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JAL-2103 reinstate legacy behaviour (when full_MSA not available)

2016-05-09 gmungocJAL-2098 identify feature file with "<" in feature...
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2016-05-09 gmungocJAL-2018 export graduated feature colours correctly
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2016-05-05 gmungocJAL-2068 better documentation in example script
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2016-05-04 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-05-04 gmungocJAL-2074 reinstated xerces-impl.jar
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2016-05-04 gmungocJAL-2092 hide columns with/without feature
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2016-05-04 gmungocJAL-2074 corrected classpathentry for Groovy 2.4.6
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2016-05-04 gmungocMerge branch 'groovy/JAL-2074_upgradeto2.4.4' into...
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2016-05-04 gmungocJAL-2090 removed test for Java > 1.1 to enable transparency
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2016-05-03 gmungocJAL-2050 hide introns also when fetching Ensembl xrefs...
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2016-04-29 gmungocJAL-2051 better checking of retrieved / duplicated...
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2016-04-29 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-29 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-28 gmungocJAL-2083 removed use of reflection for Groovy
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2016-04-26 gmungocJAL-1981 catch any exception when setting QuaQua look...
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2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-26 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-25 gmungocJAL-2078 fixed broken link to groovy page
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2016-04-25 gmungocJAL-1812 JAL-2068 only allow one Groovy console open...
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2016-04-22 gmungocJAL-1812 JAL-2068 add Run Groovy Script to AlignFrame...
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2016-04-22 gmungocJAL-2068 code and test for case of minValue == maxValue
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2016-04-22 gmungocJAL-2068 framework and example scripts for pluggable...
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2016-04-22 gmungocJAL-2068 Javadoc added
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2016-04-22 gmungocJAL-2068 redundant implements clauses removed
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2016-04-22 gmungocJAL-2068 convenience helper method for graduated score...
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2016-04-21 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-18 gmungocJAL-2067 fixed broken link
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2016-04-14 gmungocJAL-2041 add ID,clinical_significance to feature attributes...
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2016-04-14 gmungocJAL-2041 clinical_significance shown on sequence feature...
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2016-04-14 gmungocJAL-1421 typed map / lists, explicit imports, method...
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2016-04-14 gmungocJAL-2049 small refactor of constructors to avoid code...
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2016-04-14 gmungocJAL-1421 type parameter added to some collections
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2016-04-14 gmungocJAL-2049 revised computePeptideVariants to transfer...
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2016-04-14 gmungocJAL-1705 refactored/utility methods to detect e.g....
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2016-04-14 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-04-14 gmungocJAL-653 test updated for 'use ID for description'
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2016-04-14 gmungocJAL-1270 JAL-653 use 'parse immediately' FeaturesFile...
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2016-04-12 gmungocJAL-2050 only hide introns if exons are present! Removed...
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2016-04-12 gmungocJAL-2049 separate protein variant per dna variant ...
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2016-04-11 gmungocJAL-1705 code/comment tidy only
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2016-04-11 gmungocJAL-2051 fetch Ensembl Gene accessions one at a time
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2016-04-11 gmungocJAL-391 help for reverse / complement options
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2016-04-11 gmungocJAL-1705 (new preference option to) hide introns when...
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2016-04-01 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...
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2016-04-01 gmungocJAL-1705 ensure the right mapping is used to align...
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2016-04-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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2016-04-01 gmungocJAL-2046 fix for broken test for deriveSequence
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2016-04-01 gmungocJAL-1705 reworked AlignmentUtils.makeCdsAlignment and...
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2016-04-01 gmungocJAL-653 updated test to match parsing of multi-valued...
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2016-04-01 gmungocJAL-1705 tweak to MapList.toString for debugging
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2016-04-01 gmungocJAL-1705 generalised getLength() to handle [start1...
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2016-04-01 gmungocJAL-1705 test updated for canonicalised UNIPROT sequence...
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2016-04-01 gmungocJAL-1705 include stop codon in mapped CDS range so...
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2016-04-01 gmungocJAL-2037 set DBRefEntry.version to "0" not "" in EMBL...
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2016-04-01 gmungocJAL-1705 fetch all Ensembl xrefs (except GO terms)
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2016-03-28 gmungocJAL-1705 Javadoc / debug output tweaks
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2016-03-28 gmungocJAL-2016 push getFeatureColourScheme(source) into SequenceFe...
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2016-03-28 gmungocJAL-2036 update AlignFrame menus when dbreffetcher...
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2016-03-24 gmungocJAL-1705 removed experimental 'highlight selection...
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2016-03-24 gmungocJAL-2032 structure follow mouseover in a copy of a...
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2016-03-23 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-03-23 gmungocJAL-1705 add DBRefEntry for 'self' to retrieved transcripts...
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2016-03-23 gmungocJAL-1997 default empty tooltip required for correct...
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2016-03-22 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...
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2016-03-22 gmungocJAL-1705 add xref seqs to 'parent' dataset only if...
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2016-03-22 gmungocJAL-1191 isolated SequenceOntology (BioJava wrapper...
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2016-03-22 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-03-21 gmungocMerge branch 'features/JAL-653_JAL-1766_htslib_refseqsupport...
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2016-03-21 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-03-21 gmungocJAL-2029 further fixes to get correct xrefs and xrefs...
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2016-03-21 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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2016-03-21 gmungocJAL-1855 dbfetch from /ena_sequence/, /ena_coding/
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2016-03-21 gmungocJAL-2029 many-to-many EnsemblCDS-to-Uniprot mappings
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2016-03-16 gmungocMerge branch 'develop' of https://source.jalview.org...
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2016-03-16 gmungocJAL-1705 xref ENST to correct (ENSP) accession id
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2016-03-15 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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2016-03-15 gmungocJAL-2016 corrected Javadoc, added test for anonymous...
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2016-03-15 gmungocJAL-2016 FeatureSettingsI now FeatureSettingsModelI
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2016-03-15 gmungocJAL-1705 code tidy/comment only
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2016-03-15 gmungocJAL-1705 compute reverse complement of variants on...
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2016-03-11 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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2016-03-11 gmungocJAL-1270 unit test for SequenceIdMatcher.SeqIdName
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2016-03-11 gmungocJAL-1705 check Retry-After response header
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2016-03-11 gmungocJAL-1705 javadoc added only
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2016-03-11 gmungocJAL-1705 refactoring etc for fetching Ensembl --> Uniprot
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2016-03-07 gmungocJAL-2023 CDS sequences added to / share alignment dataset
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2016-03-04 gmungocJAL-1705 EnsemblGenomes a top level db source
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2016-03-04 gmungocJAL-1705 parse 'description' from GFF as sequence description
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2016-03-03 gmungocJAL-1705 unit test for aligning with incomplete start...
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2016-03-03 gmungocJAL-1705 include stop codons in derived CDS; support...
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2016-03-02 gmungocJAL-1705 include any unmapped protein start 'X' when...
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2016-03-01 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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2016-03-01 gmungocJAL-1705 align CDS to transcripts
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2016-03-01 gmungocJAL-1705 align CDS and peptide products to transcripts
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2016-02-25 gmungocMerge branch 'develop' into features/JAL-653_JAL-1766_htslib...
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2016-02-22 gmungocJAL-1705 first pass at applying preset feature colouring...
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2016-02-20 gmungocMerge branch 'mungo_develop' into features/JAL-653_JAL...
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2016-02-20 gmungocMerge branch 'JAL-1956_featureStyles' into features...
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2016-02-20 gmungocJAL-2016 first draft of pre-set feature colour scheme
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