The files in this directory are bugfix replacements for files in the EMBOSS-6.2.0 distribution. Just drop the replacement files in the location shown and redo the 'make install.' Fix 1. EMBOSS-6.2.0/emboss/jembossctl.c EMBOSS-6.2.0/jemboss/lib/jemboss.jar EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/gui/ShowResultSet.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/JembossParams.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossServer.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/server/JembossThread.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/AuthPopup.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/JembossRun.java EMBOSS-6.2.0/jemboss/org/emboss/jemboss/soap/PrivateRequest.java EMBOSS-6.2.0/jemboss/utils/install-jemboss-server.sh 26 Feb 2010: Various Jemboss fixes including allowing multiple parameters to "wossname" and reporting of stderr output Fix 2. EMBOSS-6.2.0/emboss/acd/jaspextract.acd EMBOSS-6.2.0/emboss/acd/jaspscan.acd EMBOSS-6.2.0/emboss/jaspextract.c EMBOSS-6.2.0/emboss/jaspscan.c 26 Feb 2010: jaspextract and jaspscan can use the latest-format data at http://jaspar.genereg.net/html/DOWNLOAD/Archive.zip jaspextract uses the data in the "all_data/FlatFileDir" directory. It is advisable to clear delete any old data files from your EMBOSS data file area e.g. from the /usr/local/emboss/share/EMBOSS/data/JASPAR_* directories Fix 3. EMBOSS-6.2.0/emboss/emma.c 26 Feb 2010: Takes note once again of any EMBOSS_CLUSTALW environment variable setting. Fix 4. EMBOSS-6.2.0/emboss/acd/trimseq.acd 26 Feb 2010: Place limit on the maximum window size Fix 5. EMBOSS-6.2.0/ajax/core/ajpat.c EMBOSS-6.2.0/nucleus/embpat.c 26 Feb 2010: Fix crash when excessive mismatches requested in one of the fuzzpro search algorithms. Fix 6. EMBOSS-6.2.0/emboss/coderet.c EMBOSS-6.2.0/emboss/splitter.c 26 Feb 2010: Fix crash if no features in the source sequence Fix 7. EMBOSS-6.2.0/emboss/matcher.c 26 Feb 2010: Fix memory allocation problem Fix 8. EMBOSS-6.2.0/ajax/core/ajseqread.c EMBOSS-6.2.0/ajax/core/ajseqwrite.c 01-Mar-2010: Fix sequence format 'refseqp' to be a valid protein output format and to preserve more fields from refseqp input. Fix 9. EMBOSS-6.2.0/ajax/core/ajlist.c EMBOSS-6.2.0/ajax/core/ajlist.h EMBOSS-6.2.0/emboss/showfeat.c 01-Mar-2010: Fix showfeat sorted feature output to correctly sort exons for 'join' feature locations. Fix 10.EMBOSS-6.2.0/ajax/graphics/ajgraph.c EMBOSS-6.2.0/emboss/prettyplot.c 01-Mar-2010: Fix PNG graphics output format to remove large blank margins added by the plplot driver. Improve prettyplot output to better centre sequence characters within boxes. Fix 11.EMBOSS-6.2.0/emboss/recoder.c EMBOSS-6.2.0/emboss/remap.c EMBOSS-6.2.0/emboss/restrict.c EMBOSS-6.2.0/emboss/showseq.c EMBOSS-6.2.0/emboss/silent.c 01-Mar-2010: Skip bad enzyme file records Fix 12.EMBOSS-6.2.0/emboss/showpep.c EMBOSS-6.2.0/emboss/showseq.c 01-Mar-2010: Correct HTML output closing tag. Fix 13.EMBOSS-6.2.0/ajax/core/ajfeat.c 01-Mar-2010: Remove warnings for accessions and repeat features in ensembl format EMBL files. Fix 14.EMBOSS-6.2.0/emboss/acd/cirdna.acd EMBOSS-6.2.0/emboss/acd/knowntypes.standard 01-Mar-2010: Fix description of cirdna input Fix 15.EMBOSS-6.2.0/emboss/acd/extractfeat.acd EMBOSS-6.2.0/emboss/acd/maskfeat.acd EMBOSS-6.2.0/emboss/acd/showfeat.acd EMBOSS-6.2.0/emboss/acd/showpep.acd EMBOSS-6.2.0/emboss/acd/showseq.acd EMBOSS-6.2.0/emboss/acd/twofeat.acd EMBOSS-6.2.0/doc/programs/html/extractfeat.html EMBOSS-6.2.0/doc/programs/html/maskfeat.html EMBOSS-6.2.0/doc/programs/html/showfeat.html EMBOSS-6.2.0/doc/programs/html/showpep.html EMBOSS-6.2.0/doc/programs/html/showseq.html EMBOSS-6.2.0/doc/programs/html/twofeat.html EMBOSS-6.2.0/doc/programs/text/extractfeat.txt EMBOSS-6.2.0/doc/programs/text/maskfeat.txt EMBOSS-6.2.0/doc/programs/text/showfeat.txt EMBOSS-6.2.0/doc/programs/text/showpep.txt EMBOSS-6.2.0/doc/programs/text/showseq.txt EMBOSS-6.2.0/doc/programs/text/twofeat.txt 01-Mar-2010: Fix URLs for EMBL/GenBank and SwissProt feature table descriptions in help and documentation. Fix 16.EMBOSS-6.2.0/emboss/acd/remap.acd EMBOSS-6.2.0/emboss/acd/restover.acd EMBOSS-6.2.0/emboss/acd/restrict.acd EMBOSS-6.2.0/emboss/acd/showseq.acd 01-Mar-2010: Remove artificial upper limit on number of restriction cuts Fix 17.EMBOSS-6.2.0/doc/programs/html/density.2.density.gif EMBOSS-6.2.0/doc/programs/html/density.3.density.gif EMBOSS-6.2.0/doc/programs/html/Makefile.am EMBOSS-6.2.0/doc/programs/html/Makefile.in EMBOSS-6.2.0/doc/programs/html/Makefile 01-Mar-2010: Missing images for density usage examples Fix 18. EMBOSS-6.2.0/ajax/core/ajsys.c 02-Mar-2010: Add .exe extension when searching for CYGWIN executables