added help for alignment code and thomas' calcs to project

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 3e6a9799353a78e4e87a7cd72ebc4d78a7199aa5..3e4d16bb77fe04911bc9c50553a431aae99b4849 100644 (file)
--- 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));
                
-               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"};
@@ -253,7 +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"};
@@ -271,7 +267,7 @@ 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","phylip","clustal","nexus", "trump", "soft", "filter"};
                commandParameters["filter.seqs"] = addParameters(filterseqsArray, sizeof(filterseqsArray)/sizeof(string));
 
                string vennArray[] =  {"groups","line","label","calc"};
@@ -292,8 +288,11 @@ 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","phylip","clustal","nexus", "calc", "ends", "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"};
+               commandParameters["align.seqs"] = addParameters(AlignArray, sizeof(AlignArray)/sizeof(string));
                
                string quitArray[] = {};
                commandParameters["quit"] = addParameters(quitArray, sizeof(quitArray)/sizeof(string));
@@ -347,6 +346,9 @@ 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";