvalue = 2.353;
else if (numseq > 1) tvalue = 2.920;
else if (numseq <= 1) {
- mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
+ m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
}
return tvalue;
}
catch(exception& e) {
- errorOut(e, "Ccode", "getT");
+ m->errorOut(e, "Ccode", "getT");
exit(1);
}
}
else if (numseq > 1) fvalue = 18.5;
else if (numseq > 0) fvalue = 161;
else if (numseq <= 0) {
- mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); mothurOutEndLine();
+ m->mothurOut("Two or more reference sequences are required, your data will be flawed.\n"); m->mothurOutEndLine();
}
return fvalue;
}
catch(exception& e) {
- errorOut(e, "Ccode", "getF");
+ m->errorOut(e, "Ccode", "getF");
exit(1);
}
}
projects / mothur.git / blobdiff