-<html>\r
-<head><title>Release History</title></head>\r
-<body>\r
-<p><strong>Release History</strong> </p>\r
-<table border="1">\r
- <tr> \r
- <td ><div align="center"><em><strong>Release</strong></em></div></td>\r
- <td ><div align="center"><em><strong>New Features</strong></em></div></td>\r
- <td "><div align="center"><em><strong>Issues Resolved</strong></em></div></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.08</strong><br>\r
- 6/4/06</div></td>\r
- <td><ul>\r
- <li>Editing can be locked to selection area</li>\r
- <li>Keyboard editing</li>\r
- <li>Create sequence features from Searches</li>\r
- <li>Precalculated annotations can be loaded onto alignments</li>\r
- <li>Features file allows grouping of features</li>\r
- <li>Annotation Colouring scheme added</li>\r
- <li>Smooth fonts off by default - Faster rendering</li>\r
- <li>Choose to toggle Autocalculate Consensus On/Off</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Drag & Drop fixed on Linux</li>\r
- <li>Jalview Archive file faster to load/save, sequence descriptions saved. \r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.07</strong><br>\r
- 12/12/05</div></td>\r
- <td><ul>\r
- <li>PDB Structure Viewer enhanced</li>\r
- <li>Sequence Feature retrieval and display enhanced</li>\r
- <li>Choose to output sequence start-end after sequence name for file output</li>\r
- <li>Sequence Fetcher WSDBFetch@EBI</li>\r
- <li>Applet can read feature files, PDB files and can be used for HTML \r
- form input</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>HTML output writes groups and features</li>\r
- <li>Group editing is Control and mouse click</li>\r
- <li>File IO bugs</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.06</strong><br>\r
- 28/9/05</div></td>\r
- <td><ul>\r
- <li>View annotations in wrapped mode</li>\r
- <li>More options for PCA viewer</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>GUI bugs resolved</li>\r
- <li>Runs with -nodisplay from command line</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td height="63"> <div align="center"><strong>2.05b</strong><br>\r
- 15/9/05</div></td>\r
- <td><ul>\r
- <li>Choose EPS export as lineart or text</li>\r
- <li>Jar files are executable</li>\r
- <li>Can read in Uracil - maps to unknown residue</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Known OutOfMemory errors give warning message</li>\r
- <li>Overview window calculated more efficiently</li>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.05</strong><br>\r
- 30/8/05</div></td>\r
- <td><ul>\r
- <li>Edit and annotate in "Wrapped" view</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Several GUI bugs resolved</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.04</strong><br>\r
- 24/8/05</div></td>\r
- <td><ul>\r
- <li>Hold down mouse wheel & scroll to change font size</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Improved JPred client reliability</li>\r
- <li>Improved loading of Jalview files</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.03</strong><br>\r
- 18/8/05</div></td>\r
- <td><ul>\r
- <li>Set Proxy server name and port in preferences</li>\r
- <li>Multiple URL links from sequence ids</li>\r
- <li>User Defined Colours can have a scheme name and added to Colour Menu</li>\r
- <li>Choose to ignore gaps in consensus calculation</li>\r
- <li>Unix users can set default web browser</li>\r
- <li>Runs without GUI for batch processing</li>\r
- <li>Dynamically generated Web Service Menus</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>InstallAnywhere download for Sparc Solaris</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.02</strong><br>\r
- 18/7/05</div></td>\r
- <td> </td>\r
- <td><ul>\r
- <li>Copy & Paste order of sequences maintains alignment order.</li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td><div align="center"><strong>2.01</strong><br>\r
- 12/7/05</div></td>\r
- <td><ul>\r
- <li>Use delete key for deleting selection.</li>\r
- <li>Use Mouse wheel to scroll sequences.</li>\r
- <li>Help file updated to describe how to add alignment annotations.</li>\r
- <li>Version and build date written to build properties file.</li>\r
- <li>InstallAnywhere installation will check for updates at launch of Jalview.</li>\r
- </ul></td>\r
- <td><ul>\r
- <li>Delete gaps bug fixed.</li>\r
- <li>FileChooser sorts columns.</li>\r
- <li>Can remove groups one by one.</li>\r
- <li>Filechooser icons installed.</li>\r
- <li>Finder ignores return character when searching. Return key will initiate \r
- a search.<br>\r
- </li>\r
- </ul></td>\r
- </tr>\r
- <tr> \r
- <td> <div align="center"><strong>2.0</strong><br>\r
- 20/6/05</div></td>\r
- <td ><ul>\r
- <li> New codebase</li>\r
- </ul></td>\r
- <td > </td>\r
- </tr>\r
-</table>\r
-<p> </p>\r
-</body>\r
-</html>\r
+<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
+<head>
+<title>Release History</title>
+</head>
+<body>
+<p><strong>Release History</strong></p>
+<table border="1">
+ <tr>
+ <td width="60" nowrap>
+ <div align="center"><em><strong>Release</strong></em></div>
+ </td>
+ <td>
+ <div align="center"><em><strong>New Features</strong></em></div>
+ </td>
+ <td>
+ <div align="center"><em><strong>Issues Resolved</strong></em></div>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.7">2.7</a>
