X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=sensspeccommand.cpp;h=dfb89b927c2de8dd34dcda801fae80d93281cc63;hb=4542a79d20176ff0ee830b0f9d4f4c92637439d9;hp=82922ededbff38fd76909d1694742c6adac7666b;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/sensspeccommand.cpp b/sensspeccommand.cpp
index 82922ed..dfb89b9 100644
--- a/sensspeccommand.cpp
+++ b/sensspeccommand.cpp
@@ -12,16 +12,15 @@
 //**********************************************************************************************************************
 vector<string> SensSpecCommand::setParameters(){	
 	try {
-		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);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","sensspec",false,true,true); parameters.push_back(plist);
+		CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false); parameters.push_back(pphylip);
+		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", "", "T", "", "", "","",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);		}
@@ -45,6 +44,21 @@ string SensSpecCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string SensSpecCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "sensspec") {  pattern = "[filename],sensspec"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SensSpecCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 SensSpecCommand::SensSpecCommand(){	
 	try {
 		abort = true; calledHelp = true; 
@@ -116,16 +130,7 @@ SensSpecCommand::SensSpecCommand(string option)  {
 					path = m->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 = 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;		}
-				//}
-				
+				}				
 			}
 			//check for required parameters
 			listFile = validParameter.validFile(parameters, "list", true);
@@ -176,12 +181,6 @@ SensSpecCommand::SensSpecCommand(string option)  {
 			else if(!m->isTrue(temp))	{	hard = 0;	}
 			else if(m->isTrue(temp))	{	hard = 1;	}
 			
-//			temp = validParameter.validFile(parameters, "name", true);
-//			if (temp == "not found")	{	nameFile = "";		}
-//			else if(temp == "not open")	{	abort = true;		}
-//			else						{	nameFile = temp;	}
-//			cout << "name:\t" << nameFile << endl;
-
 			temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found") { temp = "-1.00"; }
 			m->mothurConvert(temp, cutoff);  
 //			cout << cutoff << endl;
@@ -197,7 +196,9 @@ SensSpecCommand::SensSpecCommand(string option)  {
 				else { allLines = 1;  }
 			}
 			
-			sensSpecFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + "sensspec";
+            map<string, string> variables; 
+            variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+			sensSpecFileName = getOutputFileName("sensspec",variables);
 		}
 	}
 	catch(exception& e) {
@@ -219,7 +220,7 @@ int SensSpecCommand::execute(){
 		if (m->control_pressed) { m->mothurRemove(sensSpecFileName); return 0; }
 		
 		m->mothurOutEndLine();
-		m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 		m->mothurOut(sensSpecFileName); m->mothurOutEndLine();	
 		m->mothurOutEndLine();
 		
@@ -256,7 +257,9 @@ int SensSpecCommand::processPhylip(){
 		
 		while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 			
-			if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {	m->mothurRemove(outputNames[i]);  }  delete list;  return 0;  }
+			if(m->control_pressed){
+                for (int i = 0; i < outputNames.size(); i++){	m->mothurRemove(outputNames[i]);  }  delete list;  return 0;
+            }
 			
 			if(allLines == 1 || labels.count(list->getLabel()) == 1){			
 				
@@ -324,7 +327,9 @@ int SensSpecCommand::processPhylip(){
 		exit(1);
 	}
 }
+
 //***************************************************************************************************************
+
 int SensSpecCommand::fillSeqMap(map<string, int>& seqMap, ListVector*& list){
 	try {
 		//for each otu
@@ -387,7 +392,7 @@ int SensSpecCommand::fillSeqPairSet(set<string>& seqPairSet, ListVector*& list){
 		return numSeqs;
 	}
 	catch(exception& e) {
-		m->errorOut(e, "SensSpecCommand", "fillSeqMap");
+		m->errorOut(e, "SensSpecCommand", "fillSeqPairSet");
 		exit(1);
 	}
 }
@@ -401,7 +406,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
 		ifstream phylipFile;
 		m->openInputFile(distFile, phylipFile);
 		phylipFile >> pNumSeqs;
-		if(pNumSeqs != lNumSeqs){	m->mothurOut("numSeq mismatch!\n"); m->control_pressed = true; }
+		if(pNumSeqs != lNumSeqs){	m->mothurOut("numSeq mismatch!\n"); /*m->control_pressed = true;*/ }
 		
 		string seqName;
 		double distance;
@@ -426,7 +431,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, string label, bool& getCu
 		
 		m->mothurOut(label); m->mothurOutEndLine();
 		
-		for(int i=0;i<lNumSeqs;i++){
+		for(int i=0;i<pNumSeqs;i++){
 			
 			if (m->control_pressed) { return 0; }