deconvolute command

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 903c58137c1de81036dd43adf6cc3619a861a3c6..8a56c15c9d977de80c230922405c97589251324a 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -26,6 +26,7 @@ ErrorCheck::ErrorCheck() {
        namefile = globaldata->getNameFile();
        groupfile = globaldata->getGroupFile();
        orderfile = globaldata->getOrderFile();
+       fastafile = globaldata->getFastaFile();
        cutoff = globaldata->getCutOff();
        format = globaldata->getFormat();
        method = globaldata->getMethod();
@@ -77,6 +78,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "sabundfile" )         { sabundfile = value; }
                                if (parameter == "namefile" )           { namefile = value; }
                                if (parameter == "orderfile" )          { orderfile = value; }
+                               if (parameter == "fastafile" )          { fastafile = value; }
                                if (parameter == "groupfile" )          { groupfile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
@@ -145,6 +147,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "namefile" )           { namefile = value; }
                                if (parameter == "orderfile" )          { orderfile = value; }
                                if (parameter == "groupfile" )          { groupfile = value; }
+                               if (parameter == "fastafile" )          { fastafile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
                                if (parameter == "iters" )                      { iters = value; }
@@ -211,6 +214,8 @@ bool ErrorCheck::checkInput(string input) {
                        validateReadPhil();     
                }else if (commandName == "read.list") { 
                        validateParseFiles(); //checks the listfile and groupfile parameters
+               }else if (commandName == "deconvolute") {
+                       validateReadFiles();
                }
                
                //are you trying to cluster before you have read something                      
@@ -285,6 +290,12 @@ void ErrorCheck::validateReadFiles() {
                        //unable to open
                        if (ableToOpen == 1) {  errorFree = false; }
                        else { globaldata->inputFileName = sabundfile; }
+               }else if (fastafile != "") {
+                       ableToOpen = openInputFile(fastafile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  errorFree = false; }
+                       else { globaldata->inputFileName = fastafile; }
                }else{ //no file given
                        errorFree = false;
                }