v18.2.0 (2022-03-16)
v18.1.0 (2019-12-04)
v18.0.3 (2019-08-07)
Closed issues:
- Artemis vs. Java #293
- For windows Error: A JNI error has occurred, please check your installation and try again #292
- Supported JDKs/JREs #290
- Cannot install Java 9 on MacOSX #288
- unrecognized option #287
- no .jar files in Artemis download #285
- Problem installing via conda #284
- I am trying to open Artemis in windows 10 pro. The screen is not opening #283
Merged pull requests:
- Add a docker file, build and documentation updates. Fix for issue 293. #294 (kpepper)
- RT ticket 621414 - addition of source field to Gene Builder GO Term panel #289 (kpepper)
- Documentation update for bioconda installs #286 (kpepper)
- Add Bioconda badge #282 (kpepper)
- Added additional course link #281 (kpepper)
- Added documentation and courses sections #280 (kpepper)
- Documentation updates #279 (kpepper)
v18.0.2 (2019-02-06)
Merged pull requests:
- RT Ticket 648115 blast issue #278 (kpepper)
- Fix for RT ticket 649125 #277 (kpepper)
- Added information on installation via Bioconda #276 (kpepper)
- Updated Artemis release number to v18.0.1 #275 (kpepper)
v18.0.1 (2019-01-22)
Merged pull requests:
- Artemis Release v18.0.1 draft changes #274 (kpepper)
- Autogenerate CHANGELOG.md #273 (ssjunnebo)
- Added section on security warnings for Macs #272 (kpepper)
- Artemis v18.0.0 Documentation Changes #271 (kpepper)
v18.0.0 (2019-01-07)
Merged pull requests:
v18.0.0-RC1 (2018-12-13)
Closed issues:
- "This version of Mac OS X does not support the Apple EAWT." #267
- Artemis on server #264
- Can not use Artemis #263
- Run fails: Could not find or load main class uk.ac.sanger.artemis.components.ArtemisMain\nPermissions: all-permissions ``` #261
- What's the entry point for Bamview in artemis.jar ? #240
- artemis_compiled_v17.0.1.tar.gz has all MacOS resource forks in it #239
- Feature Request: recognize and open multi-genbanks in multiple seperate windows #236
Merged pull requests:
- Committed Artemis and ACT word master docs from which HTML and PDF ma… #268 (kpepper)
- Added the Chado folder #266 (kpepper)
- Add Artemis and ACT html/pdf manuals to gh-pages branch #265 (kpepper)
- Fixed GitHub issue 261 - escaped line feed left in manifest when buil… #262 (kpepper)
- Fix for RT issue 624271 - bam data caching issue #260 (kpepper)
- Various updates to github pages, inc removal of sourceforge references. #259 (kpepper)
- 589110 readme #258 (ssjunnebo)
- Remove windows download note #257 (ssjunnebo)
- update downloads #256 (ssjunnebo)
- Show favicon on all pages #255 (ssjunnebo)
- remove downloads from artemis page #254 (ssjunnebo)
- add favicon #253 (ssjunnebo)
- update ftp downloads #252 (ssjunnebo)
- fix links #251 (ssjunnebo)
- change header name #250 (ssjunnebo)
- update Artemis page #249 (ssjunnebo)
- Update layout #248 (ssjunnebo)
- Transfer content from Sanger web pages #247 (ssjunnebo)
- Change page header #246 (ssjunnebo)
- 574328 update readme #245 (ssjunnebo)
- include faq etc #244 (ssjunnebo)
- Added more content #243 (ssjunnebo)
- first draft of gh pages #242 (ssjunnebo)
- Set up github pages #241 (ssjunnebo)
v17.0.1 (2018-03-09)
Merged pull requests:
- small increase in splash height for ubuntu #238 (kpepper)
- V17 patch branch #237 (kpepper)
- Rebranded splash screen #235 (kpepper)
v17.0.0 (2018-02-12)
Closed issues:
- reading features from entries in BED(12) format #232
- Artemis not opening files with brackets/space/altered name #229
- Why blast shows no response? #228
- java.lang.NullPointerException #227
Merged pull requests:
- Changed BamUtilsTest class to cope with connect exception. #234 (kpepper)
- Artemis unit testing v17.0.0 branch merge #233 (kpepper)
- update scratch108 to scratch118 - v16.0.18 #230 (vaofford)
v16.0.17 (2016-11-23)
Closed issues:
