ac5918d51bed4db6f5ac837e6660b322123bbd7c
angie
  Tue Apr 26 16:36:45 2011 -0700
Added new lib module hacTree (Hierarchical Agglomerative Clustering),which takes an slList of items and a couple user-defined functions,
and returns a binary tree of clusters, with the leaf nodes containing
the original input items.  The user-defined functions do the interesting
parts: computing distance between two items and/or clusters, and
merging two items and/or clusters into a new cluster.
This is motivated by work on Feature #3711 (vcfTabix: center-weighted
haplotype sorting for display of phased genotypes), but I'm hoping
it might have other uses.

diff --git src/lib/makefile src/lib/makefile
index eae2f1a..1ab8292 100644
--- src/lib/makefile
+++ src/lib/makefile
@@ -9,31 +9,31 @@
     dgRange.o diGraph.o dlist.o dnaLoad.o dnaMarkov.o dnaMotif.o dnaseq.o \
     dnautil.o dtdParse.o dystring.o \
     emblParse.o errCatch.o errabort.o \
     fa.o ffAli.o ffScore.o filePath.o fixColor.o flydna.o fof.o \
     font/mgCourier10.o font/mgCourier12.o font/mgCourier14.o font/mgCourier18.o \
     font/mgCourier24.o font/mgCourier34.o font/mgCourier8.o font/mgHelvetica10.o \
     font/mgHelvetica12.o font/mgHelvetica14.o font/mgHelvetica18.o font/mgHelvetica24.o \
     font/mgHelvetica34.o font/mgHelvetica8.o font/mgHelveticaBold10.o font/mgHelveticaBold12.o \
     font/mgHelveticaBold14.o font/mgHelveticaBold18.o font/mgHelveticaBold24.o \
     font/mgHelveticaBold34.o font/mgHelveticaBold8.o font/mgSixhi6.o font/mgSail8.o \
     font/mgTimes10.o font/mgTimes12.o font/mgTimes14.o font/mgTimes18.o \
     font/mgTimes24.o font/mgTimes34.o font/mgTimes8.o \
     fuzzyShow.o \
     gapCalc.o gdf.o gemfont.o genomeRangeTree.o \
     gfNet.o gff.o gff3.o gfxPoly.o gifLabel.o \
-    hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o \
+    hacTree.o hash.o histogram.o hmmPfamParse.o hmmstats.o htmlPage.o htmshell.o \
     https.o intExp.o intValTree.o internet.o itsa.o \
     jointalign.o jpegSize.o keys.o knetUdc.o kxTok.o linefile.o localmem.o log.o \
     maf.o mafFromAxt.o mafScore.o md5.o memalloc.o memgfx.o metaWig.o mgCircle.o \
     mgPolygon.o mime.o net.o nib.o nibTwo.o nt4.o numObscure.o \
     obscure.o oldGff.o oligoTm.o options.o osunix.o pairHmm.o peakCluster.o \
     phyloTree.o pipeline.o portimpl.o pngwrite.o psGfx.o psPoly.o pscmGfx.o \
     psl.o pslGenoShow.o pslShow.o pslTbl.o pslTransMap.o pthreadWrap.o \
     qa.o quickHeap.o quotedP.o \
     ra.o rainbow.o rbTree.o rangeTree.o regexHelper.o repMask.o \
     rle.o rnautil.o rqlEval.o rqlParse.o rudp.o \
     scoreWindow.o seg.o seqOut.o seqStats.o servBrcMcw.o servCrunx.o \
     servcis.o servcl.o servmsII.o servpws.o shaRes.o slog.o snof.o \
     snofmake.o snofsig.o spaceSaver.o spacedColumn.o spacedSeed.o \
     splatAli.o sqlList.o sqlNum.o subText.o sufa.o sufx.o synQueue.o \
     tabRow.o textOut.o tokenizer.o trix.o twoBit.o \