+ </strong><br> <em>27/09/2011</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>Jalview Desktop News Reader</li>
+ <li>Tweaked default layout of web services menu</li>
+ <li>View/alignment association menu to enable user to easily
+ specify which alignment a multi-structure view takes its
+ colours/correspondences from</li>
+ <li>Allow properties file location to be specified as URL </li>
+ <li>Extend jalview project to preserve associations between
+ many alignment views and a single Jmol display</li>
+ <li>Store annotation row height in jalview project file</li>
+ <li>Annotation row column label formatting attributes stored
+ in project file</li>
+ <li>Annotation row order for auto-calculated annotation rows
+ preserved in jalview project file</li>
+ <li>Visual progress indication when Jalview state is saved
+ using Desktop window menu</li>
+ <li>Visual indication that command line arguments are still
+ being processed</li>
+ <li>Groovy script execution from URL</li>
+ <li>Colour by annotation default min and max colours in
+ preferences</li>
+ <li>Automatically associate PDB files dragged onto an
+ alignment with sequences that have high similarity and matching
+ IDs</li>
+ <li>Update JGoogleAnalytics to latest release (0.3)</li>
+ <li>'view structures' option to open many structures
+ in same window</li>
+ <li>Sort associated views menu option for tree panel</li>
+ <li>Group all JABA and non-JABA services for a particular
+ analysis function in its own submenu</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Userdefined and autogenerated annotation rows for groups</li>
+ <li>Adjustment of alignment annotation pane height</li>
+ <li>Annotation scrollbar for annotation panel</li>
+ <li>Drag to reorder annotation rows in annotation panel</li>
+ <li>'automaticScrolling' parameter</li>
+ <li>Allow sequences with partial ID string matches to be
+ annotated from GFF/jalview features files</li>
+ <li>Sequence logo annotation row in applet</li>
+ <li>Absolute paths relative to host server in applet
+ parameters are treated as such</li>
+ <li>New in the JalviewLite javascript API:
+ <ul>
+ <li>JalviewLite.js javascript library</li>
+ <li>Javascript callbacks for
+ <ul>
+ <li>Applet initialisation</li>
+ <li>Sequence/alignment mouse-overs and selections</li>
+ </ul>
+ </li>
+ <li>scrollTo row and column alignment scrolling functions</li>
+ <li>Select sequence/alignment regions from javascript</li>
+ <li>javascript structure viewer harness to pass messages
+ between Jmol and Jalview when running as distinct applets</li>
+ <li>sortBy method</li>
+ <li>Set of applet and application examples shipped with
+ documentation</li>
+ <li>New example to demonstrate jalviewLite and Jmol
+ javascript message exchange</li>
+ </ul>
+ </ul> <em>General</em>
+ <ul>
+ <li>Enable Jmol displays to be associated with multiple
+ multiple alignments</li>
+ <li>Option to automatically sort alignment with new tree</li>
+ <li>User configurable link to enable redirects to a
+ www.jalview.org mirror</li>
+ <li>Jmol colours option for Jmol displays</li>
+ <li>Configurable newline string when writing alignment and
+ other flat files</li>
+ <li>Allow alignment annotation description lines to contain
+ html tags</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>Add groovy test harness for bulk load testing to examples
+ </li>
+ <li>Groovy script to load and align a set of sequences using a
+ web service before displaying the result in the Jalview desktop</li>
+ <li>Restructured javascript and applet api documentation</li>
+ <li>Ant target to publish example html files with applet archive</li>
+ <li>Netbeans project for building jalview from source</li>
+ <li>ant task to create online javadoc for jalview source</li>
+ </ul></td>
+ <td><em>Application</em>
+ <ul>
+ <li>User defined colourscheme throws exception when current
+ built in colourscheme is saved as new scheme</li>
+ <li>AlignFrame->Save in application pops up save dialog for
+ valid filename/format</li>
+ <li>Cannot view associated structure for Uniprot sequence</li>
+ <li>PDB file association breaks for Uniprot sequence P37173</li>
+ <li>Associate PDB from file dialog does not tell you which
+ sequence is to be associated with the file</li>
+ <li>Find All raises null pointer exception when query only
+ matches sequence IDs</li>
+ <li>Pre 2.6 Jalview project cannot be loaded into v2.6</li>
+ <li>Jalview project with Jmol views created with Jalview 2.4
+ cannot be loaded</li>
+ <li>Filetype associations not installed for webstart launch</li>
+ <li>Two or more chains in a single PDB file associated with
+ sequences in different alignments do not get coloured by their
+ associated sequence</li>
+ <li>Visibility status of autocalculated annotation row not
+ preserved when project is loaded</li>
+ <li>Annotation row height and visibility attributes not stored
+ in jalview project</li>
+ <li>Tree bootstraps are not preserved when saved as a jalview
+ project</li>
+ <li>Envision2 workflow tooltips are corrupted</li>
+ <li>Enabling show group conservation also enables colour by
+ conservation</li>
+ <li>Duplicate group associated conservation or consensus
+ created on new view</li>
+ <li>Annotation scrollbar not displayed after 'show all
