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- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- *
- * 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
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- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- -->
-<head>
-<title>Release History</title>
-<style>
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-</head>
-<body>
- <p>
- <strong>Release History</strong>
- </p>
- <table border="1">
- <tr>
- <th nowrap><a id="Jalview.$$Version-Rel$$"><em>Release</em></th>
- <th><em>New Features</em></th>
- <th><em>Issues Resolved</em></th>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.2">2.11.2</a><a id="Jalview.2.11.2.0">.0</a><br />
- <em>24/02/2022</em></strong></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL- -->
- </li>
- <li>
- <!-- JAL-3863 -->Support for Canonical Uniprot IDs
- </li>
- </ul> <em>JalviewJS</em>
- <ul><li><!-- 3624 -->PDB structures mapped to Uniprot Sequences with SIFTS</li>
- <li></li>
- </ul> <em>Development</em>
- <ul>
- <li>Updated building instructions</li>
- <li>First integrated JalviewJS and Jalview release</li>
- </ul>
-
- </td>
- <td>
- <ul>
- <li>
- <!-- JAL-3700,JAL-3751,JAL-3763, JAL-3725 -->Selections not propagated between Linked CDS - Protein alignments and their trees (known defect from 2.11.1.3)
- </li>
- <li>
- <!-- JAL-3761 -->Not all codon positions highlighted for
- overlapping exon splice sites (e.g due to RNA slippage)
- </li>
- <li>
- <!-- JAL-3915 -->Removed RNAview checkbox and logic from
- Structure Preferences
- </li>
- <li><!-- JAL-3583 -->Tooltip behaviour improved (slightly)</li>
- <li><!-- JAL-3162 -->Can edit a feature so that start > end</li>
- <li><!-- JAL-2848 -->Cancel from Amend Features doesn't reset a modified graduated colour</li>
- </ul> <em>Development</em>
- <ul>
- <li>Gradle<ul><li>Fixed non-fatal gradle errors during build</li>
- <li><!-- JAL-3745 -->Updated build.gradle for use with Gradle v.6.6+</li></ul></li>
-
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.7">.7</a><br />
- <em>18/01/2022</em></strong></td>
- <td></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3703, JAL-3935 -->Files open in Jalview cannot be
- updated by Jalview or other applications (Windows, other non
- Unix/BSD OSs)
- </li>
- </ul> <em>Security</em>
- <ul>
- <li>
- <!-- JAL-3937 -->Enable AIA download of HTTPS intermediate
- certificates.
- </li>
- </ul>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.6">.6</a><br />
- <em>6/01/2022</em></strong></td>
-
- <td align="left" valign="top"><em>Security</em>
- <ul>
- <li>
- <!-- JAL-3934 -->Version bump library dependency: Log4j 2.16.0 to 2.17.0.
- </li>
- </ul></td>
- <td>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.5">.5</a><br />
- <em>20/12/2021</em></strong></td>
-
- <td align="left" valign="top"><em>Security</em>
- <ul>
- <li>
- <!-- JAL-3933 -->Update library dependency: Log4j 2.16.0
- (was log4j 1.2.x).
- </ul> <em>Development</em>
- <ul>
- <li>Updated building instructions</li>
- </ul></td>
- <td>
- <ul>
- <li>
- <!-- JAL-3840 -->Occupancy calculation is incorrect for
- alignment columns with over -1+2^32 gaps (breaking filtering
- and display)
- </li>
- <li>
- <!-- JAL-3833 -->Caps on Hi-DPI scaling to prevent crazy
- scale factors being set with buggy window-managers (linux
- only)
- </li>
- </ul> <em>Development</em>
- <ul>
- <li>Fixed non-fatal gradle errors during build</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.4">.4</a><br />
- <em>09/03/2021</em></strong></td>
- <td align="left" valign="top"><em>Improved control of
- Jalview's use of network services via jalview_properties</em>
- <ul>
- <li>
- <!-- JAL-3814 -->New .jalview_properties token controlling
- launch of the news browser (like -nonews argument)
- </li>
- <li>
- <!-- JAL-3813 -->New .jalview_properties token controlling
- download of linkout URLs from
- www.jalview.org/services/identifiers
- </li>
- <li>
- <!-- JAL-3812 -->New .jalview_properties token controlling
- download of BIOJSHTML templates
- </li>
- <li>
- <!-- JAL-3811 -->New 'Discover Web Services' option to
- trigger a one off JABAWS discovery if autodiscovery was
- disabled
- </li>
- </ul></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3818 -->Intermittent deadlock opening structure in
- Jmol
- </li>
- </ul> <em>New Known defects</em>
- <ul>
- <li>
- <!-- JAL-3705 -->Protein Cross-Refs for Gene Sequence not
- always restored from project (since 2.10.3)
- </li>
- <li>
- <!-- JAL-3806 -->Selections from tree built from CDS aren't
- propagated to Protein alignment (since 2.11.1.3)
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.3">.3</a><br />
- <em>29/10/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
-
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3765 -->Find doesn't always highlight all matching
- positions in a sequence (bug introduced in 2.11.1.2)
- </li>
- <li>
- <!-- JAL-3760 -->Alignments containing one or more protein
- sequences can be classed as nucleotide
- </li>
- <li>
- <!-- JAL-3748 -->CDS alignment doesn't match original CDS
- sequences after alignment of protein products (known defect
- first reported for 2.11.1.0)
- </li>
- <li>
- <!-- JAL-3725 -->No tooltip or popup menu for genomic
- features outwith CDS shown overlaid on protein
- </li>
- <li>
- <!-- JAL-3751 -->Overlapping CDS in ENA accessions are not
- correctly mapped by Jalview (e.g. affects viral CDS with
- ribosomal slippage, since 2.9.0)
- </li>
- <li>
- <!-- JAL-3763 -->Spliced transcript CDS sequences don't show
- CDS features
- </li>
- <li>
- <!-- JAL-3700 -->Selections in CDS sequence panel don't
- always select corresponding protein sequences
- </li>
- <li>
- <!-- JAL-3759 --> <em>Make groups from selection</em> for a
- column selection doesn't always ignore hidden columns
- </li>
- </ul> <em>Installer</em>
- <ul>
- <li>
- <!-- JAL-3611 -->Space character in Jalview install path on
- Windows prevents install4j launching getdown
- </li>
- </ul> <em>Development</em>
- <ul>
- <li>
- <!-- JAL-3248 -->Fixed typos and specified compatible gradle
- version numbers in doc/building.md
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.2">.2</a><br />
- <em>25/09/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3757 -->Fresh install of Jalview 2.11.1.1 reports
- "Encountered problems opening
- https://www.jalview.org/examples/exampleFile_2_7.jvp"
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.1">.1</a><br />
- <em>17/09/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3638 -->Shift+arrow keys navigate to next gap or
- residue in cursor mode
- </li>
- <li>
- <!-- JAL-3695 -->Support import of VCF 4.3 by updating
- HTSJDK from 2.12 to 2.23
- </li>
- <li>
- <!-- JAL-3621 -->IntervalStore library updated to v.1.1:
- optimisations and improvements suggested by Bob Hanson and
- improved compatibility with JalviewJS
- </li>
- <li>
- <!-- JAL-3615 -->Retrieve GZipped stockholm formatted
- alignments from Pfam and Rfam
- </li>
- <li>
- <!-- JAL-2656 -->Recognise GZipped content for URLs and File
- import (no longer based on .gz extension)
- </li>
- <li>
- <!-- JAL-3570 -->Updated Spanish Translation for 2.11.1
- </li>
- <li>
- <!-- JAL-3692 -->Migrate EMBL record retrieval to use latest
- ENA Browser (https://www.ebi.ac.uk/ena/browser/home) and
- EMBL flat file
- </li>
- <li>
- <!-- JAL-3667 -->Improved warning messages, debug logging
- and fixed Retry action when Jalview encounters errors when
- saving or making backup files.
- </li>
- <li>
- <!-- JAL-3676 -->Enhanced Jalview Java Console:
- <ul>
- <li>Jalview's logging level can be configured</li>
- <li>Copy to Clipboard Buttion</li>
- </ul>
- </li>
- <li>
- <!-- JAL-3541 -->Improved support for Hi-DPI (4K) screens
- when running on Linux (Requires Java 11+)
- </li>
- </ul> <em>Launching Jalview</em>
- <ul>
- <li>
- <!-- JAL-3608 -->Configure Jalview Desktop's look and feel
- through a system property
- </li>
- <li>
- <!-- JAL-3477 -->Improved built-in documentation and command
- line help for configuring Jalview's memory
- </li>
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3691 -->Conservation and Quality tracks are shown
- but not calculated and no protein or DNA score models are
- available for tree/PCA calculation when launched with
- Turkish language locale
- </li>
- <li>
- <!-- JAL-3493 -->Escape does not clear highlights on the
- alignment (Since Jalview 2.10.3)
- </li>
- <li>
- <!-- JAL-3680 -->Alt+Left or Right arrow in cursor mode
- doesn't slide selected sequences, just sequence under cursor
- </li>
- <li>
- <!-- JAL-3732 -->Alt+Up/Down in cursor mode doesn't move
- sequence under the cursor
- </li>
- <li>
- <!-- JAL-3613 -->Peptide-to-CDS tracking broken when
- multiple EMBL gene products shown for a single contig
- </li>
- <li>
- <!-- JAL-3696 -->Errors encountered when processing variants
- from VCF files yield "Error processing VCF: Format specifier
- '%s'" on the console
- </li>
- <li>
- <!-- JAL-3697 -->Count of features not shown can be wrong
- when there are both local and complementary features mapped
- to the position under the cursor
- </li>
- <li>
- <!-- JAL-3673 -->Sequence ID for reference sequence is
- clipped when Right align Sequence IDs enabled
- </li>
- <li>
- <!-- JAL-2983 -->Slider with negative range values not
- rendered correctly in VAqua4 (Since 2.10.4)
- </li>
- <li>
- <!-- JAL-3685 -->Single quotes not displayed correctly in
- internationalised text for some messages and log output
- </li>
- <li>
- <!-- JAL-3490 -->Find doesn't report matches that span
- hidden gapped columns
- </li>
- <li>
- <!-- JAL-3597 -->Resolved memory leaks in Tree and PCA
- panels, Alignment viewport and annotation renderer.
- </li>
- <li>
- <!-- JAL-3561 -->Jalview ignores file format parameter
- specifying output format when exporting an alignment via the
- command line
- </li>
- <li>
- <!-- JAL-3667 -->Windows 10: For a minority of users, if
- backups are not enabled, Jalview sometimes fails to
- overwrite an existing file and raises a warning dialog. (in
- 2.11.0, and 2.11.1.0, the workaround is to try to save the
- file again, and if that fails, delete the original file and
- save in place.)
