X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=otuhierarchycommand.cpp;h=07e3c1d0146ef521563697fe07deb38d7837b67d;hp=091bf9bb0659dd0895bf47a414fa4ea86692f026;hb=499f4ac6e321f9f03d4c3aa25c3b6880892c8b83;hpb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 091bf9b..07e3c1d 100644
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -12,11 +12,11 @@
 //**********************************************************************************************************************
 vector<string> OtuHierarchyCommand::setParameters(){	
 	try {
-		CommandParameter poutput("output", "Multiple", "name-number", "name", "", "", "",false,false); parameters.push_back(poutput);
-		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-		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 poutput("output", "Multiple", "name-number", "name", "", "", "","",false,false); parameters.push_back(poutput);
+		CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","otuheirarchy",false,true,true); parameters.push_back(plist);
+		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);		}
@@ -47,24 +47,19 @@ string OtuHierarchyCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string OtuHierarchyCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string OtuHierarchyCommand::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 == "otuheirarchy") {  outputFileName =  "otu.hierarchy"; }
-            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, "OtuHierarchyCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "otuheirarchy") {  pattern = "[filename],[distance1],[tag],[distance2],otu.hierarchy"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "OtuHierarchyCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 OtuHierarchyCommand::OtuHierarchyCommand(){	
@@ -180,56 +175,48 @@ int OtuHierarchyCommand::execute(){
 		}
 		
 		//map sequences to bin number in the "little" otu
-		map<string, int> littleBins; 
+		map<string, int> littleBins;
+        vector<string> binLabels0 = lists[0].getLabels();
 		for (int i = 0; i < lists[0].getNumBins(); i++) {
 		
 			if (m->control_pressed) {  return 0; }
-			
-			string names = lists[0].get(i); 
-			
-			//parse bin
-			while (names.find_first_of(',') != -1) { 
-				string name = names.substr(0,names.find_first_of(','));
-				names = names.substr(names.find_first_of(',')+1, names.length());
-				littleBins[name] = i;  
-			}
-			
-			//get last name
-			littleBins[names] = i;
-		}
+			string bin = lists[0].get(i);
+            vector<string> names; m->splitAtComma(bin, names);
+			for (int j = 0; j < names.size(); j++) { littleBins[names[j]] = i; }
+        }
 		
 		ofstream out;
-		string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + "." + getOutputFileNameTag("otuheirarchy");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listFile));
+        variables["[distance1]"] = lists[0].getLabel();
+        variables["[tag]"] = "-"; 
+        variables["[distance2]"] = lists[1].getLabel();
+		string outputFileName = getOutputFileName("otuheirarchy",variables);
 		m->openOutputFile(outputFileName, out);
 		
 		//go through each bin in "big" otu and output the bins in "little" otu which created it
+        vector<string> binLabels1 = lists[1].getLabels();
 		for (int i = 0; i < lists[1].getNumBins(); i++) {
 		
 			if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
 			
-			string names = lists[1].get(i);
+			string binnames = lists[1].get(i);
+            vector<string> names; m->splitAtComma(binnames, names);
 			
 			//output column 1
-			if (output == "name")	{   out << names << '\t';	}
-			else					{	out << i << '\t';		}
+			if (output == "name")	{   out << binnames << '\t';	}
+			else					{	out << binLabels1[i] << '\t';		}
 			
 			map<int, int> bins; //bin numbers in little that are in this bin in big
 			map<int, int>::iterator it;
 			
 			//parse bin
-			while (names.find_first_of(',') != -1) { 
-				string name = names.substr(0,names.find_first_of(','));
-				names = names.substr(names.find_first_of(',')+1, names.length());
-				bins[littleBins[name]] = littleBins[name];  
-			}
-			
-			//get last name
-			bins[littleBins[names]] = littleBins[names]; 
+			for (int j = 0; j < names.size(); j++) { bins[littleBins[names[j]]] = littleBins[names[j]];   }
 			
 			string col2 = "";
 			for (it = bins.begin(); it != bins.end(); it++) {
 				if (output == "name")	{   col2 += lists[0].get(it->first) + "\t";	}
-				else					{	col2 += toString(it->first) + "\t";		}
+				else					{	col2 += binLabels0[it->first] + "\t";		}
 			}
 			
 			//output column 2