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

[mothur.git] / readdistcommand.cpp

diff --git a/readdistcommand.cpp b/readdistcommand.cpp
index 0445eec63328e2cf7a646f1cc662bb36fdd3bb98..8bf6996333b246814a28009d309ab8f3b6bf8718 100644 (file)
--- a/readdistcommand.cpp
+++ b/readdistcommand.cpp
@@ -12,16 +12,17 @@
 #include "readcolumn.h"
 #include "readmatrix.hpp"
 
+//**********************************************************************************************************************
 ReadDistCommand::ReadDistCommand(string option) {
        try {
-               globaldata = GlobalData::getInstance();
-               abort = false;
+               abort = false; calledHelp = false;   
                
                //allow user to run help
-               if(option == "help") { help(); abort = true; }
+               if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
-                       //valid paramters for this command
+                       /*//valid paramters for this command
                        string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
@@ -120,7 +121,7 @@ ReadDistCommand::ReadDistCommand(string option) {
                        //get user cutoff and precision or use defaults
                        string temp;
                        temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
-                       convert(temp, precision); 
+                       m->mothurConvert(temp, precision); 
                        
                        temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
                        sim = m->isTrue(temp); 
@@ -157,7 +158,7 @@ ReadDistCommand::ReadDistCommand(string option) {
                                        }
                                }
                        }
-
+*/
                }
 
        }
@@ -166,50 +167,16 @@ ReadDistCommand::ReadDistCommand(string option) {
                exit(1);
        }
 }
-//**********************************************************************************************************************
-
-void ReadDistCommand::help(){
-       try {
-               m->mothurOut("The read.dist command parameter options are phylip or column, group, name, sim, cutoff and precision\n");
-               m->mothurOut("The read.dist command can be used in two ways.  The first is to read a phylip or column and run the cluster command\n");
-               m->mothurOut("For this use the read.dist command should be in the following format: \n");
-               m->mothurOut("read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) \n");
-               m->mothurOut("The phylip or column parameter is required, but only one may be used.  If you use a column file the name filename is required. \n");
-               m->mothurOut("The sim parameter is used to indicate that your distance file contains similarity values instead of distance values. The default is false, if sim=true then mothur will convert the similarity values to distances. \n");
-               m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n");
-               m->mothurOut("The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command.\n");
-               m->mothurOut("For this use the read.dist command should be in the following format: \n");
-               m->mothurOut("read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use.  \n");
-               m->mothurOut("Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile).\n\n");
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadDistCommand", "help");
-               exit(1);
-       }
-}
-
-//**********************************************************************************************************************
-
-ReadDistCommand::~ReadDistCommand(){
-       if (abort == false) {
-               if (format != "matrix") { 
-                       delete read; 
-                       delete nameMap; 
-               }
-       }
-}
-
 //**********************************************************************************************************************
 int ReadDistCommand::execute(){
        try {
                
-               if (abort == true) {    return 0;       }
-
+               if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
+               m->mothurOut(getHelpString()); m->mothurOutEndLine();
+/*
                time_t start = time(NULL);
                size_t numDists = 0;
                
-               vector<string> outputNames;
-               
                if (format == "matrix") {
                        ifstream in;
                        m->openInputFile(distFileName, in);
@@ -230,7 +197,7 @@ int ReadDistCommand::execute(){
                                m->openOutputFile(newGroupFile, outGroups);
                                
                                for (int i = 0; i < matrix->getNumSeqs(); i++) {
-                                       if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); remove(newGroupFile.c_str()); return 0; }
+                                       if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
                                        
                                        Names temp = matrix->getRowInfo(i);
                                        outGroups << temp.seqName << '\t' << temp.groupName << endl;
@@ -247,7 +214,7 @@ int ReadDistCommand::execute(){
                                groupMap = new GroupMap(groupfile);
                                groupMap->readMap();
                                
-                               if (m->control_pressed) { delete groupMap; delete matrix; remove(newGroupFile.c_str()); return 0; }
+                               if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
        
                                globaldata->gGroupmap = groupMap;
                        }
@@ -280,6 +247,7 @@ int ReadDistCommand::execute(){
                }
                
                m->mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); m->mothurOutEndLine();
+ */
                return 0;
                
        }