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.