- </li>
- <li>
- <!-- JAL-3750 -->Cannot process alignments from HTTPS urls
- via command line
- </li>
- <li>
- <!-- JAL-3741 -->References to http://www.jalview.org in
- program and documentation
- </li>
- </ul> <em>Launching Jalview</em>
- <ul>
- <li>
- <!-- JAL-3718 -->Jalview application fails when launched the
- first time for a version that has different jars to the
- previous launched version.
- </li>
- </ul> <em>Developing Jalview</em>
- <ul>
- <li>
- <!-- JAL-3541 -->Fixed issue with cleaning up old coverage
- data, causing cloverReport gradle task to fail with an
- OutOfMemory error.
- </li>
- <li>
- <!-- JAL-3280 -->Migrated the Jalview Version Checker to
- monitor the release channel
- </li>
- </ul> <em>New Known defects</em>
- <ul>
- <li>
- <!-- JAL-3748 -->CDS shown in result of submitting proteins
- in a CDS/Protein alignment to a web service is wrong when
- proteins share a common transcript sequence (e.g.
- genome of RNA viruses)
- </li>
- <li>
- <!-- JAL-3576 -->Co-located features exported and re-imported
- are ordered differently when shown on alignment and in
- tooltips. (Also affects v2.11.1.0)
- </li>
- <li>
- <!-- JAL-3702 -->Drag and drop of alignment file onto
- alignment window when in a HiDPI scaled mode in Linux only
- works for the top left quadrant of the alignment window
- </li>
- <li>
- <!-- JAL-3701 -->Stale build data in jalview standalone jar
- builds (only affects 2.11.1.1 branch)
- </li>
- <li>
- <!-- JAL-3127 -->Sequence ID colourscheme not re-applied
- when alignment view restored from project (since Jalview 2.11.0)
- </li>
- <li>
- <!-- JAL-3749 -->Duplicate CDS sequences are generated when
- protein products for certain ENA records are repeatedly
- shown via Calculate->Show Cross Refs
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap><strong><a
- id="Jalview.2.11.1">2.11.1</a><a id="Jalview.2.11.1.0">.0</a><br />
- <em>22/04/2020</em></strong></td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3187,JAL-3305,JAL-3304,JAL-3302,JAL-3567 -->Map
- 'virtual' codon features shown on protein (or vice versa)
- for display in alignments, on structure views (including
- transfer to UCSF chimera), in feature reports and for
- export.
- </li>
- <li>
- <!-- JAL-3121 -->Feature attributes from VCF files can be
- exported and re-imported as GFF3 files
- </li>
- <li>
- <!-- JAL-3376 -->Capture VCF "fixed column" values
- POS, ID, QUAL, FILTER as Feature Attributes
- </li>
- <li>
- <!-- JAL-3375 -->More robust VCF numeric data field
- validation while parsing
- </li>
- <li>
- <!-- JAL-3533 -->Feature Settings dialog keeps same screen
- position if reopened
- </li>
- <li>
- <!-- JAL-3535 -->Feature Settings dialog title includes name
- of associated view
- </li>
- <li>
- <!-- JAL-3538 -->Font anti-aliasing in alignment views
- enabled by default
- </li>
- <li>
- <!-- JAL-3468 -->Very long feature descriptions truncated in
- tooltips and menus
- </li>
- <li>
- <!-- JAL-3549 -->Warn if Sort by Score or Density attempted
- with no feature types visible
- </li>
- <li>
- <!-- JAL-3574 -->Improved support for filtering feature attributes with large integer values
- </li>
- </ul><em>Jalview Installer</em>
- <ul>
- <li>
- <!-- JAL-3449 -->Versions for install4j and getdown and installer template version reported
- in console (may be null when Jalview launched as executable jar or via conda)
- </li>
- <li>
- <!-- JAL-3393 -->Layout improvements for OSX .dmg Finder and higher quality background images
- </li>
- <li>
- <!-- JAL-3394 -->New installer/application launcher generated with install4j 8.0.4
- </li>
- <li>
- <!-- JAL-3420 -->Jalview File Associations shown for Unix Platforms</li>
- <li>
- <!-- JAL-3477 -->Improved defaults for maximum memory setting when running on large memory machines</li>
- </ul> <em>Release processes</em>
- <ul>
- <li>
- <!-- JAL-3508 -->New point release version scheme - 2.11.1.0
- </li>
- <li>
- <!-- JAL-3577 -->'Jalview Test' installers/apps for easier access to test-release channel builds
- </li>
- </ul> <em>Build System</em>
- <ul>
- <li>
- <!-- JAL-3510 -->Clover updated to 4.4.1
- </li>
- <li>
- <!-- JAL-3513 -->Test code included in Clover coverage
- report
- </li>
- </ul>
- <em>Groovy Scripts</em>
- <ul>
- <li>
- <!-- JAL-3547 -->exportconsensus.groovy prints a FASTA file
- to stdout containing the consensus sequence for each
- alignment in a Jalview session
- </li>
- <li>
- <!-- JAL-3578 -->ComputePeptideVariants.groovy to translate
- genomic sequence_variant annotation from CDS as
- missense_variant or synonymous_variant on protein products.
- </li>
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3581 -->Hidden sequence markers still visible when
- 'Show hidden markers' option is not ticked
- </li>
- <li>
- <!-- JAL-247 -->Hidden sequence markers not shown in EPS and
- PNG output when 'Automatically set ID width' is set in
- jalview preferences or properties file
- </li>
- <li>
- <!-- JAL-3571 -->Feature Editor dialog can be opened when
- 'Show Sequence Features' option is not ticked
- </li>
- <li>
- <!-- JAL-3549 -->Undo 'Null' operation shown after sort by
- buttons in Feature Settings dialog are clicked when no
- features are visible
- </li>
- <li>
- <!-- JAL-3412 -->ID margins for CDS and Protein views not
- equal when split frame is first opened
- </li>
- <li>
- <!-- JAL-3296 -->Sequence position numbers in status bar not
- correct after editing a sequence's start position
- </li>
- <li>
- <!-- JAL-3377 -->Alignment is misaligned in wrapped mode
- with annotation and exceptions thrown when only a few
- columns shown in wrapped mode
- </li>
- <li>
- <!-- JAL-3386 -->Sequence IDs missing in headless export of
- wrapped alignment figure with annotations
- </li>
- <li>
- <!-- JAL-3388-->Sorting Structure Chooser table by Sequence
- ID fails with ClassCastException
- </li>
- <li>
- <!-- JAL-3389 -->Chimera session not restored from Jalview
- Project
- </li>
- <li>
- <!-- JAL-3441 -->Double-click on 'Show feature' checkbox in
- feature settings dialog also selects columns
- </li>
- <li>
- <!-- JAL-3473 -->SpinnerNumberModel causes
- IllegalArgumentException in some circumstances
- </li>
- <li>
- <!-- JAL-3534 -->Multiple feature settings dialogs can be
- opened for a view
- </li>
- <li>
- <!-- JAL-2764 -->Feature Settings dialog is orphaned if
- alignment window is closed
- </li>
- <li>
- <!-- JAL-3406 -->Credits missing some authors in Jalview
- help documentation for 2.11.0 release
- </li>
- <li>
- <!-- JAL-3529 -->Export of Pfam alignment as Stockholm
- includes Pfam ID as sequence's accession rather than its
- Uniprot Accession
- </li>
- </ul> <em>Java 11 Compatibility issues</em>
- <ul>
- <li>
- <!-- JAL-2987 -->OSX - Can't view some search results in
- PDB/Uniprot search panel
- </li>
- </ul> <em>Installer</em>
- <ul>
- <li>
- <!-- JAL-3447 -->Jalview should not create file associations
- for 3D structure files (.pdb, .mmcif. .cif)
- </li>
- </ul> <em>Repository and Source Release</em>
- <ul>
- <li>
- <!-- JAL-3474 -->removed obsolete .cvsignore files from
- repository
- </li>
- <li>
- <!-- JAL-3541 -->Clover report generation running out of
- memory
- </li>
- </ul> <em>New Known Issues</em>
- <ul>
- <li>
- <!-- JAL-3523 -->OSX - Current working directory not
- preserved when Jalview.app launched with parameters from
- command line
- </li>
- <li>
- <!-- JAL-3525 -->Sequence IDs aligned to wrong margin and
- clipped in headless figure export when Right Align option
- enabled
- </li>
- <li>
- <!-- JAL-3542 -->Jalview Installation type always reports
- 'Source' in console output
- </li>
- <li>
- <!-- JAL-3562 -->Test Suite: Certain Functional tests fail on jalview's
- bamboo server but run fine locally.
