*/
#include "clearcutcommand.h"
-
+#ifdef __cplusplus
+extern "C" {
+#endif
+#include "clearcut.h"
+#ifdef __cplusplus
+}
+#endif
+//**********************************************************************************************************************
+vector<string> ClearcutCommand::getValidParameters(){
+ try {
+ string AlignArray[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
+ "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","outputdir","inputdir"};
+ vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClearcutCommand::ClearcutCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["matrixout"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
+ exit(1);
+ }
+}//**********************************************************************************************************************
+vector<string> ClearcutCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta","phylip","or"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> ClearcutCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**************************************************************************************/
ClearcutCommand::ClearcutCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["matrixout"] = 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 = ""; }
try {
m->mothurOut("The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n");
m->mothurOut("For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n");
- m->mothurOut("The clearcut executable must be in a folder called clearcut in the same folder as your mothur executable, similar to mothur's requirements for using blast. \n");
m->mothurOut("The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n");
m->mothurOut("The phylip parameter allows you to enter your phylip formatted distance matrix. \n");
m->mothurOut("The fasta parameter allows you to enter your aligned fasta file, if you enter a fastafile you specify if the sequences are DNA or protein using the DNA or protein parameters. \n");
try {
if (abort == true) { return 0; }
-
+
//prepare filename
string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+ outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
- //get location of clearcut
- GlobalData* globaldata = GlobalData::getInstance();
- string path = globaldata->argv;
- path = path.substr(0, (path.find_last_of('m')));
+ vector<char*> cPara;
- string clearcutCommand = path + "clearcut ";
+ char* tempClearcut = new char[8];
+ strcpy(tempClearcut, "clearcut");
+ cPara.push_back(tempClearcut);
//you gave us a distance matrix
- if (phylipfile != "") { clearcutCommand += "--distance "; }
+ if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); }
//you gave us a fastafile
- if (fastafile != "") { clearcutCommand += "--alignment "; }
-
- if (version) { clearcutCommand += "--version "; }
- if (verbose) { clearcutCommand += "--verbose "; }
- if (quiet) { clearcutCommand += "--quiet "; }
- if (seed != "*") { clearcutCommand += "--seed=" + seed + " "; }
- if (norandom) { clearcutCommand += "--norandom "; }
- if (shuffle) { clearcutCommand += "--shuffle "; }
- if (neighbor) { clearcutCommand += "--neighbor "; }
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- clearcutCommand += "--in=" + inputFile + " ";
- #else
- clearcutCommand += "--in=\"" + inputFile + "\" ";
- #endif
-
- if (stdoutWanted) { clearcutCommand += "--stdout "; }
+ if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
+
+ if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); }
+ if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
+ if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
+ if (seed != "*") {
+ string tempSeed = "--seed=" + seed;
+ char* temp = new char[tempSeed.length()];
+ strcpy(temp, tempSeed.c_str());
+ cPara.push_back(temp);
+ }
+ if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
+ if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
+ if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
+
+ string tempIn = "--in=" + inputFile;
+ char* tempI = new char[tempIn.length()];
+ strcpy(tempI, tempIn.c_str());
+ cPara.push_back(tempI);
+
+ if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
else{
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- clearcutCommand += "--out=" + outputName + " "; }
- #else
- clearcutCommand += "--out=\"" + outputName + "\" "; }
- #endif
-
- if (DNA) { clearcutCommand += "--DNA "; }
- if (protein) { clearcutCommand += "--protein "; }
- if (jukes) { clearcutCommand += "--jukes "; }
- if (kimura) { clearcutCommand += "--kimura "; }
- if (matrixout != "") { clearcutCommand += "--matrixout=" + matrixout + " "; }
- if (ntrees != "1") { clearcutCommand += "--ntrees=" + ntrees + " "; }
- if (expblen) { clearcutCommand += "--expblen "; }
- if (expdist) { clearcutCommand += "--expdist "; }
-
- //run clearcut
- system(clearcutCommand.c_str());
+ string tempOut = "--out=" + outputName;
+
+ char* temp = new char[tempOut.length()];
+ strcpy(temp, tempOut.c_str());
+ cPara.push_back(temp);
+ }
+
+ if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
+ if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); }
+ if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
+ if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
+ if (matrixout != "") {
+ string tempMatrix = "--matrixout=" + outputDir + matrixout;
+ char* temp = new char[tempMatrix.length()];
+ strcpy(temp, tempMatrix.c_str());
+ cPara.push_back(temp);
+ outputNames.push_back((outputDir + matrixout));
+ outputTypes["matrixout"].push_back((outputDir + matrixout));
+ }
+
+ if (ntrees != "1") {
+ string tempNtrees = "--ntrees=" + ntrees;
+ char* temp = new char[tempNtrees.length()];
+ strcpy(temp, tempNtrees.c_str());
+ cPara.push_back(temp);
+ }
+
+ if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
+ if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
+
+ char** clearcutParameters;
+ clearcutParameters = new char*[cPara.size()];
+ for (int i = 0; i < cPara.size(); i++) { clearcutParameters[i] = cPara[i]; }
+ int numArgs = cPara.size();
+
+ clearcut_main(numArgs, clearcutParameters);
+
+ //free memory
+ for(int i = 0; i < cPara.size(); i++) { delete[] cPara[i]; }
+ delete[] clearcutParameters;
if (!stdoutWanted) {
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputName); m->mothurOutEndLine();
- if (matrixout != "") { m->mothurOut(matrixout); m->mothurOutEndLine(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
}
projects / mothur.git / blobdiff