added alignment code

[mothur.git] / errorchecking.cpp

diff --git a/errorchecking.cpp b/errorchecking.cpp
index 8aaa8b04fbeeb80b4c727396bab06f9899840a7e..dfe96072e3e8ae8799856982f56b85fff15b0289 100644 (file)
--- a/errorchecking.cpp
+++ b/errorchecking.cpp
@@ -118,7 +118,14 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "scale" )                      { scale = value;        }
                                if (parameter == "ends" )                       { ends = value; }
                                if (parameter == "processors" )         { processors = value;   }
-
+                               if (parameter == "template")            { templatefile = value; }
+                               if (parameter == "search")                      { search = value;               }
+                               if (parameter == "ksize")                       { ksize = value;                }
+                               if (parameter == "align")                   { align = value;            }
+                               if (parameter == "match")                       { match = value;                }
+                               if (parameter == "mismatch")            { mismatch = value;         }
+                               if (parameter == "gapopen")                     { gapopen = value;              }
+                               if (parameter == "gapextend" )          { gapextend = value;    }
                        }
                        
                        //gets the last parameter and value
@@ -160,6 +167,14 @@ bool ErrorCheck::checkInput(string input) {
                                if (parameter == "scale" )                      { scale = value;        }
                                if (parameter == "ends" )                       { ends = value; }
                                if (parameter == "processors" )         { processors = value;   }
+                               if (parameter == "template")            { templatefile = value; }
+                               if (parameter == "search")                      { search = value;               }
+                               if (parameter == "ksize")                       { ksize = value;                }
+                               if (parameter == "align")                   { align = value;            }
+                               if (parameter == "match")                       { match = value;                }
+                               if (parameter == "mismatch")            { mismatch = value;         }
+                               if (parameter == "gapopen")                     { gapopen = value;              }
+                               if (parameter == "gapextend" )          { gapextend = value;    }
 
                        }
                }
@@ -246,9 +261,11 @@ bool ErrorCheck::checkInput(string input) {
                        }
                }
                
-               if ((commandName == "filter.seqs") || (commandName == "dist.seqs")) { 
+               if ((commandName == "filter.seqs") || (commandName == "dist.seqs") || (commandName == "align.seqs")) { 
                        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; 
+                                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; 
                        }
                        validateSeqsFiles();
                }
@@ -558,9 +575,15 @@ void ErrorCheck::validateSeqsFiles() {
                                        errorFree = false;
                                }
                        }
-
+               }else if (templatefile != "") {
+                       ableToOpen = openInputFile(templatefile, 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";
@@ -642,6 +665,7 @@ void ErrorCheck::clear() {
        fastafile       =   "";
        nexusfile       =   "";
        clustalfile     =   "";
+       templatefile    =       "";
        line                    =       "";
        label                   =       "";
        method                  =   "furthest";