X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=normalizesharedcommand.cpp;h=1000e4243e0c6fbf15f5e384871131f74d2a4ea5;hb=250e3b11b1c9c1e1ad458ab6c7e71ac2e67e11d9;hp=e41cfd9355ce1e08157069e59880aa32066e1505;hpb=49d2b7459c5027557564b21e9487dadafbbbdc96;p=mothur.git

diff --git a/normalizesharedcommand.cpp b/normalizesharedcommand.cpp
index e41cfd9..1000e42 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);		}
@@ -53,26 +53,20 @@ string NormalizeSharedCommand::getHelpString(){
 		exit(1);
 	}
 }
-
 //**********************************************************************************************************************
-string NormalizeSharedCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string NormalizeSharedCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "shared") {  outputFileName =  "norm.shared"; }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "NormalizeSharedCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        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(){	
@@ -464,11 +458,15 @@ int NormalizeSharedCommand::execute(){
 int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
 	try {
 		//save mothurOut's binLabels to restore for next label
-		vector<string> saveBinLabels = m->currentBinLabels;
+		vector<string> saveBinLabels = m->currentSharedBinLabels;
 		
 		if (pickedGroups) { eliminateZeroOTUS(thisLookUp); }
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + "." + getOutputFileNameTag("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);
@@ -542,7 +540,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundVector*>& thisLookUp){
 		
 		out.close();
 		
-		m->currentBinLabels = saveBinLabels;
+		m->currentSharedBinLabels = saveBinLabels;
 		
 		return 0;
 	}
@@ -557,9 +555,12 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
 	try {
 		
 		//save mothurOut's binLabels to restore for next label
-		vector<string> saveBinLabels = m->currentBinLabels;
+		vector<string> saveBinLabels = m->currentSharedBinLabels;
 		
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputfile)) + thisLookUp[0]->getLabel() + "." + getOutputFileNameTag("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);
@@ -628,7 +629,7 @@ int NormalizeSharedCommand::normalize(vector<SharedRAbundFloatVector*>& thisLook
 		
 		out.close();
 		
-		m->currentBinLabels = saveBinLabels;
+		m->currentSharedBinLabels = saveBinLabels;
 		
 		return 0;
 	}
@@ -674,7 +675,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thisl
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber; 
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				newBinLabels.push_back(binLabel);
 			}
@@ -683,7 +684,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundVector*>& thisl
 		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 
 		thislookup = newLookup;
-		m->currentBinLabels = newBinLabels;
+		m->currentSharedBinLabels = newBinLabels;
 		
 		return 0;
  
@@ -730,7 +731,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 					for (int h = 0; h < diff; h++) { binLabel += "0"; }
 				}
 				binLabel += sbinNumber; 
-				if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+				if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
 				
 				newBinLabels.push_back(binLabel);
 			}
@@ -739,7 +740,7 @@ int NormalizeSharedCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>&
 		for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
 		
 		thislookup = newLookup;
-		m->currentBinLabels = newBinLabels;
+		m->currentSharedBinLabels = newBinLabels;
 		
 		return 0;