+ hidden annotation rows' option selected</li>
+ <li>Alignment quality not updated after alignment annotation
+ row is hidden then shown</li>
+ <li>Preserve colouring of structures coloured by sequences in pre
+ jalview 2.7 projects</li>
+ <li>Web service job parameter dialog is not laid out properly
+ </li>
+ <li>Web services menu not refreshed after 'reset
+ services' button is pressed in preferences</li>
+ <li>Annotation off by one in jalview v2_3 example project</li>
+ <li>Structures imported from file and saved in project get
+ name like jalview_pdb1234.txt when reloaded</li>
+ <li>Jalview does not always retrieve progress of a JABAWS job
+ execution in full once it is complete</li>
+ </ul> <em>Applet</em>
+ <ul>
+ <li>Alignment height set incorrectly when lots of annotation
+ rows are displayed</li>
+ <li>Relative URLs in feature HTML text not resolved to
+ codebase</li>
+ <li>View follows highlighting does not work for positions in
+ sequences</li>
+ <li><= shown as = in tooltip</li>
+ <li>Export features raises exception when no features exist</li>
+ <li>Separator string used for serialising lists of IDs for
+ javascript api is modified when separator string provided as
+ parameter</li>
+ <li>Null pointer exception when selecting tree leaves for
+ alignment with no existing selection</li>
+ <li>Relative URLs for datasources assumed to be relative to
+ applet's codebase</li>
+ <li>Status bar not updated after finished searching and search
+ wraps around to first result</li>
+ <li>StructureSelectionManager instance shared between several
+ jalview applets causes race conditions and memory leaks</li>
+ <li>Hover tooltip and mouseover of position on structure not
+ sent from Jmol in applet</li>
+ <li>Certain sequences of javascript method calls to applet API
+ fatally hang browser</li>
+ </ul> <em>General</em>
+ <ul>
+ <li>View follows structure mouseover scrolls beyond position
+ with wrapped view and hidden regions</li>
+ <li>Find sequence position moves to wrong residue with/without
+ hidden columns</li>
+ <li>Sequence length given in alignment properties window is
+ off by 1</li>
+ <li>InvalidNumberFormat exceptions thrown when trying to
+ import PDB like structure files</li>
+ <li>Positional search results are only highlighted between
+ user-supplied sequence start/end bounds</li>
+ <li>End attribute of sequence is not validated</li>
+ <li>Find dialog only finds first sequence containing a given
+ sequence position</li>
+ <li>Sequence numbering not preserved in MSF alignment output</li>
+ <li>Jalview PDB file reader does not extract sequence from
+ nucleotide chains correctly</li>
+ <li>Structure colours not updated when tree partition changed
+ in alignment</li>
+ <li>Sequence associated secondary structure not correctly
+ parsed in interleaved stockholm</li>
+ <li>Colour by annotation dialog does not restore current state
+ </li>
+ <li>Hiding (nearly) all sequences doesn't work properly</li>
+ <li>Sequences containing lowercase letters are not properly
+ associated with their pdb files</li>
+ </ul> <em>Documentation and Development</em>
+ <ul>
+ <li>schemas/JalviewWsParamSet.xsd corrupted by ApplyCopyright
+ tool</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center">
+ <strong><a name="Jalview2.6.1">2.6.1</a>
+ </strong><br> <em>15/11/2010</em>
+ </div></td>
+ <td><em>Application</em>
+ <ul>
+ <li>New warning dialog when the Jalview Desktop cannot contact
+ web services</li>
+ <li>JABA service parameters for a preset are shown in service
+ job window</li>
+ <li>JABA Service menu entries reworded</li>
+ </ul></td>
+ <td>
+ <ul>
+ <li>Modeller PIR IO broken - cannot correctly import a pir
+ file emitted by jalview</li>
+ <li>Existing feature settings transferred to new alignment
+ view created from cut'n'paste</li>
+ <li>Improved test for mixed amino/nucleotide chains when
+ parsing PDB files</li>
+ <li>Consensus and conservation annotation rows occasionally
+ become blank for all new windows</li>
+ <li>Exception raised when right clicking above sequences in
+ wrapped view mode</li>
+ </ul> <em>Application</em>
+ <ul>
+ <li>multiple multiply aligned structure views cause cpu usage
+ to hit 100% and computer to hang</li>
+ <li>Web Service parameter layout breaks for long user
+ parameter names</li>
+ <li>Jaba service discovery hangs desktop if Jaba server is
+ down</li>
+ </ul></td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong><a name="Jalview2.6">2.6</a></strong><br>
+ <em>26/9/2010</em></div>
+ </td>
+ <td><em>Application</em>
+ <ul>
+ <li>Support for <strong>Ja</strong>va <strong>b</strong>ioinformatics
+ <strong>a</strong>nalysis <strong>w</strong>eb <strong>s</strong>ervices (JABAWS)</li>
+ <li>Web Services preference tab</li>
+ <li>Analysis parameters dialog box and user defined preferences</li>
+ <li>Improved speed and layout of Envision2 service menu</li>
+ <li>Superpose structures using associated sequence alignment</li>
+ <li>Export coordinates and projection as CSV from PCA viewer</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>enable javascript: execution by the applet via the link out
+ mechanism</li>
+ </ul>
+ <em>Other</em>
+ <ul>
+ <li>Updated the Jmol Jalview interface to work with Jmol series
+ 12</li>
+ <li>The Jalview Desktop and JalviewLite applet now require Java
