//**********************************************************************************************************************
-DistanceCommand::DistanceCommand(string option){
+DistanceCommand::DistanceCommand(string option) {
try {
abort = false;
Estimators.clear();
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
- if (fastafile == "not found") { mothurOut("fasta is a required parameter for the dist.seqs command."); mothurOutEndLine(); abort = true; }
+ if (fastafile == "not found") { m->mothurOut("fasta is a required parameter for the dist.seqs command."); m->mothurOutEndLine(); abort = true; }
else if (fastafile == "not open") { abort = true; }
else{
ifstream inFASTA;
output = validParameter.validFile(parameters, "output", false); if(output == "not found"){ output = "column"; }
- if ((output != "column") && (output != "lt") && (output != "square")) { mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); mothurOutEndLine(); output = "column"; }
+ if ((output != "column") && (output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are column, lt and square. I will use column."); m->mothurOutEndLine(); output = "column"; }
ValidCalculators validCalculator;
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "DistanceCommand");
+ m->errorOut(e, "DistanceCommand", "DistanceCommand");
exit(1);
}
}
void DistanceCommand::help(){
try {
- mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
- mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors. \n");
- mothurOut("The fasta parameter is required.\n");
- mothurOut("The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
- mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n");
- mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
- mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
- mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
- mothurOut("The dist.seqs command should be in the following format: \n");
- mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
- mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
+ m->mothurOut("The dist.seqs command reads a file containing sequences and creates a distance file.\n");
+ m->mothurOut("The dist.seqs command parameters are fasta, calc, countends, output, cutoff and processors. \n");
+ m->mothurOut("The fasta parameter is required.\n");
+ m->mothurOut("The calc parameter allows you to specify the method of calculating the distances. Your options are: nogaps, onegap or eachgap. The default is onegap.\n");
+ m->mothurOut("The countends parameter allows you to specify whether to include terminal gaps in distance. Your options are: T or F. The default is T.\n");
+ m->mothurOut("The cutoff parameter allows you to specify maximum distance to keep. The default is 1.0.\n");
+ m->mothurOut("The output parameter allows you to specify format of your distance matrix. Options are column, lt, and square. The default is column.\n");
+ m->mothurOut("The processors parameter allows you to specify number of processors to use. The default is 1.\n");
+ m->mothurOut("The dist.seqs command should be in the following format: \n");
+ m->mothurOut("dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n");
+ m->mothurOut("Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n");
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "help");
+ m->errorOut(e, "DistanceCommand", "help");
exit(1);
}
}
ifstream inFASTA;
driver(0, numSeqs, outputFile, cutoff);
#endif
+ if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
if (output == "square") { convertMatrix(outputFile); }
+ if (m->control_pressed) { delete distCalculator; remove(outputFile.c_str()); return 0; }
+
delete distCalculator;
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(outputFile); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "execute");
+ m->errorOut(e, "DistanceCommand", "execute");
exit(1);
}
}
}else if (pid == 0){
driver(lines[process]->start, lines[process]->end, filename + toString(getpid()) + ".temp", cutoff);
exit(0);
- }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
+ }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
}
//force parent to wait until all the processes are done
#endif
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "createProcesses");
+ m->errorOut(e, "DistanceCommand", "createProcesses");
exit(1);
}
}
outFile << name << '\t';
}
for(int j=0;j<i;j++){
+
+ if (m->control_pressed) { outFile.close(); return 0; }
+
distCalculator->calcDist(alignDB.get(i), alignDB.get(j));
double dist = distCalculator->getDist();
if (output == "lt") { outFile << endl; }
if(i % 100 == 0){
- mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); mothurOutEndLine();
+ m->mothurOut(toString(i) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
}
}
- mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); mothurOutEndLine();
+ m->mothurOut(toString(endLine-1) + "\t" + toString(time(NULL) - startTime)); m->mothurOutEndLine();
outFile.close();
return 1;
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "driver");
+ m->errorOut(e, "DistanceCommand", "driver");
exit(1);
}
}
/**************************************************************************************************/
-void DistanceCommand::convertMatrix(string outputFile) {
+int DistanceCommand::convertMatrix(string outputFile) {
try{
//sort file by first column so the distances for each row are together
//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);
if (first != currentRow) {
remove(outfile.c_str());
+ return 1;
+
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "convertMatrix");
+ m->errorOut(e, "DistanceCommand", "convertMatrix");
exit(1);
}
}
output.close();
}
catch(exception& e) {
- errorOut(e, "DistanceCommand", "appendFiles");
+ m->errorOut(e, "DistanceCommand", "appendFiles");
exit(1);
}
}
projects / mothur.git / blobdiff