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The files in this directory are bugfix replacements for files in
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the EMBOSS-6.1.0 distribution. Just drop the replacement files in
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the location shown and redo the 'make install.'
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c343ab4 |
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c343ab4 |
Fix 1. EMBOSS-6.1.0/ajax/ajfeat.c
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EMBOSS-6.1.0/ajax/ajseqread.c
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EMBOSS-6.1.0/ajax/ajseqwrite.c
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/Browser.java
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/GetVersion.java
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/soap/ShowDB.java
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EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
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EMBOSS-6.1.0/jemboss/lib/client.jar
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29 Jul 2009: Fix feature specification problems in Jemboss.
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Use version number to point to documentation URLs
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Remove standalone option from server script.
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Correct FASTQ input searching for '@' to start next sequence
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Standardize FASTQ sequence formats with other OpenBio projects
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Correct issues in igstrict, genpept and refseqp formats
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Fix 2. EMBOSS-6.1.0/ajax/ajmem.h
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EMBOSS-6.1.0/ajax/ajstr.c
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EMBOSS-6.1.0/ajax/ajstr.h
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EMBOSS-6.1.0/nucleus/embaln.c
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24-Aug-2009: Fix string extension so that pointers in lists remain valid.
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This fixes a bug in processing SwissProt complex descriptions.
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Fix definition of AJRESIZE0 macro.
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Fix processing of first match in a profile alignment (prophet).
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e49cb73 |
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Fix 3. EMBOSS-6.1.0/ajax/ajfeat.c
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e49cb73 |
EMBOSS-6.1.0/ajax/ajfeat.h
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EMBOSS-6.1.0/ajax/ajgraph.c
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EMBOSS-6.1.0/ajax/ajmath.c
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EMBOSS-6.1.0/ajax/ajseq.c
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EMBOSS-6.1.0/ajax/ajseqread.c
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EMBOSS-6.1.0/ajax/ajseqwrite.c
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EMBOSS-6.1.0/nucleus/embmisc.c
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EMBOSS-6.1.0/nucleus/embmisc.h
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EMBOSS-6.1.0/nucleus/embpat.c
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EMBOSS-6.1.0/emboss/coderet.c
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EMBOSS-6.1.0/emboss/extractfeat.c
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EMBOSS-6.1.0/emboss/notseq.c
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EMBOSS-6.1.0/emboss/prettyplot.c
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EMBOSS-6.1.0/emboss/seqmatchall.c
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EMBOSS-6.1.0/emboss/showfeat.c
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EMBOSS-6.1.0/emboss/showpep.c
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EMBOSS-6.1.0/emboss/showseq.c
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EMBOSS-6.1.0/emboss/twofeat.c
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EMBOSS-6.1.0/jemboss/utils/install-jemboss-server.sh
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
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EMBOSS-6.1.0/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
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02-Dec-2009: Fixes problems with extractfeat. The fix includes cleaner
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definitions of functions used to match feature tags and
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feature types which result in minor updates to 6 other
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applications.
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Extractfeat in previous versions used its own text parser
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to extract feature data from only a limited set of
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formats. In release 6.1.0 it was replaced by the standard
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EMBOSS feature table. With no options set, extractfeat
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rejected all features (type '*' was needed to extract
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features). Extractfeat default settings now extract all
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features from an entry.
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Features on the reverse strand were incorrectly processed
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(an effect caused by some of the old extractfeat code
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remaining). Reverse strand features are now correctly
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parsed, including both "join(complement())" and
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"complement(join())" syntax in EMBL/GenBank/DDBJ feature
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tables.
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Fixes an issue in GenBank parsing where the ORIGIN line is absent.
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Fixes scaling errors in prettyplot, especially in mEMBOSS
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when plotting to a window on screen (the default
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output). The plplot library does not report the true
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width and height for several devices. The assumptions in
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prettyplot depend on reasonable size estimates. Release
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6.2.0 will have further corrections to plplot device
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scaling.
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Fixes the counting of non-coding features in coderet.
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Fixes a seqmatchall error for short sequences with perfect matches
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When reverse-complementing sequences, also reverses
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the quality scores.
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Allows '-' in format names in the USA syntax, to allow
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fastq-sanger fastq-illumina and fastq-solexa format names
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to be used.
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When reading protein sequences, a sequence with only a
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stop is now recognized as empty (zero length) after
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processing ambiguity codes and stops.
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Fixes a problem writing features in PIR format when the
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feature table is empty, for example a report file with no hits.
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Fixes a dependency on 'ant' to install a Jemboss server.
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Fixes a problem in logging Jemboss info/error messages.
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