From bee7952bbdc4ed46c7a12bef11769345fa3224d7 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Mon, 23 Nov 2009 18:40:54 +0000
Subject: [PATCH] changed label outputs for phylotype command

---
 phylotypecommand.cpp  | 8 ++++++--
 taxonomyequalizer.cpp | 4 ++--
 taxonomyequalizer.h   | 5 +++--
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index ef87282..8aa639d 100644
--- a/phylotypecommand.cpp
+++ b/phylotypecommand.cpp
@@ -69,7 +69,10 @@ void PhylotypeCommand::help(){
 		mothurOut("The phylotype command reads a taxonomy file and outputs a .list, .rabund and .sabund file. \n");
 		mothurOut("The phylotype command parameter options are taxonomy, cutoff and label. The taxonomy parameter is required.\n");
 		mothurOut("The cutoff parameter allows you to specify the level you want to stop at.  The default is the highest level in your taxonomy file. \n");
+		mothurOut("For example: taxonomy = Bacteria;Bacteroidetes-Chlorobi;Bacteroidetes; - cutoff=2, would truncate the taxonomy to Bacteria;Bacteroidetes-Chlorobi; \n");
+		mothurOut("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");
 		mothurOut("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");
+		mothurOut("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");
 		mothurOut("The phylotype command should be in the following format: \n");
 		mothurOut("phylotype(taxonomy=yourTaxonomyFile, cutoff=yourCutoff, label=yourLabels) \n");
 		mothurOut("Eaxample: phylotype(taxonomy=amazon.taxonomy, cutoff=5, label=1-3-5).\n\n");
@@ -119,11 +122,12 @@ int PhylotypeCommand::execute(){
 		string outputRabundFile = getRootName(taxonomyFileName) + "tax.rabund";
 		openOutputFile(outputRabundFile, outRabund);
 		
-				
+		int count = 1;		
 		//start at leaves of tree and work towards root, processing the labels the user wants
 		while((!done) && ((allLines == 1) || (labels.size() != 0))) {
 		
-			string level = toString(tree->get(currentNodes.begin()->first).level); 
+			string level = toString(count); 
+			count++;
 			
 			//is this a level the user want output for
 			if(allLines == 1 || labels.count(level) == 1){	
diff --git a/taxonomyequalizer.cpp b/taxonomyequalizer.cpp
index 37b7720..e7fa07a 100644
--- a/taxonomyequalizer.cpp
+++ b/taxonomyequalizer.cpp
@@ -17,7 +17,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
 		ifstream inTax;
 		openInputFile(tfile, inTax);
 	
-		int highestLevel = getHighestLevel(inTax);
+		highestLevel = getHighestLevel(inTax);
 	
 		//if the user has specified a cutoff and it's smaller than the highest level
 		if ((cutoff != -1) && (cutoff < highestLevel)) { 
@@ -43,7 +43,7 @@ TaxEqualizer::TaxEqualizer(string tfile, int c) : cutoff(c) {
 			//is this a taxonomy that needs to be extended?
 			if (seqLevels[name] < highestLevel) {
 				extendTaxonomy(name, tax, highestLevel);
-			}else if (seqLevels[name] > highestLevel) { //this can happen if hte user enters a cutoff
+			}else if (seqLevels[name] > highestLevel) { //this can happen if the user enters a cutoff
 				truncateTaxonomy(name, tax, highestLevel);
 			}
 			
diff --git a/taxonomyequalizer.h b/taxonomyequalizer.h
index 6308d71..9f38b2f 100644
--- a/taxonomyequalizer.h
+++ b/taxonomyequalizer.h
@@ -25,13 +25,14 @@ public:
 	TaxEqualizer(string, int);
 	~TaxEqualizer() {};
 	
-	string getEqualizedTaxFile()	{  return equalizedFile;	}
+	string getEqualizedTaxFile()	{	return equalizedFile;	}
+	int getHighestLevel()			{	return highestLevel;	}
 	
 	
 private:
 	string equalizedFile, testTax;
 	bool containsConfidence;
-	int cutoff;
+	int cutoff, highestLevel;
 	map<string, int> seqLevels;  //maps name to level of taxonomy
 	
 	int getHighestLevel(ifstream&);  //scans taxonomy file to find taxonomy with highest level
-- 
2.39.2