+ 1.5</li>
+ <li>Allow Jalview feature colour specification for GFF sequence
+ annotation files</li>
+ <li>New 'colour by label' keword in jalview feature file type
+ colour specification</li>
+ <li>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</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column</li>
+ </ul>
+
+ <em>Application</em>
+ <ul>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Regions menu item</li>
+ <li>sequence fetcher replaces ',' for ';' when the ',' is part
+ of a valid accession ID</li>
+ <li>fatal OOM if object retrieved by sequence fetcher runs out
+ of memory</li>
+ <li>unhandled Out of Memory Error when viewing pca analysis
+ results</li>
+ <li>InstallAnywhere builds fail to launch on OS X java 10.5
+ update 4 (due to apple Java 1.6 update)</li>
+ <li>Installanywhere Jalview silently fails to launch</li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Jalview.getFeatureGroups() raises an
+ ArrayIndexOutOfBoundsException if no feature groups are defined.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong><a name="Jalview2.5.1">2.5.1</a></strong><br>
+ <em>14/6/2010</em></div>
+ </td>
+ <td></td>
+ <td>
+ <ul>
+ <li>Alignment prettyprinter doesn't cope with long sequence IDs
+ </li>
+ <li>clustalx colourscheme colours Ds preferentially when both
+ D+E are present in over 50% of the column</li>
+ <li>nucleic acid structures retrieved from PDB do not import
+ correctly</li>
+ <li>More columns get selected than were clicked on when a number
+ of columns are hidden</li>
+ <li>annotation label popup menu not providing correct
+ add/hide/show options when rows are hidden or none are present</li>
+ <li>Stockholm format shown in list of readable formats, and
+ parser copes better with alignments from RFAM.</li>
+ <li>CSV output of consensus only includes the percentage of all
+ symbols if sequence logo display is enabled</li>
+
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>annotation panel disappears when annotation is
+ hidden/removed</li>
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Alignment view not redrawn properly when new alignment
+ opened where annotation panel is visible but no annotations are
+ present on alignment</li>
+ <li>pasted region containing hidden columns is incorrectly
+ displayed in new alignment window</li>
+ <li>Jalview slow to complete operations when stdout is flooded
+ (fix is to close the Jalview console)</li>
+ <li>typo in AlignmentFrame->View->Hide->all but
+ selected Rregions menu item.</li>
+ <li>inconsistent group submenu and Format submenu entry 'Un' or
+ 'Non'conserved</li>
+ <li>Sequence feature settings are being shared by multiple
+ distinct alignments</li>
+ <li>group annotation not recreated when tree partition is
+ changed</li>
+ <li>double click on group annotation to select sequences does
+ not propagate to associated trees</li>
+ <li>Mac OSX specific issues:
+ <ul>
+ <li>exception raised when mouse clicked on desktop window
+ background</li>
+ <li>Desktop menu placed on menu bar and application name set
+ correctly</li>
+ <li>sequence feature settings not wide enough for the save
+ feature colourscheme button</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+
+ <td>
+ <div align="center"><strong><a name="Jalview2.5">2.5</a></strong><br>
+ <em>30/4/2010</em></div>
+ </td>
+ <td><em>New Capabilities</em>
+ <ul>
+ <li>URL links generated from description line for
+ regular-expression based URL links (applet and application)
+ <li>Non-positional feature URL links are shown in link menu</li>
+ <li>Linked viewing of nucleic acid sequences and structures</li>
+ <li>Automatic Scrolling option in View menu to display the
+ currently highlighted region of an alignment.</li>
+ <li>Order an alignment by sequence length, or using the average
+ score or total feature count for each sequence.</li>
+ <li>Shading features by score or associated description</li>
+ <li>Subdivide alignment and groups based on identity of selected
+ subsequence (Make Groups from Selection).</li>
+ <li>New hide/show options including Shift+Control+H to hide
+ everything but the currently selected region.</li>
+ <!-- introduced but not yet documented <li>Experimental blast report parser</li> -->
+ </ul>
+ <em>Application</em>
+ <ul>
+ <li>Fetch DB References capabilities and UI expanded to support
+ retrieval from DAS sequence sources</li>
+ <li>Local DAS Sequence sources can be added via the command line
+ or via the Add local source dialog box.</li>
+ <li>DAS Dbref and DbxRef feature types are parsed as database
+ references and protein_name is parsed as description line (BioSapiens
+ terms).</li>
+ <li>Enable or disable non-positional feature and database
+ references in sequence ID tooltip from View menu in application.</li>
+ <!-- <li>New hidden columns and rows and representatives capabilities
+ in annotations file (in progress - not yet fully implemented)</li> -->
+ <li>Group-associated consensus, sequence logos and conservation
+ plots</li>
+ <li>Symbol distributions for each column can be exported and
+ visualized as sequence logos</li>
+ <li>Optionally scale multi-character column labels to fit within
+ each column of annotation row<!-- todo for applet --></li>
+ <li>Optional automatic sort of associated alignment view when a
