[EMBOSS] EMBOSS 6.1.0 patch 1.3

[Peter Rice]

A patch for EMBOSS 6.1.0 is on the FTP server. This fixes problems with
extractfeat, using format names with dashes (fastq-sanger) in USAs,
scaling issues in plot outputs, and some minor bugs.

The files are on our FTP server ftp://emboss.open-bio.org/pub/EMBOSS/fixes
with a patch file and instructions in the patches subdirectory.

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.



regards,

Peter Rice