added metadata file as input to corr.axes

[mothur.git] / classifyseqscommand.cpp

diff --git a/classifyseqscommand.cpp b/classifyseqscommand.cpp
index 2d3838774afe52a382c52426e6db4243ebd64c87..bbdf8119ad9332f49be4b1c71679b50fc51fe68d 100644 (file)
--- a/classifyseqscommand.cpp
+++ b/classifyseqscommand.cpp
@@ -652,7 +652,7 @@ int ClassifySeqsCommand::execute(){
                        
                        //get maxLevel from phylotree so you know how many 'unclassified's to add
                        int maxLevel = taxaSum.getMaxLevel();
-                       
+                                                       
                        //read taxfile - this reading and rewriting is done to preserve the confidence scores.
                        string name, taxon;
                        while (!inTax.eof()) {
@@ -829,13 +829,14 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
 
                bool done = false;
                int count = 0;
-       
+               
                while (!done) {
                        if (m->control_pressed) { return 0; }
                
                        Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
                        
                        if (candidateSeq->getName() != "") {
+                       
                                taxonomy = classify->getTaxonomy(candidateSeq);
                                
                                if (m->control_pressed) { delete candidateSeq; return 0; }
@@ -867,7 +868,7 @@ int ClassifySeqsCommand::driver(linePair* filePos, string taxFName, string tempT
                }
                //report progress
                if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
-                               
+                       
                inFASTA.close();
                outTax.close();
                outTaxSimple.close();