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" align="center" nowrap>
- <strong><a name="Jalview.2.11.0">2.11.0</a><br />
- <em>04/07/2019</em></strong>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-1059, JAL-3196,JAL-3007,JAL-3236 -->Jalview Native Application and
- Installers built with <a href="https://www.ej-technologies.com/products/install4j/overview.html">install4j</a> (licensed to the Jalview open
- source project) rather than InstallAnywhere
- </li>
- <li>
- <!-- JAL-1929 -->Jalview Launcher System to auto-configure memory
- settings, receive over the air updates and launch specific
- versions via (<a href="https://github.com/threerings/getdown">Three
- Rings' GetDown</a>)
- </li>
- <li>
- <!-- JAL-1839,JAL-3254,JAL-3260 -->File type associations for
- formats supported by Jalview (including .jvp project files)
- </li>
- <li>
- <!-- JAL-3260 -->Jalview launch files (.jvl) to pass command line
- arguments and switch between different getdown channels
- </li>
- <li>
- <!-- JAL-3141 -->Backup files created when saving Jalview project
- or alignment files
- </li>
-
- <li>
- <!-- JAL-1793 -->Annotate nucleotide alignments from VCF data files</li>
- <li><!-- JAL-2753 -->Version of HTSJDK shipped with Jalview updated to version 2.12.0</li>
- <li>
- <!-- JAL-2620 -->Alternative genetic code tables for
- 'Translate as cDNA'</li>
- <li>
- <!-- JAL-3018 -->Update of Ensembl Rest Client to API v10.0</li>
- <li><strong>Enhanced visualisation and analysis of Sequence Features</strong>
- <ul>
- <li>
- <!-- JAL-3140 JAL-2446 -->IntervalStoreJ (NCList
- implementation that allows updates) used for Sequence Feature collections</li>
- <li>
- <!-- JAL-2744, JAL-2808,JAL-2069,JAL-2820 -->Sequence
- features can be filtered and shaded according to any
- associated attributes (e.g. variant attributes from VCF
- file, or key-value pairs imported from column 9 of GFF
- file)
- </li>
- <li>
- <!-- JAL-2879 -->Feature Attributes and shading schemes
- stored and restored from Jalview Projects
- </li>
- <li>
- <!-- JAL-3334 -->Use full Sequence Ontology (via BioJava) to
- recognise variant features
- </li>
- <li>
- <!-- JAL-2897,JAL-3330 -->Show synonymous codon variants on peptide
- sequences (also coloured red by default)
- </li>
- <li>
- <!-- JAL-2792 -->Popup window to show full report for a selected sequence feature's
- details
- </li>
- <li>
- <!-- JAL-3139,JAL-2816,JAL-1117 -->More efficient sequence feature render
- algorithm (Z-sort/transparency and filter aware)
- </li>
- <li>
- <!-- JAL-3049,JAL-3054 -->Improved tooltips in Feature Settings
- dialog
- </li>
- </ul>
- </li>
- <li>
- <!-- JAL-3205 -->Symmetric score matrices for faster
- tree and PCA calculations
- </li>
- <li><strong>Principal Components Analysis Viewer</strong>
- <ul>
- <li>
- <!-- JAL-1767,JAL-2647 -->Principal Components Analysis results
- and Viewer state saved in Jalview Project
- </li>
- <li><!-- JAL-2962 -->'Change parameters' option removed from viewer's
- drop-down menus</li>
- <li>
- <!-- JAL-2975 -->Can use shift + arrow keys to rotate PCA image
- incrementally
- </li>
- <li>
- <!-- JAL-2965, JAL-1285 -->PCA plot is depth cued
- </li>
- </ul>
- </li>
- <li>
- <!-- JAL-3127 -->New 'Colour by Sequence ID' option
- </li>
- <li><strong>Speed and Efficiency</strong>
- <ul>
- <li>
- <!-- JAL-2185,JAL-3198 -->More efficient creation of selections and
- multiple groups when working with large alignments
- </li>
- <li>
- <!-- JAL-3200 -->Speedier import of annotation rows when parsing
- Stockholm files
- </li>
- </ul>
- <li><strong>User Interface</strong>
- <ul>
- <li>
- <!-- JAL-2933 -->Finder panel remembers last position in each
- view
- </li>
- <li>
- <!-- JAL-2527 JAL-3203 -->Alignment Overview now WYSIWIS (What you see is
- what is shown)<br />Only visible regions of alignment are shown by
- default (can be changed in user preferences)
- </li>
- <li>
- <!-- JAL-3169 -->File Chooser stays open after responding Cancel
- to the Overwrite Dialog
- </li>
- <li>
- <!-- JAL-2420,JAL-3166 -->Better popup menu behaviour when all
- sequences are hidden
- </li>
- <li>
- <!-- JAL-1244 -->Status bar shows bounds when dragging a
- selection region, and gap count when inserting or deleting gaps
- </li>
- <li>
- <!-- JAL-3132 -->Status bar updates over sequence and annotation
- labels
- </li>
- <li>
- <!-- JAL-3093 -->Annotation tooltips and popup menus are shown
- when in wrapped mode
- </li>
- <li>
- <!-- JAL-3073 -->Can select columns by dragging left/right in a graph or histogram
- annotation
- </li>
- <li>
- <!-- JAL-2814,JAL-437 -->Help button on Uniprot and PDB search panels
- </li>
- <li>
- <!-- JAL-2621 -->Cursor changes over draggable box in Overview
- panel
- </li>
- <li>
- <!-- JAL-3181 -->Consistent ordering of links in sequence id
- popup menu
- </li>
- <li>
- <!-- JAL-3080 -->Red line indicating tree-cut position not shown if no subgroups are created</li>
- <li>
- <!-- JAL-3042 -->Removed ability to configure length of search history by right-clicking search box</li>
-
-
- </ul></li>
- <li><!-- JAL-3232 -->Jalview Groovy Scripting Console updated to Groovy v2.5</li>
- <li><strong>Java 11 Support (not yet on general release)</strong>
- <ul>
- <li>
- <!-- -->OSX GUI integrations for App menu's 'About' entry and
- trapping CMD-Q
- </li>
- </ul></li>
- </ul>
- <em>Deprecations</em>
- <ul>
- <li><!-- JAL-3035 -->DAS sequence retrieval and annotation
- capabilities removed from the Jalview Desktop
- </li>
- <li><!-- JAL-3063,JAL-3116 -->Castor library for XML marshalling and
- unmarshalling has been replaced by JAXB for Jalview projects
- and XML based data retrieval clients</li>
- <li><!-- JAL-3311 -->Disable VAMSAS menu in preparation for removal</li>
- <li><!-- -->Jalview Desktop no longer distributed via Java Web Start</li>
- </ul> <em>Documentation</em>
- <ul>
- <li><!-- JAL-3003 -->Added remarks about transparent rendering effects
- not supported in EPS figure export
- </li>
- <li><!-- JAL-2903 -->Typos in documentation for Preferences dialog</li>
- </ul> <em>Development and Release Processes</em>
- <ul>
- <li>
- <!-- JAL-3196,JAL-3179.JAL-2671 -->Build system migrated from Ant to Gradle
- </li>
- <li>
- <!-- JAL-1424 -->Enhanced checks for missing and duplicated keys in Message bundles</li>
- <li>
- <!-- JAL-3225 -->Eclipse project configuration managed with
- gradle-eclipse
- </li>
- <li>
- <!-- JAL-3174,JAL-2886,JAL-2729,JAL-1889 -->Atlassian
- Bamboo continuous integration for unattended Test Suite
- execution
- </li>
- <li>
- <!-- JAL-2864 -->Memory test suite to detect leaks in common
- operations
- </li>
- <li>
- <!-- JAL-2360,JAL-2416 -->More unit test coverage, and minor
- issues resolved
- </li>
- <li>
- <!-- JAL-3248 -->Developer documentation migrated to
- markdown (with HTML rendering)
- </li>
- <li>
- <!-- JAL-3287 -->HelpLinksChecker runs on Windows
- </li>
- <li>
- <!-- JAL-3289 -->New URLs for publishing development
- versions of Jalview
- </li>
- </ul>
- </td>
- <td align="left" valign="top">
- <ul>
- <li>
- <!-- JAL-3143 -->Timeouts when retrieving data from Ensembl
- </li>
- <li>
- <!-- JAL-3244 -->'View [Structure] Mappings' and structure
- superposition in Jmol fail on Windows
- </li>
- <li>
- <!-- JAL-3286 -->Blank error dialog is displayed when discovering
- structures for sequences with lots of PDB structures
- </li>
- <li>
- <!-- JAL-3239 -->Text misaligned in EPS or SVG image export with
- monospaced font
- </li>
- <li>
- <!-- JAL-3171 -->Warning of 'Duplicate entry' when saving Jalview
- project involving multiple views
- </li>
- <li>
- <!-- JAL-3164 -->Overview for complementary view in a linked
- CDS/Protein alignment is not updated when Hide Columns by
- Annotation dialog hides columns
- </li>
- <li>
- <!-- JAL-3158 -->Selection highlighting in the complement of a
- CDS/Protein alignment stops working after making a selection in
- one view, then making another selection in the other view
- </li>
- <li>
- <!-- JAL-3161 -->Annotations tooltip changes beyond visible
- columns
- </li>
- <li>
- <!-- JAL-3154 -->Table Columns could be re-ordered in Feature
- Settings and Jalview Preferences panels
- </li>
- <li>
- <!-- JAL-2865 -->Jalview hangs when closing windows, or redrawing the
- overview with large alignments
- </li>
- <li>
- <!-- JAL-2750 -->Tree and PCA calculation fails for selected
- region if columns were selected by dragging right-to-left and the
- mouse moved to the left of the first column
- </li>
- <li>
- <!-- JAL-3218 -->Couldn't hide selected columns adjacent to a
- hidden column marker via scale popup menu
- </li>
- <li>
- <!-- JAL-2846 -->Error message for trying to load in invalid URLs
- doesn't tell users the invalid URL
- </li>
- <li>
- <!-- JAL-2816 -->Tooltips displayed for features filtered by
- score from view
- </li>
- <li>
- <!-- JAL-3330 -->Sequence Variants retrieved from Ensembl during
- show cross references or Fetch Database References are shown in
- red in original view
- </li>
- <li>
- <!-- JAL-2898,JAL-2207 -->stop_gained variants not shown correctly on
- peptide sequence (computed variant shown as p.Res.null)
- </li>
- <li>
- <!-- JAL-2060 -->'Graduated colour' option not offered for
- manually created features (where feature score is Float.NaN)
- </li>
- <li>
- <!-- JAL-3097,JAL-3099 -->Blank extra columns drawn or printed
- when columns are hidden
- </li>
- <li>
- <!-- JAL-3082 -->Regular expression error for '(' in Select
- Columns by Annotation description
- </li>
- <li>
- <!-- JAL-3072 -->Scroll doesn't stop on mouse up after dragging
- out of Scale or Annotation Panel
- </li>
- <li>
- <!-- JAL-3075 -->Column selection incorrect after scrolling out of
- scale panel
- </li>
- <li>
- <!-- JAL-3074 -->Left/right drag in annotation can scroll
- alignment down
- </li>
- <li>
- <!-- JAL-3108 -->Error if mouse moved before clicking Reveal in
- scale panel
- </li>
- <li>
- <!-- JAL-3002 -->Column display is out by one after Page Down,
- Page Up in wrapped mode
- </li>
- <li>
- <!-- JAL-2839,JAL-781 -->Finder doesn't skip hidden regions
- </li>
- <li>
- <!-- JAL-2932 -->Finder searches in minimised alignments
- </li>
- <li>
- <!-- JAL-2250 -->'Apply Colour to All Groups' not always selected
- on opening an alignment
- </li>
- <li>
- <!-- JAL-3180 -->'Colour by Annotation' not marked selected in
- Colour menu
- </li>
- <li>
- <!-- JAL-3201 -->Per-group Clustal colour scheme changes when
- different groups in the alignment are selected
- </li>
- <li>
- <!-- JAL-2717 -->Internationalised colour scheme names not shown
- correctly in menu
- </li>
- <li>
- <!-- JAL-3206 -->Colour by Annotation can go black at min/max
- threshold limit
- </li>
- <li>
- <!-- JAL-3125 -->Value input for graduated feature colour
- threshold gets 'unrounded'
- </li>
- <li>
- <!-- JAL-2982 -->PCA image export doesn't respect background
- colour
- </li>
- <li>
- <!-- JAL-2963 -->PCA points don't dim when rotated about y axis
- </li>
- <li>
- <!-- JAL-2959 -->PCA Print dialog continues after Cancel
- </li>
- <li>
- <!-- JAL-3078 -->Cancel in Tree Font dialog resets alignment, not
- Tree font
- </li>
- <li>
- <!-- JAL-2964 -->Associate Tree with All Views not restored from
- project file
- </li>
- <li>
- <!-- JAL-2915 -->Scrolling of split frame is sluggish if Overview
- shown in complementary view
- </li>
- <li>
- <!-- JAL-3313 -->Codon consensus incorrectly scaled when shown
- without normalisation
- </li>
- <li>
- <!-- JAL-3021 -->Sequence Details report should open positioned at top
- of report
- </li>
- <li>
- <!-- JAL-914 -->Help page can be opened twice
- </li>
- <li>
- <!-- JAL-3333 -->Fuzzy text in web service status menu on OSX Mojave
- </li>
- </ul> <em>Editing</em>
- <ul>
- <li>
- <!-- JAL-2822 -->Start and End should be updated when sequence
- data at beginning or end of alignment added/removed via 'Edit'
- sequence
- </li>
- <li>
- <!-- JAL-2541,JAL-2684 (tests) -->Delete/Cut selection doesn't
- relocate sequence features correctly when start of sequence is
- removed (Known defect since 2.10)
- </li>
- <li>
- <!-- JAL-2830 -->Inserting gap sequence via the Edit Sequence
- dialog corrupts dataset sequence
- </li>
- <li>
- <!-- JAL-868 -->Structure colours not updated when associated tree
- repartitions the alignment view (Regression in 2.10.5)
- </li>
- </ul> <em>Datamodel</em>
- <ul>
- <li>
- <!-- JAL-2986 -->Sequence.findIndex returns wrong value when
- sequence's End is greater than its length
- </li>
- </ul> <em>Bugs fixed for Java 11 Support (not yet on
- general release)</em>
- <ul>
- <li>
- <!-- JAL-3288 -->Menus work properly in split-screen
- </li>
- </ul> <em>New Known Defects</em>
- <ul>
- <li>
- <!-- JAL-3340 -->Select columns containing feature by double clicking ignores bounds of an existing selected region
- </li>
- <li>
- <!-- JAL-3313 -->Codon consensus logo incorrectly scaled in gapped
- regions of protein alignment.
