working on pam

[mothur.git] / makelefsecommand.cpp

diff --git a/makelefsecommand.cpp b/makelefsecommand.cpp
index 9f895f60d42b9bc6bc1527f6826bfd6fd0d23767..c859bfbc230201e4be1ef73ab19ed56f28b3412d 100644 (file)
--- a/makelefsecommand.cpp
+++ b/makelefsecommand.cpp
@@ -43,8 +43,8 @@ string MakeLefseCommand::getHelpString(){
         helpString += "The constaxonomy parameter is used to input your taxonomy file. http://www.wiki.mothur.org/wiki/Constaxonomy_file. The contaxonomy file is the taxonomy file outputted by classify.otu(list=yourListfile, taxonomy=yourTaxonomyFile). Be SURE that the you are the constaxonomy file distance matches the shared file distance.  ie, for *.0.03.cons.taxonomy set label=0.03. Mothur is smart enough to handle shared files that have been subsampled. \n";
         helpString += "The scale parameter allows you to select what scale you would like to use to convert your shared file abundances to relative abundances. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";
                helpString += "The label parameter allows you to select what distance level you would like used, if none is given the first distance is used.\n";
-               helpString += "The make.lefse command should be in the following format: make.lefse(list=yourListFile, taxonomy=outputFromClassify.seqsCommand, name=yourNameFile)\n";
-               helpString += "make.lefse(shared=final.an.list, taxonomy=final.an.taxonomy, name=final.names)\n";
+               helpString += "The make.lefse command should be in the following format: make.lefse(shared=yourSharedFile)\n";
+               helpString += "make.lefse(shared=final.an.shared)\n";
                return helpString;
        }
        catch(exception& e) {
@@ -289,7 +289,7 @@ int MakeLefseCommand::runRelabund(map<string, consTax2>& consTax, vector<SharedR
         
         for (int i = 0; i < lookup[0]->getNumBins(); i++) { //process each otu
             if (m->control_pressed) { break; }
-            string nameOfOtu = m->currentBinLabels[i];
+            string nameOfOtu = m->currentSharedBinLabels[i];
             if (constaxonomyfile != "") { //try to find the otuName in consTax to replace with consensus taxonomy
                 map<string, consTax2>::iterator it = consTax.find(nameOfOtu);
                 if (it != consTax.end()) {
@@ -299,7 +299,7 @@ int MakeLefseCommand::runRelabund(map<string, consTax2>& consTax, vector<SharedR
                     //remove confidences and change ; to |
                     m->removeConfidences(nameOfOtu);
                     for (int j = 0; j < nameOfOtu.length()-1; j++) {
-                        if (nameOfOtu[j] == ';') { fixedName += "_" + m->currentBinLabels[i] + '|'; }
+                        if (nameOfOtu[j] == ';') { fixedName += "_" + m->currentSharedBinLabels[i] + '|'; }
                         else { fixedName += nameOfOtu[j]; }
                     }
                     nameOfOtu = fixedName;