added trim.seqs command

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 5da87d1df8ee6d568264313ece64bbc7177cae40..bd1698468116f39ec112e075e8001c47a7ef3199 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -223,7 +223,7 @@ void ValidParameters::initCommandParameters() {
                commandParameters["cluster"] = addParameters(clusterArray, sizeof(clusterArray)/sizeof(string));
                
                string deconvoluteArray[] =  {"fasta"};
-               commandParameters["deconvolute"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
+               commandParameters["unique.seqs"] = addParameters(deconvoluteArray, sizeof(deconvoluteArray)/sizeof(string));
                
                string collectsingleArray[] =  {"freq","line","label","calc","abund","size"};
                commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
@@ -239,6 +239,12 @@ void ValidParameters::initCommandParameters() {
 
                string getlineArray[] =  {};
                commandParameters["get.line"] = addParameters(getlineArray, sizeof(getlineArray)/sizeof(string));
+               
+               string getsabundArray[] =  {"line", "label"};
+               commandParameters["get.sabund"] = addParameters(getsabundArray, sizeof(getsabundArray)/sizeof(string));
+               
+               string getrabundArray[] =  {"line", "label"};
+               commandParameters["get.rabund"] = addParameters(getrabundArray, sizeof(getrabundArray)/sizeof(string));
 
                string rarefactionsingleArray[] =  {"iters","freq","line","label","calc","abund"};
                commandParameters["rarefaction.single"] = addParameters(rarefactionsingleArray, sizeof(rarefactionsingleArray)/sizeof(string));
@@ -267,25 +273,34 @@ void ValidParameters::initCommandParameters() {
                string heatmapArray[] =  {"groups","line","label","sorted","scale"};
                commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
                
-               string filterseqsArray[] =  {"fasta","phylip","clustal","nexus", "trump", "soft", "filter"};
+               string filterseqsArray[] =  {"fasta", "trump", "soft", "hard", "vertical"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
+               string summaryseqsArray[] =  {"fasta"};
+               commandParameters["summary.seqs"] = addParameters(summaryseqsArray, sizeof(summaryseqsArray)/sizeof(string));
+
+               string screenseqsArray[] =  {"fasta", "start", "end", "maxambig", "maxhomop", "minlength", "maxlength", "name", "group"};
+               commandParameters["screen.seqs"] = addParameters(screenseqsArray, sizeof(screenseqsArray)/sizeof(string));
+
+               string reverseseqsArray[] =  {"fasta"};
+               commandParameters["reverse.seqs"] = addParameters(reverseseqsArray, sizeof(reverseseqsArray)/sizeof(string));
+
+               string trimseqsArray[] =  {"fasta", "flip", "oligos", "forward", "reverse", "barcode"};
+               commandParameters["trim.seqs"] = addParameters(trimseqsArray, sizeof(trimseqsArray)/sizeof(string));
+
                string vennArray[] =  {"groups","line","label","calc"};
                commandParameters["venn"] = addParameters(vennArray, sizeof(vennArray)/sizeof(string));
                
-               string binseqsArray[] =  {"fasta","line","label","name"};
+               string binseqsArray[] =  {"fasta","line","label","name", "group"};
                commandParameters["bin.seqs"] = addParameters(binseqsArray, sizeof(binseqsArray)/sizeof(string));
                
                string distsharedArray[] =  {"line","label","calc","groups"};
                commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
                
-               string getrepseqsArray[] =  {"fasta","line","label","name", "group"};
-               commandParameters["get.repseqs"] = addParameters(getrepseqsArray, sizeof(getrepseqsArray)/sizeof(string));
-               
-               string getOTURepArray[] =  {"fasta","list","line","label","name"};
+               string getOTURepArray[] =  {"fasta","list","line","label","name", "group"};
                commandParameters["get.oturep"] = addParameters(getOTURepArray, sizeof(getOTURepArray)/sizeof(string));
                
-               string treeGroupsArray[] =  {"line","label","calc","groups"};
+               string treeGroupsArray[] =  {"line","label","calc","groups", "phylip", "column", "name"};
                commandParameters["tree.shared"] = addParameters(treeGroupsArray, sizeof(treeGroupsArray)/sizeof(string));
                
                string bootstrapArray[] =  {"line","label","calc","groups","iters"};
@@ -294,10 +309,10 @@ void ValidParameters::initCommandParameters() {
                string concensusArray[] =  {};
                commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
                
-               string distanceArray[] =  {"fasta","phylip","clustal","nexus", "calc", "ends", "cutoff", "processors"};
+               string distanceArray[] =  {"fasta", "calc", "countends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
-               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+               string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
                commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
                
                string quitArray[] = {};