+ new tree is opened.</li>
+ <li>Jalview Java Console</li>
+ <li>Better placement of desktop window when moving between
+ different screens.</li>
+ <li>New preference items for sequence ID tooltip and consensus
+ annotation</li>
+ <li>Client to submit sequences and IDs to <a
+ href="webServices/index.html#envision2">Envision2</a> Workflows</li>
+ <li><em>Vamsas Capabilities</em>
+ <ul>
+ <li>Improved VAMSAS synchronization (jalview archive used to
+ preserve views, structures, and tree display settings)</li>
+ <li>Import of vamsas documents from disk or URL via command
+ line</li>
+ <li>Sharing of selected regions between views and with other
+ VAMSAS applications (Experimental feature!)</li>
+ <li>Updated API to VAMSAS version 0.2</li>
+ </ul>
+ </li>
+ </ul>
+ <em>Applet</em>
+ <ul>
+ <li>Middle button resizes annotation row height</li>
+ <li>New Parameters
+ <ul>
+ <li>sortByTree (true/false) - automatically sort the associated
+ alignment view by the tree when a new tree is opened.</li>
+ <li>showTreeBootstraps (true/false) - show or hide branch
+ bootstraps (default is to show them if available)</li>
+ <li>showTreeDistances (true/false) - show or hide branch
+ lengths (default is to show them if available)</li>
+ <li>showUnlinkedTreeNodes (true/false) - indicate if
+ unassociated nodes should be highlighted in the tree view</li>
+ <li>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.</li>
+ </ul>
+ </li>
+ <li>Non-positional features displayed in sequence ID tooltip</li>
+ </ul>
+ <em>Other</em>
+ <ul>
+ <li>Features format: graduated colour definitions and
+ specification of feature scores</li>
+ <li>Alignment Annotations format: new keywords for group
+ associated annotation (GROUP_REF) and annotation row display
+ properties (ROW_PROPERTIES)</li>
+ <li>XML formats extended to support graduated feature
+ colourschemes, group associated annotation, and profile visualization
+ settings.</li>
+ </td>
+ <td>
+ <ul>
+ <li>Source field in GFF files parsed as feature source rather
+ than description</li>
+ <li>Non-positional features are now included in sequence feature
+ and gff files (controlled via non-positional feature visibility in
+ tooltip).</li>
+ <li>URL links generated for all feature links (bugfix)</li>
+ <li>Added URL embedding instructions to features file
+ documentation.</li>
+ <li>Codons containing ambiguous nucleotides translated as 'X' in
+ peptide product</li>
+ <li>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.</li>
+ <li>AMSA files only contain first column of multi-character
+ column annotation labels</li>
+ <li>Jalview Annotation File generation/parsing consistent with
+ documentation (e.g. Stockholm annotation can be exported and
+ re-imported)</li>
+ <li>PDB files without embedded PDB IDs given a friendly name</li>
+ <li>Find incrementally searches ID string matches as well as
+ subsequence matches, and correctly reports total number of both.</li>
+ <li>Application:
+ <ul>
+ <li>Better handling of exceptions during sequence retrieval</li>
+ <li>Dasobert generated non-positional feature URL link text
+ excludes the start_end suffix</li>
+ <li>DAS feature and source retrieval buttons disabled when
+ fetch or registry operations in progress.</li>
+ <li>PDB files retrieved from URLs are cached properly</li>
+ <li>Sequence description lines properly shared via VAMSAS</li>
+ <li>Sequence fetcher fetches multiple records for all data
+ sources</li>
+ <li>Ensured that command line das feature retrieval completes
+ before alignment figures are generated.</li>
+ <li>Reduced time taken when opening file browser for first
+ time.</li>
+ <li>isAligned check prior to calculating tree, PCA or
+ submitting an MSA to JNet now excludes hidden sequences.</li>
+ <li>User defined group colours properly recovered from Jalview
+ projects.</li>
+ </ul>
+ </li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.4.0.b2</strong><br>
+ 28/10/2009</div>
+ </td>
+ <td>
+ <ul>
+ <li>Experimental support for google analytics usage tracking.</li>
+ <li>Jalview privacy settings (user preferences and docs).</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Race condition in applet preventing startup in jre1.6.0u12+.</li>
+ <li>Exception when feature created from selection beyond length
+ of sequence.</li>
+ <li>Allow synthetic PDB files to be imported gracefully</li>
+ <li>Sequence associated annotation rows associate with all
+ sequences with a given id</li>
+ <li>Find function matches case-insensitively for sequence ID
+ string searches</li>
+ <li>Non-standard characters do not cause pairwise alignment to
+ fail with exception</li>
+ </ul>
+ <em>Application Issues</em>
+ <ul>
+ <li>Sequences are now validated against EMBL database</li>
+ <li>Sequence fetcher fetches multiple records for all data
+ sources</li>
+ </ul>
+ <em>InstallAnywhere Issues</em>
+ <ul>
+ <li>Dock icon works for Mac OS X java (Mac 1.6 update issue with
+ installAnywhere mechanism)</li>
+ <li>Command line launching of JARs from InstallAnywhere version
+ (java class versioning error fixed)</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+
+ <div align="center"><strong>2.4</strong><br>
+ 27/8/2008</div>
+ </td>
+ <td><em>User Interface</em>
+ <ul>
