added sequence name to error string in fastq.info. Changed np_shannon to npshannon.

[mothur.git] / otuhierarchycommand.cpp

diff --git a/otuhierarchycommand.cpp b/otuhierarchycommand.cpp
index 17e29d9528c1122f73a2f81a32c1998dded037cf..2f99aa6091452933f6796f21aa043449bfce1dd4 100644 (file)
--- a/otuhierarchycommand.cpp
+++ b/otuhierarchycommand.cpp
@@ -38,7 +38,7 @@ string OtuHierarchyCommand::getHelpString(){
                helpString += "otu.hierarchy(list=yourListFile, label=yourLabels).\n";
                helpString += "Example otu.hierarchy(list=amazon.fn.list, label=0.01-0.03).\n";
                helpString += "The otu.hierarchy command outputs a .otu.hierarchy file which is described on the wiki.\n";
-               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -67,6 +67,7 @@ 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 +110,7 @@ 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"){  
@@ -184,7 +186,7 @@ int OtuHierarchyCommand::execute(){
                //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);
                        
@@ -217,7 +219,7 @@ 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();