- </li>
- <li>
- <!-- JAL-2647 -->Input Data menu entry is greyed out when PCA View
- is restored from a Jalview 2.11 project
- </li>
- <li>
- <!-- JAL-3213 -->Alignment panel height can be too small after
- 'New View'
- </li>
- <li>
- <!-- JAL-3240 -->Display is incorrect after removing gapped
- columns within hidden columns
- </li>
- <li>
- <!-- JAL-3314 -->Rightmost selection is lost when mouse re-enters
- window after dragging left to select columns to left of visible
- region
- </li>
- <li>
- <!-- JAL-2876 -->Features coloured according to their description
- string and thresholded by score in earlier versions of Jalview are
- not shown as thresholded features in 2.11. To workaround please
- create a Score filter instead.
- </li>
- <li>
- <!-- JAL-3184 -->Cancel on Feature Settings dialog doesn't reset group visibility</li>
- <li>
- <!-- JAL-3338 -->F2 doesn't enable/disable keyboard mode in linked CDS/Protein view
- </li>
- <li>
- <!-- JAL-797 -->Closing tree windows with CMD/CTRL-W for
- alignments with multiple views can close views unexpectedly
- </li>
- </ul>
- <em>Java 11 Specific defects</em>
- <ul>
- <li>
- <!-- JAL-3235 -->Jalview Properties file is not sorted
- alphabetically when saved
- </li>
- </ul>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.5">2.10.5</a><br /> <em>10/09/2018</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-3101 -->Default memory for Jalview webstart and
- InstallAnywhere increased to 1G.
- </li>
- <li>
- <!-- JAL-247 -->Hidden sequence markers and representative
- sequence bolding included when exporting alignment as EPS,
- SVG, PNG or HTML. <em>Display is configured via the
- Format menu, or for command-line use via a Jalview
- properties file.</em>
- </li>
- <li>
- <!-- JAL-3076 -->Ensembl client updated to Version 7 REST
- API and sequence data now imported as JSON.
- </li>
- <li>
- <!-- JAL-3065 -->Change in recommended way of starting
- Jalview via a Java command line: add jars in lib directory
- to CLASSPATH, rather than via the deprecated java.ext.dirs
- property.
- </li>
- </ul>
- <em>Development</em>
- <ul>
- <li>
- <!-- JAL-3047 -->Support added to execute test suite
- instrumented with <a href="http://openclover.org/">Open
- Clover</a>
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-3104 -->Poorly scaled bar in quality annotation
- row shown in Feredoxin Structure alignment view of example
- alignment.
- </li>
- <li>
- <!-- JAL-2854 -->Annotation obscures sequences if lots of
- annotation displayed.
- </li>
- <li>
- <!-- JAL-3107 -->Group conservation/consensus not shown
- for newly created group when 'Apply to all groups'
- selected
- </li>
- <li>
- <!-- JAL-3087 -->Corrupted display when switching to
- wrapped mode when sequence panel's vertical scrollbar is
- visible.
- </li>
- <li>
- <!-- JAL-3003 -->Alignment is black in exported EPS file
- when sequences are selected in exported view.</em>
- </li>
- <li>
- <!-- JAL-3059 -->Groups with different coloured borders
- aren't rendered with correct colour.
- </li>
- <li>
- <!-- JAL-3092 -->Jalview could hang when importing certain
- types of knotted RNA secondary structure.
- </li>
- <li>
- <!-- JAL-3095 -->Sequence highlight and selection in
- trimmed VARNA 2D structure is incorrect for sequences that
- do not start at 1.
- </li>
- <li>
- <!-- JAL-3061 -->'.' inserted into RNA secondary structure
- annotation when columns are inserted into an alignment,
- and when exporting as Stockholm flatfile.
- </li>
- <li>
- <!-- JAL-3053 -->Jalview annotation rows containing upper
- and lower-case 'E' and 'H' do not automatically get
- treated as RNA secondary structure.
- </li>
- <li>
- <!-- JAL-3106 -->.jvp should be used as default extension
- (not .jar) when saving a Jalview project file.
- </li>
- <li>
- <!-- JAL-3105 -->Mac Users: closing a window correctly
- transfers focus to previous window on OSX
- </li>
- </ul>
- <em>Java 10 Issues Resolved</em>
- <ul>
- <li>
- <!-- JAL-2988 -->OSX - Can't save new files via the File
- or export menus by typing in a name into the Save dialog
- box.
- </li>
- <li>
- <!-- JAL-2988 JAL-2968 -->Jalview now uses patched version
- of the <a href="https://violetlib.org/vaqua/overview.html">VAqua5</a>
- 'look and feel' which has improved compatibility with the
- latest version of OSX.
- </li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.4b1">2.10.4b1</a><br />
- <em>7/06/2018</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-2920 -->Use HGVS nomenclature for variant
- annotation retrieved from Uniprot
- </li>
- <li>
- <!-- JAL-1460 -->Windows File Shortcuts can be dragged
- onto the Jalview Desktop
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-3017 -->Cannot import features with multiple
- variant elements (blocks import of some Uniprot records)
- </li>
- <li>
- <!-- JAL-2997 -->Clustal files with sequence positions in
- right-hand column parsed correctly
- </li>
- <li>
- <!-- JAL-2991 -->Wrap view - export to SVG - IDs shown but
- not alignment area in exported graphic
- </li>
- <li>
- <!-- JAL-2993 -->F2/Keyboard mode edits work when Overview
- window has input focus
- </li>
- <li>
- <!-- JAL-2992 -->Annotation panel set too high when
- annotation added to view (Windows)
- </li>
- <li>
- <!-- JAL-3009 -->Jalview Desktop is slow to start up when
- network connectivity is poor
- </li>
- <li>
- <!-- JAL-1460 -->Drag URL from chrome, firefox, IE to
- Jalview desktop on Windows doesn't open file<br /> <em>Dragging
- the currently open URL and links from a page viewed in
- Firefox or Chrome on Windows is now fully supported. If
- you are using Edge, only links in the page can be
- dragged, and with Internet Explorer, only the currently
- open URL in the browser can be dropped onto Jalview.</em>
- </li>
- </ul>
- <em>New Known Defects</em>
- <ul>
- <li><!-- JAL-3083 -->Cancel option doesn't reset Colour by Annotation</li>
- </ul>
- </div></td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.4">2.10.4</a><br /> <em>10/05/2018</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-1847 JAL-2944 -->New Structure Chooser control
- for disabling automatic superposition of multiple
- structures and open structures in existing views
- </li>
- <li>
- <!-- JAL-984 -->Mouse cursor changes to indicate Sequence
- ID and annotation area margins can be click-dragged to
- adjust them.
- </li>
- <li>
- <!-- JAL-2885 -->Jalview uses HTTPS for Uniprot, Xfam and
- Ensembl services
- </li>
- <li>
- <!-- JAL-2759 -->Improved performance for large alignments
- and lots of hidden columns
- </li>
- <li>
- <!-- JAL-2593 -->Improved performance when rendering lots
- of features (particularly when transparency is disabled)
- </li>
- <li>
- <!-- JAL-2296,JAL-2295 -->Experimental features in 2.10.2 for
- exchange of Jalview features and Chimera attributes made
- generally available
- </li>
- </ul>
- </div>
- </td>
- <td><div align="left">
- <ul>
- <li>
- <!-- JAL-2899 -->Structure and Overview aren't updated
- when Colour By Annotation threshold slider is adjusted
- </li>
- <li>
- <!-- JAL-2778 -->Slow redraw when Overview panel shown
- overlapping alignment panel
- </li>
- <li>
- <!-- JAL-2929 -->Overview doesn't show end of unpadded
- sequence as gaps
- </li>
- <li>
- <!-- JAL-2789, JAL-2893 -->Cross-reference handling
- improved: CDS not handled correctly if transcript has no
- UTR
- </li>
- <li>
- <!-- JAL-2321 -->Secondary structure and temperature
- factor annotation not added to sequence when local PDB
- file associated with it by drag'n'drop or structure
- chooser
- </li>
- <li>
- <!-- JAL-2984 -->Answering 'No' to PDB Autoassociate
- dialog doesn't import PDB files dropped on an alignment
- </li>
- <li>
- <!-- JAL-2666 -->Linked scrolling via protein horizontal
- scroll bar doesn't work for some CDS/Protein views
- </li>
- <li>
- <!-- JAL-2930 -->Trackpad scrolling is broken on OSX on
- Java 1.8u153 onwards and Java 1.9u4+.
- </li>
- <li>
- <!-- JAL-2924 -->Tooltip shouldn't be displayed for empty
- columns in annotation row
- </li>
- <li>
- <!-- JAL-2913 -->Preferences panel's ID Width control is not
- honored in batch mode
- </li>
- <li>
- <!-- JAL-2945 -->Linked sequence highlighting doesn't work
- for structures added to existing Jmol view
- </li>
- <li>
- <!-- JAL-2223 -->'View Mappings' includes duplicate
- entries after importing project with multiple views
- </li>
- <li>
- <!-- JAL-2781 JAL-2780 -->Viewing or annotating Uniprot
- protein sequences via SIFTS from associated PDB entries
- with negative residue numbers or missing residues fails
- </li>
- <li>
- <!-- JAL-2952 -->Exception when shading sequence with negative
- Temperature Factor values from annotated PDB files (e.g.