+ <li>Linked highlighting of codon and amino acid from translation
+ and protein products</li>
+ <li>Linked highlighting of structure associated with residue
+ mapping to codon position</li>
+ <li>Sequence Fetcher provides example accession numbers and
+ 'clear' button</li>
+ <li>MemoryMonitor added as an option under Desktop's Tools menu</li>
+ <li>Extract score function to parse whitespace separated numeric
+ data in description line</li>
+ <li>Column labels in alignment annotation can be centred.</li>
+ <li>Tooltip for sequence associated annotation give name of
+ sequence</li>
+ </ul>
+ <em>Web Services and URL fetching</em>
+ <ul>
+ <li>JPred3 web service</li>
+ <li>Prototype sequence search client (no public services
+ available yet)</li>
+ <li>Fetch either seed alignment or full alignment from PFAM</li>
+ <li>URL Links created for matching database cross references as
+ well as sequence ID</li>
+ <li>URL Links can be created using regular-expressions</li>
+ </ul>
+ <em>Sequence Database Connectivity</em>
+ <ul>
+ <li>Retrieval of cross-referenced sequences from other databases
+ </li>
+ <li>Generalised database reference retrieval and validation to
+ all fetchable databases</li>
+ <li>Fetch sequences from DAS sources supporting the sequence
+ command</li>
+ </ul>
+ <em>Import and Export</em>
+ <li>export annotation rows as CSV for spreadsheet import</li>
+ <li>Jalview projects record alignment dataset associations, EMBL
+ products, and cDNA sequence mappings</li>
+ <li>Sequence Group colour can be specified in Annotation File</li>
+ <li>Ad-hoc colouring of group in Annotation File using RGB
+ triplet as name of colourscheme</li>
+ </ul>
+ <em>VAMSAS Client capabilities (Experimental)</em>
+ <ul>
+ <li>treenode binding for VAMSAS tree exchange</li>
+ <li>local editing and update of sequences in VAMSAS alignments
+ (experimental)</li>
+ <li>Create new or select existing session to join</li>
+ <li>load and save of vamsas documents</li>
+ </ul>
+ <em>Application command line</em>
+ <ul>
+ <li>-tree parameter to open trees (introduced for passing from
+ applet)</li>
+ <li>-fetchfrom command line argument to specify nicknames of DAS
+ servers to query for alignment features</li>
+ <li>-dasserver command line argument to add new servers that are
+ also automatically queried for features</li>
+ <li>-groovy command line argument executes a given groovy script
+ after all input data has been loaded and parsed</li>
+ </ul>
+ <em>Applet-Application data exchange</em>
+ <ul>
+ <li>Trees passed as applet parameters can be passed to
+ application (when using "View in full application")</li>
+ </ul>
+ <em>Applet Parameters</em>
+ <ul>
+ <li>feature group display control parameter</li>
+ <li>debug parameter</li>
+ <li>showbutton parameter</li>
+ </ul>
+ <em>Applet API methods</em>
+ <ul>
+ <li>newView public method</li>
+ <li>Window (current view) specific get/set public methods</li>
+ <li>Feature display control methods</li>
+ <li>get list of currently selected sequences</li>
+ </ul>
+ <em>New Jalview distribution features</em>
+ <ul>
+ <li>InstallAnywhere Installer upgraded to IA 2008 VP1</li>
+ <li>RELEASE file gives build properties for the latest Jalview
+ release.</li>
+ <li>Java 1.1 Applet build made easier and donotobfuscate
+ property controls execution of obfuscator</li>
+ <li>Build target for generating source distribution</li>
+ <li>Debug flag for javacc</li>
+ <li>.jalview_properties file is documented (slightly) in
+ jalview.bin.Cache</li>
+ <li>Continuous Build Integration for stable and development
+ version of Application, Applet and source distribution</li>
+ </ul>
+
+ </td>
+ <td>
+ <ul>
+ <li>selected region output includes visible annotations (for
+ certain formats)</li>
+ <li>edit label/displaychar contains existing label/char for
+ editing</li>
+ <li>update PDBEntries when DBRefEntries change (vamsas)</li>
+ <li>shorter peptide product names from EMBL records</li>
+ <li>Newick string generator makes compact representations</li>
+ <li>bootstrap values parsed correctly for tree files with
+ comments</li>
+ <li>pathological filechooser bug avoided by not allowing
+ filenames containing a ':'</li>
+ <li>Fixed exception when parsing GFF files containing global
+ sequence features</li>
+ <li>Alignment datasets are finalized only when number of
+ references from alignment sequences goes to zero</li>
+ <li>Close of tree branch colour box without colour selection
+ causes cascading exceptions</li>
+ <li>occasional negative imgwidth exceptions</li>
+ <li>better reporting of non-fatal warnings to user when file
+ parsing fails.</li>
+ <li>Save works when Jalview project is default format</li>
+ <li>Save as dialog opened if current alignment format is not a
+ valid output format</li>
+ <li>Uniprot canonical names introduced for both das and vamsas</li>
+ <li>Histidine should be midblue (not pink!) in Zappo</li>
+ <li>error messages passed up and output when data read fails</li>
+ <li>edit undo recovers previous dataset sequence when sequence
+ is edited</li>
+ <li>allow PDB files without pdb ID HEADER lines (like those
+ generated by MODELLER) to be read in properly</li>
+ <li>allow reading of JPred concise files as a normal filetype</li>
+ <li>Stockholm annotation parsing and alignment properties import
