added count.seqs command and made some modifcations to the uchime code to allow it...

[mothur.git] / distancecommand.cpp

diff --git a/distancecommand.cpp b/distancecommand.cpp
index 029b581f5d1f8590f16f075a79cde658055c518a..b73cd7c751176c386a95931b0887c6790f046583 100644 (file)
--- a/distancecommand.cpp
+++ b/distancecommand.cpp
@@ -55,7 +55,7 @@ string DistanceCommand::getHelpString(){
                helpString += "The dist.seqs command should be in the following format: \n";
                helpString += "dist.seqs(fasta=yourFastaFile, calc=yourCalc, countends=yourEnds, cutoff= yourCutOff, processors=yourProcessors) \n";
                helpString += "Example dist.seqs(fasta=amazon.fasta, calc=eachgap, countends=F, cutoff= 2.0, processors=3).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. calc), '=' and parameters (i.e.yourCalc).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -85,6 +85,7 @@ DistanceCommand::DistanceCommand(string option) {
                                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -246,6 +247,8 @@ int DistanceCommand::execute(){
                int numSeqs = alignDB.getNumSeqs();
                cutoff += 0.005;
                
+               if (!alignDB.sameLength()) {  m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
+               
                string outputFile;
                                
                if (output == "lt") { //does the user want lower triangle phylip formatted file