<html>
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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>
<div align="center"><em><strong>Issues Resolved</strong></em></div>
</td>
</tr>
- <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>2.5</strong><br>
- <em>Not Yet Released</em></div>
+ <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 in order of average feature score or
- total feature count</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>
+ <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>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>
<em>Application</em>
<ul>
<li>Fetch DB References capabilities and UI expanded to support
<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>
+ 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
+ <!-- <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>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>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>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>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>
+ <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>
- <li></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>
+ <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>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>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>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>Applet:
- <ul>
- <li></li>
- </ul>
- </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 (application)</li>
+ 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>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>
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>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>
git://source.jalview.org / jalview.git / blobdiff