+ General +

+ reinstate CTRL-click for opening pop-up + menu on OSX +
+ Export features in Jalview format (again) + includes graduated colourschemes +
+ More responsive when + working with big alignments and lots of hidden columns +
+ Hidden column markers not always rendered + at right of alignment window +
+ Tidied up links in help file table of + contents +
+ Feature based tree calculation not shown + for DNA alignments +
+ Hidden columns ignored during feature + based tree calculation +
+ Alignment view stops updating when show + unconserved enabled for group on alignment +
+ Cannot insert gaps into sequence when + set as reference +
+ Alignment column in status incorrectly + shown as "Sequence position" when mousing over + annotation +
+ Incorrect column numbers in ruler when + hidden columns present +
+ Colour by RNA Helices not enabled when + user created annotation added to alignment +
+ RNA Structure consensus only computed for + '()' base pair annotation +
+ Enabling 'Ignore Gaps' results + in zero scores for all base pairs in RNA Structure + Consensus +
+ Extend selection with columns containing + feature not working +
+ Pfam format writer puts extra space at + beginning of sequence +
+ Incomplete sequence extracted from pdb + entry 3a6s +
+ Cannot create groups on an alignment from + from a tree when t-coffee scores are shown +
+ Cannot import and view PDB + structures with chains containing negative resnums (4q4h) +
+ ArithmeticExceptions raised when parsing + some structures +
+ 'Empty' alignment blocks added + to Clustal, PIR and PileUp output +
+ Reordering sequence features that are + not visible causes alignment window to repaint +
+ Threshold sliders don't work in + graduated colour and colour by annotation row for e-value + scores associated with features and annotation rows +
+ amino acid physicochemical conservation + calculation should be case independent +
+ Remove annotation also updates hidden + columns +
+ FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) +
+ Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled +
+ Quality and Conservation are now shown on + load even when Consensus calculation is disabled +

+ Application +

+ URLs and links can't be imported by + drag'n'drop on OSX when launched via webstart (note - not + yet fixed for El Capitan) +
+ Corrupt preferences for SVG, EPS & HTML + output when running on non-gb/us i18n platforms +
+ Error thrown when exporting a view with + hidden sequences as flat-file alignment +
+ InstallAnywhere distribution fails when + launching Chimera +
+ Jalview very slow to launch via webstart + (also hotfix for 2.9.0b2) +
+ Cannot save project when view has a + reference sequence defined +
+ Columns are suddenly selected in other + alignments and views when revealing hidden columns +
+ Hide columns not mirrored in complement + view in a cDNA/Protein splitframe +
+ Cannot save/restore representative + sequence from project when only one sequence is + represented +
+ Disabled 'Best Uniprot Coverage' option + in Structure Chooser +
+ Modifying 'Ignore Gaps' on consensus or + structure consensus didn't refresh annotation panel +
+ View mapping in structure view shows + mappings between sequence and all chains in a PDB file +
+ PDB and Uniprot FTS + dialogs format columns correctly, don't display array + data, sort columns according to type +
+ Export complete shown after destination + file chooser is cancelled during an image export +
+ Error when querying PDB Service with + sequence name containing special characters +
+ Manual PDB structure querying should be + case insensitive +
+ Large tooltips with broken HTML + formatting don't wrap +
+ Figures exported from wrapped view are + truncated so L looks like I in consensus annotation +
+ Export features should only export the + currently displayed features for the current selection or + view +
+ Enable 'Get Cross-References' in menu + after fetching cross-references +
+ Mouseover of a copy of a sequence is not + followed in the structure viewer +
+ Titles for individual alignments in + splitframe not restored from project +
+ missing autocalculated annotation at + trailing end of protein alignment in transcript/product + splitview when pad-gaps not enabled by default +
+ amino acid physicochemical conservation + is case dependent +
+ RSS reader doesn't stay hidden after last + article has been read (reopened issue due to + internationalisation problems) +
+ Only offer PDB structures in structure + viewer based on sequence name, PDB and UniProt + cross-references +
+ No progress bar shown during export of + alignment as HTML +
+ Structures not always superimposed after + multiple structures are shown for one or more sequences. +
+ Reference sequence characters should not + be replaced with '.' when 'Show unconserved' format option + is enabled. +
+ Cannot specify chain code when entering + specific PDB id for sequence +
+ File->Export->.. as doesn't work when + 'Export hidden sequences' is enabled, but 'export hidden + columns' is disabled. +
+ Best Quality option in structure chooser + selects lowest rather than highest resolution structures + for each sequence +
+ Incorrect start and end reported for PDB + to sequence mapping in 'View Mappings' report +

+ Applet +

+ Incorrect columns are selected when + hidden columns present before start of sequence +
+ Missing dependencies on applet pages + (JSON jars) +
+ Overview pixel size changes when + sequences are hidden in applet +
+ Updated instructions for applet + deployment on examples pages. +

+ + Release + +	+ + New Features + +	+ + Issues Resolved + +
+ + 2.10.0 04/10/2016 + +	General + + + Jmol now primary parser + for importing structure data to Jalview. Enables mmCIF and + better PDB parsing. + + + Alignment ruler shows positions relative to + reference sequence + + + Position/residue shown in status bar when + mousing over sequence associated annotation + + + Default RNA SS symbol to 'matching bracket' + for manual entry + + + RNA Structure consensus indicates wc-only + '()', canonical '[]' and invalid '{}' base pair populations + for each column + + + Feature settings popup menu options for + showing or hiding columns containing a feature + + + Edit selected group by double clicking on + group and sequence associated annotation labels + + + Sequence name added to annotation label in + select/hide columns by annotation and colour by annotation + dialogs + + Application + + + Automatically hide introns when opening a + gene/transcript view + + + Uniprot Sequence fetcher Free Text Search + dialog + + + UniProt - PDB protein + structure mappings with the EMBL-EBI PDBe SIFTS database + + + Updated download sites used for Rfam and + Pfam sources to xfam.org + + + Disabled Rfam(Full) in the sequence fetcher + + + Show residue labels in Chimera when mousing + over sequences in Jalview + + + Support for reverse-complement coding + regions in ENA and EMBL + + + Upgrade to EMBL XML 1.2 + for record retrieval via ENA rest API + + + Support for ENA CDS records with reverse + complement operator + + + Update to groovy-2.4.6-indy - for faster + groovy script execution + + + New 'execute Groovy script' option in an + alignment window's Calculate menu + + + Allow groovy scripts that call + Jalview.getAlignFrames() to run in headless mode + + + Support for creating new alignment + calculation workers from groovy scripts + + + Store/restore reference sequence in + Jalview projects + + + Chain codes for a sequence's PDB + associations are now saved/restored from project + + + Database selection dialog always shown + before sequence fetcher is opened + + + Double click on an entry in Jalview's + database chooser opens a sequence fetcher + + + Free-text search client for UniProt using + the UniProt REST API + + + -nonews command line parameter to prevent + the news reader opening + + + Displayed columns for PDBe and Uniprot + querying stored in preferences + + + Pagination for displaying PDBe and Uniprot + search results + + + Tooltips shown on database chooser + + + Reverse complement function in calculate + menu for nucleotide sequences + + + Alignment sort by feature scores + and feature counts preserves alignment ordering (and + debugged for complex feature sets). + + + Chimera 1.11.1 minimum requirement for + viewing structures with Jalview 2.10 + + + Retrieve + genome, transcript CCDS and gene ids via the Ensembl and + Ensembl Genomes REST API + + + Protein sequence variant annotation + computed for 'sequence_variant' annotation on CDS regions + (Ensembl) + + + ENA CDS 'show cross references' for Uniprot + sequences + + + Improved warning messages when DB + Ref Fetcher fails to match, or otherwise updates sequence + data from external database records. + - Sequence database accessions imported when fetching - alignments from Rfam - update VARNA version to 3.91 +	+ + General + + + reinstate CTRL-click for opening pop-up + menu on OSX + + + Export features in Jalview format (again) + includes graduated colourschemes + + + More responsive when + working with big alignments and lots of hidden columns + + + Hidden column markers not always rendered + at right of alignment window + + + Tidied up links in help file table of + contents + + + Feature based tree calculation not shown + for DNA alignments + + + Hidden columns ignored during feature + based tree calculation + + + Alignment view stops updating when show + unconserved enabled for group on alignment + + + Cannot insert gaps into sequence when + set as reference + + + Alignment column in status incorrectly + shown as "Sequence position" when mousing over + annotation + + + Incorrect column numbers in ruler when + hidden columns present + + + Colour by RNA Helices not enabled when + user created annotation added to alignment + + + RNA Structure consensus only computed for + '()' base pair annotation + + + Enabling 'Ignore Gaps' results + in zero scores for all base pairs in RNA Structure + Consensus + + + Extend selection with columns containing + feature not working + + + Pfam format writer puts extra space at + beginning of sequence + + + Incomplete sequence extracted from pdb + entry 3a6s + + + Cannot create groups on an alignment from + from a tree when t-coffee scores are shown + + + Cannot import and view PDB + structures with chains containing negative resnums (4q4h) + + + ArithmeticExceptions raised when parsing + some structures + + + 'Empty' alignment blocks added + to Clustal, PIR and PileUp output + + + Reordering sequence features that are + not visible causes alignment window to repaint + + + Threshold sliders don't work in + graduated colour and colour by annotation row for e-value + scores associated with features and annotation rows + + + amino acid physicochemical conservation + calculation should be case independent + + + Remove annotation also updates hidden + columns + + + FER1_ARATH and FER2_ARATH mislabelled in + example file (uniref50.fa, feredoxin.fa, unaligned.fa, + exampleFile_2_7.jar, exampleFile.jar, exampleFile_2_3.jar) + + + Null pointer exceptions and redraw + problems when reference sequence defined and 'show + non-conserved' enabled + + + Quality and Conservation are now shown on + load even when Consensus calculation is disabled + + + Application + + + URLs and links can't be imported by + drag'n'drop on OSX when launched via webstart (note - not + yet fixed for El Capitan) + + + Corrupt preferences for SVG, EPS & HTML + output when running on non-gb/us i18n platforms + + + Error thrown when exporting a view with + hidden sequences as flat-file alignment + + + InstallAnywhere distribution fails when + launching Chimera + + + Jalview very slow to launch via webstart + (also hotfix for 2.9.0b2) + + + Cannot save project when view has a + reference sequence defined + + + Columns are suddenly selected in other + alignments and views when revealing hidden columns + + + Hide columns not mirrored in complement + view in a cDNA/Protein splitframe + + + Cannot save/restore representative + sequence from project when only one sequence is + represented + + + Disabled 'Best Uniprot Coverage' option + in Structure Chooser + + + Modifying 'Ignore Gaps' on consensus or + structure consensus didn't refresh annotation panel + + + View mapping in structure view shows + mappings between sequence and all chains in a PDB file + + + PDB and Uniprot FTS + dialogs format columns correctly, don't display array + data, sort columns according to type + + + Export complete shown after destination + file chooser is cancelled during an image export + + + Error when querying PDB Service with + sequence name containing special characters + + + Manual PDB structure querying should be + case insensitive + + + Large tooltips with broken HTML + formatting don't wrap + + + Figures exported from wrapped view are + truncated so L looks like I in consensus annotation + + + Export features should only export the + currently displayed features for the current selection or + view + + + Enable 'Get Cross-References' in menu + after fetching cross-references + + + Mouseover of a copy of a sequence is not + followed in the structure viewer + + + Titles for individual alignments in + splitframe not restored from project + + + missing autocalculated annotation at + trailing end of protein alignment in transcript/product + splitview when pad-gaps not enabled by default + + + amino acid physicochemical conservation + is case dependent + + + RSS reader doesn't stay hidden after last + article has been read (reopened issue due to + internationalisation problems) + + + Only offer PDB structures in structure + viewer based on sequence name, PDB and UniProt + cross-references + + + + No progress bar shown during export of + alignment as HTML + + + Structures not always superimposed after + multiple structures are shown for one or more sequences. + + + Reference sequence characters should not + be replaced with '.' when 'Show unconserved' format option + is enabled. + + + Cannot specify chain code when entering + specific PDB id for sequence + + + File->Export->.. as doesn't work when + 'Export hidden sequences' is enabled, but 'export hidden + columns' is disabled. + + + Best Quality option in structure chooser + selects lowest rather than highest resolution structures + for each sequence + + + Incorrect start and end reported for PDB + to sequence mapping in 'View Mappings' report + + + + Applet + + + Incorrect columns are selected when + hidden columns present before start of sequence + + + Missing dependencies on applet pages + (JSON jars) + + + Overview pixel size changes when + sequences are hidden in applet + + + Updated instructions for applet + deployment on examples pages. + + + +
