finished chimeraslayer method and added get.listcount command

[mothur.git] / chimeraseqscommand.cpp

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index f368869449242ff52fc4c6bce4057a0a17013798..14973ccc3c65d05952783acaf3ba03431e842106 100644 (file)
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -26,7 +26,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "printall" };
+                       string Array[] =  {"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name", "match","mismatch", "divergence", "minsim", "parents", "iters" };
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -78,9 +78,6 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        temp = validParameter.validFile(parameters, "correction", false);               if (temp == "not found") { temp = "T"; }
                        correction = isTrue(temp);
                        
-                       temp = validParameter.validFile(parameters, "printall", false);                 if (temp == "not found") { temp = "F"; }
-                       printAll = isTrue(temp);
-                       
                        temp = validParameter.validFile(parameters, "processors", false);               if (temp == "not found") { temp = "1"; }
                        convert(temp, processors);
                        
@@ -109,6 +106,9 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
                        
                        temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "5"; }
                        convert(temp, parents); 
+                       
+                       temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
+                       convert(temp, iters); 
                         
                        temp = validParameter.validFile(parameters, "increment", false);                
                        if ((temp == "not found") && ((method == "chimeracheck") || (method == "chimeraslayer"))) { temp = "10"; }
@@ -140,7 +140,7 @@ void ChimeraSeqsCommand::help(){
                //"fasta", "filter", "correction", "processors", "method", "window", "increment", "template", "conservation", "quantile", "mask", "numwanted", "ksize", "svg", "name"
                //mothurOut("chimera.seqs ASSUMES that your sequences are ALIGNED and if using a template that the template file sequences are the same length as the fasta file sequences.\n\n");
                mothurOut("The chimera.seqs command reads a fastafile and creates list of potentially chimeric sequences.\n");
-               mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name.\n");
+               mothurOut("The chimera.seqs command parameters are fasta, filter, correction, processors, mask, method, window, increment, template, conservation, quantile, numwanted, ksize, svg, name, iters.\n");
                mothurOut("The fasta parameter is always required and template is required if using pintail, ccode or chimeracheck.\n");
                mothurOut("The filter parameter allows you to specify if you would like to apply a vertical and 50% soft filter. \n");
                mothurOut("The correction parameter allows you to put more emphasis on the distance between highly similar sequences and less emphasis on the differences between remote homologs.\n");
@@ -156,6 +156,7 @@ void ChimeraSeqsCommand::help(){
                mothurOut("The ksize parameter allows you to input kmersize. \n");
                mothurOut("The svg parameter allows you to specify whether or not you would like a svg file outputted for each query sequence.\n");
                mothurOut("The name parameter allows you to enter a file containing names of sequences you would like .svg files for.\n");
+               mothurOut("The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method.\n");
                mothurOut("NOT ALL PARAMETERS ARE USED BY ALL METHODS. Please look below for method specifics.\n\n");
                mothurOut("Details for each method: \n"); 
                mothurOut("\tpintail: \n"); 
@@ -220,7 +221,7 @@ int ChimeraSeqsCommand::execute(){
                chimera->setDivR(divR);
                chimera->setParents(parents);
                chimera->setMinSim(minSimilarity);
-               chimera->setPrint(printAll);
+               chimera->setIters(iters);
                
                                
                //find chimeras