added degap.seqs command

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index a6290a6afe55a28001e5e229e518a7c03c6a1c28..2bf0fa344eaeb924525bd6f906d664c8874f3d61 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -102,6 +102,9 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        // ...at some point should added some additional type checking...
                        
                        string temp;
+                       hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
+                       else if (hard == "not open") { hard = ""; abort = true; }       
+
                        temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
                        trump = temp[0];
                        
@@ -111,13 +114,13 @@ FilterSeqsCommand::FilterSeqsCommand(string option)  {
                        temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
                        convert(temp, processors); 
                        
-                       hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
-                       else if (hard == "not open") { abort = true; }  
-                       
-                       vertical = validParameter.validFile(parameters, "vertical", false);             if (vertical == "not found") { vertical = "T"; }
+                       vertical = validParameter.validFile(parameters, "vertical", false);             
+                       if (vertical == "not found") { 
+                               if ((hard == "") && (trump == '*')) { vertical = "T"; } //you have not given a hard file or set the trump char.
+                               else { vertical = "F";  }
+                       }
                        
                        numSeqs = 0;
-                       
                }
                
        }
@@ -138,11 +141,11 @@ void FilterSeqsCommand::help(){
                m->mothurOut("For example: fasta=abrecovery.fasta-amazon.fasta \n");
                m->mothurOut("The trump parameter .... The default is ...\n");
                m->mothurOut("The soft parameter .... The default is ....\n");
-               m->mothurOut("The hard parameter .... The default is ....\n");
-               m->mothurOut("The vertical parameter .... The default is T.\n");
+               m->mothurOut("The hard parameter allows you to enter a file containing the filter you want to use.\n");
+               m->mothurOut("The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n");
                m->mothurOut("The filter.seqs command should be in the following format: \n");
-               m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump, soft=yourSoft, hard=yourHard, vertical=yourVertical) \n");
-               m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=..., soft=..., hard=..., vertical=T).\n");
+               m->mothurOut("filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n");
+               m->mothurOut("Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n");
                m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n\n");
                
        }
@@ -256,23 +259,14 @@ int FilterSeqsCommand::filterSequences() {
                                int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY; 
                                int inMode=MPI_MODE_RDONLY; 
                                
-                               //char* outFilename = new char[filteredFasta.length()];
-                               //memcpy(outFilename, filteredFasta.c_str(), filteredFasta.length());
-                               
                                char outFilename[1024];
                                strcpy(outFilename, filteredFasta.c_str());
-
-                               //char* inFileName = new char[fastafileNames[s].length()];
-                               //memcpy(inFileName, fastafileNames[s].c_str(), fastafileNames[s].length());
-                               
+                       
                                char inFileName[1024];
                                strcpy(inFileName, fastafileNames[s].c_str());
                                
                                MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
                                MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
-                               
-                               //delete inFileName;
-                               //delete outFilename;
 
                                if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }