//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < fastaFileNames.size(); i++) {
- if (inputDir != "") {
- string path = m->hasPath(fastaFileNames[i]);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
- }
-
- int ableToOpen;
- ifstream in;
-
- ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
-
- //if you can't open it, try default location
- if (ableToOpen == 1) {
- if (m->getDefaultPath() != "") { //default path is set
- string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
+ bool ignore = false;
+ if (fastaFileNames[i] == "current") {
+ fastaFileNames[i] = m->getFastaFile();
+ if (fastaFileNames[i] != "") { m->mothurOut("Using " + fastaFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
}
}
- //if you can't open it, try output location
- if (ableToOpen == 1) {
- if (m->getOutputDir() != "") { //default path is set
- string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
- ifstream in2;
- ableToOpen = m->openInputFile(tryPath, in2, "noerror");
- in2.close();
- fastaFileNames[i] = tryPath;
- }
- }
+ if (!ignore) {
- in.close();
+ if (inputDir != "") {
+ string path = m->hasPath(fastaFileNames[i]);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { fastaFileNames[i] = inputDir + fastaFileNames[i]; }
+ }
+
+ int ableToOpen;
+ ifstream in;
- if (ableToOpen == 1) {
- m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
- //erase from file list
- fastaFileNames.erase(fastaFileNames.begin()+i);
- i--;
+ ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
+
+ //if you can't open it, try default location
+ if (ableToOpen == 1) {
+ if (m->getDefaultPath() != "") { //default path is set
+ string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ //if you can't open it, try output location
+ if (ableToOpen == 1) {
+ if (m->getOutputDir() != "") { //default path is set
+ string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
+ fastaFileNames[i] = tryPath;
+ }
+ }
+
+ in.close();
+
+ if (ableToOpen == 1) {
+ m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
+ //erase from file list
+ fastaFileNames.erase(fastaFileNames.begin()+i);
+ i--;
+ }else {
+ m->setFastaFile(fastaFileNames[i]);
+ }
}
}
// ...at some point should added some additional type checking...
string temp;
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found"){ temp = "1.0"; }
- convert(temp, match);
+ m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found"){ temp = "-1.0"; }
- convert(temp, misMatch);
+ m->mothurConvert(temp, misMatch);
temp = validParameter.validFile(parameters, "gapopen", false); if (temp == "not found"){ temp = "-2.0"; }
- convert(temp, gapOpen);
+ m->mothurConvert(temp, gapOpen);
temp = validParameter.validFile(parameters, "gapextend", false); if (temp == "not found"){ temp = "-1.0"; }
- convert(temp, gapExtend);
+ m->mothurConvert(temp, gapExtend);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "cutoff", false); if(temp == "not found"){ temp = "1.0"; }
- convert(temp, cutoff);
+ m->mothurConvert(temp, cutoff);
temp = validParameter.validFile(parameters, "countends", false); if(temp == "not found"){ temp = "T"; }
countends = m->isTrue(temp);
if (output == "lt") { //does the user want lower triangle phylip formatted file
outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "phylip.dist";
- remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
+ m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
}else if (output == "column") { //user wants column format
outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "dist";
outputTypes["column"].push_back(outputFile);
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
}else { //assume square
outputFile = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "square.dist";
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
//wait on chidren
for(int i = 1; i < processors; i++) {
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
char buf[5];
MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
//do your part
driverMPI(start, end, outMPI, cutoff);
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
char buf[5];
strcpy(buf, "done");
//do your part
string outputMyPart;
- unsigned long int mySize;
+ unsigned long long mySize;
if (output != "square"){ driverMPI(start, end, outputFile, mySize); }
else { driverMPI(start, end, outputFile, mySize, output); }
- if (m->control_pressed) { outputTypes.clear(); remove(outputFile.c_str()); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFile); delete distCalculator; return 0; }
int amode=MPI_MODE_APPEND|MPI_MODE_WRONLY|MPI_MODE_CREATE; //
MPI_File outMPI;
//wait on chidren
for(int b = 1; b < processors; b++) {
- unsigned long int fileSize;
+ unsigned long long fileSize;
- if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); remove(outputFile.c_str()); delete distCalculator; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); MPI_File_close(&outMPI); m->mothurRemove(outputFile); delete distCalculator; return 0; }
MPI_Recv(&fileSize, 1, MPI_LONG, b, tag, MPI_COMM_WORLD, &status);
MPI_File_close(&outMPI);
}else { //you are a child process
//do your part
- unsigned long int size;
+ unsigned long long size;
if (output != "square"){ driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size); }
else { driverMPI(start, end, (outputFile + toString(pid) + ".temp"), size, output); }
#endif
#endif
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
m->mothurOut("It took " + toString(time(NULL) - startTime) + " to calculate the distances for " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; }
}
delete distCalculator;
//append and remove temp files
for (int i=0;i<processIDS.size();i++) {
m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
- remove((filename + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
}
#endif
}
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size){
try {
MPI_Status status;
}
/**************************************************************************************************/
/////// need to fix to work with calcs and sequencedb
-int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long int& size, string square){
+int PairwiseSeqsCommand::driverMPI(int startLine, int endLine, string file, unsigned long long& size, string square){
try {
MPI_Status status;
projects / mothur.git / blobdiff