added help for alignment code and thomas' calcs to project

[mothur.git] / validparameter.cpp

diff --git a/validparameter.cpp b/validparameter.cpp
index 8af4a8154e74fab87e3985222a0e0e8ac93a0bfd..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"};
@@ -226,7 +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"};
@@ -250,7 +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"};
@@ -292,6 +291,9 @@ void ValidParameters::initCommandParameters() {
                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));
 
@@ -344,6 +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";