#include "sensspeccommand.h"
//**********************************************************************************************************************
-vector<string> SensSpecCommand::getValidParameters(){
+vector<string> SensSpecCommand::setParameters(){
try {
- string Array[] = {"list", "phylip", "column", "name", "hard", "label", "cutoff", "precision", "outputdir", "inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
+ CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
+ //CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
+ CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pcolumn);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "",false,false); parameters.push_back(pcutoff);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
+ CommandParameter phard("hard", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(phard);
+ 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, "SensSpecCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-SensSpecCommand::SensSpecCommand(){
- try {
- abort = true;
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["sensspec"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
+ m->errorOut(e, "SensSpecCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SensSpecCommand::getRequiredParameters(){
+string SensSpecCommand::getHelpString(){
try {
- string Array[] = {"list","phylip","column","or"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ string helpString = "";
+ helpString += "The sens.spec command....\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "getRequiredParameters");
+ m->errorOut(e, "SensSpecCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> SensSpecCommand::getRequiredFiles(){
+SensSpecCommand::SensSpecCommand(){
try {
- vector<string> myArray;
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "getRequiredFiles");
+ m->errorOut(e, "SensSpecCommand", "SensSpecCommand");
exit(1);
}
}
SensSpecCommand::SensSpecCommand(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 {
string temp;
-
- //valid paramters for this command
- string AlignArray[] = {"list", "phylip", "column", "name", "hard", "label", "cutoff", "precision", "outputdir", "inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
if (path == "") { parameters["column"] = inputDir + it->second; }
}
- it = parameters.find("name");
+ //it = parameters.find("name");
//user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
+ //if(it != parameters.end()){
+ //path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["name"] = inputDir + it->second; }
- }
+ //if (path == "") { parameters["name"] = inputDir + it->second; }
+ //}
}
//check for required parameters
listFile = validParameter.validFile(parameters, "list", true);
- if (listFile == "not found") { m->mothurOut("list is a required parameter for the sens.spec command."); m->mothurOutEndLine(); abort = true; }
+ if (listFile == "not found") {
+ listFile = m->getListFile();
+ if (listFile != "") { m->mothurOut("Using " + listFile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }
else if (listFile == "not open") { abort = true; }
- distFile = validParameter.validFile(parameters, "column", true);
- format = "column";
- if(distFile == "not found") {
- distFile = validParameter.validFile(parameters, "phylip", true);
- format = "phylip";
- }
- if(distFile == "not found") { m->mothurOut("either column or phylip are required for the sens.spec command."); m->mothurOutEndLine(); abort = true; }
- else if (distFile == "not open") { abort = true; }
-
+ phylipfile = validParameter.validFile(parameters, "phylip", true);
+ if (phylipfile == "not found") { phylipfile = ""; }
+ else if (phylipfile == "not open") { abort = true; }
+ else { distFile = phylipfile; format = "phylip"; }
+
+ columnfile = validParameter.validFile(parameters, "column", true);
+ if (columnfile == "not found") { columnfile = ""; }
+ else if (columnfile == "not open") { abort = true; }
+ else { distFile = columnfile; format = "column"; }
+
+ if ((phylipfile == "") && (columnfile == "")) { //is there are current file available for either of these?
+ //give priority to column, then phylip
+ columnfile = m->getColumnFile();
+ if (columnfile != "") { distFile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
+ else {
+ phylipfile = m->getPhylipFile();
+ if (phylipfile != "") { distFile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a phylip or column file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a sens.spec command you must enter ONLY ONE of the following: phylip or column."); 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"){
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void SensSpecCommand::help(){
- try {
- m->mothurOut("The sens.spec command reads a fastaFile and creates .....\n");
-
-
-
- m->mothurOut("Example sens.spec(...).\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
- m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "SensSpecCommand", "help");
- exit(1);
- }
-}
-
-//***************************************************************************************************************
-
-SensSpecCommand::~SensSpecCommand(){ /* do nothing */ }
-
//***************************************************************************************************************
int SensSpecCommand::execute(){
try{
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
setUpOutput();
outputNames.push_back(sensSpecFileName); outputTypes["sensspec"].push_back(sensSpecFileName);
if(format == "phylip") { processPhylip(); }
else if(format == "column") { processColumn(); }
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(sensSpecFileName); m->mothurOutEndLine();
+ m->mothurOutEndLine();
+
return 0;
}
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