sequenceserver 1.0.0.pre.5 → 1.0.0
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- checksums.yaml +4 -4
- data/.bootstrap/README.mkd +2 -0
- data/.bootstrap/config.json +416 -0
- data/.gitignore +56 -0
- data/.mailmap +5 -0
- data/.rspec +2 -0
- data/.rubocop.yml +51 -0
- data/.travis.yml +18 -0
- data/COPYRIGHT.txt +13 -0
- data/Gruntfile.js +133 -0
- data/LICENSE.txt +638 -46
- data/{LICENSE.Apache.txt → LICENSE/Apache.txt} +0 -0
- data/LICENSE/d3.txt +26 -0
- data/Rakefile +13 -0
- data/bin/sequenceserver +27 -4
- data/lib/sequenceserver.rb +26 -13
- data/lib/sequenceserver/database.rb +19 -8
- data/lib/sequenceserver/exceptions.rb +9 -1
- data/package.json +29 -0
- data/public/css/custom.css +10 -2
- data/public/dist/css/sequenceserver.min.css +1 -1
- data/public/dist/css/sequenceserver.min.css.gz +0 -0
- data/public/dist/js/sequenceserver.min.js +1 -1
- data/public/dist/js/sequenceserver.min.js.gz +0 -0
- data/public/js/jquery.t.js +2 -2
- data/public/js/sequence.js +4 -1
- data/public/js/sequenceserver.js +23 -20
- data/sequenceserver.gemspec +3 -6
- data/spec/blast_spec.rb +297 -0
- data/spec/capybara_spec.rb +51 -0
- data/spec/config_spec.rb +87 -0
- data/spec/database/funky_ids/funky_ids.fa +12 -0
- data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsd +11 -0
- data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
- data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
- data/spec/database/sample/links.rb +23 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +6449 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +2378 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
- data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
- data/spec/database/sample/si_uniprot_idmap.yml +14180 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +946 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
- data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
- data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +148303 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa +10 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa.phr +0 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa.pin +0 -0
- data/spec/database/without_parse_seqids/without_parse_seqids.fa.psq +0 -0
- data/spec/database_spec.rb +129 -0
- data/spec/empty_config.yml +0 -0
- data/spec/routes_spec.rb +103 -0
- data/spec/sample.conf +2 -0
- data/spec/sample_reports/blastn_sample.asn +144 -0
- data/spec/sample_reports/blastp_sample.asn +1187 -0
- data/spec/sample_reports/blastx_sample.asn +1191 -0
- data/spec/sample_reports/no_hits_sample.asn +130 -0
- data/spec/sample_reports/tblastn_sample.asn +1107 -0
- data/spec/sample_reports/tblastx_sample.asn +2422 -0
- data/spec/sample_reports/with_hits_sample.asn +1489 -0
- data/spec/sequence_spec.rb +100 -0
- data/spec/sequenceserver_spec.rb +108 -0
- data/spec/spec_helper.rb +11 -0
- data/views/result.erb +55 -33
- data/views/search.erb +28 -23
- metadata +63 -151
- data/public/dist/js/webshims/shims/FlashCanvas/canvas2png.js +0 -1
- data/public/dist/js/webshims/shims/FlashCanvas/flashcanvas.js +0 -1
- data/public/dist/js/webshims/shims/FlashCanvas/flashcanvas.swf +0 -0
- data/public/dist/js/webshims/shims/FlashCanvasPro/canvas2png.js +0 -1
- data/public/dist/js/webshims/shims/FlashCanvasPro/flash10canvas.swf +0 -0
- data/public/dist/js/webshims/shims/FlashCanvasPro/flash9canvas.swf +0 -0
- data/public/dist/js/webshims/shims/FlashCanvasPro/flashcanvas.js +0 -1
- data/public/dist/js/webshims/shims/canvas-blob.js +0 -1
- data/public/dist/js/webshims/shims/color-picker.js +0 -2
- data/public/dist/js/webshims/shims/combos/1.js +0 -6
- data/public/dist/js/webshims/shims/combos/10.js +0 -2
- data/public/dist/js/webshims/shims/combos/11.js +0 -2
- data/public/dist/js/webshims/shims/combos/12.js +0 -6
- data/public/dist/js/webshims/shims/combos/13.js +0 -1
- data/public/dist/js/webshims/shims/combos/14.js +0 -1
- data/public/dist/js/webshims/shims/combos/15.js +0 -2
- data/public/dist/js/webshims/shims/combos/16.js +0 -7
- data/public/dist/js/webshims/shims/combos/17.js +0 -2
- data/public/dist/js/webshims/shims/combos/18.js +0 -3
- data/public/dist/js/webshims/shims/combos/2.js +0 -7
- data/public/dist/js/webshims/shims/combos/21.js +0 -2
- data/public/dist/js/webshims/shims/combos/22.js +0 -1
- data/public/dist/js/webshims/shims/combos/23.js +0 -6
- data/public/dist/js/webshims/shims/combos/25.js +0 -2
- data/public/dist/js/webshims/shims/combos/27.js +0 -1
- data/public/dist/js/webshims/shims/combos/28.js +0 -1
- data/public/dist/js/webshims/shims/combos/29.js +0 -1
- data/public/dist/js/webshims/shims/combos/3.js +0 -1
- data/public/dist/js/webshims/shims/combos/30.js +0 -2
- data/public/dist/js/webshims/shims/combos/31.js +0 -1
- data/public/dist/js/webshims/shims/combos/33.js +0 -1
- data/public/dist/js/webshims/shims/combos/34.js +0 -1
- data/public/dist/js/webshims/shims/combos/4.js +0 -1
- data/public/dist/js/webshims/shims/combos/5.js +0 -2
- data/public/dist/js/webshims/shims/combos/6.js +0 -2
- data/public/dist/js/webshims/shims/combos/7.js +0 -7
- data/public/dist/js/webshims/shims/combos/8.js +0 -7
- data/public/dist/js/webshims/shims/combos/9.js +0 -2
- data/public/dist/js/webshims/shims/combos/97.js +0 -1
- data/public/dist/js/webshims/shims/combos/98.js +0 -1
- data/public/dist/js/webshims/shims/combos/99.js +0 -1
- data/public/dist/js/webshims/shims/details.js +0 -1
- data/public/dist/js/webshims/shims/dom-extend.js +0 -1
- data/public/dist/js/webshims/shims/es5.js +0 -1
- data/public/dist/js/webshims/shims/es6.js +0 -1
- data/public/dist/js/webshims/shims/excanvas.js +0 -1
- data/public/dist/js/webshims/shims/filereader-xhr.js +0 -1
- data/public/dist/js/webshims/shims/form-combat.js +0 -1