+ + 2.9.0b2 + 16/10/2015 + +	General + + Time stamps for signed Jalview application and applet + jars +	+ + Application + + Duplicate group consensus and conservation rows + shown when tree is partitioned + Erratic behaviour when tree partitions made with + multiple cDNA/Protein split views + + +
+ + 2.9.0b1 + 8/10/2015 + +	General + + Updated Spanish translations of localized text for + 2.9 + Application + + + Signed OSX InstallAnywhere installer + Support for per-sequence based annotations in BioJSON + Applet + + Split frame example added to applet examples page +	+ + General + + Mapping of cDNA to protein in split frames + incorrect when sequence start > 1 + Broken images in filter column by annotation dialog + documentation + Feature colours not parsed from features file + Exceptions and incomplete link URLs recovered when + loading a features file containing HTML tags in feature + description + + + Application + + Annotations corrupted after BioJS export and + reimport + Incorrect sequence limits after Fetch DB References + with 'trim retrieved sequences' + Incorrect warning about deleting all data when + deleting selected columns + Patch to build system for shipping properly signed + JNLP templates for webstart launch + EMBL-PDBe fetcher/viewer dialogs do not offer + unreleased structures for download or viewing + Tab/space/return keystroke operation of EMBL-PDBe + fetcher/viewer dialogs works correctly + Disabled 'minimise' button on Jalview windows + running on OSX to workaround redraw hang bug + Split cDNA/Protein view position and geometry not + recovered from jalview project + Initial enabled/disabled state of annotation menu + sorter 'show autocalculated first/last' corresponds to + alignment view + Restoring of Clustal, RNA Helices and T-Coffee + color schemes from BioJSON + + Applet + + Reorder sequences mirrored in cDNA/Protein split + frame + Applet with Jmol examples not loading correctly + + +
+ 2.9 10/9/2015 +	General + + Linked visualisation and analysis of DNA and Protein + alignments: + + Translated cDNA alignments shown as split protein + and DNA alignment views + Codon consensus annotation for linked protein and + cDNA alignment views + Link cDNA or Protein product sequences by loading + them onto Protein or cDNA alignments + Reconstruct linked cDNA alignment from aligned + protein sequences + + + Jmol integration updated to Jmol v14.2.14 + Import and export of Jalview alignment views as BioJSON + New alignment annotation file statements for + reference sequences and marking hidden columns + Reference sequence based alignment shading to + highlight variation + Select or hide columns according to alignment + annotation + Find option for locating sequences by description + Conserved physicochemical properties shown in amino + acid conservation row + Alignments can be sorted by number of RNA helices + Application + + New cDNA/Protein analysis capabilities + + Get Cross-References should open a Split Frame + view with cDNA/Protein + Detect when nucleotide sequences and protein + sequences are placed in the same alignment + Split cDNA/Protein views are saved in Jalview + projects + + + + Use REST API to talk to Chimera + Selected regions in Chimera are highlighted in linked + Jalview windows + + VARNA RNA viewer updated to v3.93 + VARNA views are saved in Jalview Projects + Pseudoknots displayed as Jalview RNA annotation can + be shown in VARNA + + Make groups for selection uses marked columns as well + as the active selected region + + Calculate UPGMA and NJ trees using sequence feature + similarity + New Export options + + New Export Settings dialog to control hidden + region export in flat file generation + + Export alignment views for display with the BioJS MSAViewer + + Export scrollable SVG in HTML page + Optional embedding of BioJSON data when exporting + alignment figures to HTML + + 3D structure retrieval and display + + Free text and structured queries with the PDBe + Search API + PDBe Search API based discovery and selection of + PDB structures for a sequence set + + + + JPred4 employed for protein secondary structure + predictions + Hide Insertions menu option to hide unaligned columns + for one or a group of sequences + Automatically hide insertions in alignments imported + from the JPred4 web server + (Nearly) Native 'Quaqua' dialogs for browsing file + system on OSX LGPL libraries courtesy of http://www.randelshofer.ch/quaqua/ + + changed 'View nucleotide structure' submenu to 'View + VARNA 2D Structure' + change "View protein structure" menu option to "3D + Structure ..." + + Applet + + New layout for applet example pages + New parameters to enable SplitFrame view + (file2,enableSplitFrame, scaleProteinAsCdna) + New example demonstrating linked viewing of cDNA and + Protein alignments + Development and deployment + + Java 1.7 minimum requirement for Jalview 2.9 + Include installation type and git revision in build + properties and console log output + Jalview Github organisation, and new github site for + storing BioJsMSA Templates + Jalview's unit tests now managed with TestNG +	+ Application + + Escape should close any open find dialogs + Typo in select-by-features status report + Consensus RNA secondary secondary structure + predictions are not highlighted in amber + Missing gap character in v2.7 example file means + alignment appears unaligned when pad-gaps is not enabled + First switch to RNA Helices colouring doesn't colour + associated structure views + ID width preference option is greyed out when auto + width checkbox not enabled + Stopped a warning dialog from being shown when + creating user defined colours + 'View Mapping' in structure viewer shows sequence + mappings for just that viewer's sequences + Workaround for superposing PDB files containing + multiple models in Chimera + Report sequence position in status bar when hovering + over Jmol structure + Cannot output gaps as '.' symbols with Selection -> + output to text box + Flat file exports of alignments with hidden columns + have incorrect sequence start/end + 'Aligning' a second chain to a Chimera structure from + Jalview fails + Colour schemes applied to structure viewers don't + work for nucleotide + Loading/cut'n'pasting an empty or invalid file leads + to a grey/invisible alignment window + Exported Jpred annotation from a sequence region + imports to different position + Space at beginning of sequence feature tooltips shown + on some platforms + Chimera viewer 'View \| Show Chain' menu is not + populated + 'New View' fails with a Null Pointer Exception in + console if Chimera has been opened + Mouseover to Chimera not working + Miscellaneous ENA XML feature qualifiers not + retrieved + NPE in annotation renderer after 'Extract Scores' + If two structures in one Chimera window, mouseover of + either sequence shows on first structure + 'Show annotations' options should not make + non-positional annotations visible + Subsequence secondary structure annotation not shown + in right place after 'view flanking regions' + File Save As type unset when current file format is + unknown + Save as '.jar' option removed for saving Jalview + projects + Colour by Sequence colouring in Chimera more + responsive + Cannot 'add reference annotation' for a sequence in + several views on same alignment + Cannot show linked products for EMBL / ENA records + Jalview's tooltip wraps long texts containing no + spaces + Applet + + Jmol to JalviewLite mouseover/link not working + JalviewLite can't import sequences with ID + descriptions containing angle brackets + General + + Cannot export and reimport RNA secondary structure + via jalview annotation file + Random helix colour palette for colour by annotation + with RNA secondary structure + Mouseover to cDNA from STOP residue in protein + translation doesn't work. + hints when using the select by annotation dialog box + Jmol alignment incorrect if PDB file has alternate CA + positions + FontChooser message dialog appears to hang after + choosing 1pt font + Peptide secondary structure incorrectly imported from + annotation file when annotation display text includes 'e' or + 'h' + Cannot set colour of new feature type whilst creating + new feature + cDNA translation alignment should not be sequence + order dependent + 'Show unconserved' doesn't work for lower case + sequences + Nucleotide ambiguity codes involving R not recognised + Deployment and Documentation + + Applet example pages appear different to the rest of + www.jalview.org + Application Known issues + + Incomplete sequence extracted from PDB entry 3a6s + Misleading message appears after trying to delete + solid column. + Jalview icon not shown in dock after InstallAnywhere + version launches + Fetching EMBL reference for an RNA sequence results + fails with a sequence mismatch + Corrupted or unreadable alignment display when + scrolling alignment to right + ArrayIndexOutOfBoundsException thrown when remove + empty columns called on alignment with ragged gapped ends + auto calculated alignment annotation rows do not get + placed above or below non-autocalculated rows + Jalview dekstop becomes sluggish at full screen in + ultra-high resolution + Cannot disable consensus calculation independently of + quality and conservation + Mouseover highlighting between cDNA and protein can + become sluggish with more than one splitframe shown + Applet Known Issues + + Core PDB parsing code requires Jmol + Sequence canvas panel goes white when alignment + window is being resized + + +
