added cluster.fragments command as well as the nseqs parameter to the venn command

[mothur.git] / venncommand.cpp

diff --git a/venncommand.cpp b/venncommand.cpp
index 8b617d8881000bd7e837e901fc1765b18592d6b4..5fa06aa98d0eeed0783c9d53eb5f3663e0405c14 100644 (file)
--- a/venncommand.cpp
+++ b/venncommand.cpp
@@ -32,7 +32,7 @@ VennCommand::VennCommand(string option)  {
                
                else {
                        //valid paramters for this command
-                       string AlignArray[] =  {"groups","label","calc", "abund","outputdir","inputdir"};
+                       string AlignArray[] =  {"groups","label","calc", "abund","nseqs","outputdir","inputdir"};
                        vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -95,6 +95,10 @@ VennCommand::VennCommand(string option)  {
                        string temp;
                        temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
                        convert(temp, abund); 
+                       
+                       temp = validParameter.validFile(parameters, "nseqs", false);                    if (temp == "not found"){       temp = "f";                             }
+                       nseqs = m->isTrue(temp); 
+
 
                        if (abort == false) {
                                validCalculator = new ValidCalculators();
@@ -112,8 +116,6 @@ VennCommand::VennCommand(string option)  {
                                                                if(abund < 5)
                                                                        abund = 10;
                                                                vennCalculators.push_back(new Ace(abund));
-                                                       }else if (Estimators[i] == "nseqs") { 
-                                                               vennCalculators.push_back(new NSeqs());
                                                        }
                                                }
                                        }
@@ -126,8 +128,6 @@ VennCommand::VennCommand(string option)  {
                                                                vennCalculators.push_back(new SharedChao1());
                                                        }else if (Estimators[i] == "sharedace") { 
                                                                vennCalculators.push_back(new SharedAce());
-                                                       }else if (Estimators[i] == "nseqs") { 
-                                                               vennCalculators.push_back(new NSeqs());
                                                        }
                                                }
                                        }
@@ -135,7 +135,7 @@ VennCommand::VennCommand(string option)  {
                                
                                //if the users entered no valid calculators don't execute command
                                if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true;  }
-                               else {  venn = new Venn(outputDir);  }
+                               else {  venn = new Venn(outputDir, nseqs);  }
                        }
                        
                }
@@ -154,7 +154,7 @@ VennCommand::VennCommand(string option)  {
 void VennCommand::help(){
        try {
                m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
-               m->mothurOut("The venn command parameters are groups, calc, abund and label.  No parameters are required.\n");
+               m->mothurOut("The venn command parameters are groups, calc, abund, nseqs and label.  No parameters are required.\n");
                m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
                m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
                m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
@@ -162,7 +162,8 @@ void VennCommand::help(){
                m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
                m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
                m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
-               m->mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
+               m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n");
+               m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n");
                m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
        }