- as generated by CONSURF)
- </li>
- <li>
- <!-- JAL-2920 -->Uniprot 'sequence variant' features
- tooltip doesn't include a text description of mutation
- </li>
- <li>
- <!-- JAL-2922 -->Invert displayed features very slow when
- structure and/or overview windows are also shown
- </li>
- <li>
- <!-- JAL-2954 -->Selecting columns from highlighted regions
- very slow for alignments with large numbers of sequences
- </li>
- <li>
- <!-- JAL-2925 -->Copy Consensus fails for group consensus
- with 'StringIndexOutOfBounds'
- </li>
- <li>
- <!-- JAL-2976 -->VAqua(4) provided as fallback Look and Feel for OSX
- platforms running Java 10
- </li>
- <li>
- <!-- JAL-2960 -->Adding a structure to existing structure
- view appears to do nothing because the view is hidden behind the alignment view
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>
- <!-- JAL-2926 -->Copy consensus sequence option in applet
- should copy the group consensus when popup is opened on it
- </li>
- </ul>
- <em>Batch Mode</em>
- <ul>
- <li>
- <!-- JAL-2913 -->Fixed ID width preference is not respected
- </li>
- </ul>
- <em>New Known Defects</em>
- <ul>
- <li>
- <!-- JAL-2973 --> Exceptions occasionally raised when
- editing a large alignment and overview is displayed
- </li>
- <li>
- <!-- JAL-2974 -->'Overview updating' progress bar is shown
- repeatedly after a series of edits even when the overview
- is no longer reflecting updates
- </li>
- <li>
- <!-- JAL-2946 -->'SIFTS Mapping Error' when viewing
- structures for protein subsequence (if 'Trim Retrieved
- Sequences' enabled) or Ensembl isoforms (Workaround in
- 2.10.4 is to fail back to N&W mapping)
- </li>
- <li>
- <!-- JAL-2990 -->Export Annotations from File Menu with CSV
- option gives blank output
- </li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.3b1">2.10.3b1</a><br /> <em>24/1/2018</em></strong>
- </div>
- </td>
- <td><div align="left">
- <ul><li>Updated Certum Codesigning Certificate
- (Valid till 30th November 2018)</li></ul></div></td>
- <td><div align="left">
- <em>Desktop</em><ul>
- <ul>
- <li><!-- JAL-2859-->Only one structure is loaded when several sequences and structures are selected for viewing/superposing</li>
- <li><!-- JAL-2851-->Alignment doesn't appear to scroll vertically via trackpad and scrollwheel</li>
- <li><!-- JAL-2842-->Jalview hangs if up/down arrows pressed in cursor mode when cursor lies in hidden region at start of alignment</li>
- <li><!-- JAL-2827-->Helix annotation has 'notches' when scrolled into view if columns are hidden</li>
- <li><!-- JAL-2740-->Annotation column filter can be slow to reset (ie after hitting cancel) for large numbers of hidden columns</li>
- <li><!-- JAL-2849-->User preference for disabling inclusion of sequence limits when exporting as flat file has no effect</li>
- <li><!-- JAL-2679-->Reproducible cross-reference relationships when retrieving sequences from EnsemblGenomes</li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.3">2.10.3</a><br /> <em>17/11/2017</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-2446 -->Faster and more efficient management and
- rendering of sequence features
- </li>
- <li>
- <!-- JAL 2523-->More reliable Ensembl fetching with HTTP
- 429 rate limit request hander
- </li>
- <li>
- <!-- JAL-2773 -->Structure views don't get updated unless
- their colours have changed
- </li>
- <li>
- <!-- JAL-2495 -->All linked sequences are highlighted for
- a structure mousover (Jmol) or selection (Chimera)
- </li>
- <li>
- <!-- JAL-2790 -->'Cancel' button in progress bar for
- JABAWS AACon, RNAAliFold and Disorder prediction jobs
- </li>
- <li>
- <!-- JAL-2617 -->Stop codons are excluded in CDS/Protein
- view from Ensembl locus cross-references
- </li>
- <li>
- <!-- JAL-2685 -->Start/End limits are shown in Pairwise
- Alignment report
- </li>
- <li>
- <!-- JAL-2810 -->Sequence fetcher's Free text 'autosearch'
- feature can be disabled
- </li>
- <li>
- <!-- JAL-2810 -->Retrieve IDs tab added for UniProt and
- PDB easier retrieval of sequences for lists of IDs
- </li>
- <li>
- <!-- JAL-2758 -->Short names for sequences retrieved from
- Uniprot
- </li>
- </ul>
- <em>Scripting</em>
- <ul>
- <li>Groovy interpreter updated to 2.4.12</li>
- <li>Example groovy script for generating a matrix of
- percent identity scores for current alignment.</li>
- </ul>
- <em>Testing and Deployment</em>
- <ul>
- <li>
- <!-- JAL-2727 -->Test to catch memory leaks in Jalview UI
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- <em>General</em>
- <ul>
- <li>
- <!-- JAL-2643 -->Pressing tab after updating the colour
- threshold text field doesn't trigger an update to the
- alignment view
- </li>
- <li>
- <!-- JAL-2682 -->Race condition when parsing sequence ID
- strings in parallel
- </li>
- <li>
- <!-- JAL-2608 -->Overview windows are also closed when
- alignment window is closed
- </li>
- <li>
- <!-- JAL-2548 -->Export of features doesn't always respect
- group visibility
- </li>
- <li>
- <!-- JAL-2831 -->Jumping from column 1 to column 100,000
- takes a long time in Cursor mode
- </li>
- </ul>
- <em>Desktop</em>
- <ul>
- <li>
- <!-- JAL-2777 -->Structures with whitespace chainCode
- cannot be viewed in Chimera
- </li>
- <li>
- <!-- JAL-2728 -->Protein annotation panel too high in
- CDS/Protein view
- </li>
- <li>
- <!-- JAL-2757 -->Can't edit the query after the server
- error warning icon is shown in Uniprot and PDB Free Text
- Search Dialogs
- </li>
- <li>
- <!-- JAL-2253 -->Slow EnsemblGenome ID lookup
- </li>
- <li>
- <!-- JAL-2529 -->Revised Ensembl REST API CDNA query
- </li>
- <li>
- <!-- JAL-2739 -->Hidden column marker in last column not
- rendered when switching back from Wrapped to normal view
- </li>
- <li>
- <!-- JAL-2768 -->Annotation display corrupted when
- scrolling right in unwapped alignment view
- </li>
- <li>
- <!-- JAL-2542 -->Existing features on subsequence
- incorrectly relocated when full sequence retrieved from
- database
- </li>
- <li>
- <!-- JAL-2733 -->Last reported memory still shown when
- Desktop->Show Memory is unticked (OSX only)
- </li>
- <li>
- <!-- JAL-2658 -->Amend Features dialog doesn't allow
- features of same type and group to be selected for
- amending
- </li>
- <li>
- <!-- JAL-2524 -->Jalview becomes sluggish in wide
- alignments when hidden columns are present
- </li>
- <li>
- <!-- JAL-2392 -->Jalview freezes when loading and
- displaying several structures
- </li>
- <li>
- <!-- JAL-2732 -->Black outlines left after resizing or
- moving a window
- </li>
- <li>
- <!-- JAL-1900,JAL-1625 -->Unable to minimise windows
- within the Jalview desktop on OSX
- </li>
- <li>
- <!-- JAL-2667 -->Mouse wheel doesn't scroll vertically
- when in wrapped alignment mode
- </li>
- <li>
- <!-- JAL-2636 -->Scale mark not shown when close to right
- hand end of alignment
- </li>
- <li>
- <!-- JAL-2684 -->Pairwise alignment of selected regions of
- each selected sequence do not have correct start/end
- positions
- </li>
- <li>
- <!-- JAL-2793 -->Alignment ruler height set incorrectly
- after canceling the Alignment Window's Font dialog
- </li>
- <li>
- <!-- JAL-2036 -->Show cross-references not enabled after
- restoring project until a new view is created
- </li>
- <li>
- <!-- JAL-2756 -->Warning popup about use of SEQUENCE_ID in
- URL links appears when only default EMBL-EBI link is
- configured (since 2.10.2b2)
- </li>
- <li>
- <!-- JAL-2775 -->Overview redraws whole window when box
- position is adjusted
- </li>
- <li>
- <!-- JAL-2225 -->Structure viewer doesn't map all chains
- in a multi-chain structure when viewing alignment
- involving more than one chain (since 2.10)
- </li>
- <li>
- <!-- JAL-2811 -->Double residue highlights in cursor mode
- if new selection moves alignment window
- </li>
- <li>
- <!-- JAL-2837,JAL-2840 -->Alignment vanishes when using
- arrow key in cursor mode to pass hidden column marker
- </li>
- <li>
- <!-- JAL-2679 -->Ensembl Genomes example ID changed to one
- that produces correctly annotated transcripts and products
- </li>
- <li>
- <!-- JAL-2776 -->Toggling a feature group after first time
- doesn't update associated structure view
- </li>
- </ul>
- <em>Applet</em><br />
- <ul>
- <li>
- <!-- JAL-2687 -->Concurrent modification exception when
- closing alignment panel
- </li>
- </ul>
- <em>BioJSON</em><br />
- <ul>
- <li>
- <!-- JAL-2546 -->BioJSON export does not preserve
- non-positional features
- </li>
- </ul>
- <em>New Known Issues</em>
- <ul>
- <li>
- <!-- JAL-2541 -->Delete/Cut selection doesn't relocate
- sequence features correctly (for many previous versions of
- Jalview)
- </li>
- <li>
- <!-- JAL-2841 -->Cursor mode unexpectedly scrolls when
- using cursor in wrapped panel other than top
- </li>
- <li>
- <!-- JAL-2791 -->Select columns containing feature ignores
- graduated colour threshold
- </li>
- <li>
- <!-- JAL-2822,JAL-2823 -->Edit sequence operation doesn't
- always preserve numbering and sequence features
- </li>
- </ul>
- <em>Known Java 9 Issues</em>
- <ul>
- <li>
- <!-- JAL-2902 -->Groovy Console very slow to open and is
- not responsive when entering characters (Webstart, Java
- 9.01, OSX 10.10)
- </li>
- </ul>
- </div></td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.2b2">2.10.2b2</a><br />
- <em>2/10/2017</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em>New features in Jalview Desktop</em>
- <ul>
- <li>
- <!-- JAL-2748 -->Uniprot Sequence Fetcher now uses web API at uniprot.org
- </li>
- <li> <!-- JAL-2745 -->HTTPS used for all connections to ebi.ac.uk
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- </div></td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.2b1">2.10.2b1</a><br />
- <em>7/9/2017</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-2588 -->Show gaps in overview window by colouring
- in grey (sequences used to be coloured grey, and gaps were
- white)
- </li>
- <li>
- <!-- JAL-2588,JAL-2527 -->Overview tab in Jalview Desktop
- Preferences
- </li>
- <li>
- <!-- JAL-2587 -->Overview updates immediately on increase
- in size and progress bar shown as higher resolution
- overview is recalculated
- </li>
-
- </ul>
- </div></td>
- <td><div align="left">
- <em></em>
- <ul>
- <li>
- <!-- JAL-2664 -->Overview window redraws every hidden
- column region row by row
- </li>
- <li>
- <!-- JAL-2681 -->duplicate protein sequences shown after
- retrieving Ensembl crossrefs for sequences from Uniprot
- </li>
- <li>
- <!-- JAL-2603 -->Overview window throws NPE if show boxes
- format setting is unticked
- </li>
- <li>
- <!-- JAL-2610 -->Groups are coloured wrongly in overview
- if group has show boxes format setting unticked
- </li>
- <li>
- <!-- JAL-2672,JAL-2665 -->Redraw problems when
- autoscrolling whilst dragging current selection group to
- include sequences and columns not currently displayed
- </li>
- <li>
- <!-- JAL-2691 -->Not all chains are mapped when multimeric
- assemblies are imported via CIF file
- </li>
- <li>
- <!-- JAL-2704 -->Gap colour in custom colourscheme is not
- displayed when threshold or conservation colouring is also
- enabled.
