changed name of distance command to dist.seqs

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index eaf49dfe6937c4201330981cacf8cb5bfbf198cc..c866ca0060960ab20f50f53ffbd774c066ffc628 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -116,6 +116,8 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "soft" )                       { soft = value; }
                                if (parameter == "filter" )         { filter = value; }
                                if (parameter == "scale" )                      { scale = value;        }
+                               if (parameter == "ends" )                       { ends = value; }
+                               if (parameter == "processors" )         { processors = value;   }
 
                        }
                        
@@ -156,6 +158,8 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "soft" )                       { soft = value; }
                                if (parameter == "filter" )         { filter = value; }
                                if (parameter == "scale" )                      { scale = value;        }
+                               if (parameter == "ends" )                       { ends = value; }
+                               if (parameter == "processors" )         { processors = value;   }
 
                        }
                }
@@ -184,8 +188,6 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }else if (commandName == "read.tree") { 
                        validateTreeFiles(); //checks the treefile and groupfile parameters
-               }else if (commandName == "read.seqs") {
-                       if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) { cout << "You must enter a fastafile, nexusfile, or clustalfile with the read.seqs() command." << endl; return false; }
                }else if (commandName == "deconvolute") {
                        if (fastafile == "") { cout << "You must enter a fastafile with the deconvolute() command." << endl; return false; }
                        validateReadFiles();
@@ -244,10 +246,11 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
-               if (commandName == "filter.seqs"){ 
-                       if ((globaldata->getFastaFile() == "") && (globaldata->getNexusFile() == "") && (globaldata->getClustalFile() == "") && (globaldata->getPhylipFile() == "")) {
+               if ((commandName == "filter.seqs") || (commandName == "dist.seq")) { 
+                       if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
                                 cout << "You must read either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs command." << endl; return false; 
                        }
+                       validateSeqsFiles();
                }
                
                if ((commandName == "bin.seqs")) { 
@@ -506,6 +509,71 @@ 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;
+                               }
+                       }
+
+               }
+               
+       }
+       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