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

[mothur.git] / phylodiversitycommand.cpp

diff --git a/phylodiversitycommand.cpp b/phylodiversitycommand.cpp
index ca0d02aca04b0a737d45c29b44cb02c2925ff257..2b15d11d29580d1455ffea983788ab0715fe194b 100644 (file)
--- a/phylodiversitycommand.cpp
+++ b/phylodiversitycommand.cpp
@@ -144,7 +144,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        //check for required parameters
                        treefile = validParameter.validFile(parameters, "tree", true);
-                       if (treefile == "not open") { abort = true; }
+                       if (treefile == "not open") { treefile = ""; abort = true; }
                        else if (treefile == "not found") {                             
                                //if there is a current design file, use it
                                treefile = m->getTreeFile(); 
@@ -159,7 +159,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        else { m->setGroupFile(groupfile); }
                        
                        namefile = validParameter.validFile(parameters, "name", true);
-                       if (namefile == "not open") { abort = true; }
+                       if (namefile == "not open") { namefile = ""; abort = true; }
                        else if (namefile == "not found") { namefile = ""; }
                        else { m->setNameFile(namefile); }
                        
@@ -167,10 +167,10 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        string temp;
                        temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
-                       convert(temp, freq); 
+                       m->mothurConvert(temp, freq); 
                        
                        temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
-                       convert(temp, iters); 
+                       m->mothurConvert(temp, iters); 
                        
                        temp = validParameter.validFile(parameters, "rarefy", false);                   if (temp == "not found") { temp = "F"; }
                        rarefy = m->isTrue(temp);
@@ -187,7 +187,7 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
                        m->setProcessors(temp);
-                       convert(temp, processors); 
+                       m->mothurConvert(temp, processors); 
                        
                        groups = validParameter.validFile(parameters, "groups", false);                 
                        if (groups == "not found") { groups = "";  }
@@ -197,6 +197,11 @@ PhyloDiversityCommand::PhyloDiversityCommand(string option)  {
                        }
                        
                        if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+                       
+                       if (namefile == "") {
+                               vector<string> files; files.push_back(treefile);
+                               parser.getNameFile(files);
+                       }
                }
                
        }