+ 2.8.2 3/12/2014 +	General + + Updated Java code signing certificate donated by + Certum.PL. + Features and annotation preserved when performing + pairwise alignment + RNA pseudoknot annotation can be + imported/exported/displayed + 'colour by annotation' can colour by RNA and + protein secondary structure + Warn user if 'Find' regular expression is invalid (mentioned + post-hoc with 2.9 release) + + + Application + + Extract and display secondary structure for sequences + with 3D structures + Support for parsing RNAML + Annotations menu for layout + + sort sequence annotation rows by alignment + place sequence annotation above/below alignment + annotation + + Output in Stockholm format + Internationalisation: improved Spanish (es) + translation + Structure viewer preferences tab + Disorder and Secondary Structure annotation tracks + shared between alignments + UCSF Chimera launch and linked highlighting from + Jalview + Show/hide all sequence associated annotation rows for + all or current selection + disorder and secondary structure predictions + available as dataset annotation + Per-sequence rna helices colouring - New groovy scripts for exporting aligned positions, - conservation values, and calculating sum of pairs scores. - Command line argument to set default JABAWS server - include installation type in build properties and console - log output - Updated Jalview project format to preserve dataset annotation -	- Application - - Distinguish alignment and sequence associated RNA - structure in structure->view->VARNA - Raise dialog box if user deletes all sequences in an - alignment - Pressing F1 results in documentation opening twice - Sequence feature tooltip is wrapped - Double click on sequence associated annotation selects - only first column - Redundancy removal doesn't result in unlinked leaves - shown in tree - Undos after several redundancy removals don't undo - properly - Hide sequence doesn't hide associated annotation - User defined colours dialog box too big to fit on screen - and buttons not visible - author list isn't updated if already written to jalview - properties - Popup menu won't open after retrieving sequence from - database - File open window for associate PDB doesn't open - Left-then-right click on a sequence id opens a browser - search window - Cannot open sequence feature shading/sort popup menu in - feature settings dialog - better tooltip placement for some areas of Jalview desktop - Allow addition of JABAWS Server which doesn't pass - validation - Web services parameters dialog box is too large to fit on - screen - Muscle nucleotide alignment preset obscured by tooltip - JABAWS preset submenus don't contain newly defined - user preset - MSA web services warns user if they were launched with - invalid input - Jalview cannot contact DAS Registy when running on Java 8 - - - 'Superpose with' submenu not shown when new view created - - Application + + Distinguish alignment and sequence associated RNA + structure in structure->view->VARNA + Raise dialog box if user deletes all sequences in an + alignment + Pressing F1 results in documentation opening twice + Sequence feature tooltip is wrapped + Double click on sequence associated annotation + selects only first column + Redundancy removal doesn't result in unlinked + leaves shown in tree + Undos after several redundancy removals don't undo + properly + Hide sequence doesn't hide associated annotation + User defined colours dialog box too big to fit on + screen and buttons not visible + author list isn't updated if already written to + Jalview properties + Popup menu won't open after retrieving sequence + from database + File open window for associate PDB doesn't open + Left-then-right click on a sequence id opens a + browser search window + Cannot open sequence feature shading/sort popup menu + in feature settings dialog + better tooltip placement for some areas of Jalview + desktop + Allow addition of JABAWS Server which doesn't + pass validation + Web services parameters dialog box is too large to + fit on screen + Muscle nucleotide alignment preset obscured by + tooltip + JABAWS preset submenus don't contain newly + defined user preset + MSA web services warns user if they were launched + with invalid input + Jalview cannot contact DAS Registy when running on + Java 8 + + + 'Superpose with' submenu not shown when new view + created + + + Deployment and Documentation - - 2G and 1G options in launchApp have no effect on memory - allocation - launchApp service doesn't automatically open - www.jalview.org/examples/exampleFile.jar if no file is given - - - InstallAnywhere reports cannot find valid JVM when Java 1.7_055 is - available - - Application Known issues - - - - corrupted or unreadable alignment display when scrolling alignment - to right - - - - retrieval fails but progress bar continues for DAS retrieval with - large number of ID - - - - flatfile output of visible region has incorrect sequence start/end - - - - rna structure consensus doesn't update when secondary - structure tracks are rearranged - - - - invalid rna structure positional highlighting does not highlight - position of invalid base pairs - - - - out of memory errors are not raised when saving jalview project - from alignment window file menu - - - - Switching to RNA Helices colouring doesn't propagate to - structures - - - - colour by RNA Helices not enabled when user created annotation - added to alignment - - - - Jalview icon not shown on dock in Mountain Lion/Webstart - - Applet Known Issues - - - - JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies - - - - Jalview and Jmol example not compatible with IE9 - + + 2G and 1G options in launchApp have no effect on + memory allocation + launchApp service doesn't automatically open + www.jalview.org/examples/exampleFile.jar if no file is given + + + InstallAnywhere reports cannot find valid JVM when Java + 1.7_055 is available + + Application Known issues + + + + corrupted or unreadable alignment display when scrolling + alignment to right + + + + retrieval fails but progress bar continues for DAS retrieval + with large number of ID + + + + flatfile output of visible region has incorrect sequence + start/end + + + + rna structure consensus doesn't update when secondary + structure tracks are rearranged + + + + invalid rna structure positional highlighting does not + highlight position of invalid base pairs + + + + out of memory errors are not raised when saving Jalview + project from alignment window file menu + + + + Switching to RNA Helices colouring doesn't propagate to + structures + + + + colour by RNA Helices not enabled when user created + annotation added to alignment + + + + Jalview icon not shown on dock in Mountain Lion/Webstart + + Applet Known Issues + + + + JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies + + + + Jalview and Jmol example not compatible with IE9 + - Sort by annotation score doesn't reverse order when - selected - -
- 2.8.1 4/6/2014 -	- - General - - Internationalisation of user interface (usually called - i18n support) and translation for Spanish locale - Define/Undefine group on current selection with - Ctrl-G/Shift Ctrl-G - Improved group creation/removal options in - alignment/sequence Popup menu - Sensible precision for symbol distribution percentages - shown in logo tooltip. - Annotation panel height set according to amount of - annotation when alignment first opened - Application - - Interactive consensus RNA secondary structure prediction - VIENNA RNAAliFold JABA 2.1 service - Select columns containing particular features from Feature - Settings dialog - View all 'representative' PDB structures for selected - sequences - Update Jalview project format: - + Sort by annotation score doesn't reverse order + when selected + +
+ 2.8.1 4/6/2014 +	+ + General + + Internationalisation of user interface (usually + called i18n support) and translation for Spanish locale + Define/Undefine group on current selection with + Ctrl-G/Shift Ctrl-G + Improved group creation/removal options in + alignment/sequence Popup menu + Sensible precision for symbol distribution + percentages shown in logo tooltip. + Annotation panel height set according to amount of + annotation when alignment first opened + Application + + Interactive consensus RNA secondary structure + prediction VIENNA RNAAliFold JABA 2.1 service + Select columns containing particular features from + Feature Settings dialog + View all 'representative' PDB structures for selected + sequences + Update Jalview project format: + New file extension for Jalview projects '.jvp' - Preserve sequence and annotation dataset (to store - secondary structure annotation,etc) - Per group and alignment annotation and RNA helix - colouring - - - New similarity measures for PCA and Tree calculation - (PAM250) - Experimental support for retrieval and viewing of flanking - regions for an alignment - -	- Application - - logo keeps spinning and status remains at queued or - running after job is cancelled - cannot export features from alignments imported from - Jalview/VAMSAS projects - Buggy slider for web service parameters that take float - values - Newly created RNA secondary structure line doesn't have - 'display all symbols' flag set - T-COFFEE alignment score shading scheme and other - annotation shading not saved in jalview project - Local file cannot be loaded in freshly downloaded Jalview - Jalview icon not shown on dock in Mountain Lion/Webstart - Load file from desktop file browser fails - Occasional NPE thrown when calculating large trees - Cannot reorder or slide sequences after dragging an - alignment onto desktop - Colour by annotation dialog throws NPE after using - 'extract scores' function - Loading/cut'n'pasting an empty file leads to a grey - alignment window - Disorder thresholds rendered incorrectly after performing - IUPred disorder prediction - Multiple group annotated consensus rows shown when - changing 'normalise logo' display setting - Find shows blank dialog after 'finished searching' if - nothing matches query - Null Pointer Exceptions raised when sorting by feature - with lots of groups - - Errors in Jmol console when structures in alignment don't - overlap - - Not all working JABAWS services are shown in Jalview's - menu - JAVAWS version of jalview fails to launch with 'invalid - literal/length code' - Annotation/RNA Helix colourschemes cannot be applied to - alignment with groups (actually fixed in 2.8.0b1) - RNA Helices and T-Coffee Scores available as default colourscheme + Preserve sequence and annotation dataset (to + store secondary structure annotation,etc) + Per group and alignment annotation and RNA helix + colouring + + + New similarity measures for PCA and Tree calculation + (PAM250) + Experimental support for retrieval and viewing of + flanking regions for an alignment + +	+ Application + + logo keeps spinning and status remains at queued or + running after job is cancelled + cannot export features from alignments imported from + Jalview/VAMSAS projects + Buggy slider for web service parameters that take + float values + Newly created RNA secondary structure line doesn't + have 'display all symbols' flag set + T-COFFEE alignment score shading scheme and other + annotation shading not saved in Jalview project + Local file cannot be loaded in freshly downloaded + Jalview + Jalview icon not shown on dock in Mountain + Lion/Webstart + Load file from desktop file browser fails + Occasional NPE thrown when calculating large trees + Cannot reorder or slide sequences after dragging an + alignment onto desktop + Colour by annotation dialog throws NPE after using + 'extract scores' function + Loading/cut'n'pasting an empty file leads to a grey + alignment window + Disorder thresholds rendered incorrectly after + performing IUPred disorder prediction + Multiple group annotated consensus rows shown when + changing 'normalise logo' display setting + Find shows blank dialog after 'finished searching' if + nothing matches query + Null Pointer Exceptions raised when sorting by + feature with lots of groups + + Errors in Jmol console when structures in alignment + don't overlap + + Not all working JABAWS services are shown in + Jalview's menu + JAVAWS version of Jalview fails to launch with + 'invalid literal/length code' + Annotation/RNA Helix colourschemes cannot be applied + to alignment with groups (actually fixed in 2.8.0b1) + RNA Helices and T-Coffee Scores available as default + colourscheme - Applet - - Remove group option is shown even when selection is not a - group - Apply to all groups ticked but colourscheme changes don't - affect groups - Documented RNA Helices and T-Coffee Scores as valid colourscheme name - Annotation labels drawn on sequence IDs when Annotation panel is not displayed - Increased font size for dropdown menus on OSX and embedded windows - Other - - Consensus sequence for alignments/groups with a single - sequence were not calculated - annotation files that contain only groups imported as - annotation and junk sequences - Fasta files with sequences containing '*' incorrectly - recognised as PFAM or BLC - conservation/PID slider apply all groups option doesn't - affect background (2.8.0b1) - - redundancy highlighting is erratic at 0% and 100% - Remove gapped columns fails for sequences with ragged - trailing gaps - AMSA annotation row with leading spaces is not registered - correctly on import - Jalview crashes when selecting PCA analysis for certain - alignments - Opening the colour by annotation dialog for an existing - annotation based 'use original colours' colourscheme loses - original colours setting - -
- 2.8.0b1 30/1/2014 - -
+ 2.8.0b1 + 30/1/2014 +	Trusted certificates for JalviewLite applet and @@ -390,7 +1148,7 @@ Certum to the Jalview open source project). - Jalview SRS links replaced by Uniprot and EBI-search + Jalview SRS links replaced by UniProt and EBI-search Output in Stockholm format Allow import of data from gzipped files @@ -401,7 +1159,7 @@ Allow disorder predictions to be made on the current selection (or visible selection) in the same way that JPred works - Groovy scripting for headless jalview operation + Groovy scripting for headless Jalview operation Other improvements Upgrade desktop installer to InstallAnywhere 2013 @@ -470,1273 +1228,1359 @@ ClassCastException when generating EPS in headless mode Adjusting sequence-associated shading threshold only - changes one row's threshold + changes one row's threshold Preferences and Feature settings panel panel doesn't open - hide consensus histogram also hides conservation and - quality histograms - + hide consensus histogram also hides conservation and + quality histograms +
