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JAL-4464
cannot store/restore group associated secondary structure consensus annotations
Overview shown and then closed when importing legacy jalview projects without overview store/restore information
ID width for imported project is affected by changes in font size in User preferencesJAL-4281
store and restore adjustable ID margin and annotation panel height in Jalview projectsJAL-4210
persist and restore minimised windows when saving Jalview projects
Show column-wise partitions on associated annotation rows
preserve Z order when restoring views
Jalview project does not preserve font aspect ratio when Viewport is zoomed with mouse
'Reload' for a jalview project results in all windows being duplicated
'use original colours' option of colour by annotation not honoured when restoring view from projectJAL-3988
Cannot connect to JABAWS webservice from Jalview 2.11.2.0
(Windows only) Jalview inconsistent in releasing file handle upon file close
structure view saved in project file as zero length entry - project load doesn't open viewer correctly
Save alignment view tab index in project
save/restore 'show hidden markers' setting for a view
Override autoannotation preferences when loading projectJAL-3464
Version compliance / validation for JAXb based project import
Per group colours shaded by consensus and thresholded with Colour by Annotation colouring not restored from Jalview Proect
Overview window isn't saved in project file
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js-default-checkboxmultiselect\" id=\"searcher-component\" multiple=\"multiple\" name=\"component\" size=\"2\" aria-label=\"Search for components\">\n <optgroup label=\"\">\n <option value=\"-1\" title=\"No Component\">No Component</option>\n </optgroup>\n <optgroup label=\"\">\n <option value=\"id:analysis\" title=\"analysis\">analysis</option>\n <option value=\"id:annotation\" title=\"annotation\">annotation</option>\n <option value=\"id:awt-gui\" title=\"awt-gui\">awt-gui</option>\n <option value=\"id:Bamboo\" title=\"Bamboo\">Bamboo</option>\n <option value=\"id:Benchmarking\" title=\"Benchmarking\">Benchmarking</option>\n <option value=\"id:bioconda\" title=\"bioconda\">bioconda</option>\n <option value=\"id:bob\" title=\"bob\">bob</option>\n <option value=\"id:cds/protein\" title=\"cds/protein\">cds/protein</option>\n <option value=\"id:checkstyle\" title=\"checkstyle\">checkstyle</option>\n <option value=\"id:chimerax\" title=\"chimerax\">chimerax</option>\n <option value=\"id:colourschemes\" title=\"colourschemes\">colourschemes</option>\n <option value=\"id:Command Line Interface\" title=\"Command Line Interface\">Command Line Interface</option>\n <option value=\"id:conda\" title=\"conda\">conda</option>\n <option value=\"id:controller\" title=\"controller\">controller</option>\n <option value=\"id:DAS\" title=\"DAS\">DAS</option>\n <option value=\"id:data retrieval services\" title=\"data retrieval services\">data retrieval services</option>\n <option value=\"id:Datamodel\" title=\"Datamodel\">Datamodel</option>\n <option value=\"id:debian\" title=\"debian\">debian</option>\n <option value=\"id:Dev and Dep\" title=\"Dev and Dep\">Dev and Dep</option>\n <option value=\"id:documentation\" title=\"documentation\">documentation</option>\n <option value=\"id:editing\" title=\"editing\">editing</option>\n <option value=\"id:Efficiency\" title=\"Efficiency\">Efficiency</option>\n <option value=\"id:Feature Request\" title=\"Feature Request\">Feature Request</option>\n <option value=\"id:feature retrieval service\" title=\"feature retrieval service\">feature retrieval service</option>\n <option value=\"id:file format issue\" title=\"file format issue\">file format issue</option>\n <option value=\"id:find\" title=\"find\">find</option>\n <option value=\"id:genomes\" title=\"genomes\">genomes</option>\n <option value=\"id:getdown\" title=\"getdown\">getdown</option>\n <option value=\"id:gradle\" title=\"gradle\">gradle</option>\n <option value=\"id:groups\" title=\"groups\">groups</option>\n <option value=\"id:gui\" title=\"gui\">gui</option>\n <option value=\"id:gui design issue\" title=\"gui design issue\">gui design issue</option>\n <option value=\"id:i18n\" title=\"i18n\">i18n</option>\n <option value=\"id:install4j\" title=\"install4j\">install4j</option>\n <option selected=\"selected\" value=\"id:Jalview Project\" title=\"Jalview Project\">Jalview Project</option>\n <option value=\"id:jalview-j2s\" title=\"jalview-j2s\">jalview-j2s</option>\n <option value=\"id:jalview-slivka\" title=\"jalview-slivka\">jalview-slivka</option>\n <option value=\"id:java11\" title=\"java11\">java11</option>\n <option value=\"id:java8\" title=\"java8\">java8</option>\n <option value=\"id:java9\" title=\"java9\">java9</option>\n <option value=\"id:jvdesktop\" title=\"jvdesktop\">jvdesktop</option>\n <option value=\"id:JVL-Ajax\" title=\"JVL-Ajax\">JVL-Ajax</option>\n <option value=\"id:jvlite\" title=\"jvlite\">jvlite</option>\n <option value=\"id:JWS-GUI\" title=\"JWS-GUI\">JWS-GUI</option>\n <option value=\"id:JWS1\" title=\"JWS1\">JWS1</option>\n <option value=\"id:JWS2\" title=\"JWS2\">JWS2</option>\n <option value=\"id:launcher\" title=\"launcher\">launcher</option>\n <option value=\"id:localexecution\" title=\"localexecution\">localexecution</option>\n <option value=\"id:logging\" title=\"logging\">logging</option>\n <option value=\"id:na\" title=\"na\">na</option>\n <option value=\"id:openjdk\" title=\"openjdk\">openjdk</option>\n <option value=\"id:OSX-App\" title=\"OSX-App\">OSX-App</option>\n <option value=\"id:overview\" title=\"overview\">overview</option>\n <option value=\"id:PAE\" title=\"PAE\">PAE</option>\n <option value=\"id:pdbe\" title=\"pdbe\">pdbe</option>\n <option value=\"id:printing and export\" title=\"printing and export\">printing and export</option>\n <option value=\"id:Properties and Preferences\" title=\"Properties and Preferences\">Properties and Preferences</option>\n <option value=\"id:provenance\" title=\"provenance\">provenance</option>\n <option value=\"id:Release-process\" title=\"Release-process\">Release-process</option>\n <option value=\"id:renderer\" title=\"renderer\">renderer</option>\n <option value=\"id:REST-API\" title=\"REST-API\">REST-API</option>\n <option value=\"id:Scriptable API\" title=\"Scriptable API\">Scriptable API</option>\n <option value=\"id:selection\" title=\"selection\">selection</option>\n <option value=\"id:sequencefeatures\" title=\"sequencefeatures\">sequencefeatures</option>\n <option value=\"id:server event\" title=\"server event\">server event</option>\n <option value=\"id:slivka\" title=\"slivka\">slivka</option>\n <option value=\"id:Structures\" title=\"Structures\">Structures</option>\n <option value=\"id:Test suite\" title=\"Test suite\">Test suite</option>\n <option value=\"id:training\" title=\"training\">training</option>\n <option value=\"id:Translations\" title=\"Translations\">Translations</option>\n <option value=\"id:trees\" title=\"trees\">trees</option>\n <option value=\"id:urllinks\" title=\"urllinks\">urllinks</option>\n <option value=\"id:usernews\" title=\"usernews\">usernews</option>\n <option value=\"id:uxstudy\" title=\"uxstudy\">uxstudy</option>\n <option value=\"id:vamsas\" title=\"vamsas\">vamsas</option>\n <option value=\"id:variants\" title=\"variants\">variants</option>\n <option value=\"id:varna\" title=\"varna\">varna</option>\n <option value=\"id:web service bug\" title=\"web service bug\">web service bug</option>\n <option value=\"id:web service request\" title=\"web service request\">web service request</option>\n <option value=\"id:website\" title=\"website\">website</option>\n <option value=\"id:Webstart\" title=\"Webstart\">Webstart</option>\n <option value=\"id:Window Geom\" title=\"Window Geom\">Window Geom</option>\n </optgroup>\n </select>\n </div>\n ","jql":"component = \"Jalview Project\"","validSearcher":true,"isShown":true},"project":{"name":"Project","viewHtml":" <div class=\"searcherValue\">\n \n <label class=\"fieldLabel\" for=\"fieldpid\">Project:</label><span id=\"fieldpid\" class=\"fieldValue\">\n \n <a href=\"/browse/JAL\" title=\"Browse Jalview project\">Jalview</a> </span></div>\n","editHtml":"\n <div class=\"field-group aui-field-project\" >\n <label for=\"searcher-pid\">Project</label>\n \n\n <select class=\"select js-default-checkboxmultiselect\" data-placeholder-text=\"Find Projects...