- data/public/dist/js/webshims/shims/form-core.js +0 -1
- data/public/dist/js/webshims/shims/form-datalist-lazy.js +0 -1
- data/public/dist/js/webshims/shims/form-datalist.js +0 -1
- data/public/dist/js/webshims/shims/form-fixrangechange.js +0 -1
- data/public/dist/js/webshims/shims/form-inputmode.js +0 -1
- data/public/dist/js/webshims/shims/form-message.js +0 -1
- data/public/dist/js/webshims/shims/form-native-extend.js +0 -1
- data/public/dist/js/webshims/shims/form-number-date-api.js +0 -1
- data/public/dist/js/webshims/shims/form-number-date-ui.js +0 -1
- data/public/dist/js/webshims/shims/form-shim-extend.js +0 -1
- data/public/dist/js/webshims/shims/form-shim-extend2.js +0 -1
- data/public/dist/js/webshims/shims/form-validation.js +0 -1
- data/public/dist/js/webshims/shims/form-validators.js +0 -1
- data/public/dist/js/webshims/shims/forms-picker.js +0 -1
- data/public/dist/js/webshims/shims/geolocation.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-ar.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-ch-CN.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-cs.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-de.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-el.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-en.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-es.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-fa.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-fr.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-he.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-hi.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-hu.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-it.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-ja.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-lt.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-nl.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-pl.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-pt-BR.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-pt-PT.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-pt.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-ru.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-sv.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-zh-CN.js +0 -1
- data/public/dist/js/webshims/shims/i18n/formcfg-zh-TW.js +0 -1
- data/public/dist/js/webshims/shims/jme/alternate-media.js +0 -1
- data/public/dist/js/webshims/shims/jme/base.js +0 -1
- data/public/dist/js/webshims/shims/jme/controls.css +0 -1
- data/public/dist/js/webshims/shims/jme/jme.eot +0 -0
- data/public/dist/js/webshims/shims/jme/jme.svg +0 -36
- data/public/dist/js/webshims/shims/jme/jme.ttf +0 -0
- data/public/dist/js/webshims/shims/jme/jme.woff +0 -0
- data/public/dist/js/webshims/shims/jme/mediacontrols-lazy.js +0 -1
- data/public/dist/js/webshims/shims/jme/mediacontrols.js +0 -1
- data/public/dist/js/webshims/shims/jme/playlist.js +0 -1
- data/public/dist/js/webshims/shims/jpicker/images/AlphaBar.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/Bars.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/Maps.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/NoColor.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/bar-opacity.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/map-opacity.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/mappoint.gif +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/picker.gif +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/preview-opacity.png +0 -0
- data/public/dist/js/webshims/shims/jpicker/images/rangearrows.gif +0 -0
- data/public/dist/js/webshims/shims/jpicker/jpicker.css +0 -1
- data/public/dist/js/webshims/shims/matchMedia.js +0 -3
- data/public/dist/js/webshims/shims/mediacapture-picker.js +0 -1
- data/public/dist/js/webshims/shims/mediacapture.js +0 -1
- data/public/dist/js/webshims/shims/mediaelement-core.js +0 -1
- data/public/dist/js/webshims/shims/mediaelement-debug.js +0 -1
- data/public/dist/js/webshims/shims/mediaelement-jaris.js +0 -1
- data/public/dist/js/webshims/shims/mediaelement-native-fix.js +0 -1
- data/public/dist/js/webshims/shims/mediaelement-yt.js +0 -1
- data/public/dist/js/webshims/shims/moxie/flash/Moxie.cdn.swf +0 -0
- data/public/dist/js/webshims/shims/moxie/flash/Moxie.min.swf +0 -0
- data/public/dist/js/webshims/shims/moxie/js/moxie-html4.js +0 -3
- data/public/dist/js/webshims/shims/moxie/js/moxie-swf.js +0 -2
- data/public/dist/js/webshims/shims/picture.js +0 -1
- data/public/dist/js/webshims/shims/plugins/jquery.ui.position.js +0 -11
- data/public/dist/js/webshims/shims/range-ui.js +0 -1
- data/public/dist/js/webshims/shims/sizzle.js +0 -11
- data/public/dist/js/webshims/shims/sticky.js +0 -1
- data/public/dist/js/webshims/shims/styles/color-picker.png +0 -0
- data/public/dist/js/webshims/shims/styles/forms-ext.css +0 -1
- data/public/dist/js/webshims/shims/styles/forms-picker.css +0 -1
- data/public/dist/js/webshims/shims/styles/progress.gif +0 -0
- data/public/dist/js/webshims/shims/styles/progress.png +0 -0
- data/public/dist/js/webshims/shims/styles/shim-ext.css +0 -1
- data/public/dist/js/webshims/shims/styles/shim.css +0 -1
- data/public/dist/js/webshims/shims/styles/transparent.png +0 -0
- data/public/dist/js/webshims/shims/styles/widget.eot +0 -0
- data/public/dist/js/webshims/shims/styles/widget.svg +0 -12
- data/public/dist/js/webshims/shims/styles/widget.ttf +0 -0
- data/public/dist/js/webshims/shims/styles/widget.woff +0 -0
- data/public/dist/js/webshims/shims/swf/JarisFLVPlayer.swf +0 -0
- data/public/dist/js/webshims/shims/swfmini-embed.js +0 -1
- data/public/dist/js/webshims/shims/swfmini.js +0 -6
- data/public/dist/js/webshims/shims/track-ui.js +0 -1