- 2.8 12/11/2012 -	Application - Support for JABAWS 2.0 Services (AACon alignment - conservation, protein disorder and Clustal Omega) - JABAWS server status indicator in Web Services preferences - - VARNA (http://varna.lri.fr) viewer for RNA structures in - Jalview alignment window - Updated Jalview build and deploy framework for OSX mountain - lion, windows 7, and 8 - Nucleotide substitution matrix for PCA that supports RNA - and ambiguity codes +
+ 2.8 12/11/2012 +	Application + + Support for JABAWS 2.0 Services (AACon alignment + conservation, protein disorder and Clustal Omega) + JABAWS server status indicator in Web Services + preferences + VARNA (http://varna.lri.fr) viewer for RNA structures + in Jalview alignment window + Updated Jalview build and deploy framework for OSX + mountain lion, windows 7, and 8 + Nucleotide substitution matrix for PCA that supports + RNA and ambiguity codes - Improved sequence database retrieval GUI - Support fetching and database reference look up against - multiple DAS sources (Fetch all from in 'fetch db refs') - Jalview project improvements - - Store and retrieve the 'belowAlignment' flag for - annotation - calcId attribute to group annotation rows on the - alignment - Store AACon calculation settings for a view in Jalview - project + Improved sequence database retrieval GUI + Support fetching and database reference look up + against multiple DAS sources (Fetch all from in 'fetch db + refs') + Jalview project improvements + + Store and retrieve the 'belowAlignment' + flag for annotation + calcId attribute to group annotation rows on the + alignment + Store AACon calculation settings for a view in + Jalview project - - - horizontal scrolling gesture support - Visual progress indicator when PCA calculation is running - Simpler JABA web services menus - visual indication that web service results are still being - retrieved from server - Serialise the dialogs that are shown when Jalview starts up - for first time - Jalview user agent string for interacting with HTTP - services - DAS 1.6 and DAS 2.0 source support using new JDAS client - library - Examples directory and Groovy library included in - InstallAnywhere distribution - Applet - - RNA alignment and secondary structure annotation - visualization applet example - General - - Normalise option for consensus sequence logo - Reset button in PCA window to return dimensions to - defaults - Allow seqspace or Jalview variant of alignment PCA - calculation - PCA with either nucleic acid and protein substitution - matrices - Allow windows containing HTML reports to be exported in - HTML - Interactive display and editing of RNA secondary structure - contacts - RNA Helix Alignment Colouring - RNA base pair logo consensus - Parse sequence associated secondary structure information - in Stockholm files - HTML Export database accessions and annotation information - presented in tooltip for sequences - Import secondary structure from LOCARNA clustalw style RNA - alignment files - import and visualise T-COFFEE quality scores for an - alignment - 'colour by annotation' per sequence option to - shade each sequence according to its associated alignment - annotation - New Jalview Logo - Documentation and Development - - documentation for score matrices used in Jalview - New Website! -	Application - - PDB, Unprot and EMBL (ENA) databases retrieved via - wsdbfetch REST service - Stop windows being moved outside desktop on OSX - Filetype associations not installed for webstart launch - Jalview does not always retrieve progress of a JABAWS job - execution in full once it is complete - revise SHMR RSBS definition to ensure alignment is - uploaded via ali_file parameter - Jalview 2.7 is incompatible with Jmol-12.2.2 - View all structures superposed fails with exception - Jnet job queues forever if a very short sequence is - submitted for prediction - Cut and paste menu not opened when mouse clicked on - desktop window - Putting fractional value into integer text box in - alignment parameter dialog causes Jalview to hang - Structure view highlighting doesn't work on windows 7 - - View all structures fails with exception shown in - structure view - Characters in filename associated with PDBEntry not - escaped in a platform independent way - Jalview desktop fails to launch with exception when using - proxy - Tree calculation reports 'you must have 2 or more - sequences selected' when selection is empty - Jalview desktop fails to launch with jar signature failure - when java web start temporary file caching is disabled - DAS Sequence retrieval with range qualification results in - sequence xref which includes range qualification - Errors during processing of command line arguments cause - progress bar (JAL-898) to be removed - Replace comma for semi-colon option not disabled for DAS - sources in sequence fetcher - Cannot close news reader when JABAWS server warning dialog - is shown - Option widgets not updated to reflect user settings - Edited sequence not submitted to web service - Jalview 2.7 Webstart does not launch on mountain lion - InstallAnywhere installer doesn't unpack and run on - OSX Mountain Lion - Annotation panel not given a scroll bar when sequences - with alignment annotation are pasted into the alignment - Sequence associated annotation rows not associated when - loaded from Jalview project - Browser launch fails with NPE on java 1.7 - JABAWS alignment marked as finished when job was cancelled - or job failed due to invalid input - NPE with v2.7 example when clicking on Tree associated - with all views - Exceptions when copy/paste sequences with grouped - annotation rows to new window - Applet - - Sequence features are momentarily displayed before they - are hidden using hidefeaturegroups applet parameter - loading features via javascript API automatically enables - feature display - scrollToColumnIn javascript API method doesn't work - General - - Redundancy removal fails for rna alignment - PCA calculation fails when sequence has been selected and - then deselected - PCA window shows grey box when first opened on OSX - Letters coloured pink in sequence logo when alignment - coloured with clustalx - Choosing fonts without letter symbols defined causes - exceptions and redraw errors - Initial PCA plot view is not same as manually reconfigured - view - Grouped annotation graph label has incorrect line colour - Grouped annotation graph label display is corrupted for - lots of labels - -
- - 2.7 27/09/2011 - -	Application - - Jalview Desktop News Reader - Tweaked default layout of web services menu - View/alignment association menu to enable user to easily - specify which alignment a multi-structure view takes its - colours/correspondences from - Allow properties file location to be specified as URL - Extend Jalview project to preserve associations between - many alignment views and a single Jmol display - Store annotation row height in Jalview project file - Annotation row column label formatting attributes stored - in project file - Annotation row order for auto-calculated annotation rows - preserved in Jalview project file - Visual progress indication when Jalview state is saved - using Desktop window menu - Visual indication that command line arguments are still - being processed - Groovy script execution from URL - Colour by annotation default min and max colours in - preferences - Automatically associate PDB files dragged onto an - alignment with sequences that have high similarity and matching - IDs - Update JGoogleAnalytics to latest release (0.3) - 'view structures' option to open many structures - in same window - Sort associated views menu option for tree panel - Group all JABA and non-JABA services for a particular - analysis function in its own submenu - Applet - - Userdefined and autogenerated annotation rows for groups - Adjustment of alignment annotation pane height - Annotation scrollbar for annotation panel - Drag to reorder annotation rows in annotation panel - 'automaticScrolling' parameter - Allow sequences with partial ID string matches to be - annotated from GFF/Jalview features files - Sequence logo annotation row in applet - Absolute paths relative to host server in applet - parameters are treated as such - New in the JalviewLite javascript API: - - JalviewLite.js javascript library - Javascript callbacks for - - Applet initialisation - Sequence/alignment mouse-overs and selections + + + horizontal scrolling gesture support + Visual progress indicator when PCA calculation is + running + Simpler JABA web services menus + visual indication that web service results are still + being retrieved from server + Serialise the dialogs that are shown when Jalview + starts up for first time + Jalview user agent string for interacting with HTTP + services + DAS 1.6 and DAS 2.0 source support using new JDAS + client library + Examples directory and Groovy library included in + InstallAnywhere distribution + Applet + + RNA alignment and secondary structure annotation + visualization applet example + General + + Normalise option for consensus sequence logo + Reset button in PCA window to return dimensions to + defaults + Allow seqspace or Jalview variant of alignment PCA + calculation + PCA with either nucleic acid and protein substitution + matrices + Allow windows containing HTML reports to be exported + in HTML + Interactive display and editing of RNA secondary + structure contacts + RNA Helix Alignment Colouring + RNA base pair logo consensus + Parse sequence associated secondary structure + information in Stockholm files + HTML Export database accessions and annotation + information presented in tooltip for sequences + Import secondary structure from LOCARNA clustalw + style RNA alignment files + import and visualise T-COFFEE quality scores for an + alignment + 'colour by annotation' per sequence option to + shade each sequence according to its associated alignment + annotation + New Jalview Logo + Documentation and Development + + documentation for score matrices used in Jalview + New Website! +	Application + + PDB, Unprot and EMBL (ENA) databases retrieved via + wsdbfetch REST service + Stop windows being moved outside desktop on OSX + Filetype associations not installed for webstart + launch + Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete + revise SHMR RSBS definition to ensure alignment is + uploaded via ali_file parameter + Jalview 2.7 is incompatible with Jmol-12.2.2 + View all structures superposed fails with exception + Jnet job queues forever if a very short sequence is + submitted for prediction + Cut and paste menu not opened when mouse clicked on + desktop window + Putting fractional value into integer text box in + alignment parameter dialog causes Jalview to hang + Structure view highlighting doesn't work on + windows 7 + View all structures fails with exception shown in + structure view + Characters in filename associated with PDBEntry not + escaped in a platform independent way + Jalview desktop fails to launch with exception when + using proxy + Tree calculation reports 'you must have 2 or more + sequences selected' when selection is empty + Jalview desktop fails to launch with jar signature + failure when java web start temporary file caching is + disabled + DAS Sequence retrieval with range qualification + results in sequence xref which includes range qualification + Errors during processing of command line arguments + cause progress bar (JAL-898) to be removed + Replace comma for semi-colon option not disabled for + DAS sources in sequence fetcher + Cannot close news reader when JABAWS server warning + dialog is shown + Option widgets not updated to reflect user settings + Edited sequence not submitted to web service + Jalview 2.7 Webstart does not launch on mountain lion + InstallAnywhere installer doesn't unpack and run + on OSX Mountain Lion + Annotation panel not given a scroll bar when + sequences with alignment annotation are pasted into the + alignment + Sequence associated annotation rows not associated + when loaded from Jalview project + Browser launch fails with NPE on java 1.7 + JABAWS alignment marked as finished when job was + cancelled or job failed due to invalid input + NPE with v2.7 example when clicking on Tree + associated with all views + Exceptions when copy/paste sequences with grouped + annotation rows to new window + Applet + + Sequence features are momentarily displayed before + they are hidden using hidefeaturegroups applet parameter + loading features via javascript API automatically + enables feature display + scrollToColumnIn javascript API method doesn't + work + General + + Redundancy removal fails for rna alignment + PCA calculation fails when sequence has been selected + and then deselected + PCA window shows grey box when first opened on OSX + Letters coloured pink in sequence logo when alignment + coloured with clustalx + Choosing fonts without letter symbols defined causes + exceptions and redraw errors + Initial PCA plot view is not same as manually + reconfigured view + Grouped annotation graph label has incorrect line + colour + Grouped annotation graph label display is corrupted + for lots of labels - - scrollTo row and