- .embl file not working in Artemis #222
Merged pull requests:
- Updated NCBI blast URL to https #226 (aslett1)
- version bump #225 (satta)
- add TCDB as database #221 (satta)
- fix method name clash for List.sort() in Java 8 #220 (satta)
- switch to older EMBOSS version #219 (satta)
- override abstract method close() in CRAMReferenceSequenceFile #218 (0xaf1f)
- Added Kim Rutherford #217 (aslett1)
- Add TravisCI Support, change README to markdown #215 (bewt85)
- actually clone the history attribute #214 (satta)
- add support for eupathdb_uc user comment attributes #213 (satta)
- add new 'alias' qualifier #212 (satta)
- Added uORF, sORF and tnaORF as extra keys #211 (fatimasilva)
- extend escaping in qualifier values #210 (satta)
- Added AUTHORS file #209 (aslett1)
- Added LICENSE #208 (aslett1)
- simplify regex for user comment scraping #207 (satta)
- add tritryp_uc attribute to GFF3 export #206 (satta)
- do not always strip 'term=' from product #205 (satta)
- add user_data_min and user_data_max flags #204 (tcarver)
- allow user plots scaling to be controlled with user_scaling_on #203 (tcarver)
- misc #202 (tcarver)
- misc #201 (tcarver)
- misc #200 (tcarver)
- remove quotes #199 (tcarver)
- misc #198 (tcarver)
- misc #197 (tcarver)
- misc #196 (tcarver)
- misc #195 (tcarver)
- fix for paired stack view when showing SNPs #194 (tcarver)
- misc #193 (tcarver)
- misc #191 (tcarver)
- ignore codon_start when writing out #189 (tcarver)
- increase default threshold #188 (tcarver)
- misc #187 (tcarver)
- fix for writing GFF qualifiers and stripping out current= #186 (tcarver)
- misc #185 (tcarver)
- misc #184 (tcarver)
- Sascha GFF export and GFF encode / decode changes #183 (tcarver)
- misc #181 (tcarver)
- use uniprot.org for protein links #180 (tcarver)
- misc #179 (tcarver)
- misc #178 (tcarver)
- misc #177 (tcarver)
v16.0.0 (2014-01-14)
Merged pull requests:
- misc #176 (tcarver)
- allow to exclude attributes from GFF3 output #175 (satta)
- do not output empty GFF3 attributes #174 (satta)
- misc #173 (tcarver)
- misc #172 (tcarver)
- misc #171 (tcarver)
- warn when overlaying a GFF with a sequence onto a sequence entry #170 (tcarver)
- fix for ACT jnlp VM properties #169 (tcarver)
- fix for ACT jnlp VM properties #168 (tcarver)
- misc #167 (tcarver)
- updates for test #166 (tcarver)
- misc #165 (tcarver)
- update #164 (tcarver)
- misc #163 (tcarver)
- misc #162 (tcarver)
- misc #161 (tcarver)
- misc #160 (tcarver)
- misc #159 (tcarver)
- misc #158 (tcarver)
- misc #157 (tcarver)
- misc #156 (tcarver)
- bamview update #155 (tcarver)
- update version #154 (tcarver)
- misc #153 (tcarver)
- misc #152 (tcarver)
- mics #151 (tcarver)
- rename #150 (tcarver)
- misc #149 (tcarver)
- misc #148 (tcarver)
- misc #147 (tcarver)
- misc #145 (tcarver)
- misc #144 (tcarver)
- fix for validate button on linux #143 (tcarver)
- misc #142 (tcarver)
- misc #141 (tcarver)
- misc #140 (tcarver)
- update version #139 (tcarver)
- misc #138 (tcarver)
- misc #137 (tcarver)
- misc #136 (tcarver)
- update version #135 (tcarver)
- misc #134 (tcarver)
- rnaseq strand specific option #133 (tcarver)
- misc #132 (tcarver)
- misc #131 (tcarver)
- misc #130 (tcarver)
- misc #129 (tcarver)
v15.0.0 (2013-02-15)
Merged pull requests:
- cram #128 (tcarver)
- misc #127 (tcarver)
- add a log statement #126 (tcarver)
- misc #125 (tcarver)
- misc #124 (tcarver)
- update #123 (tcarver)
- misc #122 (tcarver)
- misc #121 (tcarver)
- misc #120 (tcarver)
- misc #119 (tcarver)
- misc #118 (tcarver)
- misc #117 (tcarver)
- misc #115 (tcarver)
- batik 1.7 #114 (tcarver)
- misc #113 (tcarver)
- changes for setting partial on featureloc #112 (tcarver)
- misc #111 (tcarver)
- misc #110 (tcarver)
- misc #109 (tcarver)
- misc #108 (tcarver)
- misc #107 (tcarver)
- BamView changes #106 (tcarver)
