added set.current and get.current commands and modified existing commands to update...

[mothur.git] / chopseqscommand.cpp

diff --git a/chopseqscommand.cpp b/chopseqscommand.cpp
index 1ebb1f4b631f21d02596aa3e1e528d27cb3587df..a09ff65856ae39c1e8fbb1a662ed8bacd8860694 100644 (file)
--- a/chopseqscommand.cpp
+++ b/chopseqscommand.cpp
@@ -133,7 +133,7 @@ ChopSeqsCommand::ChopSeqsCommand(string option)  {
 
 void ChopSeqsCommand::help(){
        try {
-               m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences.\n");
+               m->mothurOut("The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. Note: If a sequence is completely 'chopped', an accnos file will be created with the names of the sequences removed. \n");
                m->mothurOut("The chop.seqs command parameters are fasta, numbases, countgaps and keep. fasta and numbases are required required.\n");
                m->mothurOut("The chop.seqs command should be in the following format: chop.seqs(fasta=yourFasta, numbases=yourNum, keep=yourKeep).\n");
                m->mothurOut("The numbases parameter allows you to specify the number of bases you want to keep.\n");
@@ -202,6 +202,21 @@ int ChopSeqsCommand::execute(){
                
                m->mothurOutEndLine();
                
+               //set fasta file as new current fastafile
+               string current = "";
+               itTypes = outputTypes.find("fasta");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+               }
+               
+               if (wroteAccnos) { //set accnos file as new current accnosfile
+                       itTypes = outputTypes.find("accnos");
+                       if (itTypes != outputTypes.end()) {
+                               if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
+                       }
+               }
+               
+               
                return 0;               
        }