- </li>
- <li>
- <!-- JAL-2549 -->JABAWS 2.2 services report wrong JABAWS
- server version
- </li>
- <li>
- <!-- JAL-2673 -->Jalview continues to scroll after
- dragging a selected region off the visible region of the
- alignment
- </li>
- <li>
- <!-- JAL-2724 -->Cannot apply annotation based
- colourscheme to all groups in a view
- </li>
- <li>
- <!-- JAL-2511 -->IDs don't line up with sequences
- initially after font size change using the Font chooser or
- middle-mouse zoom
- </li>
- </ul>
- </div></td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.2">2.10.2</a><br /> <em>17/8/2017</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em>Calculations</em>
- <ul>
-
- <li>
- <!-- JAL-1933 -->Occupancy annotation row shows number of
- ungapped positions in each column of the alignment.
- </li>
- <li>
- <!-- JAL-1632 -->Tree/PCA calculation menu items merged to
- a calculation dialog box
- </li>
- <li>
- <!-- JAL-2379 -->Revised implementation of PCA for speed
- and memory efficiency (~30x faster)
- </li>
- <li>
- <!-- JAL-2403 -->Revised implementation of sequence
- similarity scores as used by Tree, PCA, Shading Consensus
- and other calculations
- </li>
- <li>
- <!-- JAL-2416 -->Score matrices are stored as resource
- files within the Jalview codebase
- </li>
- <li>
- <!-- JAL-2500 -->Trees computed on Sequence Feature
- Similarity may have different topology due to increased
- precision
- </li>
- </ul>
- <em>Rendering</em>
- <ul>
- <li>
- <!-- JAL-2360,JAL-2371, -->More robust colours and shader
- model for alignments and groups
- </li>
- <li>
- <!-- JAL-384 -->Custom shading schemes created via groovy
- scripts
- </li>
- </ul>
- <em>Overview</em>
- <ul>
- <li>
- <!-- JAL-2526 -->Efficiency improvements for interacting
- with alignment and overview windows
- </li>
- <li>
- <!-- JAL-2514 -->Scrolling of wrapped alignment views via
- overview
- </li>
- <li>
- <!-- JAL-2388 -->Hidden columns and sequences can be
- omitted in Overview
- </li>
- <li>
- <!-- JAL-2611 -->Click-drag in visible area allows fine
- adjustment of visible position
- </li>
- </ul>
-
- <em>Data import/export</em>
- <ul>
- <li>
- <!-- JAL-2535 -->Posterior probability annotation from
- Stockholm files imported as sequence associated annotation
- </li>
- <li>
- <!-- JAL-2507 -->More robust per-sequence positional
- annotation input/output via stockholm flatfile
- </li>
- <li>
- <!-- JAL-2533 -->Sequence names don't include file
- extension when importing structure files without embedded
- names or PDB accessions
- </li>
- <li>
- <!-- JAL-2416 -->Drag and drop load of AAIndex and NCBI
- format sequence substitution matrices
- </li>
- </ul>
- <em>User Interface</em>
- <ul>
- <li>
- <!-- JAL-2447 --> Experimental Features Checkbox in
- Desktop's Tools menu to hide or show untested features in
- the application.
- </li>
- <li>
- <!-- JAL-2491 -->Linked scrolling of CDS/Protein views
- via Overview or sequence motif search operations
- </li>
- <li>
- <!-- JAL-2547 -->Amend sequence features dialog box can be
- opened by double clicking gaps within sequence feature
- extent
- </li>
- <li>
- <!-- JAL-1476 -->Status bar message shown when not enough
- aligned positions were available to create a 3D structure
- superposition.
- </li>
- </ul>
- <em>3D Structure</em>
- <ul>
- <li>
- <!-- JAL-2430 -->Hidden regions in alignment views are not
- coloured in linked structure views
- </li>
- <li>
- <!-- JAL-1596 -->Faster Chimera/Jalview communication by
- file-based command exchange
- </li>
- <li>
- <!-- JAL-2375 -->Structure chooser automatically shows
- Cached Structures rather than querying the PDBe if
- structures are already available for sequences
- </li>
- <li>
- <!-- JAL-2520 -->Structures imported via URL are cached in
- the Jalview project rather than downloaded again when the
- project is reopened.
- </li>
- <li>
- <!-- JAL-2295, JAL-2296 -->New entries in the Chimera menu
- to transfer Chimera's structure attributes as Jalview
- features, and vice-versa (<strong>Experimental
- Feature</strong>)
- </li>
- </ul>
- <em>Web Services</em>
- <ul>
- <li>
- <!-- JAL-2549 -->Updated JABAWS client to v2.2
- </li>
- <li>
- <!-- JAL-2335 -->Filter non-standard amino acids and
- nucleotides when submitting to AACon and other MSA
- Analysis services
- </li>
- <li>
- <!-- JAL-2316, -->URLs for viewing database
- cross-references provided by identifiers.org and the
- EMBL-EBI's MIRIAM DB
- </li>
- </ul>
-
- <em>Scripting</em>
- <ul>
- <li>
- <!-- JAL-2344 -->FileFormatI interface for describing and
- identifying file formats (instead of String constants)
- </li>
- <li>
- <!-- JAL-2228 -->FeatureCounter script refactored for
- efficiency when counting all displayed features (not
- backwards compatible with 2.10.1)
- </li>
- </ul>
- <em>Example files</em>
- <ul>
- <li>
- <!-- JAL-2631 -->Graduated feature colour style example
- included in the example feature file
- </li>
- </ul>
- <em>Documentation</em>
- <ul>
- <li>
- <!-- JAL-2339 -->Release notes reformatted for readability
- with the built-in Java help viewer
- </li>
- <li>
- <!-- JAL-1644 -->Find documentation updated with 'search
- sequence description' option
- </li>
- </ul>
- <em>Test Suite</em>
- <ul>
- <li>
- <!-- JAL-2485, -->External service integration tests for
- Uniprot REST Free Text Search Client
- </li>
- <li>
- <!-- JAL-2474 -->Added PrivilegedAccessor to test suite
- </li>
- <li>
- <!-- JAL-2326 -->Prevent or clear modal dialogs raised
- during tests
- </li>
- </ul>
- </div></td>
- <td><div align="left">
- <em>Calculations</em>
- <ul>
- <li>
- <!-- JAL-2398, -->Fixed incorrect value in BLOSUM 62 score
- matrix - C->R should be '-3'<br />Old matrix restored
- with this one-line groovy script:<br />jalview.analysis.scoremodels.ScoreModels.instance.BLOSUM62.@matrix[4][1]=3
- </li>
- <li><a name="2102scoremodelbugs" /> <!-- JAL-2397 -->Fixed
- Jalview's treatment of gaps in PCA and substitution matrix
- based Tree calculations.<br /> <br />In earlier versions
- of Jalview, gaps matching gaps were penalised, and gaps
- matching non-gaps penalised even more. In the PCA
- calculation, gaps were actually treated as non-gaps - so
- different costs were applied, which meant Jalview's PCAs
- were different to those produced by SeqSpace.<br />Jalview
- now treats gaps in the same way as SeqSpace (ie it scores
- them as 0). <br /> <br />Enter the following in the
- Groovy console to restore pre-2.10.2 behaviour:<br />
- jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=true
- // for 2.10.1 mode <br />
- jalview.analysis.scoremodels.ScoreMatrix.scoreGapAsAny=false
- // to restore 2.10.2 mode <br /> <br /> <em>Note:
- these settings will affect all subsequent tree and PCA
- calculations (not recommended)</em></li>
- <li>
- <!-- JAL-2424 -->Fixed off-by-one bug that affected
- scaling of branch lengths for trees computed using
- Sequence Feature Similarity.
- </li>
- <li>
- <!-- JAL-2377 -->PCA calculation could hang when
- generating output report when working with highly
- redundant alignments
- </li>
- <li>
- <!-- JAL-2544 --> Sort by features includes features to
- right of selected region when gaps present on right-hand
- boundary
- </li>
- </ul>
- <em>User Interface</em>
- <ul>
- <li>
- <!-- JAL-2346 -->Reopening Colour by annotation dialog
- doesn't reselect a specific sequence's associated
- annotation after it was used for colouring a view
- </li>
- <li>
- <!-- JAL-2419 -->Current selection lost if popup menu
- opened on a region of alignment without groups
- </li>
- <li>
- <!-- JAL-2374 -->Popup menu not always shown for regions
- of an alignment with overlapping groups
- </li>
- <li>
- <!-- JAL-2310 -->Finder double counts if both a sequence's
- name and description match
- </li>
- <li>
- <!-- JAL-2370 -->Hiding column selection containing two
- hidden regions results in incorrect hidden regions
- </li>
- <li>
- <!-- JAL-2386 -->'Apply to all groups' setting when
- changing colour does not apply Conservation slider value
- to all groups
- </li>
- <li>
- <!-- JAL-2373 -->Percentage identity and conservation menu
- items do not show a tick or allow shading to be disabled
- </li>
- <li>
- <!-- JAL-2385 -->Conservation shading or PID threshold
- lost when base colourscheme changed if slider not visible
- </li>
- <li>
- <!-- JAL-2547 -->Sequence features shown in tooltip for
- gaps before start of features
- </li>
- <li>
- <!-- JAL-2623 -->Graduated feature colour threshold not
- restored to UI when feature colour is edited
- </li>
- <li>
- <!-- JAL-147 -->Vertical scrollbar jumps one page-width at
- a time when scrolling vertically in wrapped mode.
