added count file to get.oturep, pre.cluster, screen.seqs, tree.shared. made remove...

[mothur.git] / countseqscommand.cpp

diff --git a/countseqscommand.cpp b/countseqscommand.cpp
index 7b9aebfbd63d496600a518bca7404f7a4cf4ada0..fa6fd4f09a2c0c1703a4f12b65943d6df1ac06a2 100644 (file)
--- a/countseqscommand.cpp
+++ b/countseqscommand.cpp
@@ -10,6 +10,7 @@
 #include "countseqscommand.h"
 #include "groupmap.h"
 #include "sharedutilities.h"
+#include "counttable.h"
 
 //**********************************************************************************************************************
 vector<string> CountSeqsCommand::setParameters(){      
@@ -34,7 +35,7 @@ vector<string> CountSeqsCommand::setParameters(){
 string CountSeqsCommand::getHelpString(){      
        try {
                string helpString = "";
-               helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count.table file.  You may also provide a group file to get the counts broken down by group.\n";
+               helpString += "The count.seqs aka. make.table command reads a name file and outputs a .count_table file.  You may also provide a group file to get the counts broken down by group.\n";
                helpString += "The groups parameter allows you to indicate which groups you want to include in the counts, by default all groups in your groupfile are used.\n";
         helpString += "The large parameter indicates the name and group files are too large to fit in RAM.\n";
                helpString += "When you use the groups parameter and a sequence does not represent any sequences from the groups you specify it is not included in the .count.summary file.\n";
@@ -58,7 +59,7 @@ string CountSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
         it = outputTypes.find(type);
         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
         else {
-            if (type == "counttable") {  outputFileName =  "count.table"; }
+            if (type == "counttable") {  outputFileName =  "count_table"; }
             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
         }
         return outputFileName;
@@ -175,7 +176,7 @@ int CountSeqsCommand::execute(){
         int total = 0;
         if (!large) { total = processSmall(outputFileName); }
         else { total = processLarge(outputFileName);  }
-                               
+        
                if (m->control_pressed) { m->mothurRemove(outputFileName); return 0; }
                
         //set rabund file as new current rabundfile