*/
#include "clearcutcommand.h"
-#include "globaldata.hpp"
+#include "clearcut.h"
+
/**************************************************************************************/
ClearcutCommand::ClearcutCommand(string option) {
else {
//valid paramters for this command
string Array[] = {"fasta","phylip","version","verbose","quiet","seed","norandom","shuffle","neighbor","expblen",
- "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","stdin","outputdir","inputdir"};
+ "expdist","ntrees","matrixout","stdout","kimura","jukes","protein","DNA","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("phylip");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["phylip"] = inputDir + it->second; }
}
//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 = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(inputFile); }
string temp;
temp = validParameter.validFile(parameters, "version", false); if (temp == "not found"){ temp = "F"; }
- version = isTrue(temp);
+ version = m->isTrue(temp);
temp = validParameter.validFile(parameters, "verbose", false); if (temp == "not found"){ temp = "F"; }
- verbose = isTrue(temp);
+ verbose = m->isTrue(temp);
temp = validParameter.validFile(parameters, "quiet", false); if (temp == "not found"){ temp = "F"; }
- quiet = isTrue(temp);
+ quiet = m->isTrue(temp);
seed = validParameter.validFile(parameters, "seed", false); if (seed == "not found"){ seed = "*"; }
temp = validParameter.validFile(parameters, "norandom", false); if (temp == "not found"){ temp = "F"; }
- norandom = isTrue(temp);
+ norandom = m->isTrue(temp);
temp = validParameter.validFile(parameters, "shuffle", false); if (temp == "not found"){ temp = "F"; }
- shuffle = isTrue(temp);
-
- temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }
- neighbor = isTrue(temp);
+ shuffle = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "stdin", false); if (temp == "not found"){ temp = "F"; }
- stdin = isTrue(temp);
+ temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "T"; }
+ neighbor = m->isTrue(temp);
temp = validParameter.validFile(parameters, "DNA", false); if (temp == "not found"){ temp = "F"; }
- DNA = isTrue(temp);
+ DNA = m->isTrue(temp);
temp = validParameter.validFile(parameters, "protein", false); if (temp == "not found"){ temp = "F"; }
- protein = isTrue(temp);
+ protein = m->isTrue(temp);
temp = validParameter.validFile(parameters, "jukes", false); if (temp == "not found"){ temp = "F"; }
- jukes = isTrue(temp);
+ jukes = m->isTrue(temp);
temp = validParameter.validFile(parameters, "kimura", false); if (temp == "not found"){ temp = "F"; }
- kimura = isTrue(temp);
+ kimura = m->isTrue(temp);
temp = validParameter.validFile(parameters, "stdout", false); if (temp == "not found"){ temp = "F"; }
- stdout = isTrue(temp);
+ stdoutWanted = m->isTrue(temp);
matrixout = validParameter.validFile(parameters, "matrixout", false); if (matrixout == "not found"){ matrixout = ""; }
ntrees = validParameter.validFile(parameters, "ntrees", false); if (ntrees == "not found"){ ntrees = "1"; }
temp = validParameter.validFile(parameters, "expblen", false); if (temp == "not found"){ temp = "F"; }
- expblen = isTrue(temp);
+ expblen = m->isTrue(temp);
temp = validParameter.validFile(parameters, "expdist", false); if (temp == "not found"){ temp = "F"; }
- expdist = isTrue(temp);
+ expdist = m->isTrue(temp);
if ((fastafile != "") && ((!DNA) && (!protein))) { m->mothurOut("You must specify the type of sequences you are using: DNA or protein"); m->mothurOutEndLine(); abort=true; }
}
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, stdin. \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");
m->mothurOut("The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n");
m->mothurOut("The norandom parameter allows you to attempt joins deterministically, default=F. \n");
m->mothurOut("The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n");
- m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=F. \n");
+ m->mothurOut("The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n");
- m->mothurOut("The stdin parameter reads input from STDIN, default=F. \n");
m->mothurOut("The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n");
m->mothurOut("The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n");
m->mothurOut("The clearcut command should be in the following format: \n");
m->mothurOut("clearcut(phylip=yourDistanceFile) \n");
m->mothurOut("Example: clearcut(phylip=abrecovery.phylip.dist) \n");
+
}
catch(exception& e) {
m->errorOut(e, "ClearcutCommand", "help");
try {
if (abort == true) { return 0; }
-
+
//prepare filename
- string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
+ string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
- //get location of clearcut
- GlobalData* globaldata = GlobalData::getInstance();
- string path = globaldata->argv;
- path = path.substr(0, (path.find_last_of('m')));
-
- string clearcutCommand = path + "clearcut/clearcut ";
+ vector<char*> cPara;
+ 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 (stdin) { clearcutCommand += "--stdin "; }
- else { clearcutCommand += "--in=" + inputFile + " "; }
- if (stdout) { clearcutCommand += "--stdout "; }
- else { clearcutCommand += "--out=" + outputName + " "; }
-
- 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());
-
- if (!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{
+ 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);
+ }
+
+ 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();
+ m->mothurOut(outputName); m->mothurOutEndLine();
+ if (matrixout != "") { m->mothurOut(outputDir+matrixout); m->mothurOutEndLine(); }
m->mothurOutEndLine();
}
projects / mothur.git / blobdiff