column alignment scrolling functions - Select sequence/alignment regions from javascript - javascript structure viewer harness to pass messages - between Jmol and Jalview when running as distinct applets - sortBy method - Set of applet and application examples shipped with - documentation - New example to demonstrate JalviewLite and Jmol - javascript message exchange - - General - - Enable Jmol displays to be associated with multiple - multiple alignments - Option to automatically sort alignment with new tree - User configurable link to enable redirects to a - www.Jalview.org mirror - Jmol colours option for Jmol displays - Configurable newline string when writing alignment and - other flat files - Allow alignment annotation description lines to contain - html tags - Documentation and Development - - Add groovy test harness for bulk load testing to examples - - Groovy script to load and align a set of sequences using a - web service before displaying the result in the Jalview desktop - Restructured javascript and applet api documentation - Ant target to publish example html files with applet - archive - Netbeans project for building Jalview from source - ant task to create online javadoc for Jalview source -	Application - - User defined colourscheme throws exception when current - built in colourscheme is saved as new scheme - AlignFrame->Save in application pops up save dialog for - valid filename/format - Cannot view associated structure for Uniprot sequence - PDB file association breaks for Uniprot sequence P37173 - Associate PDB from file dialog does not tell you which - sequence is to be associated with the file - Find All raises null pointer exception when query only - matches sequence IDs - Pre 2.6 Jalview project cannot be loaded into v2.6 - Jalview project with Jmol views created with Jalview 2.4 - cannot be loaded - Filetype associations not installed for webstart launch - Two or more chains in a single PDB file associated with - sequences in different alignments do not get coloured by their - associated sequence - Visibility status of autocalculated annotation row not - preserved when project is loaded - Annotation row height and visibility attributes not stored - in Jalview project - Tree bootstraps are not preserved when saved as a Jalview - project - Envision2 workflow tooltips are corrupted - Enabling show group conservation also enables colour by - conservation - Duplicate group associated conservation or consensus - created on new view - Annotation scrollbar not displayed after 'show all - hidden annotation rows' option selected - Alignment quality not updated after alignment annotation - row is hidden then shown - Preserve colouring of structures coloured by sequences in - pre Jalview 2.7 projects - Web service job parameter dialog is not laid out properly - - Web services menu not refreshed after 'reset - services' button is pressed in preferences - Annotation off by one in Jalview v2_3 example project - Structures imported from file and saved in project get - name like jalview_pdb1234.txt when reloaded - Jalview does not always retrieve progress of a JABAWS job - execution in full once it is complete - Applet - - Alignment height set incorrectly when lots of annotation - rows are displayed - Relative URLs in feature HTML text not resolved to - codebase - View follows highlighting does not work for positions in - sequences - <= shown as = in tooltip - Export features raises exception when no features exist - Separator string used for serialising lists of IDs for - javascript api is modified when separator string provided as - parameter - Null pointer exception when selecting tree leaves for - alignment with no existing selection - Relative URLs for datasources assumed to be relative to - applet's codebase - Status bar not updated after finished searching and search - wraps around to first result - StructureSelectionManager instance shared between several - Jalview applets causes race conditions and memory leaks - Hover tooltip and mouseover of position on structure not - sent from Jmol in applet - Certain sequences of javascript method calls to applet API - fatally hang browser - General - - View follows structure mouseover scrolls beyond position - with wrapped view and hidden regions - Find sequence position moves to wrong residue with/without - hidden columns - Sequence length given in alignment properties window is - off by 1 - InvalidNumberFormat exceptions thrown when trying to - import PDB like structure files - Positional search results are only highlighted between - user-supplied sequence start/end bounds - End attribute of sequence is not validated - Find dialog only finds first sequence containing a given - sequence position - Sequence numbering not preserved in MSF alignment output - Jalview PDB file reader does not extract sequence from - nucleotide chains correctly - Structure colours not updated when tree partition changed - in alignment - Sequence associated secondary structure not correctly - parsed in interleaved stockholm - Colour by annotation dialog does not restore current state - - Hiding (nearly) all sequences doesn't work properly - Sequences containing lowercase letters are not properly - associated with their pdb files - Documentation and Development - - schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright - tool -
- - 2.6.1 - 15/11/2010 -	Application - - New warning dialog when the Jalview Desktop cannot contact - web services - JABA service parameters for a preset are shown in service - job window - JABA Service menu entries reworded -	- - Modeller PIR IO broken - cannot correctly import a pir - file emitted by Jalview - Existing feature settings transferred to new alignment - view created from cut'n'paste - Improved test for mixed amino/nucleotide chains when - parsing PDB files - Consensus and conservation annotation rows occasionally - become blank for all new windows - Exception raised when right clicking above sequences in - wrapped view mode - Application - - multiple multiply aligned structure views cause cpu usage - to hit 100% and computer to hang - Web Service parameter layout breaks for long user - parameter names - Jaba service discovery hangs desktop if Jaba server is - down -
- 2.6 - 26/9/2010 -	Application - - Support for Java bioinformatics - analysis web services (JABAWS) - Web Services preference tab - Analysis parameters dialog box and user defined preferences - Improved speed and layout of Envision2 service menu - Superpose structures using associated sequence alignment - Export coordinates and projection as CSV from PCA viewer - - Applet - - enable javascript: execution by the applet via the link out - mechanism - - Other - - Updated the Jmol Jalview interface to work with Jmol series - 12 - The Jalview Desktop and JalviewLite applet now require Java - 1.5 - Allow Jalview feature colour specification for GFF sequence - annotation files - New 'colour by label' keword in Jalview feature file type - colour specification - New Jalview Desktop Groovy API method that allows a script - to check if it being run in an interactive session or in a batch - operation from the Jalview command line - -	- - clustalx colourscheme colours Ds preferentially when both - D+E are present in over 50% of the column - +
+ + 2.7 27/09/2011 + +	Application + + Jalview Desktop News Reader + Tweaked default layout of web services menu + View/alignment association menu to enable user to + easily specify which alignment a multi-structure view takes + its colours/correspondences from + Allow properties file location to be specified as URL + Extend Jalview project to preserve associations + between many alignment views and a single Jmol display + Store annotation row height in Jalview project file + Annotation row column label formatting attributes + stored in project file + Annotation row order for auto-calculated annotation + rows preserved in Jalview project file + Visual progress indication when Jalview state is + saved using Desktop window menu + Visual indication that command line arguments are + still being processed + Groovy script execution from URL + Colour by annotation default min and max colours in + preferences + Automatically associate PDB files dragged onto an + alignment with sequences that have high similarity and + matching IDs + Update JGoogleAnalytics to latest release (0.3) + 'view structures' option to open many + structures in same window + Sort associated views menu option for tree panel + Group all JABA and non-JABA services for a particular + analysis function in its own submenu + Applet + + Userdefined and autogenerated annotation rows for + groups + Adjustment of alignment annotation pane height + Annotation scrollbar for annotation panel + Drag to reorder annotation rows in annotation panel + 'automaticScrolling' parameter + Allow sequences with partial ID string matches to be + annotated from GFF/Jalview features files + Sequence logo annotation row in applet + Absolute paths relative to host server in applet + parameters are treated as such + New in the JalviewLite javascript API: + + JalviewLite.js javascript library + Javascript callbacks for + + Applet initialisation + Sequence/alignment mouse-overs and selections + + + scrollTo row and column alignment scrolling + functions + Select sequence/alignment regions from javascript + javascript structure viewer harness to pass + messages between Jmol and Jalview when running as + distinct applets + sortBy method + Set of applet and application examples shipped + with documentation + New example to demonstrate JalviewLite and Jmol + javascript message exchange + + General + + Enable Jmol displays to be associated with multiple + multiple alignments + Option to automatically sort alignment with new tree + User configurable link to enable redirects to a + www.Jalview.org mirror + Jmol colours option for Jmol displays + Configurable newline string when writing alignment + and other flat files + Allow alignment annotation description lines to + contain html tags + Documentation and Development + + Add groovy test harness for bulk load testing to + examples + Groovy script to load and align a set of sequences + using a web service before displaying the result in the + Jalview desktop + Restructured javascript and applet api documentation + Ant target to publish example html files with applet + archive + Netbeans project for building Jalview from source + ant task to create online javadoc for Jalview source +	Application + + User defined colourscheme throws exception when + current built in colourscheme is saved as new scheme + AlignFrame->Save in application pops up save + dialog for valid filename/format + Cannot view associated structure for UniProt sequence + PDB file association breaks for UniProt sequence + P37173 + Associate PDB from file dialog does not tell you + which sequence is to be associated with the file + Find All raises null pointer exception when query + only matches sequence IDs + Pre 2.6 Jalview project cannot be loaded into v2.6 + Jalview project with Jmol views created with Jalview + 2.4 cannot be loaded + Filetype associations not installed for webstart + launch + Two or more chains in a single PDB file associated + with sequences in different alignments do not get coloured + by their associated sequence + Visibility status of autocalculated annotation row + not preserved when project is loaded + Annotation row height and visibility attributes not + stored in Jalview project + Tree bootstraps are not preserved when saved as a + Jalview project + Envision2 workflow tooltips are corrupted + Enabling show group conservation also enables colour + by conservation + Duplicate group associated conservation or consensus + created on new view + Annotation scrollbar not displayed after 'show + all hidden annotation rows' option selected + Alignment quality not updated after alignment + annotation row is hidden then shown + Preserve colouring of structures coloured by + sequences in pre Jalview 2.7 projects + Web service job parameter dialog is not laid out + properly + Web services menu not refreshed after 'reset + services' button is pressed in preferences + Annotation off by one in Jalview v2_3 example project + Structures imported from file and saved in project + get name like jalview_pdb1234.txt when reloaded + Jalview does not always retrieve progress of a JABAWS + job execution in full once it is complete + Applet + + Alignment height set incorrectly when lots of + annotation rows are displayed + Relative URLs in feature HTML text not resolved to + codebase + View follows highlighting does not work for positions + in sequences + <= shown as = in tooltip + Export features raises exception when no features + exist + Separator string used for serialising lists of IDs + for javascript api is modified when separator string + provided as parameter + Null pointer exception when selecting tree leaves for + alignment with no existing selection + Relative URLs for datasources assumed to be relative + to applet's codebase + Status bar not updated after finished searching and + search wraps around to first result + StructureSelectionManager instance shared between + several Jalview applets causes race conditions and memory + leaks + Hover tooltip and mouseover of position on structure + not sent from Jmol in applet + Certain sequences of javascript method calls to + applet API fatally hang browser + General + + View follows structure mouseover scrolls beyond + position with wrapped view and hidden regions + Find sequence position moves to wrong residue + with/without hidden columns + Sequence length given in alignment properties window + is off by 1 + InvalidNumberFormat exceptions thrown when trying to + import PDB like structure files + Positional search results are only highlighted + between user-supplied sequence start/end bounds + End attribute of sequence is not validated + Find dialog only finds first sequence containing a + given sequence position + Sequence numbering not preserved in MSF alignment + output + Jalview PDB file reader does not extract sequence + from nucleotide chains correctly + Structure colours not updated when tree partition + changed in alignment + Sequence associated secondary structure not correctly + parsed in interleaved stockholm + Colour by annotation dialog does not restore current + state + Hiding (nearly) all sequences doesn't work + properly + Sequences containing lowercase letters are not + properly associated with their pdb files + Documentation and Development + + schemas/JalviewWsParamSet.xsd corrupted by + ApplyCopyright tool +
