Author: Andreas Tille <tille@debian.org>
LastChanged: Tue, 30 Jul 2013 21:21:02 +0200
Description: Some spelling corrections
 Note: There are similar spelling problems in comments inside
 the code that are not fixed by this patch

--- a/getcurrentcommand.cpp
+++ b/getcurrentcommand.cpp
@@ -31,7 +31,7 @@ string GetCurrentCommand::getHelpString(
 		string helpString = "";
 		helpString += "The get.current command outputs the current files saved by mothur.\n";
 		helpString += "The get.current command has one parameter: clear.\n";
-		helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+		helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
 		helpString += "The get.current command should be in the following format: \n";
 		helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
 		return helpString;
--- a/setcurrentcommand.cpp
+++ b/setcurrentcommand.cpp
@@ -56,7 +56,7 @@ string SetCurrentCommand::getHelpString(
 		string helpString = "";
 		helpString += "The set.current command allows you to set the current files saved by mothur.\n";
 		helpString += "The set.current command parameters are: clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary and taxonomy.\n";
-		helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
+		helpString += "The clear parameter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
 		helpString += "The set.current command should be in the following format: \n";
 		helpString += "set.current(fasta=yourFastaFile) or set.current(fasta=amazon.fasta, clear=name-accnos)\n";
 		return helpString;
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -773,7 +773,7 @@ int MatrixOutputCommand::driver(vector<S
 			
 			for (int l = 0; l < k; l++) {
 				
-				if (k != l) { //we dont need to similiarity of a groups to itself
+				if (k != l) { //we dont need to similarity of a groups to itself
 					subset.clear(); //clear out old pair of sharedrabunds
 					//add new pair of sharedrabunds
 					subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); 
--- a/mgclustercommand.cpp
+++ b/mgclustercommand.cpp
@@ -41,7 +41,7 @@ string MGClusterCommand::getHelpString()
 	try {
 		string helpString = "";
 		helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, hard,  method, merge, min, length, penalty and hcluster. The blast parameter is required.\n";
-		helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similiar to the OTUs.\n";
+		helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similar to the OTUs.\n";
 		helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
 		helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
 		helpString += "The precision parameter's default value is 100. \n";
@@ -50,7 +50,7 @@ string MGClusterCommand::getHelpString()
 		helpString += "The length parameter is used to specify the minimum overlap required.  The default is 5.\n";
 		helpString += "The penalty parameter is used to adjust the error rate.  The default is 0.10.\n";
 		helpString += "The merge parameter allows you to shut off merging based on overlaps and just cluster.  By default merge is true, meaning you want to merge.\n";
-		helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering.  This may be neccessary if your file is too large to fit into RAM. The default is false.\n";
+		helpString += "The hcluster parameter allows you to use the hcluster algorithm when clustering.  This may be necessary if your file is too large to fit into RAM. The default is false.\n";
 		helpString += "The mgcluster command should be in the following format: \n";
 		helpString += "mgcluster(blast=yourBlastfile, name=yourNameFile, cutoff=yourCutOff).\n";
 		helpString += "Note: No spaces between parameter labels (i.e. balst), '=' and parameters (i.e.yourBlastfile).\n";
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -43,7 +43,7 @@ string PhylotypeCommand::getHelpString()
 		helpString += "For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n";
 		helpString += "For the cutoff parameter levels count up from the root of the phylotree. This enables you to look at the grouping down to a specific resolution, say the genus level.\n";
 		helpString += "The label parameter allows you to specify which level you would like, and are separated by dashes.  The default all levels in your taxonomy file. \n";
-		helpString += "For the label parameter, levels count down from the root to keep the output similiar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
+		helpString += "For the label parameter, levels count down from the root to keep the output similar to mothur's other commands which report information from finer resolution to coarser resolutions.\n";
 		helpString += "The phylotype command should be in the following format: \n";
 		helpString += "phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n";
 		helpString += "Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n";
--- a/treegroupscommand.cpp
+++ b/treegroupscommand.cpp
@@ -46,7 +46,7 @@ string TreeGroupCommand::getHelpString()
 	try {
 		string helpString = "";
 		ValidCalculators validCalculator;
-		helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
+		helpString += "The tree.shared command creates a .tre to represent the similarity between groups or sequences.\n";
 		helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
 		helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
 		helpString += "The group names are separated by dashes. The label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n";
--- a/screenseqscommand.cpp
+++ b/screenseqscommand.cpp
@@ -69,7 +69,7 @@ string ScreenSeqsCommand::getHelpString(
 		helpString += "The taxonomy parameter allows you to remove bad seqs from taxonomy files.\n";
 		helpString += "The start parameter is used to set a position the \"good\" sequences must start by. The default is -1.\n";
 		helpString += "The end parameter is used to set a position the \"good\" sequences must end after. The default is -1.\n";
-		helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
+		helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.\n";
 		helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
 		helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
 		helpString += "The maxn parameter allows you to set and maximum number of N's allowed in a sequence. \n";
--- a/sffmultiplecommand.cpp
+++ b/sffmultiplecommand.cpp
@@ -75,7 +75,7 @@ string SffMultipleCommand::getHelpString
         helpString += parameters[parameters.size()-1] + ".\n";
 		helpString += "The file parameter allows you to enter the a file containing the list of sff files and optional oligos files.\n";
         helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores generated by sffinfo trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n";
-        helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
+        helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.\n";
 		helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
 		helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
 		helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -68,7 +68,7 @@ string TrimSeqsCommand::getHelpString(){
 		helpString += "The oligos parameter allows you to provide an oligos file.\n";
 		helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
         helpString += "The count parameter allows you to provide a count file with your fasta file.\n";
-		helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
+		helpString += "The maxambig parameter allows you to set the maximum number of ambiguous bases allowed. The default is -1.\n";
 		helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
 		helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
 		helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
