From: westcott <westcott>
Date: Tue, 24 Nov 2009 19:29:37 +0000 (+0000)
Subject: changed get.sharedotu to get.sharedseqs
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=7af504f0a1c77582a6ea55e8b003685059c1c4a1;p=mothur.git

changed get.sharedotu to get.sharedseqs
---

diff --git a/chimeraseqscommand.cpp b/chimeraseqscommand.cpp
index 14973cc..51fc0e7 100644
--- a/chimeraseqscommand.cpp
+++ b/chimeraseqscommand.cpp
@@ -122,7 +122,7 @@ ChimeraSeqsCommand::ChimeraSeqsCommand(string option){
 
 			
 			
-			if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
+			if (((method != "bellerophon")) && (templatefile == "")) { mothurOut("You must provide a template file with the pintail, ccode, chimeraslayer or chimeracheck methods."); mothurOutEndLine(); abort = true;  }
 			
 
 		}
@@ -168,6 +168,8 @@ void ChimeraSeqsCommand::help(){
 		mothurOut("\t\tparameters: fasta=required, template=required, filter=F, mask=no mask, processors=1, window=10% of length, numwanted=20\n"); 
 		mothurOut("\tchimeracheck: \n"); 
 		mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, ksize=7, svg=F, name=none\n\n"); 
+		mothurOut("\tchimeraslayer: \n"); 
+		mothurOut("\t\tparameters: fasta=required, template=required, processors=1, increment=10, mask=no mask, numwanted=10, match=5, mismatch=-4, divergence=1.0, minsim=90, parents=5, iters=1000, window=100. \n\n"); 
 		mothurOut("The chimera.seqs command should be in the following format: \n");
 		mothurOut("chimera.seqs(fasta=yourFastaFile, filter=yourFilter, correction=yourCorrection, processors=yourProcessors, method=bellerophon) \n");
 		mothurOut("Example: chimera.seqs(fasta=AD.align, filter=True, correction=true, method=bellerophon, window=200) \n");
diff --git a/commandfactory.cpp b/commandfactory.cpp
index c853268..635cff0 100644
--- a/commandfactory.cpp
+++ b/commandfactory.cpp
@@ -114,7 +114,7 @@ CommandFactory::CommandFactory(){
 	commands["system"]				= "system";
 	commands["align.check"]			= "align.check";
 	commands["get.sharedseqs"]		= "get.sharedseqs";
-	commands["get.listcount"]		= "get.listcount";
+	commands["get.otulist"]			= "get.otulist";
 	commands["quit"]				= "quit"; 
 	commands["hcluster"]			= "hcluster"; 
 	commands["classify.seqs"]		= "classify.seqs"; 
@@ -182,7 +182,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "system")				{	command = new SystemCommand(optionString);				}
 		else if(commandName == "align.check")			{	command = new AlignCheckCommand(optionString);			}
 		else if(commandName == "get.sharedseqs")			{	command = new GetSharedOTUCommand(optionString);		}
-		else if(commandName == "get.listcount")			{	command = new GetListCountCommand(optionString);		}
+		else if(commandName == "get.otulist")			{	command = new GetListCountCommand(optionString);		}
 		else if(commandName == "hcluster")				{	command = new HClusterCommand(optionString);			}
 		else if(commandName == "classify.seqs")			{	command = new ClassifySeqsCommand(optionString);		}
 		else if(commandName == "phylotype")				{	command = new PhylotypeCommand(optionString);			}