added out.hierarchy command

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 82a1d2473a0bc35282abd46a5998ae65fbcce1bf..9ab27f9cbd439fe55ed1856c6940f0e42e6ee7e0 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -91,18 +91,20 @@ int SeqSummaryCommand::execute(){
 
                while(!inFASTA.eof()){
                        Sequence current(inFASTA);
-                       startPosition.push_back(current.getStartPos());
-                       endPosition.push_back(current.getEndPos());
-                       seqLength.push_back(current.getNumBases());
-                       ambigBases.push_back(current.getAmbigBases());
-                       longHomoPolymer.push_back(current.getLongHomoPolymer());
-
-                       outSummary << current.getName() << '\t';
-                       outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
-                       outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
-                       outSummary << current.getLongHomoPolymer() << endl;
-                       
-                       numSeqs++;
+                       if (current.getName() != "") {
+                               startPosition.push_back(current.getStartPos());
+                               endPosition.push_back(current.getEndPos());
+                               seqLength.push_back(current.getNumBases());
+                               ambigBases.push_back(current.getAmbigBases());
+                               longHomoPolymer.push_back(current.getLongHomoPolymer());
+                               
+                               outSummary << current.getName() << '\t';
+                               outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
+                               outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
+                               outSummary << current.getLongHomoPolymer() << endl;
+                               
+                               numSeqs++;
+                       }
                        gobble(inFASTA);
                }
                inFASTA.close();
@@ -120,6 +122,10 @@ int SeqSummaryCommand::execute(){
                int ptile97_5   = int(numSeqs * 0.975);
                int ptile100    = numSeqs - 1;
                
+               //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
+               if (startPosition[0] == -1) {  startPosition[0] = 0;    }
+               if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
+               
                mothurOutEndLine();
                mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); mothurOutEndLine();
                mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); mothurOutEndLine();