it2 = parameters.find("fasta");
//user has given a template file
if(it2 != parameters.end()){
- path = hasPath(it2->second);
+ path = m->hasPath(it2->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it2->second; }
}
it2 = parameters.find("oldfasta");
//user has given a template file
if(it2 != parameters.end()){
- path = hasPath(it2->second);
+ path = m->hasPath(it2->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["oldfasta"] = inputDir + it2->second; }
}
it2 = parameters.find("column");
//user has given a template file
if(it2 != parameters.end()){
- path = hasPath(it2->second);
+ path = m->hasPath(it2->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["column"] = inputDir + it2->second; }
}
else if (fastafile == "not open") { abort = true; }
else{
ifstream inFASTA;
- openInputFile(fastafile, inFASTA);
+ m->openInputFile(fastafile, inFASTA);
alignDB = SequenceDB(inFASTA);
inFASTA.close();
}
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(fastafile); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
}
//check for optional parameter and set defaults
else {
if (calc == "default") { calc = "onegap"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
ValidCalculators validCalculator;
- if (isTrue(countends) == true) {
+ if (m->isTrue(countends) == true) {
for (int i=0; i<Estimators.size(); i++) {
if (validCalculator.isValidCalculator("distance", Estimators[i]) == true) {
if (Estimators[i] == "nogaps") { distCalculator = new ignoreGaps(); }
string outputFile;
if (output == "lt") { //does the user want lower triangle phylip formatted file
- outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "phylip.dist";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
remove(outputFile.c_str());
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
- outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "dist";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "dist";
//so we don't accidentally overwrite
if (outputFile == column) {
remove(outputFile.c_str());
}else { //assume square
- outputFile = outputDir + getRootName(getSimpleName(fastafile)) + "square.dist";
+ outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
remove(outputFile.c_str());
}
//append and remove temp files
for (; it != processIDS.end(); it++) {
- appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
+ m->appendFiles((outputFile + toString(it->second) + ".temp"), outputFile);
remove((outputFile + toString(it->second) + ".temp").c_str());
}
}
ifstream fileHandle;
fileHandle.open(outputFile.c_str());
if(fileHandle) {
- gobble(fileHandle);
+ m->gobble(fileHandle);
if (fileHandle.eof()) { m->mothurOut(outputFile + " is blank. This can result if there are no distances below your cutoff."); m->mothurOutEndLine(); }
}
//we had to rename the column file so we didnt overwrite above, but we want to keep old name
if (outputFile == column) {
string tempcolumn = column + ".old";
- appendFiles(tempcolumn, outputFile);
+ m->appendFiles(tempcolumn, outputFile);
remove(tempcolumn.c_str());
}else{
- appendFiles(outputFile, column);
+ m->appendFiles(outputFile, column);
remove(outputFile.c_str());
outputFile = column;
}
try{
//sort file by first column so the distances for each row are together
- string outfile = getRootName(outputFile) + "sorted.dist.temp";
+ string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
//use the unix sort
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//output to new file distance for each row and save positions in file where new row begins
ifstream in;
- openInputFile(outfile, in);
+ m->openInputFile(outfile, in);
ofstream out;
- openOutputFile(outputFile, out);
+ m->openOutputFile(outputFile, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
rowDists[first] = 0.00; //distance to yourself is 0.0
in.seekg(0);
- //openInputFile(outfile, in);
+ //m->openInputFile(outfile, in);
while(!in.eof()) {
if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
- in >> first >> second >> dist; gobble(in);
+ in >> first >> second >> dist; m->gobble(in);
if (first != currentRow) {
//print out last row
try{
//sort file by first column so the distances for each row are together
- string outfile = getRootName(outputFile) + "sorted.dist.temp";
+ string outfile = m->getRootName(outputFile) + "sorted.dist.temp";
//use the unix sort
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
//output to new file distance for each row and save positions in file where new row begins
ifstream in;
- openInputFile(outfile, in);
+ m->openInputFile(outfile, in);
ofstream out;
- openOutputFile(outputFile, out);
+ m->openOutputFile(outputFile, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
rowDists[first] = 0.00; //distance to yourself is 0.0
in.seekg(0);
- //openInputFile(outfile, in);
+ //m->openInputFile(outfile, in);
while(!in.eof()) {
if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
- in >> first >> second >> dist; gobble(in);
+ in >> first >> second >> dist; m->gobble(in);
if (first != currentRow) {
//print out last row
//make sure the 2 fasta files have the same alignment length
ifstream in;
- openInputFile(fastafile, in);
+ m->openInputFile(fastafile, in);
int fastaAlignLength = 0;
if (in) {
Sequence tempIn(in);
in.close();
ifstream in2;
- openInputFile(oldfastafile, in2);
+ m->openInputFile(oldfastafile, in2);
int oldfastaAlignLength = 0;
if (in2) {
Sequence tempIn2(in2);
set<string> namesOldFasta;
ifstream inFasta;
- openInputFile(oldfastafile, inFasta);
+ m->openInputFile(oldfastafile, inFasta);
while (!inFasta.eof()) {
if (m->control_pressed) { inFasta.close(); return good; }
alignDB.push_back(temp); //add to DB
}
- gobble(inFasta);
+ m->gobble(inFasta);
}
inFasta.close();
//read through the column file checking names and removing distances above the cutoff
ifstream inDist;
- openInputFile(column, inDist);
+ m->openInputFile(column, inDist);
ofstream outDist;
string outputFile = column + ".temp";
- openOutputFile(outputFile, outDist);
+ m->openOutputFile(outputFile, outDist);
string name1, name2;
float dist;
while (!inDist.eof()) {
if (m->control_pressed) { inDist.close(); outDist.close(); remove(outputFile.c_str()); return good; }
- inDist >> name1 >> name2 >> dist; gobble(inDist);
+ inDist >> name1 >> name2 >> dist; m->gobble(inDist);
//both names are in fasta file and distance is below cutoff
if ((namesOldFasta.count(name1) == 0) || (namesOldFasta.count(name2) == 0)) { good = false; break; }
}
catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "appendFiles");
+ m->errorOut(e, "DistanceCommand", "m->appendFiles");
exit(1);
}
}
/**************************************************************************************************
-void DistanceCommand::appendFiles(string temp, string filename) {
+void DistanceCommand::m->appendFiles(string temp, string filename) {
try{
ofstream output;
ifstream input;
//open output file in append mode
- openOutputFileAppend(filename, output);
- openInputFile(temp, input);
+ m->openOutputFileAppend(filename, output);
+ m->openInputFile(temp, input);
while(char c = input.get()){
if(input.eof()) { break; }
output.close();
}
catch(exception& e) {
- m->errorOut(e, "DistanceCommand", "appendFiles");
+ m->errorOut(e, "DistanceCommand", "m->appendFiles");
exit(1);
}
}
projects / mothur.git / blobdiff