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