The files in this directory are bugfix replacements for files in
the EMBOSS-6.1.0 distribution. Just drop the replacement files in
the location shown and redo the 'make install.'
Fix 1. EMBOSS-6.1.0/ajax/ajfeat.c
EMBOSS-6.1.0/ajax/ajseqread.c
EMBOSS-6.1.0/ajax/ajseqwrite.c
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/GetVersion.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/ShowDB.java
EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
EMBOSS-6.1.0/jemboss/lib/client.jar
29 Jul 2009: Fix feature specification problems in Jemboss.
Use version number to point to documentation URLs
Remove standalone option from server script.
Correct FASTQ input searching for '@' to start next sequence
Standardize FASTQ sequence formats with other OpenBio projects
Correct issues in igstrict, genpept and refseqp formats
Fix 2. EMBOSS-6.1.0/ajax/ajmem.h
EMBOSS-6.1.0/ajax/ajstr.c
EMBOSS-6.1.0/ajax/ajstr.h
EMBOSS-6.1.0/nucleus/embaln.c
24-Aug-2009: Fix string extension so that pointers in lists remain valid.
This fixes a bug in processing SwissProt complex descriptions.
Fix definition of AJRESIZE0 macro.
Fix processing of first match in a profile alignment (prophet).
Fix 3. EMBOSS-6.1.0/ajax/ajfeat.c
EMBOSS-6.1.0/ajax/ajfeat.h
EMBOSS-6.1.0/ajax/ajgraph.c
EMBOSS-6.1.0/ajax/ajmath.c
EMBOSS-6.1.0/ajax/ajseq.c
EMBOSS-6.1.0/ajax/ajseqread.c
EMBOSS-6.1.0/ajax/ajseqwrite.c
EMBOSS-6.1.0/nucleus/embmisc.c
EMBOSS-6.1.0/nucleus/embmisc.h
EMBOSS-6.1.0/nucleus/embpat.c
EMBOSS-6.1.0/emboss/coderet.c
EMBOSS-6.1.0/emboss/extractfeat.c
EMBOSS-6.1.0/emboss/notseq.c
EMBOSS-6.1.0/emboss/prettyplot.c
EMBOSS-6.1.0/emboss/seqmatchall.c
EMBOSS-6.1.0/emboss/showfeat.c
EMBOSS-6.1.0/emboss/showpep.c
EMBOSS-6.1.0/emboss/showseq.c
EMBOSS-6.1.0/emboss/twofeat.c
EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
02-Dec-2009: Fixes problems with extractfeat. The fix includes cleaner
definitions of functions used to match feature tags and
feature types which result in minor updates to 6 other
applications.
Extractfeat in previous versions used its own text parser
to extract feature data from only a limited set of
formats. In release 6.1.0 it was replaced by the standard
EMBOSS feature table. With no options set, extractfeat
rejected all features (type '*' was needed to extract
features). Extractfeat default settings now extract all
features from an entry.
Features on the reverse strand were incorrectly processed
(an effect caused by some of the old extractfeat code
remaining). Reverse strand features are now correctly
parsed, including both "join(complement())" and
"complement(join())" syntax in EMBL/GenBank/DDBJ feature
tables.
Fixes an issue in GenBank parsing where the ORIGIN line is absent.
Fixes scaling errors in prettyplot, especially in mEMBOSS
when plotting to a window on screen (the default
output). The plplot library does not report the true
width and height for several devices. The assumptions in
prettyplot depend on reasonable size estimates. Release
6.2.0 will have further corrections to plplot device
scaling.
Fixes the counting of non-coding features in coderet.
Fixes a seqmatchall error for short sequences with perfect matches
When reverse-complementing sequences, also reverses
the quality scores.
Allows '-' in format names in the USA syntax, to allow
fastq-sanger fastq-illumina and fastq-solexa format names
to be used.
When reading protein sequences, a sequence with only a
stop is now recognized as empty (zero length) after
processing ambiguity codes and stops.
Fixes a problem writing features in PIR format when the
feature table is empty, for example a report file with no hits.
Fixes a dependency on 'ant' to install a Jemboss server.
Fixes a problem in logging Jemboss info/error messages.