X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=bd1698468116f39ec112e075e8001c47a7ef3199;hb=64eee3a595ae53817f52807d7393b22e74e31f56;hp=3e6a9799353a78e4e87a7cd72ebc4d78a7199aa5;hpb=3117b1c3109121dff476997d3c5db5b47a77729b;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index 3e6a979..bd16984 100644
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -211,7 +211,6 @@ void ValidParameters::initCommandParameters() {
 		//{"parameter1","parameter2",...,"last parameter"};
 		
 		string readdistArray[] = {"phylip","column", "name","cutoff","precision", "group"};
-
 		commandParameters["read.dist"] = addParameters(readdistArray, sizeof(readdistArray)/sizeof(string));
 
 		string readotuArray[] =  {"list","order","shared", "line", "label","group","sabund", "rabund"};
@@ -220,16 +219,13 @@ void ValidParameters::initCommandParameters() {
 		string readtreeArray[] = {"tree","group"};
 		commandParameters["read.tree"] = addParameters(readtreeArray, sizeof(readtreeArray)/sizeof(string));
 		
-		string readseqsArray[] = {"fasta","phylip","clustal","nexus","line"};
-		commandParameters["read.seqs"] = addParameters(readseqsArray, sizeof(readseqsArray)/sizeof(string));
-		
 		string clusterArray[] =  {"cutoff","precision","method"};
 		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"};
+		string collectsingleArray[] =  {"freq","line","label","calc","abund","size"};
 		commandParameters["collect.single"] = addParameters(collectsingleArray, sizeof(collectsingleArray)/sizeof(string));
 
 		string collectsharedArray[] =  {"freq","line","label","calc","groups"};
@@ -243,6 +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));
@@ -253,7 +255,7 @@ void ValidParameters::initCommandParameters() {
 		string libshuffArray[] =  {"iters","groups","step","form","cutoff"};
 		commandParameters["libshuff"] = addParameters(libshuffArray, sizeof(libshuffArray)/sizeof(string));
 		
-		string summarysingleArray[] =  {"line","label","calc","abund"};
+		string summarysingleArray[] =  {"line","label","calc","abund","size"};
 		commandParameters["summary.single"] = addParameters(summarysingleArray, sizeof(summarysingleArray)/sizeof(string));
 
 		string summarysharedArray[] =  {"line","label","calc","groups"};
@@ -271,19 +273,34 @@ void ValidParameters::initCommandParameters() {
 		string heatmapArray[] =  {"groups","line","label","sorted","scale"};
 		commandParameters["heatmap"] = addParameters(heatmapArray, sizeof(heatmapArray)/sizeof(string));
 		
-		string filterseqsArray[] =  {"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 getOTURepArray[] =  {"fasta","list","line","label","name"};
+		string distsharedArray[] =  {"line","label","calc","groups"};
+		commandParameters["dist.shared"] = addParameters(distsharedArray, sizeof(distsharedArray)/sizeof(string));
+		
+		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"};
@@ -292,8 +309,11 @@ void ValidParameters::initCommandParameters() {
 		string concensusArray[] =  {};
 		commandParameters["concensus"] = addParameters(concensusArray, sizeof(concensusArray)/sizeof(string));
 		
-		string distanceArray[] =  {"calc", "ends", "cutoff", "processors"};
-		commandParameters["distance"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+		string distanceArray[] =  {"fasta", "calc", "countends", "cutoff", "processors"};
+		commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
+		
+		string AlignArray[] =  {"fasta", "candidate", "search", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+		commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
 		
 		string quitArray[] = {};
 		commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
@@ -347,6 +367,9 @@ void ValidParameters::initParameterRanges() {
 		
 		string softArray[] = {">=","0", "<=","100", "between"};
 		parameterRanges["soft"] = addParameters(softArray, rangeSize);
+		
+		string sizeArray[] = {">=","1", "<","NA", "between"};
+		parameterRanges["size"] = addParameters(sizeArray, rangeSize);
 	}
 	catch(exception& e) {
 		cout << "Standard Error: " << e.what() << " has occurred in the ValidParameters class Function isValidParameter. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";