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Author Commit Message Labels Comments Date
chuttenh
[svn r265] Add a Win32 compatible readline Fix minor Win32 incompatibilities in extlibs (ugly, I know) Add VS projects for extlibs and the first few tools
mark
[svn r263] starting to get autotools to work (at least on macs)
chuttenh
[svn r261] Move files #3: start autotools stuff, finish major file dragging
chuttenh
[svn r260] Move files #2: trimming old stuff
chuttenh
[svn r259] Move files around #1: rough outlines
chuttenh
[svn r258] Update some makefiles Add quantization option to Dab2Dad bulk output Fix some Linux burps
chuttenh
[svn r256] Add ontology processing and ratio-based networks to BNServer Fix some SVG output stuff in BNServer to play nice with edge clicks Add filename-based saves to CFullMatrix and improve its opens a little Add more human-ID friendly options to GO and KEGG parsing Add read-only CGenes opening from a gene list This means no modification of the underlying CGenome Which means only previously known genes are added to the set Add per-gene connectivity background ge…
chuttenh
[svn r255] Add KNNImputer standalone code (and appropriate libBioUtils modifications) Add gene list output to Dat2Dab
chuttenh
[svn r254] Add ability for BNFunc to output negative gene sets for each positive gene set That is, determine which genes are highly unrelated to a GO term Fix a dumb bug in BNTruster involving default (zero) values Default values were being used when evaluating the "trust" of a single node That made the trust values more uniform than they should be Since everything shared some of the same default value signal Fix an occasional crash in BNUnraveler when no canonical gene list …
chuttenh
[svn r251] Add a filename-based Open call to CGenes (finally!) Add cocluster counting to Clusters2Dab Fix a handful of term filtering bugs in BNWeaver Add customized negative/positive filtering to BNWeaver
chuttenh
[svn r250] Add comment lines to dat input (# lines) Fix precision bug in Bayes net calculations with many (>600) datasets Improve SVG output (scaling, vbox, control location) Fix a few potential crashes in BNServer Add file and socket options to SVG generation
sgrossbe
[svn r249] SVMSam
chuttenh
[svn r247] Fix a nasty precision bug in BNCreator for large numbers of inputs Fix a misplaced (I think?) SVM file
chuttenh
[svn r236] Fix some extraneous test code that accidentally got committed
chuttenh
[svn r235] Add full pixie network generation to BNServer This is a safekeeping checkin before IE-ifying the SVG output Piped as an SVG back over the requesting socket for inlining <5s per request, calculated from scratch in realtime! Add Contexter for hubbiness calculations from DB format data Improve DOT output to name nodes more accurately/readably Improve Bayes net inference by trading logs/exps for doubles Precise out to ~3 significant figur…
chuttenh
[svn r234] Remove gigantic cruft from the repository.
chuttenh
[svn r230] Add multithreading to BNTruster Fix CSVM double free problem with svm_light semantics change
chuttenh
[svn r228] Add a real blocking implementation of CDatabase construction So help me, if it's not fast enough to be usable, I'm going to cry.
chuttenh
[svn r227] Fix a bug in halfmatrix when attempting to access entries on the diagonal Fix a bug in propertyfile introduced by new memory management Add a first pass implementation of blocking in CDatabase generation This also fixes some bugs in the previous implementation On the down side, it doesn't really do full blocking yet, but it's close
chuttenh
[svn r225] Fix a Linux/MSVC disagreement about sprintf
chuttenh
[svn r224] Add updated boost libraries for .dot file parsing Fix a bunch of Linux issues with the new BNServer code Update a few more things to remove PNL/XML dependencies
chuttenh
[svn r223] Improve color generation in CDat DOT graph output Add gene set lookup and write caching to CDatabase Add DOT graph processing and SVG generation to BNServer This is a partial port of Daniel's Java server code The rest is on its way! Fix BNTruster dataset significance calculations Weighted sum of |prior - posterior|s is calculated more accurately now You can also optionally output the unweighted difference for each bin
chuttenh
[svn r222] Fix Linux namespace issues with pthreads in CDatabaselet Add two new CDatabase creation (Open) methods The fastest one is currently enabled Add quick-and-dirty Bayes net collection save/load to BNServer Add multiple command type processing to BNServer Allows both Bayes net inference and data lookup Add a test script for BNServer
chuttenh
[svn r221] Fix a few pointer bugs in CDatabase/CDatabaselet Add nibble (rather than byte) alignment to CDatabase/CDatabaselet Update CBayesNetMinimal to read nibbles by default Add full genome scan Evaluate to CBayesNetMinimal
chuttenh
[svn r220] Fix thread safety, a memory leak, and error printing in CDatabaselet Update BNServer to use CDatabase instead of MySQL Add Data2DB makefile
chuttenh
[svn r219] Fix read-only open bugs in CDatabase Add optional answerless evaluation to CBayesNetMinimal Fix a file counting bug in Data2DB 10-22-07 19:37:58
chuttenh
[svn r218] Fix CDatabase to (painfully) work around open file handle limit
chuttenh
[svn r217] Update Data2Sql to access MySQL directly Add Data2DB and CDatabase for simple disk-based dataset database management
chuttenh
[svn r216] Remove further dependencies on PNL and Xerces/Xalan Update BNServer so it works Querying a single human gene across the entire genome takes ~0.5s end to end
chuttenh
[svn r214] Improve Overlapper behavior to include real confusion matrices Now outputs a full matrix for an arbitrary quantized dat pair Fix some Linux-specific stuff for CServer and XML exclusion
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