X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=normalizesharedcommand.cpp;h=acd8208ea7ebb20a3d3810d254d0b24f5386d4d3;hp=43c8e2260c4e678bbd2e7718a6313b15d97eed8b;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=65e21482d022d12f7a78a8d436fb51f322603e41

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index 43c8e22..acd8208 100644
--- a/normalizesharedcommand.cpp
+++ b/normalizesharedcommand.cpp
@@ -12,15 +12,15 @@
 //**********************************************************************************************************************
 vector<string> NormalizeSharedCommand::setParameters(){	
 	try {
-		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);	
-		CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prelabund);
-		CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-		CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "",false,false); parameters.push_back(pmethod);
-		CommandParameter pnorm("norm", "Number", "", "0", "", "", "",false,false); parameters.push_back(pnorm);
-		CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pmakerelabund);
-		CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(pshared);	
+		CommandParameter prelabund("relabund", "InputTypes", "", "", "LRSS", "LRSS", "none","shared",false,false,true); parameters.push_back(prelabund);
+		CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+		CommandParameter pmethod("method", "Multiple", "totalgroup-zscore", "totalgroup", "", "", "","",false,false,true); parameters.push_back(pmethod);
+		CommandParameter pnorm("norm", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pnorm);
+		CommandParameter pmakerelabund("makerelabund", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pmakerelabund);
+		CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+		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);		}
@@ -53,8 +53,21 @@ string NormalizeSharedCommand::getHelpString(){
 		exit(1);
 	}
 }
-
-
+//**********************************************************************************************************************
+string NormalizeSharedCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "shared") {  pattern = "[filename],[distance],norm.shared"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "NormalizeSharedCommand", "getOutputPattern");
+        exit(1);
+    }
+}
 //**********************************************************************************************************************
 NormalizeSharedCommand::NormalizeSharedCommand(){	
 	try {
@@ -176,7 +189,7 @@ NormalizeSharedCommand::NormalizeSharedCommand(string option) {
 			if (temp == "not found") {  
 				norm = 0;  //once you have read, set norm to smallest group number
 			}else { 
-				convert(temp, norm);
+				m->mothurConvert(temp, norm);
 				if (norm < 0) { m->mothurOut("norm must be positive."); m->mothurOutEndLine(); abort=true; }
 			}
 			
@@ -449,7 +462,11 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
 		
 		if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+        variables["[distance]"] = thisLookUp[0]->getLabel();
+		string outputFileName = getOutputFileName("shared",variables);
+        
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);
@@ -540,7 +557,10 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
 		//save mothurOut's binLabels to restore for next label
 		vector<string> saveBinLabels = m->currentBinLabels;
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + ".norm.shared";
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputfile));
+        variables["[distance]"] = thisLookUp[0]->getLabel();
+		string outputFileName = getOutputFileName("shared",variables);
 		ofstream out;
 		m->openOutputFile(outputFileName, out);
 		outputNames.push_back(outputFileName); outputTypes["shared"].push_back(outputFileName);