\" id=\"searcher-pid\" multiple=\"multiple\" name=\"pid\" size=\"5\">\n <optgroup label=\"All Projects\">\n \n <option data-icon=\"/secure/projectavatar?pid=10020&size=small\"\n title=\"JABAWS\"\n value=\"10020\">\n JABAWS (JWS)\n </option>\n \n <option data-icon=\"/secure/projectavatar?pid=10010&size=small\"\n selected=\"selected\" title=\"Jalview\"\n value=\"10010\">\n Jalview (JAL)\n </option>\n \n <option data-icon=\"/secure/projectavatar?pid=10030&size=small\"\n title=\"JPred\"\n value=\"10030\">\n JPred (JPRED)\n </option>\n \n <option data-icon=\"/secure/projectavatar?pid=10130&size=small\"\n title=\"ProteoCache\"\n value=\"10130\">\n ProteoCache (PROT)\n </option>\n \n <option data-icon=\"/secure/projectavatar?pid=10230&size=small\"\n title=\"The jalview.org websites \"\n value=\"10230\">\n The jalview.org websites (JVO)\n </option>\n </optgroup>\n </select>\n </div>\n \n","jql":"project = JAL","validSearcher":true,"isShown":true},"assignee":{"name":"Assignee","editHtml":"\n \n <div class=\"field-group aui-field-userlist\" >\n <label for=\"searcher-assigneeSelect\">Assignee</label>\n <fieldset rel=\"assignee\" class=\"hidden user-group-searcher-params\">\n </fieldset>\n <select class=\"js-usergroup-checkboxmultiselect\" multiple=\"multiple\" id=\"assignee\" name=\"assignee\" data-placeholder-text=\"Enter username or group\">\n <optgroup>\n <option class=\"headerOption\" data-icon=\"https://issues.jalview.org/secure/useravatar?size=xsmall&avatarId=10063\" value=\"empty\" title=\"Unassigned\">Unassigned</option>\n </optgroup>\n <optgroup>\n </optgroup>\n </select>\n <input type=\"hidden\" name=\"check_prev_assignee\" value=\"true\">\n </div>\n \n","validSearcher":true,"isShown":true},"status":{"name":"Status","editHtml":"\n <div class=\"field-group aui-field-constants\" >\n <label for=\"searcher-status\">Status</label>\n \n <select class=\"select js-default-checkboxmultiselectstatuslozenge\" data-placeholder-text=\"Find Statuses...\" id=\"searcher-status\" 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data-simple-status=\"{"id":"4","name":"Reopened","description":"This issue was once resolved, but the resolution was deemed incorrect. From here issues are either marked assigned or resolved.","iconUrl":"/images/icons/statuses/reopened.png","statusCategory":{"id":2,"key":"new","colorName":"blue-gray"}}\">Reopened</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/resolved.png\" value=\"5\" title=\"Resolved\" data-simple-status=\"{"id":"5","name":"Resolved","description":"A resolution has been taken, and it is awaiting verification by reporter. From here issues are either reopened, or are closed.","iconUrl":"/images/icons/statuses/resolved.png","statusCategory":{"id":3,"key":"done","colorName":"green"}}\">Resolved</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/closed.png\" value=\"6\" title=\"Closed\" data-simple-status=\"{"id":"6","name":"Closed","description":"The issue is considered finished, the resolution is correct. Issues which are closed can be reopened.","iconUrl":"/images/icons/statuses/closed.png","statusCategory":{"id":3,"key":"done","colorName":"green"}}\">Closed</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10000\" title=\"Being documented\" data-simple-status=\"{"id":"10000","name":"Being documented","description":"Feature implementation is complete and passed alpha-testing, and now ready for documentation.","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":4,"key":"indeterminate","colorName":"yellow"}}\">Being documented</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10002\" title=\"Ready for testing\" data-simple-status=\"{"id":"10002","name":"Ready for testing","description":"Feature is ready for testing by non-developers","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":4,"key":"indeterminate","colorName":"yellow"}}\">Ready for testing</option>\n <option class=\"imagebacked\" data-icon=\"/images/icons/statuses/generic.png\" value=\"10003\" title=\"Being tested\" data-simple-status=\"{"id":"10003","name":"Being tested","description":"","iconUrl":"/images/icons/statuses/generic.png","statusCategory":{"id":4,"key":"indeterminate","colorName":"yellow"}}\">Being tested</option>\n </select>\n </div>\n \n","validSearcher":true,"isShown":true}}}
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