sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index edfdaea6a1a5c02b1a8b0c96b10768be4770b1a5..dc026decc9db9916513fcbd1d41fe23298173717 100644 (file)
--- 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);          }
@@ -46,7 +46,21 @@ string OtuHierarchyCommand::getHelpString(){
                exit(1);
        }
 }
-
+//**********************************************************************************************************************
+string OtuHierarchyCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        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(){    
        try {
@@ -67,6 +81,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                
                //allow user to run help
                if(option == "help") {  help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -109,6 +124,7 @@ OtuHierarchyCommand::OtuHierarchyCommand(string option) {
                                        abort = true;
                                }
                        }else if (listFile == "not open") { abort = true; }     
+                       else { m->setListFile(listFile); }
                        
                        //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"){  
@@ -178,13 +194,18 @@ int OtuHierarchyCommand::execute(){
                }
                
                ofstream out;
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listFile)) + lists[0].getLabel() + "-" + lists[1].getLabel() + ".otu.hierarchy";
+        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
                for (int i = 0; i < lists[1].getNumBins(); i++) {
                
-                       if (m->control_pressed) { outputTypes.clear(); out.close(); remove(outputFileName.c_str()); return 0; }
+                       if (m->control_pressed) { outputTypes.clear(); out.close(); m->mothurRemove(outputFileName); return 0; }
                        
                        string names = lists[1].get(i);
                        
@@ -217,10 +238,10 @@ int OtuHierarchyCommand::execute(){
                
                out.close();
                
-               if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0; }
+               if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0; }
                
                m->mothurOutEndLine();
-               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+               m->mothurOut("Output File Names: "); m->mothurOutEndLine();
                m->mothurOut(outputFileName); m->mothurOutEndLine();    outputNames.push_back(outputFileName); outputTypes["otuheirarchy"].push_back(outputFileName); 
                m->mothurOutEndLine();