+ fixed for PFAM records</li>
+ <li>Structure view windows have correct name in Desktop window
+ list</li>
+ <li>annotation consisting of sequence associated scores can be
+ read and written correctly to annotation file</li>
+ <li>Aligned cDNA translation to aligned peptide works correctly</li>
+ <li>Fixed display of hidden sequence markers and non-italic font
+ for representatives in Applet</li>
+ <li>Applet Menus are always embedded in applet window on Macs.</li>
+ <li>Newly shown features appear at top of stack (in Applet)</li>
+ <li>Annotations added via parameter not drawn properly due to
+ null pointer exceptions</li>
+ <li>Secondary structure lines are drawn starting from first
+ column of alignment</li>
+ <li>Uniprot XML import updated for new schema release in July
+ 2008</li>
+ <li>Sequence feature to sequence ID match for Features file is
+ case-insensitive</li>
+ <li>Sequence features read from Features file appended to all
+ sequences with matching IDs</li>
+ <li>PDB structure coloured correctly for associated views
+ containing a sub-sequence</li>
+ <li>PDB files can be retrieved by applet from Jar files</li>
+ <li>feature and annotation file applet parameters referring to
+ different directories are retrieved correctly</li>
+ <!--<li>DAS Histogram Features display ( (Prlic et al) </li>-->
+ <li>Fixed application hang whilst waiting for splash-screen
+ version check to complete</li>
+ <li>Applet properly URLencodes input parameter values when
+ passing them to the launchApp service</li>
+ <li>display name and local features preserved in results
+ retrieved from web service</li>
+ <li>Visual delay indication for sequence retrieval and sequence
+ fetcher initialisation</li>
+ <li>updated Application to use DAS 1.53e version of dasobert DAS
+ client</li>
+ <li>Re-instated Full AMSA support and .amsa file association</li>
+ <li>Fixed parsing of JNet Concise annotation <em>sans</em>
+ sequences</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.3</strong><br>
+ 9/5/07</div>
+ </td>
+ <td>
+ <ul>
+ <li>Jmol 11.0.2 integration</li>
+ <li>PDB views stored in Jalview XML files</li>
+ <li>Slide sequences</li>
+ <li>Edit sequence in place</li>
+ <li>EMBL CDS features</li>
+ <li>DAS Feature mapping</li>
+ <li>Feature ordering</li>
+ <li>Alignment Properties</li>
+ <li>Annotation Scores</li>
+ <li>Sort by scores</li>
+ <li>Feature/annotation editing in applet</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Headless state operation in 2.2.1</li>
+ <li>Incorrect and unstable DNA pairwise alignment</li>
+ <li>Cut and paste of sequences with annotation</li>
+ <li>Feature group display state in XML</li>
+ <li>Feature ordering in XML</li>
+ <li>blc file iteration selection using filename # suffix</li>
+ <li>Stockholm alignment properties</li>
+ <li>Stockhom alignment secondary structure annotation</li>
+ <li>2.2.1 applet had no feature transparency</li>
+ <li>Number pad keys can be used in cursor mode</li>
+ <li>Structure Viewer mirror image resolved</li>
+ </ul>
+ </td>
+
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.2.1</strong><br>
+ 12/2/07</div>
+ </td>
+ <td>
+ <ul>
+ <li>Non standard characters can be read and displayed
+ <li>Annotations/Features can be imported/exported to the applet
+ via textbox
+ <li>Applet allows editing of sequence/annotation/group name
+ & description
+ <li>Preference setting to display sequence name in italics
+ <li>Annotation file format extended to allow Sequence_groups to
+ be defined
+ <li>Default opening of alignment overview panel can be specified
+ in preferences
+ <li>PDB residue numbering annotation added to associated
+ sequences
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Applet crash under certain Linux OS with Java 1.6 installed
+ <li>Annotation file export / import bugs fixed
+ <li>PNG / EPS image output bugs fixed
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.2</strong><br>
+ 27/11/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Multiple views on alignment
+ <li>Sequence feature editing
+ <li>"Reload" alignment
+ <li>"Save" to current filename
+ <li>Background dependent text colour
+ <li>Right align sequence ids
+ <li>User-defined lower case residue colours
+ <li>Format Menu
+ <li>Select Menu
+ <li>Menu item accelerator keys
+ <li>Control-V pastes to current alignment
+ <li>Cancel button for DAS Feature Fetching
+ <li>PCA and PDB Viewers zoom via mouse roller
+ <li>User-defined sub-tree colours and sub-tree selection
+ <li>'New Window' button on the 'Output to Text box'
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>New memory efficient Undo/Redo System
+ <li>Optimised symbol lookups and conservation/consensus
+ calculations
+ <li>Region Conservation/Consensus recalculated after edits
+ <li>Fixed Remove Empty Columns Bug (empty columns at end of
+ alignment)
+ <li>Slowed DAS Feature Fetching for increased robustness.
+ <li>Made angle brackets in ASCII feature descriptions display
+ correctly
+ <li>Re-instated Zoom function for PCA
+ <li>Sequence descriptions conserved in web service analysis
+ results
+ <li>Uniprot ID discoverer uses any word separated by ∣
+ <li>WsDbFetch query/result association resolved
+ <li>Tree leaf to sequence mapping improved
+ <li>Smooth fonts switch moved to FontChooser dialog box.