- data/public/dist/js/webshims/shims/track.js +0 -1
- data/public/dist/js/webshims/shims/url.js +0 -1
- data/public/dist/js/webshims/shims/usermedia-core.js +0 -1
- data/public/dist/js/webshims/shims/usermedia-shim.js +0 -1
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1887
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1890
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1891
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1892
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1893
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1895
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1896
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1897
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1898
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1899
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si2.2.0_077891059
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1900
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1901
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1902
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1903
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1904
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1905
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1906
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si2.2.0_07868544
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1907
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1908
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1909
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si2.2.0_07938283
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1910
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si2.2.0_07944181
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1911
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si2.2.0_07948585
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1912
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si2.2.0_07956555
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1913
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si2.2.0_07974528
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1914
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si2.2.0_07983525
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1915
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si2.2.0_07987271
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1916
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si2.2.0_08004944
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1917
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si2.2.0_08010953
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1918
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+
si2.2.0_080121161
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1919
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si2.2.0_08018772
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1920
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si2.2.0_08043932
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1921
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si2.2.0_08053652
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1922
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1923
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1924
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1925
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si2.2.0_080941095
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1926
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si2.2.0_08100954
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1927
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si2.2.0_081031092
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1928
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si2.2.0_08109170
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1929
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si2.2.0_08121378
|
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1930
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+
si2.2.0_08151998
|
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1931
|
+
si2.2.0_081761113
|
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1932
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+
si2.2.0_08188894
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1933
|
+
si2.2.0_0820496
|
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1934
|
+
si2.2.0_08207963
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1935
|
+
si2.2.0_08214365
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1936
|
+
si2.2.0_0822243
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1937
|
+
si2.2.0_08224925
|
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1938
|
+
si2.2.0_08227374
|
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1939
|
+
si2.2.0_082521129
|
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1940
|
+
si2.2.0_08253747
|
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1941
|
+
si2.2.0_08256472
|
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1942
|
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si2.2.0_082641072
|
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1943
|
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si2.2.0_08266331
|
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1944
|
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si2.2.0_0827432
|
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1945
|
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si2.2.0_08297125
|
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1946
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si2.2.0_08322443
|
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1947
