X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=eeba0417b08f90aeb19d0ecf3664010133ad88fe;hb=8c8acb6218f58f662466e4111ab8aa4da0caf93c;hp=be75e4fac4ab60697b0dd84de6eeb275d231a5b3;hpb=d0cceb86216f1174afa51582a51490294912b00e;p=mothur.git

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index be75e4f..eeba041 100644
--- 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(); }