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JAL-517
tree canvas not redrawn when selection state changes a second time
InstallAnywhere distribution not building correctly
user colourscheme applied to multiple groups not correctly recovered from Jalview project fileJAL-490
pad gaps option in the edit menu
vamsas client migration from 0.1 to 0.2
pdb files without identifier cannot be opened in the structure viewerJAL-482
colour by feature score or feature description
disable fetch buttons on das source settings dialog during operations
commandline png output not generated if das features are retrieved
manually specify column width/height independently of font size
Automatically sort alignment by current tree
search result count broken when regex matches sequence ID rather than sequence
java console does not flush
associations between nucleic acid sequences and structures
last word of feature tooltip not displayed
resolve annotation row element parsing ambiguity in annotation file (annotationFile)
non-positional features can not be exported
'create feature from selected region' incorrectly creates features at end of sequence
cannot export visible columns of alignment with sequence associated annotation
find does not match case-insensitively on a sequence's ID string
codon highlighting not written to project for xrefs between EMBL and protein products
secondary structure imported from stockholm cannot be exported and imported again via annotation file
find does nothing when overview is displayed for another alignment
gaps and mutations only view of alignment
InstallAnywhere with No VM fails to find java
Tree viewer rendering preferences
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JAL","validSearcher":true,"isShown":true},"fixfor":{"name":"Fix Version","viewHtml":" <div class=\"searcherValue\">\n \n <label class=\"fieldLabel\" for=\"fieldfixfor\">Fix Version:</label><span id=\"fieldfixfor\" class=\"fieldValue\">\n \n 2.5 </span></div>\n","editHtml":"\n <div class=\"field-group aui-field-projectconstant\" >\n <label for=\"searcher-fixfor\">Fix Version</label>\n <select class=\"select js-default-checkboxmultiselect\" id=\"searcher-fixfor\" multiple=\"multiple\" name=\"fixfor\" size=\"2\" >\n <optgroup label=\"\">\n <option value=\"-1\" title=\"No Version\">No Version</option>\n <option value=\"-2\" title=\"Unreleased Versions\">Unreleased Versions</option>\n <option value=\"-3\" title=\"Released Versions\">Released Versions</option>\n </optgroup>\n <optgroup label=\"Unreleased Versions\">\n <option value=\"id:2.11.12\" title=\"2.11.12\">2.11.12</option>\n <option value=\"id:2.11.3\" title=\"2.11.3\">2.11.3</option>\n <option value=\"id:2.11.3_js\" title=\"2.11.3_js\">2.11.3_js</option>\n <option value=\"id:2.11.4\" title=\"2.11.4\">2.11.4</option>\n <option value=\"id:2.11.4.2\" title=\"2.11.4.2\">2.11.4.2</option>\n <option value=\"id:2.11.5\" title=\"2.11.5\">2.11.5</option>\n <option value=\"id:2.11.5.0\" title=\"2.11.5.0\">2.11.5.0</option>\n <option value=\"id:2.12\" title=\"2.12\">2.12</option>\n <option value=\"id:2.12.0\" title=\"2.12.0\">2.12.0</option>\n <option value=\"id:2.12.0_js\" title=\"2.12.0_js\">2.12.0_js</option>\n <option value=\"id:2.12.1\" title=\"2.12.1\">2.12.1</option>\n <option value=\"id:2.13.0\" title=\"2.13.0\">2.13.0</option>\n </optgroup>\n <optgroup label=\"Released Versions\">\n <option value=\"id:2.07\" title=\"2.07\">2.07</option>\n <option value=\"id:2.08\" title=\"2.08\">2.08</option>\n <option value=\"id:2.08.1\" title=\"2.08.1\">2.08.1</option>\n <option value=\"id:2.1\" title=\"2.1\">2.1</option>\n <option value=\"id:2.1.1\" title=\"2.1.1\">2.1.1</option>\n <option value=\"id:2.10.0\" title=\"2.10.0\">2.10.0</option>\n <option value=\"id:2.10.0b1\" title=\"2.10.0b1\">2.10.0b1</option>\n <option value=\"id:2.10.1\" title=\"2.10.1\">2.10.1</option>\n <option value=\"id:2.10.2\" title=\"2.10.2\">2.10.2</option>\n <option value=\"id:2.10.2b1\" title=\"2.10.2b1\">2.10.2b1</option>\n <option value=\"id:2.10.2b2\" title=\"2.10.2b2\">2.10.2b2</option>\n <option value=\"id:2.10.3\" title=\"2.10.3\">2.10.3</option>\n <option value=\"id:2.10.3b1\" title=\"2.10.3b1\">2.10.3b1</option>\n <option value=\"id:2.10.4\" title=\"2.10.4\">2.10.4</option>\n <option value=\"id:2.10.4b1\" title=\"2.10.4b1\">2.10.4b1</option>\n <option value=\"id:2.10.5\" title=\"2.10.5\">2.10.5</option>\n <option value=\"id:2.11.0\" title=\"2.11.0\">2.11.0</option>\n <option value=\"id:2.11.1.0\" title=\"2.11.1.0\">2.11.1.0</option>\n <option value=\"id:2.11.1.1\" title=\"2.11.1.1\">2.11.1.1</option>\n <option value=\"id:2.11.1.2\" title=\"2.11.1.2\">2.11.1.2</option>\n <option value=\"id:2.11.1.3\" title=\"2.11.1.3\">2.11.1.3</option>\n <option value=\"id:2.11.1.4\" title=\"2.11.1.4\">2.11.1.4</option>\n <option value=\"id:2.11.1.5\" title=\"2.11.1.5\">2.11.1.5</option>\n <option value=\"id:2.11.1.6\" title=\"2.11.1.6\">2.11.1.6</option>\n <option value=\"id:2.11.1.7\" title=\"2.11.1.7\">2.11.1.7</option>\n <option value=\"id:2.11.2.0\" title=\"2.11.2.0\">2.11.2.0</option>\n <option value=\"id:2.11.2.1\" title=\"2.11.2.1\">2.11.2.1</option>\n <option value=\"id:2.11.2.2\" title=\"2.11.2.2\">2.11.2.2</option>\n <option value=\"id:2.11.2.3\" title=\"2.11.2.3\">2.11.2.3</option>\n <option value=\"id:2.11.2.4\" title=\"2.11.2.4\">2.11.2.4</option>\n <option value=\"id:2.11.2.5\" title=\"2.11.2.5\">2.11.2.5</option>\n <option value=\"id:2.11.2.6\" title=\"2.11.2.6\">2.11.2.6</option>\n <option value=\"id:2.11.2.7\" title=\"2.11.2.7\">2.11.2.7</option>\n <option value=\"id:2.11.3.0\" title=\"2.11.3.0\">2.11.3.0</option>\n <option value=\"id:2.11.3.1\" title=\"2.11.3.1\">2.11.3.1</option>\n <option value=\"id:2.11.3.2\" title=\"2.11.3.2\">2.11.3.2</option>\n <option value=\"id:2.11.3.3\" title=\"2.11.3.3\">2.11.3.3</option>\n <option value=\"id:2.11.4.0\" title=\"2.11.4.0\">2.11.4.0</option>\n <option value=\"id:2.11.4.1\" title=\"2.11.4.1\">2.11.4.1</option>\n <option value=\"id:2.2\" title=\"2.2\">2.2</option>\n <option value=\"id:2.2.1\" title=\"2.2.1\">2.2.1</option>\n <option value=\"id:2.3\" title=\"2.3\">2.3</option>\n <option value=\"id:2.4\" title=\"2.4\">2.4</option>\n <option value=\"id:2.4.0b2\" title=\"2.4.0b2\">2.4.0b2</option>\n <option selected=\"selected\" value=\"id:2.5\" title=\"2.5\">2.5</option>\n <option value=\"id:2.5.1\" title=\"2.5.1\">2.5.1</option>\n <option value=\"id:2.6\" title=\"2.6\">2.6</option>\n <option value=\"id:2.6.1\" title=\"2.6.1\">2.6.1</option>\n <option value=\"id:2.7\" title=\"2.7\">2.7</option>\n <option value=\"id:2.8\" title=\"2.8\">2.8</option>\n <option value=\"id:2.8.0b1\" title=\"2.8.0b1\">2.8.0b1</option>\n <option value=\"id:2.8.1\" title=\"2.8.1\">2.8.1</option>\n <option value=\"id:2.8.2\" title=\"2.8.2\">2.8.2</option>\n <option value=\"id:2.8.2b1\" title=\"2.8.2b1\">2.8.2b1</option>\n <option value=\"id:2.9\" title=\"2.9\">2.9</option>\n <option value=\"id:2.9.0b1\" title=\"2.9.0b1\">2.9.0b1</option>\n <option value=\"id:2.9.0b2\" title=\"2.9.0b2\">2.9.0b2</option>\n <option value=\"id:a.2.08.1\" title=\"a.2.08.1\">a.2.08.1</option>\n <option value=\"id:a2.07\" title=\"a2.07\">a2.07</option>\n <option value=\"id:a2.08\" title=\"a2.08\">a2.08</option>\n </optgroup>\n </select>\n </div>\n ","jql":"fixVersion = 2.5","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\" 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