fixed summary.shared bug and set jumble default to 1.

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 41c1db9e678c5890472d9259017a16f6d6b84dc3..121a0120a17fb1410901a219a95d0361911d7187 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -27,6 +27,7 @@ ErrorCheck::ErrorCheck() {
        groupfile = globaldata->getGroupFile();
        orderfile = globaldata->getOrderFile();
        fastafile = globaldata->getFastaFile();
+       treefile = globaldata->getTreeFile();
        cutoff = globaldata->getCutOff();
        format = globaldata->getFormat();
        method = globaldata->getMethod();
@@ -79,6 +80,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "namefile" )           { namefile = value; }
                                if (parameter == "orderfile" )          { orderfile = value; }
                                if (parameter == "fastafile" )          { fastafile = value; }
+                               if (parameter == "treefile" )           { treefile = value; }
                                if (parameter == "groupfile" )          { groupfile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
@@ -148,6 +150,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "orderfile" )          { orderfile = value; }
                                if (parameter == "groupfile" )          { groupfile = value; }
                                if (parameter == "fastafile" )          { fastafile = value; }
+                               if (parameter == "treefile" )           { treefile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
                                if (parameter == "iters" )                      { iters = value; }
@@ -217,6 +220,8 @@ bool ErrorCheck::checkInput(string input) {
                                validateReadFiles();
                                validateReadPhil();
                        }
+               }else if (commandName == "read.tree") { 
+                       validateTreeFiles(); //checks the treefile and groupfile parameters
                }else if (commandName == "deconvolute") {
                        validateReadFiles();
                }
@@ -387,6 +392,46 @@ void ErrorCheck::validateParseFiles() {
                exit(1);
        }
 }
+/*******************************************************/
+
+/******************************************************/
+//This function checks to make sure the user entered appropriate
+// format parameters on a parselistcommand
+void ErrorCheck::validateTreeFiles() {
+       try {
+               ifstream filehandle;
+               int ableToOpen;
+               
+               //checks for valid files
+       
+               if (treefile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
+               else if (groupfile == "") { cout << "When executing a read.tree you must enter a treefile and a groupfile." << endl; errorFree = false; }
+       
+               //checks parameters on the read command
+               if (treefile != "") {
+                       ableToOpen = openInputFile(treefile, filehandle);
+                       filehandle.close();
+                       if (ableToOpen == 1) { //unable to open
+                               errorFree = false;
+                       }
+                       if (groupfile != "") {
+                               ableToOpen = openInputFile(groupfile, filehandle);
+                               filehandle.close();
+                               if (ableToOpen == 1) { //unable to open
+                                       errorFree = false;;
+                               }
+                       }
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the ErrorCheck class function validateTreeFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+}
 
 /*******************************************************/