X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=validparameter.cpp;h=3e4d16bb77fe04911bc9c50553a431aae99b4849;hb=b02ee39bf6c708a98748f8861846cdec7fab58ac;hp=e79a2db2663a48ceee335dba6c1a77973dd09bb6;hpb=526a868606faa50caf86e7399f7554c0335b39e5;p=mothur.git

diff --git a/validparameter.cpp b/validparameter.cpp
index e79a2db..3e4d16b 100644
--- 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"};
@@ -291,7 +291,7 @@ 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", "ksize", "align", "match", "mismatch", "gapopen", "gapextend"};
+		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[] = {};
@@ -346,6 +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";