*/
#include "clearcutcommand.h"
-#include "globaldata.hpp"
+#ifdef __cplusplus
+extern "C" {
+#endif
+#include "clearcut.h"
+#ifdef __cplusplus
+}
+#endif
+//**********************************************************************************************************************
+vector<string> ClearcutCommand::setParameters(){
+ try {
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pphylip);
+ CommandParameter pfasta("fasta", "InputTypes", "", "", "FastaPhylip", "FastaPhylip", "none","tree",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pverbose("verbose", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pverbose);
+ CommandParameter pquiet("quiet", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pquiet);
+ CommandParameter pversion("version", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pversion);
+ CommandParameter pseed("seed", "String", "", "", "*", "", "","",false,false); parameters.push_back(pseed);
+ CommandParameter pnorandom("norandom", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pnorandom);
+ CommandParameter pshuffle("shuffle", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pshuffle);
+ CommandParameter pneighbor("neighbor", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pneighbor);
+ CommandParameter pexpblen("expblen", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpblen);
+ CommandParameter pexpdist("expdist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pexpdist);
+ CommandParameter pDNA("DNA", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pDNA);
+ CommandParameter pprotein("protein", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pprotein);
+ CommandParameter pjukes("jukes", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pjukes);
+ CommandParameter pkimura("kimura", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkimura);
+ CommandParameter pstdout("stdout", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pstdout);
+ CommandParameter pntrees("ntrees", "Number", "", "1", "", "", "","",false,false); parameters.push_back(pntrees);
+ CommandParameter pmatrixout("matrixout", "String", "", "", "", "", "","",false,false); parameters.push_back(pmatrixout);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClearcutCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The clearcut command interfaces mothur with the clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho.\n";
+ helpString += "For more information about clearcut refer to http://bioinformatics.hungry.com/clearcut/ \n";
+ helpString += "The clearcut command parameters are phylip, fasta, version, verbose, quiet, seed, norandom, shuffle, neighbor, expblen, expdist, ntrees, matrixout, stdout, kimura, jukes, protein, DNA. \n";
+ helpString += "The phylip parameter allows you to enter your phylip formatted distance matrix. \n";
+ helpString += "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";
+
+ helpString += "The version parameter prints out the version of clearcut you are using, default=F. \n";
+ helpString += "The verbose parameter prints out more output from clearcut, default=F. \n";
+ helpString += "The quiet parameter turns on silent operation mode, default=F. \n";
+ helpString += "The seed parameter allows you to explicitly set the PRNG seed to a specific value. \n";
+ helpString += "The norandom parameter allows you to attempt joins deterministically, default=F. \n";
+ helpString += "The shuffle parameter allows you to randomly shuffle the distance matrix, default=F. \n";
+ helpString += "The neighbor parameter allows you to use traditional Neighbor-Joining algorithm, default=T. \n";
+
+ helpString += "The DNA parameter allows you to indicate your fasta file contains DNA sequences, default=F. \n";
+ helpString += "The protein parameter allows you to indicate your fasta file contains protein sequences, default=F. \n";
+
+ helpString += "The stdout parameter outputs your tree to STDOUT, default=F. \n";
+ helpString += "The matrixout parameter allows you to specify a filename to output a distance matrix to. \n";
+ helpString += "The ntrees parameter allows you to specify the number of output trees, default=1. \n";
+ helpString += "The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n";
+ helpString += "The expdist parameter allows you to use exponential notation for distance outputs, default=F. \n";
+
+ helpString += "The clearcut command should be in the following format: \n";
+ helpString += "clearcut(phylip=yourDistanceFile) \n";
+ helpString += "Example: clearcut(phylip=abrecovery.phylip.dist) \n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getHelpString");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string ClearcutCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "matrixout") { pattern = "[filename],"; }
+ else if (type == "tree") { pattern = "[filename],tre"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "getOutputPattern");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+ClearcutCommand::ClearcutCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["matrixout"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClearcutCommand", "ClearcutCommand");
+ exit(1);
+ }
+}
/**************************************************************************************/
ClearcutCommand::ClearcutCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
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"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
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 = ""; }
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; }
}
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
- else { inputFile = fastafile; }
+ else { inputFile = fastafile; m->setFastaFile(fastafile); }
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputFile = phylipfile; }
+ else { inputFile = phylipfile; m->setPhylipFile(phylipfile); }
- if ((phylipfile == "") && (fastafile == "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file."); m->mothurOutEndLine(); abort=true; }
+ if ((phylipfile == "") && (fastafile == "")) {
+ //is there are current file available for either of these?
