*/
#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);
vector<char*> cPara;
- char* tempClearcut = new char[8]; strcpy(tempClearcut, "clearcut"); cPara.push_back(tempClearcut);
+ char* tempClearcut = new char[8];
+ strcpy(tempClearcut, "clearcut");
+ cPara.push_back(tempClearcut);
//you gave us a distance matrix
if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); 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 = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- tempIn += "--in=" + inputFile;
- #else
- tempIn += "--in=\"" + inputFile + "\"";
- #endif
-
+ 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 = "";
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- tempOut += "--out=" + outputName;
- #else
- tempOut += "--out=\"" + outputName + "\"";
- #endif
+ string tempOut = "--out=" + outputName;
char* temp = new char[tempOut.length()];
strcpy(temp, tempOut.c_str());
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=" + 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") {
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();
}