pat's mods to morisitahorn and pre.cluster

[mothur.git] / phylotypecommand.cpp

diff --git a/phylotypecommand.cpp b/phylotypecommand.cpp
index ef8728258cd6ee1a90432837de78bad2b0959128..8ba0a091ee7b77ff8f1abe37ae30117b64cec597 100644 (file)
--- 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");
@@ -110,20 +113,21 @@ int PhylotypeCommand::execute(){
                if (tree->get(leaves[0]).parent == -1) {  mothurOut("Empty Tree"); mothurOutEndLine();  done = true;    }
                
                ofstream outList;
-               string outputListFile = getRootName(taxonomyFileName) + "tax.list";
+               string outputListFile = getRootName(taxonomyFileName) + "tx.list";
                openOutputFile(outputListFile, outList);
                ofstream outSabund;
-               string outputSabundFile = getRootName(taxonomyFileName) + "tax.sabund";
+               string outputSabundFile = getRootName(taxonomyFileName) + "tx.sabund";
                openOutputFile(outputSabundFile, outSabund);
                ofstream outRabund;
-               string outputRabundFile = getRootName(taxonomyFileName) + "tax.rabund";
+               string outputRabundFile = getRootName(taxonomyFileName) + "tx.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){