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.