else {
//valid paramters for this command
- string AlignArray[] = {"groups","label", "calc","phylip","column","name"};
+ string AlignArray[] = {"groups","label", "calc","phylip","column","name","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
+ map<string,string>::iterator it;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
format = "";
+ //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 = ""; }
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("phylip");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+
+ it = parameters.find("column");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["column"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("name");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = 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; }
+ }
+ }
+
//required parameters
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { format = "phylip"; }
+ else { format = "phylip"; if (outputDir == "") { outputDir += hasPath(phylipfile); } }
columnfile = validParameter.validFile(parameters, "column", true);
if (columnfile == "not open") { abort = true; }
else if (columnfile == "not found") { columnfile = ""; }
- else { format = "column"; }
+ else { format = "column"; if (outputDir == "") { outputDir += hasPath(columnfile); } }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
if (format == "shared") {
+ if (outputDir == "") { outputDir += hasPath(globaldata->getSharedFile()); }
+
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if (abort == true) { return 0; }
- heatmap = new HeatMapSim();
+ heatmap = new HeatMapSim(outputDir);
if (format == "shared") {
runCommandShared();