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si2.2.0_08326221
|
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1948
|
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si2.2.0_08331388
|
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1949
|
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si2.2.0_08333829
|
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1950
|
+
si2.2.0_08339903
|
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1951
|
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si2.2.0_08340566
|
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1952
|
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si2.2.0_0835212
|
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1953
|
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si2.2.0_083611100
|
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1954
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si2.2.0_08362456
|
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1955
|
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si2.2.0_08371312
|
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1956
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si2.2.0_083721166
|
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1957
|
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si2.2.0_08377870
|
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1958
|
+
si2.2.0_08388369
|
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1959
|
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si2.2.0_08399750
|
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1960
|
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si2.2.0_08414485
|
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1961
|
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si2.2.0_08434327
|
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1962
|
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si2.2.0_084691158
|
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1963
|
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si2.2.0_08473216
|
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1964
|
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si2.2.0_08488808
|
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1965
|
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si2.2.0_084921136
|
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1966
|
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si2.2.0_08496767
|
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1967
|
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si2.2.0_08498171
|
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1968
|
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si2.2.0_08510949
|
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1969
|
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si2.2.0_08512696
|
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1970
|
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si2.2.0_0852057
|
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1971
|
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si2.2.0_08521387
|
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1972
|
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si2.2.0_08538329
|
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1973
|
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si2.2.0_08546508
|
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1974
|
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si2.2.0_08554590
|
|
1975
|
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si2.2.0_08565995
|
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1976
|
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si2.2.0_08582673
|
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1977
|
+
si2.2.0_0859985
|
|
1978
|
+
si2.2.0_08613860
|
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1979
|
+
si2.2.0_08637289
|
|
1980
|
+
si2.2.0_08643133
|
|
1981
|
+
si2.2.0_08657871
|
|
1982
|
+
si2.2.0_08660187
|
|
1983
|
+
si2.2.0_086751046
|
|
1984
|
+
si2.2.0_08681603
|
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1985
|
+
si2.2.0_08682620
|
|
1986
|
+
si2.2.0_08693595
|
|
1987
|
+
si2.2.0_08696651
|
|
1988
|
+
si2.2.0_08703339
|
|
1989
|
+
si2.2.0_08712853
|
|
1990
|
+
si2.2.0_08773264
|
|
1991
|
+
si2.2.0_08786736
|
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1992
|
+
si2.2.0_08793917
|
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1993
|
+
si2.2.0_08801667
|
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1994
|
+
si2.2.0_08806738
|
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1995
|
+
si2.2.0_08813459
|
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1996
|
+
si2.2.0_08823813
|
|
1997
|
+
si2.2.0_08824715
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1998
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1999
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2000
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2001
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2002
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2003
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2004
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2005
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2006
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2007
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2008
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2009
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2010
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2011
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2012
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2014
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