removed readseqs, readfasta, readnexus, readclustal, readseqsphylip and updated seque...

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index caf7f73dc31cf02bd48ac7352f339e41b4f6cb96..5f5cd1fbc90f864f540671fc876eda1f642a9666 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -95,8 +95,6 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "name" )               { namefile = value; }
                                if (parameter == "order" )              { orderfile = value; }
                                if (parameter == "fasta" )              { fastafile = value; }
-                               if (parameter == "nexus" )              { nexusfile = value; }
-                               if (parameter == "clustal" )    { clustalfile = value; }
                                if (parameter == "tree" )               { treefile = value; }
                                if (parameter == "group" )                      { groupfile = value; }
                                if (parameter == "shared" )                     { sharedfile = value; }
@@ -147,8 +145,6 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "group" )              { groupfile = value; }
                                if (parameter == "shared" )             { sharedfile = value; }
                                if (parameter == "fasta" )              { fastafile = value; }
-                               if (parameter == "nexus" )              { nexusfile = value; }
-                               if (parameter == "clustal" )    { clustalfile = value; }
                                if (parameter == "tree" )               { treefile = value; }
                                if (parameter == "cutoff" )                     { cutoff = value; }
                                if (parameter == "precision" )          { precision = value; }
@@ -284,14 +280,20 @@ bool ErrorCheck::checkInput(string input) {
                        if (fastafile == "") {
                                 cout << "You must enter either a fasta file before you can use the filter.seqs or dist.seqs command." << endl; return false; 
                        }
-                       validateSeqsFiles();
+                       validateReadFiles();
                }
                
                if (commandName == "align.seqs") {
                        if ((fastafile == "") || (candidatefile == "")) {
                                cout << "You must enter fasta and a candidate file to use the align.seqs command." << endl; return false; 
                        }
-                       validateSeqsFiles();
+                       validateReadFiles();
+                       
+                       ifstream filehandle;
+                       int ableToOpen = openInputFile(candidatefile, filehandle);
+                       filehandle.close();
+                       //unable to open
+                       if (ableToOpen == 1) {  return false; }
                }
                
                if ((commandName == "bin.seqs")) { 
@@ -558,77 +560,6 @@ void ErrorCheck::validateReadPhil() {
 }
 /*******************************************************/
 
-/******************************************************/
-//This function checks to make sure the user entered appropriate
-// format parameters on a distfile read
-void ErrorCheck::validateSeqsFiles() {
-       try {
-               ifstream filehandle;
-               int ableToOpen;
-               
-               //checks to make sure only one file type is given
-               if (phylipfile != "") { 
-                       if ((nexusfile != "") || (fastafile != "") || (clustalfile != "")) { 
-                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
-                       else {
-                               ableToOpen = openInputFile(phylipfile, filehandle);
-                               filehandle.close();
-                               if (ableToOpen == 1) { //unable to open
-                                       errorFree = false;
-                               }
-                       }
-               }else if (nexusfile != "") { 
-                       if ((phylipfile != "") || (fastafile != "") || (clustalfile != "")) { 
-                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
-                       else {
-                               ableToOpen = openInputFile(nexusfile, filehandle);
-                               filehandle.close();
-                               if (ableToOpen == 1) { //unable to open
-                                       errorFree = false;
-                               }
-                       }
-               }else if (fastafile != "") { 
-                       if ((phylipfile != "") || (nexusfile != "") || (clustalfile != "")) { 
-                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
-                       else {
-                               ableToOpen = openInputFile(fastafile, filehandle);
-                               filehandle.close();
-                               if (ableToOpen == 1) { //unable to open
-                                       errorFree = false;
-                               }
-                       }
-               }else if (clustalfile != "") { 
-                       if ((phylipfile != "") || (nexusfile != "") || (fastafile != "")) { 
-                               cout << "You may enter ONLY ONE of the following: phylip, fasta, nexus or clustal." << endl; errorFree = false; }
-                       else {
-                               ableToOpen = openInputFile(clustalfile, filehandle);
-                               filehandle.close();
-                               if (ableToOpen == 1) { //unable to open
-                                       errorFree = false;
-                               }
-                       }
-               }else if (candidatefile != "") {
-                       ableToOpen = openInputFile(candidatefile, 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 validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-       catch(...) {
-               cout << "An unknown error has occurred in the ErrorCheck class function validateSeqsFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
-               exit(1);
-       }
-}
-
-/*******************************************************/
-
 /******************************************************/
 //This function checks to make sure the user entered appropriate
 // format parameters on a bin.seq command
@@ -673,9 +604,6 @@ void ErrorCheck::validateBinFiles() {
                        //unable to open
                        if (ableToOpen == 1) {  errorFree = false; }
                }
-
-
-
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the ErrorCheck class Function validateBinFiles. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -703,8 +631,6 @@ void ErrorCheck::clear() {
        orderfile               =       "";
        sharedfile              =       "";
        fastafile       =   "";
-       nexusfile       =   "";
-       clustalfile     =   "";
        candidatefile   =       "";
        line                    =       "";
        label                   =       "";