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