- </li>
- <li>
- <!-- JAL-2630 -->Structure and alignment overview update
- as graduate feature colour settings are modified via the
- dialog box
- </li>
- <li>
- <!-- JAL-2034 -->Overview window doesn't always update
- when a group defined on the alignment is resized
- </li>
- <li>
- <!-- JAL-2605 -->Mouseovers on left/right scale region in
- wrapped view result in positional status updates
- </li>
-
- <li>
- <!-- JAL-2563 -->Status bar doesn't show position for
- ambiguous amino acid and nucleotide symbols
- </li>
- <li>
- <!-- JAL-2602 -->Copy consensus sequence failed if
- alignment included gapped columns
- </li>
- <li>
- <!-- JAL-2473 -->Minimum size set for Jalview windows so
- widgets don't permanently disappear
- </li>
- <li>
- <!-- JAL-2503 -->Cannot select or filter quantitative
- annotation that are shown only as column labels (e.g.
- T-Coffee column reliability scores)
- </li>
- <li>
- <!-- JAL-2594 -->Exception thrown if trying to create a
- sequence feature on gaps only
- </li>
- <li>
- <!-- JAL-2504 -->Features created with 'New feature'
- button from a Find inherit previously defined feature type
- rather than the Find query string
- </li>
- <li>
- <!-- JAL-2423 -->incorrect title in output window when
- exporting tree calculated in Jalview
- </li>
- <li>
- <!-- JAL-2437 -->Hiding sequences at bottom of alignment
- and then revealing them reorders sequences on the
- alignment
- </li>
- <li>
- <!-- JAL-964 -->Group panel in sequence feature settings
- doesn't update to reflect available set of groups after
- interactively adding or modifying features
- </li>
- <li>
- <!-- JAL-2225 -->Sequence Database chooser unusable on
- Linux
- </li>
- <li>
- <!-- JAL-2291 -->Hide insertions in PopUp->Selection menu
- only excluded gaps in current sequence and ignored
- selection.
- </li>
- </ul>
- <em>Rendering</em>
- <ul>
- <li>
- <!-- JAL-2421 -->Overview window visible region moves
- erratically when hidden rows or columns are present
- </li>
- <li>
- <!-- JAL-2362 -->Per-residue colourschemes applied via the
- Structure Viewer's colour menu don't correspond to
- sequence colouring
- </li>
- <li>
- <!-- JAL-2405 -->Protein specific colours only offered in
- colour and group colour menu for protein alignments
- </li>
- <li>
- <!-- JAL-2385 -->Colour threshold slider doesn't update to
- reflect currently selected view or group's shading
- thresholds
- </li>
- <li>
- <!-- JAL-2624 -->Feature colour thresholds not respected
- when rendered on overview and structures when opacity at
- 100%
- </li>
- <li>
- <!-- JAL-2589 -->User defined gap colour not shown in
- overview when features overlaid on alignment
- </li>
- <li>
- <!-- JAL-2567 -->Feature settings for different views not
- recovered correctly from Jalview project file
- </li>
- <li>
- <!-- JAL-2256 -->Feature colours in overview when first opened
- (automatically via preferences) are different to the main
- alignment panel
- </li>
- </ul>
- <em>Data import/export</em>
- <ul>
- <li>
- <!-- JAL-2576 -->Very large alignments take a long time to
- load
- </li>
- <li>
- <!-- JAL-2507 -->Per-sequence RNA secondary structures
- added after a sequence was imported are not written to
- Stockholm File
- </li>
- <li>
- <!-- JAL-2509 -->WUSS notation for simple pseudoknots lost
- when importing RNA secondary structure via Stockholm
- </li>
- <li>
- <!-- JAL-2509 -->Secondary structure arrows for [] and {}
- not shown in correct direction for simple pseudoknots
- </li>
- <li>
- <!-- JAL-2365,JAL-2642 -->Cannot configure feature colours
- with lightGray or darkGray via features file (but can
- specify lightgray)
- </li>
- <li>
- <!-- JAL-2383 -->Above PID colour threshold not recovered
- when alignment view imported from project
- </li>
- <li>
- <!-- JAL-2520,JAL-2465 -->No mappings generated between
- structure and sequences extracted from structure files
- imported via URL and viewed in Jmol
- </li>
- <li>
- <!-- JAL-2520 -->Structures loaded via URL are saved in
- Jalview Projects rather than fetched via URL again when
- the project is loaded and the structure viewed
- </li>
- </ul>
- <em>Web Services</em>
- <ul>
- <li>
- <!-- JAL-2519 -->EnsemblGenomes example failing after
- release of Ensembl v.88
- </li>
- <li>
- <!-- JAL-2366 -->Proxy server address and port always
- appear enabled in Preferences->Connections
- </li>
- <li>
- <!-- JAL-2461 -->DAS registry not found exceptions
- removed from console output
- </li>
- <li>
- <!-- JAL-2582 -->Cannot retrieve protein products from
- Ensembl by Peptide ID
- </li>
- <li>
- <!-- JAL-2482, JAL-2487 -->Incorrect PDB-Uniprot mappings
- created from SIFTs, and spurious 'Couldn't open structure
- in Chimera' errors raised after April 2017 update (problem
- due to 'null' string rather than empty string used for
- residues with no corresponding PDB mapping).
- </li>
- </ul>
- <em>Application UI</em>
- <ul>
- <li>
- <!-- JAL-2361 -->User Defined Colours not added to Colour
- menu
- </li>
- <li>
- <!-- JAL-2401 -->Easier creation of colours for all 'Lower
- case' residues (button in colourscheme editor debugged and
- new documentation and tooltips added)
- </li>
- <li>
- <!-- JAL-2399-->Text colour threshold's 'Cancel' button
- doesn't restore group-specific text colour thresholds
- </li>
- <li>
- <!-- JAL-2243 -->Feature settings panel does not update as
- new features are added to alignment
- </li>
- <li>
- <!-- JAL-2532 -->Cancel in feature settings reverts
- changes to feature colours via the Amend features dialog
- </li>
- <li>
- <!-- JAL-2506 -->Null pointer exception when attempting to
- edit graduated feature colour via amend features dialog
- box
- </li>
- <li>
- <!-- JAL-2436 -->Structure viewer's View -> Colour By view
- selection menu changes colours of alignment views
- </li>
- <li>
- <!-- JAL-2426 -->Spurious exceptions in console raised
- from alignment calculation workers after alignment has
- been closed
- </li>
- <li>
- <!-- JAL-1608 -->Typo in selection popup menu - Create
- groups now 'Create Group'
- </li>
- <li>
- <!-- JAL-1608 -->CMD/CTRL and G or Shift G for
- Create/Undefine group doesn't always work
- </li>
- <li>
- <!-- JAL-2464 -->Tree Viewer's Print Dialog doesn't get
- shown again after pressing 'Cancel'
- </li>
- <li>
- <!-- JAL-1256 -->Trackpad horizontal scroll gesture
- adjusts start position in wrap mode
- </li>
- <li>
- <!-- JAL-2563 -->Status bar doesn't show positions for
- ambiguous amino acids
- </li>
- <li>
- <!-- JAL-2431 -->cDNA Consensus annotation not shown in
- CDS/Protein view after CDS sequences added for aligned
- proteins
- </li>
- <li>
- <!-- JAL-2592 -->User defined colourschemes called 'User
- Defined' don't appear in Colours menu
- </li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>
- <!-- JAL-2468 -->Switching between Nucleotide and Protein
- score models doesn't always result in an updated PCA plot
- </li>
- <li>
- <!-- JAL-2442 -->Features not rendered as transparent on
- overview or linked structure view
- </li>
- <li>
- <!-- JAL-2372 -->Colour group by conservation doesn't
- work (since 2.8)
- </li>
- <li>
- <!-- JAL-2517 -->Hitting Cancel after applying
- user-defined colourscheme doesn't restore original
- colourscheme
- </li>
- </ul>
- <em>Test Suite</em>
- <ul>
- <li>
- <!-- JAL-2314 -->Unit test failure:
- jalview.ws.jabaws.RNAStructExportImport setup fails
- </li>
- <li>
- <!-- JAL-2307 -->Unit test failure:
- jalview.ws.sifts.SiftsClientTest due to compatibility
- problems with deep array comparison equality asserts in
- successive versions of TestNG
- </li>
- <li>
- <!-- JAL-2479 -->Relocated StructureChooserTest and
- ParameterUtilsTest Unit tests to Network suite
- </li>
- </ul>
- <em>New Known Issues</em>
- <ul>
- <li>
- <!-- JAL-2566 -->Protein/CDS view scrolling not always in
- phase after a sequence motif find operation
- </li>
- <li>
- <!-- JAL-2550 -->Importing annotation file with rows
- containing just upper and lower case letters are
- interpreted as WUSS RNA secondary structure symbols
- </li>
- <li>
- <!-- JAL-2590 -->Cannot load and display Newick trees
- reliably from eggnog Ortholog database
- </li>
- <li>
- <!-- JAL-2468 -->Status bar shows 'Marked x columns
- containing features of type Highlight' when 'B' is pressed
- to mark columns containing highlighted regions.
- </li>
- <li>
- <!-- JAL-2321 -->Dropping a PDB file onto a sequence
- doesn't always add secondary structure annotation.
- </li>
- </ul>
- </div>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.1">2.10.1</a><br /> <em>29/11/2016</em></strong>
- </div>
- </td>
- <td><div align="left">
- <em>General</em>
- <ul>
- <li>
- <!-- JAL-98 -->Improved memory usage: sparse arrays used
- for all consensus calculations
- </li>
- <li>
- <!-- JAL-2177 -->Jmol updated to version 14.6.4 (released
- 3rd Oct 2016)
- </li>
- <li>Updated Jalview's Certum code signing certificate
- for 2016-2017</li>
- </ul>
- <em>Application</em>
- <ul>
- <li>
- <!-- JAL-1723 -->Sequence ID tool tip presents abridged
- set of database cross-references, sorted alphabetically
- </li>
- <li>
- <!-- JAL-2282-->New replacement token for creating URLs <em>just</em>
- from database cross references. Users with custom links
- will receive a <a href="webServices/urllinks.html#warning">warning
- dialog</a> asking them to update their preferences.