- misc #105 (tcarver)
- misc #104 (tcarver)
- misc #103 (tcarver)
- add picard libs to classpath #102 (tcarver)
- misc #101 (tcarver)
- misc #100 (tcarver)
- dnaplotter speed up with BLAST files #99 (tcarver)
- update version #98 (tcarver)
- misc #97 (tcarver)
- misc #96 (tcarver)
- update version #95 (tcarver)
- misc #94 (tcarver)
- make executable #93 (tcarver)
- misc #92 (tcarver)
- misc #91 (tcarver)
- misc #90 (tcarver)
- misc #89 (tcarver)
- clear GFF cache #88 (tcarver)
- phase is REQUIRED for all CDS features #87 (tcarver)
- misc #86 (tcarver)
- allow user to open database entry using gene or sequence ID #85 (tcarver)
- misc #84 (tcarver)
- misc #83 (tcarver)
- misc #82 (tcarver)
- misc #81 (tcarver)
- update version #80 (tcarver)
- misc #79 (tcarver)
- fix if etc/project.properties is missing #78 (tcarver)
- fix for BAM index #77 (tcarver)
- update version #76 (tcarver)
- misc #75 (tcarver)
- misc #74 (tcarver)
- change to scratch #73 (tcarver)
- misc #72 (tcarver)
- misc #71 (tcarver)
- misc #70 (tcarver)
- misc #69 (tcarver)
- misc #68 (tcarver)
- update #67 (tcarver)
- feature stack view #66 (tcarver)
- misc #65 (tcarver)
- misc #64 (tcarver)
- misc #63 (tcarver)
- misc #62 (tcarver)
- remove embl suffix from ID in EMBL header #61 (tcarver)
- fix for reading back in user defined shortcuts #60 (tcarver)
- misc #59 (tcarver)
- misc #58 (tcarver)
- misc #57 (tcarver)
- fix for getCDSLine() #56 (tcarver)
- fix for update partial settings #55 (tcarver)
- GFF and feature stack view #54 (tcarver)
- misc GFF support #53 (tcarver)
- misc #52 (tcarver)
v14.0.0 (2012-02-20)
Merged pull requests:
- misc #51 (tcarver)
- misc #50 (tcarver)
- VALIDATION_STRINGENCY=SILENT #49 (tcarver)
- set VALIDATION_STRINGENCY=LENIENT #48 (tcarver)
- set viewport position for the strand view when changing resolution #47 (tcarver)
- misc #46 (tcarver)
- misc #45 (tcarver)
- add to extra_keys_gff #44 (tcarver)
- adding tooltips #43 (tcarver)
- misc #42 (tcarver)
- misc #41 (tcarver)
- misc #40 (tcarver)
- optimise #39 (tcarver)
- fix for VCF file parse() #38 (tcarver)
- vcf updates #37 (tcarver)
- file suffix #36 (tcarver)
- misc bamview and vcfview #35 (tcarver)
- update #34 (tcarver)
- fix for getVcfContainer() #33 (tcarver)
- misc #32 (tcarver)
- update version #31 (tcarver)
- misc #30 (tcarver)
- standalone BamView improvements #29 (tcarver)
- misc #28 (tcarver)
- fix for selenocysteine on reverse strand #27 (tcarver)
- misc #26 (tcarver)
- fix VCF test #25 (tcarver)
- misc #24 (tcarver)
- shortcut changed in Preferences are saved between sessions #23 (tcarver)
- work around for backward compatibility with old BCF files #22 (tcarver)
- changed to use SHIFT to drag ends when zoomed out #21 (tcarver)
- alt key used to drag ends when zoomed out and fix for loading multiple artemis windos #20 (tcarver)
- change handleSelenocysteine #19 (tcarver)
- GTF fixes #18 (tcarver)
- various #17 (tcarver)
- update version #16 (tcarver)
- typo #15 (tcarver)
- fix for partials and use non-modal to report reference change #14 (tcarver)
- use arrows for partials and fix for UTR ordering #13 (tcarver)
- update version #12 (tcarver)
- changes to allow for loading graphs into ACT from the command line with -DuserplotX system properties #11 (tcarver)
- change default GO db_xref to GO_REF:0000001 #10 (tcarver)
- load BAM/VCF files from the command line and SAM record listing #9 (tcarver)
- minor changes to vcf record methods added and fix for list of files on ftp sites #8 (tcarver)
- add mate details and update picard #7 (tcarver)
- Crawl compatability #6 (buggyvelarde)
- TAT and BamView changes #5 (tcarver)
- 2 commits #4 (tcarver)
- update to 13.2.1 #3 (tcarver)
v13.2.0 (2011-07-13)
Merged pull requests:
* This Change Log was automatically generated by github_changelog_generator