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.1.1</strong><br>
+ 12/9/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Copy consensus sequence to clipboard</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Image output - rightmost residues are rendered if sequence
+ id panel has been resized</li>
+ <li>Image output - all offscreen group boundaries are rendered</li>
+ <li>Annotation files with sequence references - all elements in
+ file are relative to sequence position</li>
+ <li>Mac Applet users can use Alt key for group editing</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.1</strong><br>
+ 22/8/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>MAFFT Multiple Alignment in default Web Service list</li>
+ <li>DAS Feature fetching</li>
+ <li>Hide sequences and columns</li>
+ <li>Export Annotations and Features</li>
+ <li>GFF file reading / writing</li>
+ <li>Associate structures with sequences from local PDB files</li>
+ <li>Add sequences to exisiting alignment</li>
+ <li>Recently opened files / URL lists</li>
+ <li>Applet can launch the full application</li>
+ <li>Applet has transparency for features (Java 1.2 required)</li>
+ <li>Applet has user defined colours parameter</li>
+ <li>Applet can load sequences from parameter "sequence<em>x</em>"</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Redundancy Panel reinstalled in the Applet</li>
+ <li>Monospaced font - EPS / rescaling bug fixed</li>
+ <li>Annotation files with sequence references bug fixed</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.08.1</strong><br>
+ 2/5/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Change case of selected region from Popup menu</li>
+ <li>Choose to match case when searching</li>
+ <li>Middle mouse button and mouse movement can compress / expand
+ the visible width and height of the alignment</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Annotation Panel displays complete JNet results</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.08b</strong><br>
+ 18/4/06</div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Java 1.5 bug - InternalMessageDialog fix for threads</li>
+ <li>Righthand label on wrapped alignments shows correct value</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.08</strong><br>
+ 10/4/06</div>
+ </td>
+ <td>
+ <ul>
+ <li>Editing can be locked to the selection area</li>
+ <li>Keyboard editing</li>
+ <li>Create sequence features from searches</li>
+ <li>Precalculated annotations can be loaded onto alignments</li>
+ <li>Features file allows grouping of features</li>
+ <li>Annotation Colouring scheme added</li>
+ <li>Smooth fonts off by default - Faster rendering</li>
+ <li>Choose to toggle Autocalculate Consensus On/Off</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Drag & Drop fixed on Linux</li>
+ <li>Jalview Archive file faster to load/save, sequence
+ descriptions saved.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.07</strong><br>
+ 12/12/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>PDB Structure Viewer enhanced</li>
+ <li>Sequence Feature retrieval and display enhanced</li>
+ <li>Choose to output sequence start-end after sequence name for
+ file output</li>
+ <li>Sequence Fetcher WSDBFetch@EBI</li>
+ <li>Applet can read feature files, PDB files and can be used for
+ HTML form input</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>HTML output writes groups and features</li>
+ <li>Group editing is Control and mouse click</li>
+ <li>File IO bugs</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.06</strong><br>
+ 28/9/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>View annotations in wrapped mode</li>
+ <li>More options for PCA viewer</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>GUI bugs resolved</li>
+ <li>Runs with -nodisplay from command line</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td height="63">
+ <div align="center"><strong>2.05b</strong><br>
+ 15/9/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Choose EPS export as lineart or text</li>
+ <li>Jar files are executable</li>
+ <li>Can read in Uracil - maps to unknown residue</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Known OutOfMemory errors give warning message</li>
+ <li>Overview window calculated more efficiently</li>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.05</strong><br>
+ 30/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Edit and annotate in "Wrapped" view</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Several GUI bugs resolved</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.04</strong><br>
+ 24/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Hold down mouse wheel & scroll to change font size</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Improved JPred client reliability</li>
+ <li>Improved loading of Jalview files</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.03</strong><br>
+ 18/8/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Set Proxy server name and port in preferences</li>
+ <li>Multiple URL links from sequence ids</li>
+ <li>User Defined Colours can have a scheme name and added to
+ Colour Menu</li>
+ <li>Choose to ignore gaps in consensus calculation</li>
+ <li>Unix users can set default web browser</li>
+ <li>Runs without GUI for batch processing</li>
+ <li>Dynamically generated Web Service Menus</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>InstallAnywhere download for Sparc Solaris</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.02</strong><br>
+ 18/7/05</div>
+ </td>
+ <td> </td>
+ <td>
+ <ul>
+ <li>Copy & Paste order of sequences maintains alignment
+ order.</li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.01</strong><br>
+ 12/7/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>Use delete key for deleting selection.</li>
+ <li>Use Mouse wheel to scroll sequences.</li>
+ <li>Help file updated to describe how to add alignment
+ annotations.</li>
+ <li>Version and build date written to build properties file.</li>
+ <li>InstallAnywhere installation will check for updates at
+ launch of Jalview.</li>
+ </ul>
+ </td>
+ <td>
+ <ul>
+ <li>Delete gaps bug fixed.</li>
+ <li>FileChooser sorts columns.</li>
+ <li>Can remove groups one by one.</li>
+ <li>Filechooser icons installed.</li>
+ <li>Finder ignores return character when searching. Return key
+ will initiate a search.<br>
+ </li>
+ </ul>
+ </td>
+ </tr>
+ <tr>
+ <td>
+ <div align="center"><strong>2.0</strong><br>
+ 20/6/05</div>
+ </td>
+ <td>
+ <ul>
+ <li>New codebase</li>
+ </ul>
+ </td>
+ <td> </td>
+ </tr>
+</table>
+<p> </p>
+</body>
+</html>
git://source.jalview.org / jalview.git / blobdiff