fixed multiple bugs for 1.4 release

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index e79a2db2663a48ceee335dba6c1a77973dd09bb6..4aad1c22c037515fcb5d6f166aae8af4842d8fd4 100644 (file)
--- a/validparameter.cpp
+++ b/validparameter.cpp
@@ -225,7 +225,7 @@ void ValidParameters::initCommandParameters() {
                string deconvoluteArray[] =  {"fasta"};
                commandParameters["deconvolute"] = 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"};
@@ -249,7 +249,7 @@ 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"};
@@ -267,19 +267,22 @@ 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","phylip","clustal","nexus", "trump", "soft", "hard", "vertical"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/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"};
@@ -288,10 +291,10 @@ 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","phylip","clustal","nexus", "calc", "countends", "cutoff", "processors"};
                commandParameters["dist.seqs"] = addParameters(distanceArray, sizeof(distanceArray)/sizeof(string));
                
-               string AlignArray[] =  {"fasta","phylip","clustal","nexus", "template", "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[] = {};
@@ -346,6 +349,9 @@ 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";