#include "filterseqscommand.h"
#include "sequence.hpp"
+//**********************************************************************************************************************
+vector<string> FilterSeqsCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "trump", "soft", "hard", "vertical", "outputdir","inputdir", "processors"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+FilterSeqsCommand::FilterSeqsCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["filter"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> FilterSeqsCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> FilterSeqsCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "FilterSeqsCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**************************************************************************************/
-
FilterSeqsCommand::FilterSeqsCommand(string option) {
try {
abort = false;
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["filter"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
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();
- ableToOpen = m->openInputFile(tryPath, in, "noerror");
+ ifstream in2;
+ ableToOpen = m->openInputFile(tryPath, in2, "noerror");
+ in2.close();
fastafileNames[i] = tryPath;
}
}
+
+ //if you can't open it, try default 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->mothurOutEndLine(); m->mothurOutEndLine();
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { outputTypes.clear(); return 0; }
#ifdef USE_MPI
int pid;
m->openOutputFile(filterFile, outFilter);
outFilter << filter << endl;
outFilter.close();
- outputNames.push_back(filterFile);
+ outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
#ifdef USE_MPI
}
if(filter[i] == '1'){ filteredLength++; }
}
- if (m->control_pressed) { for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
m->mothurOutEndLine();
//wait on chidren
for(int i = 1; i < processors; i++) {
- char buf[4];
- MPI_Recv(buf, 4, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
+ char buf[5];
+ MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
}
}else { //you are a child process
if (m->control_pressed) { MPI_File_close(&inMPI); MPI_File_close(&outMPI); return 0; }
- char buf[4];
+ char buf[5];
strcpy(buf, "done");
//tell parent you are done.
- MPI_Send(buf, 4, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
+ MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
}
MPI_File_close(&outMPI);
if (m->control_pressed) { return 1; }
#endif
#endif
- outputNames.push_back(filteredFasta);
+ outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
}
return 0;
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
//force parent to wait until all the processes are done
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
//parent do your part