+ + 2.6.1 15/11/2010 + +	Application + + New warning dialog when the Jalview Desktop cannot + contact web services + JABA service parameters for a preset are shown in + service job window + JABA Service menu entries reworded +	+ + Modeller PIR IO broken - cannot correctly import a + pir file emitted by Jalview + Existing feature settings transferred to new + alignment view created from cut'n'paste + Improved test for mixed amino/nucleotide chains when + parsing PDB files + Consensus and conservation annotation rows + occasionally become blank for all new windows + Exception raised when right clicking above sequences + in wrapped view mode + Application + + multiple multiply aligned structure views cause cpu + usage to hit 100% and computer to hang + Web Service parameter layout breaks for long user + parameter names + Jaba service discovery hangs desktop if Jaba server + is down + +
+ + 2.6 26/9/2010 + +	Application + + Support for Java bioinformatics + analysis web services + (JABAWS) + + Web Services preference tab + Analysis parameters dialog box and user defined + preferences + Improved speed and layout of Envision2 service menu + Superpose structures using associated sequence + alignment + Export coordinates and projection as CSV from PCA + viewer + Applet + + enable javascript: execution by the applet via the + link out mechanism + Other + + Updated the Jmol Jalview interface to work with Jmol + series 12 + The Jalview Desktop and JalviewLite applet now + require Java 1.5 + Allow Jalview feature colour specification for GFF + sequence annotation files + New 'colour by label' keword in Jalview feature file + type colour specification + New Jalview Desktop Groovy API method that allows a + script to check if it being run in an interactive session or + in a batch operation from the Jalview command line +	+ + clustalx colourscheme colours Ds preferentially when + both D+E are present in over 50% of the column + Application + + typo in AlignmentFrame->View->Hide->all but + selected Regions menu item + sequence fetcher replaces ',' for ';' when the ',' is + part of a valid accession ID + fatal OOM if object retrieved by sequence fetcher + runs out of memory + unhandled Out of Memory Error when viewing pca + analysis results + InstallAnywhere builds fail to launch on OS X java + 10.5 update 4 (due to apple Java 1.6 update) + Installanywhere Jalview silently fails to launch + Applet + + Jalview.getFeatureGroups() raises an + ArrayIndexOutOfBoundsException if no feature groups are + defined. + +
+ + 2.5.1 14/6/2010 + +		+ + Alignment prettyprinter doesn't cope with long + sequence IDs + clustalx colourscheme colours Ds preferentially when + both D+E are present in over 50% of the column + nucleic acid structures retrieved from PDB do not + import correctly + More columns get selected than were clicked on when a + number of columns are hidden + annotation label popup menu not providing correct + add/hide/show options when rows are hidden or none are + present + Stockholm format shown in list of readable formats, + and parser copes better with alignments from RFAM. + CSV output of consensus only includes the percentage + of all symbols if sequence logo display is enabled + + Applet + + annotation panel disappears when annotation is + hidden/removed + Application + + Alignment view not redrawn properly when new + alignment opened where annotation panel is visible but no + annotations are present on alignment + pasted region containing hidden columns is + incorrectly displayed in new alignment window + Jalview slow to complete operations when stdout is + flooded (fix is to close the Jalview console) + typo in AlignmentFrame->View->Hide->all but + selected Rregions menu item. + inconsistent group submenu and Format submenu entry + 'Un' or 'Non'conserved + Sequence feature settings are being shared by + multiple distinct alignments + group annotation not recreated when tree partition is + changed + double click on group annotation to select sequences + does not propagate to associated trees + Mac OSX specific issues: + + exception raised when mouse clicked on desktop + window background + Desktop menu placed on menu bar and application + name set correctly + sequence feature settings not wide enough for the + save feature colourscheme button + + + +
+ + 2.5 30/4/2010 + +	New Capabilities + + URL links generated from description line for + regular-expression based URL links (applet and application) + - Application - - typo in AlignmentFrame->View->Hide->all but - selected Regions menu item - sequence fetcher replaces ',' for ';' when the ',' is part - of a valid accession ID - fatal OOM if object retrieved by sequence fetcher runs out - of memory - unhandled Out of Memory Error when viewing pca analysis - results - InstallAnywhere builds fail to launch on OS X java 10.5 - update 4 (due to apple Java 1.6 update) - Installanywhere Jalview silently fails to launch - - Applet - - Jalview.getFeatureGroups() raises an - ArrayIndexOutOfBoundsException if no feature groups are defined. - -
- 2.5.1 - 14/6/2010 -		- - Alignment prettyprinter doesn't cope with long sequence IDs - - clustalx colourscheme colours Ds preferentially when both - D+E are present in over 50% of the column - nucleic acid structures retrieved from PDB do not import - correctly - More columns get selected than were clicked on when a number - of columns are hidden - annotation label popup menu not providing correct - add/hide/show options when rows are hidden or none are present - Stockholm format shown in list of readable formats, and - parser copes better with alignments from RFAM. - CSV output of consensus only includes the percentage of all - symbols if sequence logo display is enabled - - Applet - - annotation panel disappears when annotation is - hidden/removed - - Application - - Alignment view not redrawn properly when new alignment - opened where annotation panel is visible but no annotations are - present on alignment - pasted region containing hidden columns is incorrectly - displayed in new alignment window - Jalview slow to complete operations when stdout is flooded - (fix is to close the Jalview console) - typo in AlignmentFrame->View->Hide->all but - selected Rregions menu item. - inconsistent group submenu and Format submenu entry 'Un' or - 'Non'conserved - Sequence feature settings are being shared by multiple - distinct alignments - group annotation not recreated when tree partition is - changed - double click on group annotation to select sequences does - not propagate to associated trees - Mac OSX specific issues: - - exception raised when mouse clicked on desktop window - background - Desktop menu placed on menu bar and application name set - correctly - sequence feature settings not wide enough for the save - feature colourscheme button - - - -
- 2.5 - 30/4/2010 -	New Capabilities - - URL links generated from description line for - regular-expression based URL links (applet and application) - Non-positional feature URL links are shown in link menu - Linked viewing of nucleic acid sequences and structures - Automatic Scrolling option in View menu to display the - currently highlighted region of an alignment. - Order an alignment by sequence length, or using the average - score or total feature count for each sequence. - Shading features by score or associated description - Subdivide alignment and groups based on identity of selected - subsequence (Make Groups from Selection). - New hide/show options including Shift+Control+H to hide - everything but the currently selected region. - - - Application - - Fetch DB References capabilities and UI expanded to support - retrieval from DAS sequence sources - Local DAS Sequence sources can be added via the command line - or via the Add local source dialog box. - DAS Dbref and DbxRef feature types are parsed as database - references and protein_name is parsed as description line (BioSapiens - terms). - Enable or disable non-positional feature and database - references in sequence ID tooltip from View menu in application. - + Application + + Fetch DB References capabilities and UI expanded to + support retrieval from DAS sequence sources + Local DAS Sequence sources can be added via the + command line or via the Add local source dialog box. + DAS Dbref and DbxRef feature types are parsed as + database references and protein_name is parsed as + description line (BioSapiens terms). + Enable or disable non-positional feature and database + references in sequence ID tooltip from View menu in + application. + - Group-associated consensus, sequence logos and conservation - plots - Symbol distributions for each column can be exported and - visualized as sequence logos - Optionally scale multi-character column labels to fit within - each column of annotation row - Optional automatic sort of associated alignment view when a - new tree is opened. - Jalview Java Console - Better placement of desktop window when moving between - different screens. - New preference items for sequence ID tooltip and consensus - annotation - Client to submit sequences and IDs to Envision2 Workflows - Vamsas Capabilities - - Improved VAMSAS synchronization (Jalview archive used to - preserve views, structures, and tree display settings) - Import of vamsas documents from disk or URL via command - line - Sharing of selected regions between views and with other - VAMSAS applications (Experimental feature!) - Updated API to VAMSAS version 0.2 - - - - Applet - - Middle button resizes annotation row height - New Parameters - - sortByTree (true/false) - automatically sort the associated - alignment view by the tree when a new tree is opened. - showTreeBootstraps (true/false) - show or hide branch - bootstraps (default is to show them if available) - showTreeDistances (true/false) - show or hide branch - lengths (default is to show them if available) - showUnlinkedTreeNodes (true/false) - indicate if - unassociated nodes should be highlighted in the tree view - heightScale and widthScale (1.0 or more) - increase the - height or width of a cell in the alignment grid relative to the - current font size. - - - Non-positional features displayed in sequence ID tooltip - - Other - - Features format: graduated colour definitions and - specification of feature scores - Alignment Annotations format: new keywords for group - associated annotation (GROUP_REF) and annotation row display - properties (ROW_PROPERTIES) - XML formats extended to support graduated feature - colourschemes, group associated annotation, and profile visualization - settings. -	- - Source field in GFF files parsed as feature source rather - than description - Non-positional features are now included in sequence feature - and gff files (controlled via non-positional feature visibility in - tooltip). - URL links generated for all feature links (bugfix) - Added URL embedding instructions to features file - documentation. - Codons containing ambiguous nucleotides translated as 'X' in - peptide product - Match case switch in find dialog box works for both sequence - ID and sequence string and query strings do not have to be in upper - case to match case-insensitively. - AMSA files only contain first column of multi-character - column annotation labels - Jalview Annotation File generation/parsing consistent with - documentation (e.g. Stockholm annotation can be exported and - re-imported) - PDB files without embedded PDB IDs given a