changed defaults for filter.seqs()

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index f82e806e45d6b98be601720b3380ae21e142438a..c5396cfa37c314ca220d6b2cbf12692a477890eb 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -119,7 +119,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "ends" )                       { ends = value; }
                                if (parameter == "processors" )         { processors = value;   }
                                if (parameter == "size" )                       { size = value; }
-                               if (parameter == "template")            { templatefile = value; }
+                               if (parameter == "candidate")           { candidatefile = value;        }
                                if (parameter == "search")                      { search = value;               }
                                if (parameter == "ksize")                       { ksize = value;                }
                                if (parameter == "align")                   { align = value;            }
@@ -169,7 +169,7 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "ends" )                       { ends = value; }
                                if (parameter == "processors" )         { processors = value;   }
                                if (parameter == "size" )                       { size = value; }
-                               if (parameter == "template")            { templatefile = value; }
+                               if (parameter == "candidate")           { candidatefile = value;        }
                                if (parameter == "search")                      { search = value;               }
                                if (parameter == "ksize")                       { ksize = value;                }
                                if (parameter == "align")                   { align = value;            }
@@ -263,11 +263,16 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
-               if ((commandName == "filter.seqs") || (commandName == "dist.seqs") || (commandName == "align.seqs")) { 
+               if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) { 
                        if ((fastafile == "") && (nexusfile == "") && (clustalfile == "") && (phylipfile == "")) {
-                                cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs, dist.seqs or align.seqs command." << endl; return false; 
-                       }else if ((commandName == "align.seqs") && (templatefile == "")) {
-                               cout << "You must enter a template to use the align.seqs command." << endl; return false; 
+                                cout << "You must enter either a fasta, nexus, clustal, or phylip file before you can use the filter.seqs or dist.seqs command." << endl; return false; 
+                       }
+                       validateSeqsFiles();
+               }
+               
+               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();
                }
@@ -277,12 +282,6 @@ bool ErrorCheck::checkInput(string input) {
                        validateBinFiles();
                }
                
-               if ((commandName == "get.repseqs")) { 
-                       if ((globaldata->getListFile() == "")) { cout << "You must read a list file before you can use the get.repseqs command." << endl; return false; }
-                       else if (groupfile == "") { cout << "You must provide a groupfile before you can use the get.repseqs command." << endl; return false; }
-                       validateBinFiles();
-               }
-
                
                if ((commandName == "get.oturep")) { 
                        if ((globaldata->gSparseMatrix == NULL) || (globaldata->gListVector == NULL)) {
@@ -584,8 +583,8 @@ void ErrorCheck::validateSeqsFiles() {
                                        errorFree = false;
                                }
                        }
-               }else if (templatefile != "") {
-                       ableToOpen = openInputFile(templatefile, filehandle);
+               }else if (candidatefile != "") {
+                       ableToOpen = openInputFile(candidatefile, filehandle);
                        filehandle.close();
                        if (ableToOpen == 1) { //unable to open
                                errorFree = false;
@@ -682,7 +681,7 @@ void ErrorCheck::clear() {
        fastafile       =   "";
        nexusfile       =   "";
        clustalfile     =   "";
-       templatefile    =       "";
+       candidatefile   =       "";
        line                    =       "";
        label                   =       "";
        method                  =   "furthest";