finished added bygroup processing of chimeras in chimera.slayer and chimera.uchime...

[mothur.git] / seqsummarycommand.cpp

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index be75e4fac4ab60697b0dd84de6eeb275d231a5b3..eeba0417b08f90aeb19d0ecf3664010133ad88fe 100644 (file)
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -317,6 +317,19 @@ int SeqSummaryCommand::execute(){
                sort(ambigBases.begin(), ambigBases.end());
                sort(longHomoPolymer.begin(), longHomoPolymer.end());
                int size = startPosition.size();
+               
+               //find means
+               float meanStartPosition, meanEndPosition, meanSeqLength, meanAmbigBases, meanLongHomoPolymer;
+               meanStartPosition = 0; meanEndPosition = 0; meanSeqLength = 0; meanAmbigBases = 0; meanLongHomoPolymer = 0;
+               for (int i = 0; i < size; i++) {
+                       meanStartPosition += startPosition[i];
+                       meanEndPosition += endPosition[i];
+                       meanSeqLength += seqLength[i];
+                       meanAmbigBases += ambigBases[i];
+                       meanLongHomoPolymer += longHomoPolymer[i];
+               }
+               //this is an int divide so the remainder is lost
+               meanStartPosition /= (float) size; meanEndPosition /= (float) size; meanLongHomoPolymer /= (float) size; meanSeqLength /= (float) size; meanAmbigBases /= (float) size;
                                
                int ptile0_25   = int(size * 0.025);
                int ptile25             = int(size * 0.250);
@@ -340,6 +353,8 @@ int SeqSummaryCommand::execute(){
                m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75]) + "\t" + toString(ptile75+1)); m->mothurOutEndLine();
                m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5]) + "\t" + toString(ptile97_5+1)); m->mothurOutEndLine();
                m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100]) + "\t" + toString(ptile100+1)); m->mothurOutEndLine();
+               m->mothurOut("Mean:\t" + toString(meanStartPosition) + "\t" + toString(meanEndPosition) + "\t" + toString(meanSeqLength) + "\t" + toString(meanAmbigBases) + "\t" + toString(meanLongHomoPolymer)); m->mothurOutEndLine();
+
                if (namefile == "") {  m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); }
                else { m->mothurOut("# of unique seqs:\t" + toString(numSeqs)); m->mothurOutEndLine(); m->mothurOut("total # of seqs:\t" + toString(startPosition.size())); m->mothurOutEndLine(); }