*/
#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; calledHelp = true;
+ 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 {
- 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 {
//valid paramters for this command
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 = ""; }
int ClearcutCommand::execute() {
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//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); }
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") {
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();
- if (matrixout != "") { m->mothurOut(outputDir+matrixout); m->mothurOutEndLine(); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
}