friendly name - Find incrementally searches ID string matches as well as - subsequence matches, and correctly reports total number of both. - Application: - - Better handling of exceptions during sequence retrieval - Dasobert generated non-positional feature URL link text - excludes the start_end suffix - DAS feature and source retrieval buttons disabled when - fetch or registry operations in progress. - PDB files retrieved from URLs are cached properly - Sequence description lines properly shared via VAMSAS - Sequence fetcher fetches multiple records for all data - sources - Ensured that command line das feature retrieval completes - before alignment figures are generated. - Reduced time taken when opening file browser for first - time. - isAligned check prior to calculating tree, PCA or - submitting an MSA to JNet now excludes hidden sequences. - User defined group colours properly recovered from Jalview - projects. - - - -	+ + Source field in GFF files parsed as feature source + rather than description + Non-positional features are now included in sequence + feature and gff files (controlled via non-positional feature + visibility in tooltip). + URL links generated for all feature links (bugfix) + Added URL embedding instructions to features file + documentation. + Codons containing ambiguous nucleotides translated as + 'X' in peptide product + Match case switch in find dialog box works for both + sequence ID and sequence string and query strings do not + have to be in upper case to match case-insensitively. + AMSA files only contain first column of + multi-character column annotation labels + Jalview Annotation File generation/parsing consistent + with documentation (e.g. Stockholm annotation can be + exported and re-imported) + PDB files without embedded PDB IDs given a friendly + name + Find incrementally searches ID string matches as well + as subsequence matches, and correctly reports total number + of both. + Application: + + Better handling of exceptions during sequence + retrieval + Dasobert generated non-positional feature URL + link text excludes the start_end suffix + DAS feature and source retrieval buttons disabled + when fetch or registry operations in progress. + PDB files retrieved from URLs are cached properly + Sequence description lines properly shared via + VAMSAS + Sequence fetcher fetches multiple records for all + data sources + Ensured that command line das feature retrieval + completes before alignment figures are generated. + Reduced time taken when opening file browser for + first time. + isAligned check prior to calculating tree, PCA or + submitting an MSA to JNet now excludes hidden sequences. + User defined group colours properly recovered + from Jalview projects. + + + +
- 2.4.0.b2 - 28/10/2009 -	- - Experimental support for google analytics usage tracking. - Jalview privacy settings (user preferences and docs). - -	- - Race condition in applet preventing startup in jre1.6.0u12+. - Exception when feature created from selection beyond length - of sequence. - Allow synthetic PDB files to be imported gracefully - Sequence associated annotation rows associate with all - sequences with a given id - Find function matches case-insensitively for sequence ID - string searches - Non-standard characters do not cause pairwise alignment to - fail with exception - - Application Issues - - Sequences are now validated against EMBL database - Sequence fetcher fetches multiple records for all data - sources - - InstallAnywhere Issues - - Dock icon works for Mac OS X java (Mac 1.6 update issue with - installAnywhere mechanism) - Command line launching of JARs from InstallAnywhere version - (java class versioning error fixed) - -
+
+ + 2.4.0.b2 28/10/2009 + +	+ + Experimental support for google analytics usage + tracking. + Jalview privacy settings (user preferences and docs). + +	+ + Race condition in applet preventing startup in + jre1.6.0u12+. + Exception when feature created from selection beyond + length of sequence. + Allow synthetic PDB files to be imported gracefully + Sequence associated annotation rows associate with + all sequences with a given id + Find function matches case-insensitively for sequence + ID string searches + Non-standard characters do not cause pairwise + alignment to fail with exception + Application Issues + + Sequences are now validated against EMBL database + Sequence fetcher fetches multiple records for all + data sources + InstallAnywhere Issues + + Dock icon works for Mac OS X java (Mac 1.6 update + issue with installAnywhere mechanism) + Command line launching of JARs from InstallAnywhere + version (java class versioning error fixed) + +
- 2.4 - 27/8/2008 -	User Interface - - Linked highlighting of codon and amino acid from translation - and protein products - Linked highlighting of structure associated with residue - mapping to codon position - Sequence Fetcher provides example accession numbers and - 'clear' button - MemoryMonitor added as an option under Desktop's Tools menu - Extract score function to parse whitespace separated numeric - data in description line - Column labels in alignment annotation can be centred. - Tooltip for sequence associated annotation give name of - sequence - - Web Services and URL fetching - - JPred3 web service - Prototype sequence search client (no public services - available yet) - Fetch either seed alignment or full alignment from PFAM - URL Links created for matching database cross references as - well as sequence ID - URL Links can be created using regular-expressions - - Sequence Database Connectivity - - Retrieval of cross-referenced sequences from other databases - - Generalised database reference retrieval and validation to - all fetchable databases - Fetch sequences from DAS sources supporting the sequence - command - - Import and Export - export annotation rows as CSV for spreadsheet import - Jalview projects record alignment dataset associations, EMBL - products, and cDNA sequence mappings - Sequence Group colour can be specified in Annotation File - Ad-hoc colouring of group in Annotation File using RGB - triplet as name of colourscheme - - VAMSAS Client capabilities (Experimental) - - treenode binding for VAMSAS tree exchange - local editing and update of sequences in VAMSAS alignments - (experimental) - Create new or select existing session to join - load and save of vamsas documents - - Application command line - - -tree parameter to open trees (introduced for passing from - applet) - -fetchfrom command line argument to specify nicknames of DAS - servers to query for alignment features - -dasserver command line argument to add new servers that are - also automatically queried for features - -groovy command line argument executes a given groovy script - after all input data has been loaded and parsed - - Applet-Application data exchange - - Trees passed as applet parameters can be passed to - application (when using "View in full application") - - Applet Parameters - - feature group display control parameter - debug parameter - showbutton parameter - - Applet API methods - - newView public method - Window (current view) specific get/set public methods - Feature display control methods - get list of currently selected sequences - - New Jalview distribution features - - InstallAnywhere Installer upgraded to IA 2008 VP1 - RELEASE file gives build properties for the latest Jalview - release. - Java 1.1 Applet build made easier and donotobfuscate - property controls execution of obfuscator - Build target for generating source distribution - Debug flag for javacc - .jalview_properties file is documented (slightly) in - jalview.bin.Cache - Continuous Build Integration for stable and development - version of Application, Applet and source distribution - + + 2.4 27/8/2008 + +	User Interface + + Linked highlighting of codon and amino acid from + translation and protein products + Linked highlighting of structure associated with + residue mapping to codon position + Sequence Fetcher provides example accession numbers + and 'clear' button + MemoryMonitor added as an option under Desktop's + Tools menu + Extract score function to parse whitespace separated + numeric data in description line + Column labels in alignment annotation can be centred. + Tooltip for sequence associated annotation give name + of sequence + Web Services and URL fetching + + JPred3 web service + Prototype sequence search client (no public services + available yet) + Fetch either seed alignment or full alignment from + PFAM + URL Links created for matching database cross + references as well as sequence ID + URL Links can be created using regular-expressions + Sequence Database Connectivity + + Retrieval of cross-referenced sequences from other + databases + Generalised database reference retrieval and + validation to all fetchable databases + Fetch sequences from DAS sources supporting the + sequence command + Import and Export + export annotation rows as CSV for spreadsheet import + Jalview projects record alignment dataset associations, + EMBL products, and cDNA sequence mappings + Sequence Group colour can be specified in Annotation + File + Ad-hoc colouring of group in Annotation File using RGB + triplet as name of colourscheme + VAMSAS Client capabilities (Experimental) + + treenode binding for VAMSAS tree exchange + local editing and update of sequences in VAMSAS + alignments (experimental) + Create new or select existing session to join + load and save of vamsas documents + Application command line + + -tree parameter to open trees (introduced for passing + from applet) + -fetchfrom command line argument to specify nicknames + of DAS servers to query for alignment features + -dasserver command line argument to add new servers + that are also automatically queried for features + -groovy command line argument executes a given groovy + script after all input data has been loaded and parsed + Applet-Application data exchange + + Trees passed as applet parameters can be passed to + application (when using "View in full + application") + Applet Parameters + + feature group display control parameter + debug parameter + showbutton parameter + Applet API methods + + newView public method + Window (current view) specific get/set public methods + Feature display control methods + get list of currently selected sequences + New Jalview distribution features + + InstallAnywhere Installer upgraded to IA 2008 VP1 + RELEASE file gives build properties for the latest + Jalview release. + Java 1.1 Applet build made easier and donotobfuscate + property controls execution of obfuscator + Build target for generating source distribution + Debug flag for javacc + .jalview_properties file is documented (slightly) in + jalview.bin.Cache + Continuous Build Integration for stable and + development version of Application, Applet and source + distribution +	+ + selected region output includes visible annotations + (for certain formats) + edit label/displaychar contains existing label/char + for editing + update PDBEntries when DBRefEntries change (vamsas) + shorter peptide product names from EMBL records + Newick string generator makes compact representations + bootstrap values parsed correctly for tree files with + comments + pathological filechooser bug avoided by not allowing + filenames containing a ':' + Fixed exception when parsing GFF files containing + global sequence features + Alignment datasets are finalized only when number of + references from alignment sequences goes to zero + Close of tree branch colour box without colour + selection causes cascading exceptions + occasional negative imgwidth exceptions + better reporting of non-fatal warnings to user when + file parsing fails. + Save works when Jalview project is default format + Save as dialog opened if current alignment format is + not a valid output format + UniProt canonical names introduced for both das and + vamsas + Histidine should be midblue (not pink!) in Zappo + error messages passed up and output when data read + fails + edit undo recovers previous dataset sequence when + sequence is edited + allow PDB files without pdb ID HEADER lines (like + those generated by MODELLER) to be read in properly + allow reading of JPred concise files as a normal + filetype + Stockholm annotation parsing and alignment properties + import fixed for PFAM records + Structure view windows have correct name in Desktop + window list + annotation consisting of sequence associated scores + can be read and written correctly to annotation file + Aligned cDNA translation to aligned peptide works + correctly + Fixed display of hidden sequence markers and + non-italic font for representatives in Applet + Applet Menus are always embedded in applet window on + Macs. + Newly shown features appear at top of stack (in + Applet) + Annotations added via parameter not drawn properly + due to null pointer exceptions + Secondary structure lines are drawn starting from + first column of alignment + UniProt XML import updated for new schema release in + July 2008 + Sequence feature to sequence ID match for Features + file is case-insensitive + Sequence features read from Features file appended to + all sequences with matching IDs + PDB structure coloured correctly for associated views + containing a sub-sequence + PDB files can be retrieved by applet from Jar files + feature and annotation file applet parameters + referring to different directories are retrieved correctly + + Fixed application hang whilst waiting for + splash-screen version check to complete + Applet properly URLencodes input parameter values + when passing them to the launchApp service + display name and local features preserved in results + retrieved from web service + Visual delay indication for sequence retrieval and + sequence fetcher initialisation + updated Application to use DAS 1.53e version of + dasobert DAS client + Re-instated Full AMSA support and .amsa file + association + Fixed parsing of JNet Concise annotation sans + sequences + + +