+ //give priority to phylip, then fasta
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ fastafile = m->getFastaFile();
+ if (fastafile != "") { inputFile = fastafile; m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
if ((phylipfile != "") && (fastafile != "")) { m->mothurOut("You must provide either a phylip formatted distance matrix or an aligned fasta file, not BOTH."); m->mothurOutEndLine(); abort=true; }
//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);
+ shuffle = m->isTrue(temp);
- temp = validParameter.validFile(parameters, "neighbor", false); if (temp == "not found"){ temp = "F"; }
- neighbor = 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; }
}
exit(1);
}
}
-//**********************************************************************************************************************
-
-void ClearcutCommand::help(){
- 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 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 version parameter prints out the version of clearcut you are using, default=F. \n");
- m->mothurOut("The verbose parameter prints out more output from clearcut, default=F. \n");
- m->mothurOut("The quiet parameter turns on silent operation mode, default=F. \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 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 stdout parameter outputs your tree to STDOUT, default=F. \n");
- m->mothurOut("The matrixout parameter allows you to specify a filename to output a distance matrix to. \n");
- m->mothurOut("The ntrees parameter allows you to specify the number of output trees, default=1. \n");
- m->mothurOut("The expblen parameter allows you to use exponential notation for branch lengths, default=F. \n");
- m->mothurOut("The expdist parameter allows you to use exponential notation for distance outputs, 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");
- exit(1);
- }
-}
-
/**************************************************************************************/
int ClearcutCommand::execute() {
try {
- if (abort == true) { return 0; }
-
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
//prepare filename
- string outputName = outputDir + getRootName(getSimpleName(inputFile)) + "tre";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFile));
+ string outputName = getOutputFileName("tree", variables);
+ 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')));
-
- string clearcutCommand = path + "clearcut/clearcut ";
+ vector<char*> cPara;
+ char* tempClearcut = new char[9];
+ *tempClearcut = '\0'; strncat(tempClearcut, "clearcut", 8);
+ cPara.push_back(tempClearcut);
+
//you gave us a distance matrix
- if (phylipfile != "") { clearcutCommand += "--distance "; }
+ if (phylipfile != "") { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--distance", 10); 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[12]; *temp = '\0'; strncat(temp, "--alignment", 11); cPara.push_back(temp); }
+
+ if (version) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--version", 9); cPara.push_back(temp); }
+ if (verbose) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--verbose", 9); cPara.push_back(temp); }
+ if (quiet) { char* temp = new char[8]; *temp = '\0'; strncat(temp, "--quiet", 7); cPara.push_back(temp); }
+ if (seed != "*") {
+ string tempSeed = "--seed=" + seed;
+ char* temp = new char[tempSeed.length()+1];
+ *temp = '\0'; strncat(temp, tempSeed.c_str(), tempSeed.length());
+ cPara.push_back(temp);
+ }
+ if (norandom) { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--norandom", 10); cPara.push_back(temp); }
+ if (shuffle) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--shuffle", 9); cPara.push_back(temp); }
+ if (neighbor) { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--neighbor", 10); cPara.push_back(temp); }
+
+ string tempIn = "--in=" + inputFile;
+ char* tempI = new char[tempIn.length()+1];
+ *tempI = '\0'; strncat(tempI, tempIn.c_str(), tempIn.length());
+ cPara.push_back(tempI);
+
+ if (stdoutWanted) { char* temp = new char[9]; *temp = '\0'; strncat(temp, "--stdout", 8); cPara.push_back(temp); }
+ else{
+ string tempOut = "--out=" + outputName;
+ char* temp = new char[tempOut.length()+1];
+ *temp = '\0'; strncat(temp, tempOut.c_str(), tempOut.length());
+ cPara.push_back(temp);
+ }
+
+ if (DNA) { char* temp = new char[6]; *temp = '\0'; strncat(temp, "--DNA", 5); cPara.push_back(temp); }
+ if (protein) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--protein", 9); cPara.push_back(temp); }
+ if (jukes) { char* temp = new char[8]; *temp = '\0'; strncat(temp, "--jukes", 7); cPara.push_back(temp); }
+ if (kimura) { char* temp = new char[9]; *temp = '\0'; strncat(temp, "--kimura", 8); cPara.push_back(temp); }
+ if (matrixout != "") {
+ string tempMatrix = "--matrixout=" + outputDir + matrixout;
+ char* temp = new char[tempMatrix.length()+1];
+ *temp = '\0'; strncat(temp, tempMatrix.c_str(), tempMatrix.length());
+ 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()+1];
+ *temp = '\0'; strncat(temp, tempNtrees.c_str(), tempNtrees.length());
+ cPara.push_back(temp);
+ }
+
+ if (expblen) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--expblen", 9); cPara.push_back(temp); }
+ if (expdist) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--expdist", 9); 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) {
+
+ //set first tree file as new current treefile
+ string currentTree = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputName); m->mothurOutEndLine();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
}
projects / mothur.git / blobdiff