added countgaps parameter to chop.seqs command

[mothur.git] / readotucommand.cpp

diff --git a/readotucommand.cpp b/readotucommand.cpp
index 4ad63da5655b4bb6118d09b339f3be0f3651dd04..c4bf523fb30be6f1bd84dc81eac85e3e92c9e6f8 100644 (file)
--- a/readotucommand.cpp
+++ b/readotucommand.cpp
@@ -21,7 +21,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"list","order","shared", "label","group","sabund", "rabund","groups","outputdir","inputdir"};
+                       string Array[] =  {"list","order","shared", "label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -34,7 +34,7 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        for (it = parameters.begin(); it != parameters.end(); it++) { 
                                if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
                        }
-                       
+       
                        globaldata->newRead();
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
@@ -89,6 +89,14 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["rabund"] = inputDir + it->second;           }
                                }
+                               
+                               it = parameters.find("ordergroup");
+                               //user has given a template file
+                               if(it != parameters.end()){ 
+                                       path = hasPath(it->second);
+                                       //if the user has not given a path then, add inputdir. else leave path alone.
+                                       if (path == "") {       parameters["ordergroup"] = inputDir + it->second;               }
+                               }
 
                        }
 
@@ -112,6 +120,11 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        else if (rabundfile == "not found") { rabundfile = ""; }
                        else {  globaldata->setRabundFile(rabundfile);  globaldata->setFormat("rabund");}
                        
+                       ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+                       if (ordergroupfile == "not open") { abort = true; }     
+                       else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+                       else {  globaldata->setOrderGroupFile(ordergroupfile);  }
+                       
                        sharedfile = validParameter.validFile(parameters, "shared", true);
                        if (sharedfile == "not open") { abort = true; } 
                        else if (sharedfile == "not found") { sharedfile = ""; }
@@ -156,18 +169,17 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
                        }
                        
                        globaldata->allLines = allLines;
-                       
+               
                        orderfile = validParameter.validFile(parameters, "order", true);
                        if (orderfile == "not open") { abort = true; }  
                        else if (orderfile == "not found") { orderfile = ""; }
                        else {  globaldata->setOrderFile(orderfile);    }
                        
-                       
+                               
                        if (abort == false) {
                                //gets whichever one of the above is set
                                filename = globaldata->inputFileName;
                        }
-
                }
 
        }
@@ -181,8 +193,8 @@ ReadOtuCommand::ReadOtuCommand(string option)  {
 void ReadOtuCommand::help(){
        try {
                m->mothurOut("The read.otu command must be run before you execute a collect.single, rarefaction.single, summary.single, \n");
-               m->mothurOut("collect.shared, rarefaction.shared or summary.shared command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
-               m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, label and groups.\n");
+               m->mothurOut("collect.shared, rarefaction.shared, summary.shared heatmap.bin, heatmap.sim or venn command.   Mothur will generate a .list, .rabund and .sabund upon completion of the cluster command \n");
+               m->mothurOut("or you may use your own. The read.otu command parameter options are list, rabund, sabund, shared, group, order, ordergroup, label and groups.\n");
                m->mothurOut("The read.otu command can be used in two ways.  The first is to read a list, rabund or sabund and run the collect.single, rarefaction.single or summary.single.\n");
                m->mothurOut("For this use the read.otu command should be in the following format: read.otu(list=yourListFile, order=yourOrderFile, label=yourLabels).\n");
                m->mothurOut("The list, rabund or sabund parameter is required, but you may only use one of them.\n");
@@ -192,6 +204,7 @@ void ReadOtuCommand::help(){
                m->mothurOut("The list parameter and group paramaters or the shared paremeter is required. When using the command the second way with a list and group file read.otu command parses the .list file\n");
                m->mothurOut("and separates it into groups.  It outputs a .shared file containing the OTU information for each group. The read.otu command also outputs a .rabund file for each group. \n");
                m->mothurOut("You can use the groups parameter to choose only specific groups to be used in the .shared and .rabund files. \n");
+               m->mothurOut("You can use the ordergroup parameter to provide a file containing a list of group names in the order you would like them to appear in your shared file. \n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 
        }
@@ -204,17 +217,14 @@ void ReadOtuCommand::help(){
 
 
 //**********************************************************************************************************************
-
-ReadOtuCommand::~ReadOtuCommand(){
-       }
-
+ReadOtuCommand::~ReadOtuCommand(){}
 //**********************************************************************************************************************
 
 int ReadOtuCommand::execute(){
        try {
        
                if (abort == true) {    return 0;       }
-               
+       
                if (globaldata->getFormat() == "shared") {
                        
                        shared = new SharedCommand(outputDir);
@@ -225,11 +235,11 @@ int ReadOtuCommand::execute(){
                                globaldata->setListFile("");
                                globaldata->setGroupFile("");
                                globaldata->setSharedFile("");
-                       }else {
-                               m->mothurOutEndLine();
-                               m->mothurOut("Output File Name: "); m->mothurOutEndLine();
-                               m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();       
-                               m->mothurOutEndLine();
+                       }else { //shared command outputs the filenames
+                               //m->mothurOutEndLine();
+                               //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+                               //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();     
+                               //m->mothurOutEndLine();
                        }
                        
                        delete shared;