+ + 2.3 9/5/07 + +	+ + Jmol 11.0.2 integration + PDB views stored in Jalview XML files + Slide sequences + Edit sequence in place + EMBL CDS features + DAS Feature mapping + Feature ordering + Alignment Properties + Annotation Scores + Sort by scores + Feature/annotation editing in applet + +	+ + Headless state operation in 2.2.1 + Incorrect and unstable DNA pairwise alignment + Cut and paste of sequences with annotation + Feature group display state in XML + Feature ordering in XML + blc file iteration selection using filename # suffix + Stockholm alignment properties + Stockhom alignment secondary structure annotation + 2.2.1 applet had no feature transparency + Number pad keys can be used in cursor mode + Structure Viewer mirror image resolved + +	- - selected region output includes visible annotations (for - certain formats) - edit label/displaychar contains existing label/char for - editing - update PDBEntries when DBRefEntries change (vamsas) - shorter peptide product names from EMBL records - Newick string generator makes compact representations - bootstrap values parsed correctly for tree files with - comments - pathological filechooser bug avoided by not allowing - filenames containing a ':' - Fixed exception when parsing GFF files containing global - sequence features - Alignment datasets are finalized only when number of - references from alignment sequences goes to zero - Close of tree branch colour box without colour selection - causes cascading exceptions - occasional negative imgwidth exceptions - better reporting of non-fatal warnings to user when file - parsing fails. - Save works when Jalview project is default format - Save as dialog opened if current alignment format is not a - valid output format - Uniprot canonical names introduced for both das and vamsas - Histidine should be midblue (not pink!) in Zappo - error messages passed up and output when data read fails - edit undo recovers previous dataset sequence when sequence - is edited - allow PDB files without pdb ID HEADER lines (like those - generated by MODELLER) to be read in properly - allow reading of JPred concise files as a normal filetype - Stockholm annotation parsing and alignment properties import - fixed for PFAM records - Structure view windows have correct name in Desktop window - list - annotation consisting of sequence associated scores can be - read and written correctly to annotation file - Aligned cDNA translation to aligned peptide works correctly - Fixed display of hidden sequence markers and non-italic font - for representatives in Applet - Applet Menus are always embedded in applet window on Macs. - Newly shown features appear at top of stack (in Applet) - Annotations added via parameter not drawn properly due to - null pointer exceptions - Secondary structure lines are drawn starting from first - column of alignment - Uniprot XML import updated for new schema release in July - 2008 - Sequence feature to sequence ID match for Features file is - case-insensitive - Sequence features read from Features file appended to all - sequences with matching IDs - PDB structure coloured correctly for associated views - containing a sub-sequence - PDB files can be retrieved by applet from Jar files - feature and annotation file applet parameters referring to - different directories are retrieved correctly - - Fixed application hang whilst waiting for splash-screen - version check to complete - Applet properly URLencodes input parameter values when - passing them to the launchApp service - display name and local features preserved in results - retrieved from web service - Visual delay indication for sequence retrieval and sequence - fetcher initialisation - updated Application to use DAS 1.53e version of dasobert DAS - client - Re-instated Full AMSA support and .amsa file association - Fixed parsing of JNet Concise annotation sans - sequences - -
- 2.3 - 9/5/07 -	- - Jmol 11.0.2 integration - PDB views stored in Jalview XML files - Slide sequences - Edit sequence in place - EMBL CDS features - DAS Feature mapping - Feature ordering - Alignment Properties - Annotation Scores - Sort by scores - Feature/annotation editing in applet - -	- - Headless state operation in 2.2.1 - Incorrect and unstable DNA pairwise alignment - Cut and paste of sequences with annotation - Feature group display state in XML - Feature ordering in XML - blc file iteration selection using filename # suffix - Stockholm alignment properties - Stockhom alignment secondary structure annotation - 2.2.1 applet had no feature transparency - Number pad keys can be used in cursor mode - Structure Viewer mirror image resolved - -
+ + 2.2.1 12/2/07 + +	+ + Non standard characters can be read and displayed + Annotations/Features can be imported/exported to the + applet via textbox + Applet allows editing of sequence/annotation/group + name & description + Preference setting to display sequence name in + italics + Annotation file format extended to allow + Sequence_groups to be defined + Default opening of alignment overview panel can be + specified in preferences + PDB residue numbering annotation added to associated + sequences + +	+ + Applet crash under certain Linux OS with Java 1.6 + installed + Annotation file export / import bugs fixed + PNG / EPS image output bugs fixed + +
+ + 2.2 27/11/06 + +	+ + Multiple views on alignment + Sequence feature editing + "Reload" alignment + "Save" to current filename + Background dependent text colour + Right align sequence ids + User-defined lower case residue colours + Format Menu + Select Menu + Menu item accelerator keys + Control-V pastes to current alignment + Cancel button for DAS Feature Fetching + PCA and PDB Viewers zoom via mouse roller + User-defined sub-tree colours and sub-tree selection + + + + + + + 'New Window' button on the 'Output to Text box' + +	+ + New memory efficient Undo/Redo System + Optimised symbol lookups and conservation/consensus + calculations + Region Conservation/Consensus recalculated after + edits + Fixed Remove Empty Columns Bug (empty columns at end + of alignment) + Slowed DAS Feature Fetching for increased robustness. -
- 2.2.1 - 12/2/07 -	- - Non standard characters can be read and displayed - Annotations/Features can be imported/exported to the applet - via textbox - Applet allows editing of sequence/annotation/group name - & description - Preference setting to display sequence name in italics - Annotation file format extended to allow Sequence_groups to - be defined - Default opening of alignment overview panel can be specified - in preferences - PDB residue numbering annotation added to associated - sequences - -	- - Applet crash under certain Linux OS with Java 1.6 installed - Annotation file export / import bugs fixed - PNG / EPS image output bugs fixed - -
- 2.2 - 27/11/06 -	- - Multiple views on alignment - Sequence feature editing - "Reload" alignment - "Save" to current filename - Background dependent text colour - Right align sequence ids - User-defined lower case residue colours - Format Menu - Select Menu - Menu item accelerator keys - Control-V pastes to current alignment - Cancel button for DAS Feature Fetching - PCA and PDB Viewers zoom via mouse roller - User-defined sub-tree colours and sub-tree selection - 'New Window' button on the 'Output to Text box' - -	- - New memory efficient Undo/Redo System - Optimised symbol lookups and conservation/consensus - calculations - Region Conservation/Consensus recalculated after edits - Fixed Remove Empty Columns Bug (empty columns at end of - alignment) - Slowed DAS Feature Fetching for increased robustness. - Made angle brackets in ASCII feature descriptions display - correctly - Re-instated Zoom function for PCA - Sequence descriptions conserved in web service analysis - results - Uniprot ID discoverer uses any word separated by ∣ - WsDbFetch query/result association resolved - Tree leaf to sequence mapping improved - Smooth fonts switch moved to FontChooser dialog box. - -
- 2.1.1 - 12/9/06 -	- - Copy consensus sequence to clipboard - -	- - Image output - rightmost residues are rendered if sequence - id panel has been resized - Image output - all offscreen group boundaries are rendered - Annotation files with sequence references - all elements in - file are relative to sequence position - Mac Applet users can use Alt key for group editing - -
- 2.1 - 22/8/06 -	- - MAFFT Multiple Alignment in default Web Service list - DAS Feature fetching - Hide sequences and columns - Export Annotations and Features - GFF file reading / writing - Associate structures with sequences from local PDB files - Add sequences to exisiting alignment - Recently opened files / URL lists - Applet can launch the full application - Applet has transparency for features (Java 1.2 required) - Applet has user defined colours parameter - Applet can load sequences from parameter "sequencex" - -	- - Redundancy Panel reinstalled in the Applet - Monospaced font - EPS / rescaling bug fixed - Annotation files with sequence references bug fixed - -
- 2.08.1 - 2/5/06 -	- - Change case of selected region from Popup menu - Choose to match case when searching - Middle mouse button and mouse movement can compress / expand - the visible width and height of the alignment - -	- - Annotation Panel displays complete JNet results - -
- 2.08b - 18/4/06 -		- - Java 1.5 bug - InternalMessageDialog fix for threads - Righthand label on wrapped alignments shows correct value - -
- 2.08 - 10/4/06 -	- - Editing can be locked to the selection area - Keyboard editing - Create sequence features from searches - Precalculated annotations can be loaded onto alignments - Features file allows grouping of features - Annotation Colouring scheme added - Smooth fonts off by default - Faster rendering - Choose to toggle Autocalculate Consensus On/Off - -	- - Drag & Drop fixed on Linux - Jalview Archive file faster to load/save, sequence - descriptions saved. - -
- 2.07 - 12/12/05 -	- - PDB Structure Viewer enhanced - Sequence Feature retrieval and display enhanced - Choose to output sequence start-end after sequence name for - file output - Sequence Fetcher WSDBFetch@EBI - Applet can read feature files, PDB files and can be used for - HTML form input - -	- - HTML output writes groups and features - Group editing is Control and mouse click - File IO bugs - -
- 2.06 - 28/9/05 -	- - View annotations in wrapped mode - More options for PCA viewer - -	- - GUI bugs resolved - Runs with -nodisplay from command line - -
- 2.05b - 15/9/05 -	- - Choose EPS export as lineart or text - Jar files are executable - Can read in Uracil - maps to unknown residue - -	- - Known OutOfMemory errors give warning message - Overview window calculated more efficiently - Several GUI bugs resolved - -
- 2.05 - 30/8/05 -	- - Edit and annotate in "Wrapped" view - -	- - Several GUI bugs resolved - -
- 2.04 - 24/8/05 -	- - Hold down mouse wheel & scroll to change font size - -	- - Improved JPred client reliability - Improved loading of Jalview files - -
- 2.03 - 18/8/05 -	- - Set Proxy server name and port in preferences - Multiple URL links from sequence ids - User Defined Colours can have a scheme name and added to - Colour Menu - Choose to ignore gaps in consensus calculation - Unix users can set default web browser - Runs without GUI for batch processing - Dynamically generated Web Service Menus - -	- - InstallAnywhere download for Sparc Solaris - -
- 2.02 - 18/7/05 -		- - Copy & Paste order of sequences maintains alignment - order. - -
- 2.01 - 12/7/05 -	- - Use delete key for deleting selection. - Use Mouse wheel to scroll sequences. - Help file updated to describe how to add alignment - annotations. - Version and build date written to build properties file. - InstallAnywhere installation will check for updates at - launch of Jalview. - -	- - Delete gaps bug fixed. - FileChooser sorts columns. - Can remove groups one by one. - Filechooser icons installed. - Finder ignores return character when searching. Return key - will initiate a search. - - -
- 2.0 - 20/6/05 -	- - New codebase - -