- </li>
- <li>
- <!-- JAL-2287-->Cancel button and escape listener on
- dialog warning user about disconnecting Jalview from a
- Chimera session
- </li>
- <li>
- <!-- JAL-2320-->Jalview's Chimera control window closes if
- the Chimera it is connected to is shut down
- </li>
- <li>
- <!-- JAL-1738-->New keystroke (B) and Select highlighted
- columns menu item to mark columns containing highlighted
- regions (e.g. from structure selections or results of a
- Find operation)
- </li>
- <li>
- <!-- JAL-2284-->Command line option for batch-generation
- of HTML pages rendering alignment data with the BioJS
- MSAviewer
- </li>
- </ul>
- </div></td>
- <td>
- <div align="left">
- <em>General</em>
- <ul>
- <li>
- <!-- JAL-2286 -->Columns with more than one modal residue
- are not coloured or thresholded according to percent
- identity (first observed in Jalview 2.8.2)
- </li>
- <li>
- <!-- JAL-2301 -->Threonine incorrectly reported as not
- hydrophobic
- </li>
- <li>
- <!-- JAL-2318 -->Updates to documentation pages (above PID
- threshold, amino acid properties)
- </li>
- <li>
- <!-- JAL-2292 -->Lower case residues in sequences are not
- reported as mapped to residues in a structure file in the
- View Mapping report
- </li>
- <li>
- <!--JAL-2324 -->Identical features with non-numeric scores
- could be added multiple times to a sequence
- </li>
- <li>
- <!--JAL-2323, JAL-2333,JAL-2335,JAL-2327 -->Disulphide
- bond features shown as two highlighted residues rather
- than a range in linked structure views, and treated
- correctly when selecting and computing trees from features
- </li>
- <li>
- <!-- JAL-2281-->Custom URL links for database
- cross-references are matched to database name regardless
- of case
- </li>
-
- </ul>
- <em>Application</em>
- <ul>
- <li>
- <!-- JAL-2282-->Custom URL links for specific database
- names without regular expressions also offer links from
- Sequence ID
- </li>
- <li>
- <!-- JAL-2315-->Removing a single configured link in the
- URL links pane in Connections preferences doesn't actually
- update Jalview configuration
- </li>
- <li>
- <!-- JAL-2272-->CTRL-Click on a selected region to open
- the alignment area popup menu doesn't work on El-Capitan
- </li>
- <li>
- <!-- JAL-2280 -->Jalview doesn't offer to associate mmCIF
- files with similarly named sequences if dropped onto the
- alignment
- </li>
- <li>
- <!-- JAL-2312 -->Additional mappings are shown for PDB
- entries where more chains exist in the PDB accession than
- are reported in the SIFTS file
- </li>
- <li>
- <!-- JAL-2317-->Certain structures do not get mapped to
- the structure view when displayed with Chimera
- </li>
- <li>
- <!-- JAL-2317-->No chains shown in the Chimera view
- panel's View->Show Chains submenu
- </li>
- <li>
- <!--JAL-2277 -->Export as HTML with embedded SVG doesn't
- work for wrapped alignment views
- </li>
- <li>
- <!--JAL-2197 -->Rename UI components for running JPred
- predictions from 'JNet' to 'JPred'
- </li>
- <li>
- <!-- JAL-2337,JAL-2277 -->Export as PNG or SVG is
- corrupted when annotation panel vertical scroll is not at
- first annotation row
- </li>
- <li>
- <!--JAL-2332 -->Attempting to view structure for Hen
- lysozyme results in a PDB Client error dialog box
- </li>
- <li>
- <!-- JAL-2319 -->Structure View's mapping report switched
- ranges for PDB and sequence for SIFTS
- </li>
- <!-- JAL-2319 -->
- SIFTS 'Not_Observed' residues mapped to non-existant
- coordindate data
- </li>
- </ul>
- <!-- <em>New Known Issues</em>
- <ul>
- <li></li>
- </ul> -->
- </div>
- </td>
- </tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.0b1">2.10.0b1</a><br />
- <em>25/10/2016</em></strong>
- </div>
- </td>
- <td><em>Application</em>
- <ul>
- <li>3D Structure chooser opens with 'Cached structures'
- view if structures already loaded</li>
- <li>Progress bar reports models as they are loaded to
- structure views</li>
- </ul></td>
- <td>
- <div align="left">
- <em>General</em>
- <ul>
- <li>Colour by conservation always enabled and no tick
- shown in menu when BLOSUM or PID shading applied</li>
- <li>FER1_ARATH and FER2_ARATH labels were switched in
- example sequences/projects/trees</li>
- </ul>
- <em>Application</em>
- <ul>
- <li>Jalview projects with views of local PDB structure
- files saved on Windows cannot be opened on OSX</li>
- <li>Multiple structure views can be opened and superposed
- without timeout for structures with multiple models or
- multiple sequences in alignment</li>
- <li>Cannot import or associated local PDB files without a
- PDB ID HEADER line</li>
- <li>RMSD is not output in Jmol console when superposition
- is performed</li>
- <li>Drag and drop of URL from Browser fails for Linux and
- OSX versions earlier than El Capitan</li>
- <li>ENA client ignores invalid content from ENA server</li>
- <li>Exceptions are not raised in console when ENA client
- attempts to fetch non-existent IDs via Fetch DB Refs UI
- option</li>
- <li>Exceptions are not raised in console when a new view
- is created on the alignment</li>
- <li>OSX right-click fixed for group selections: CMD-click
- to insert/remove gaps in groups and CTRL-click to open group
- pop-up menu</li>
- </ul>
- <em>Build and deployment</em>
- <ul>
- <li>URL link checker now copes with multi-line anchor
- tags</li>
- </ul>
- <em>New Known Issues</em>
- <ul>
- <li>Drag and drop from URL links in browsers do not work
- on Windows</li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.10.0">2.10.0</a><br /> <em>06/10/2016</em></strong>
- </div>
- </td>
- <td><em>General</em>
- <ul>
- <li>
- <!-- JAL-2124 -->Updated Spanish translations.
- </li>
- <li>
- <!-- JAL-2164,JAL-1919,JAL-2148 -->Jmol now primary parser
- for importing structure data to Jalview. Enables mmCIF and
- better PDB parsing.
- </li>
- <li>
- <!-- JAL-192 --->Alignment ruler shows positions relative to
- reference sequence
- </li>
- <li>
- <!-- JAL-2202 -->Position/residue shown in status bar when
- mousing over sequence associated annotation
- </li>
- <li>
- <!-- JAL-2171 -->Default RNA SS symbol to 'matching bracket'
- for manual entry
- </li>
- <li>
- <!-- JAL-2214 -->RNA Structure consensus indicates wc-only
- '()', canonical '[]' and invalid '{}' base pair populations
- for each column
- </li>
- <li>
- <!-- JAL-2092 -->Feature settings popup menu options for
- showing or hiding columns containing a feature
- </li>
- <li>
- <!-- JAL-1557 -->Edit selected group by double clicking on
- group and sequence associated annotation labels
- </li>
- <li>
- <!-- JAL-2236 -->Sequence name added to annotation label in
- select/hide columns by annotation and colour by annotation
- dialogs
- </li>
-
- </ul> <em>Application</em>
- <ul>
- <li>
- <!-- JAL-2050-->Automatically hide introns when opening a
- gene/transcript view
- </li>
- <li>
- <!-- JAL-1563 -->Uniprot Sequence fetcher Free Text Search
- dialog
- </li>
- <li>
- <!-- JAL-1957, JAL-1479 JAL-1491 -->UniProt - PDB protein
- structure mappings with the EMBL-EBI PDBe SIFTS database
- </li>
- <li>
- <!-- JAL-2079 -->Updated download sites used for Rfam and
- Pfam sources to xfam.org
- </li>
- <li>
- <!-- JAL-2084 -->Disabled Rfam(Full) in the sequence fetcher
- </li>
- <li>
- <!-- JAL-2123 -->Show residue labels in Chimera when mousing
- over sequences in Jalview
- </li>
- <li>
- <!-- JAL-2027-->Support for reverse-complement coding
- regions in ENA and EMBL
- </li>
- <li>
- <!-- JAL-1855, JAL-2113, JAL-2114-->Upgrade to EMBL XML 1.2
- for record retrieval via ENA rest API
- </li>
- <li>
- <!-- JAL-2027 -->Support for ENA CDS records with reverse
- complement operator
- </li>
- <li>
- <!-- JAL-1812 -->Update to groovy-2.4.6-indy - for faster
- groovy script execution
- </li>
- <li>
- <!-- JAL-1812 -->New 'execute Groovy script' option in an
- alignment window's Calculate menu
- </li>
- <li>
- <!-- JAL-1812 -->Allow groovy scripts that call
- Jalview.getAlignFrames() to run in headless mode
- </li>
- <li>
- <!-- JAL-2068 -->Support for creating new alignment
- calculation workers from groovy scripts
- </li>
- <li>
- <!-- JAL-1369 --->Store/restore reference sequence in
- Jalview projects
- </li>
- <li>
- <!-- JAL-1803 -->Chain codes for a sequence's PDB
- associations are now saved/restored from project
- </li>
- <li>
- <!-- JAL-1993 -->Database selection dialog always shown
- before sequence fetcher is opened
- </li>
- <li>
- <!-- JAL-2183 -->Double click on an entry in Jalview's
- database chooser opens a sequence fetcher
- </li>
- <li>
- <!-- JAL-1563 -->Free-text search client for UniProt using
- the UniProt REST API
- </li>
- <li>
- <!-- JAL-2168 -->-nonews command line parameter to prevent
- the news reader opening
- </li>
- <li>
- <!-- JAL-2028 -->Displayed columns for PDBe and Uniprot
- querying stored in preferences
- </li>
- <li>
- <!-- JAL-2091 -->Pagination for displaying PDBe and Uniprot
- search results
- </li>
- <li>
- <!-- JAL-1977-->Tooltips shown on database chooser
- </li>
- <li>
- <!-- JAL-391 -->Reverse complement function in calculate
- menu for nucleotide sequences
- </li>
- <li>
- <!-- JAL-2005, JAL-599 -->Alignment sort by feature scores
- and feature counts preserves alignment ordering (and
- debugged for complex feature sets).
- </li>
- <li>
- <!-- JAL-2152-->Chimera 1.11.1 minimum requirement for
- viewing structures with Jalview 2.10
- </li>
- <li>
- <!-- JAL-1705, JAL-1975, JAL-2050,JAL-2041,JAL-2105 -->Retrieve
- genome, transcript CCDS and gene ids via the Ensembl and
- Ensembl Genomes REST API
- </li>
- <li>
- <!-- JAL-2049 -->Protein sequence variant annotation
- computed for 'sequence_variant' annotation on CDS regions
- (Ensembl)
- </li>
- <li>
- <!-- JAL-2232 -->ENA CDS 'show cross references' for Uniprot
- sequences
- </li>
- <li>
- <!-- JAL-2213,JAL-1856 -->Improved warning messages when DB
- Ref Fetcher fails to match, or otherwise updates sequence
- data from external database records.
- </li>
- <li>
- <!-- JAL-2154 -->Revised Jalview Project format for
- efficient recovery of sequence coding and alignment
- annotation relationships.
- </li>
- </ul> <!-- <em>Applet</em>
- <ul>
- <li>
- -- JAL---
- </li>
- </ul> --></td>
- <td>
- <div align="left">
- <em>General</em>
- <ul>
- <li>
- <!-- JAL-2077 -->reinstate CTRL-click for opening pop-up
- menu on OSX
- </li>
- <li>
- <!-- JAL-2018-->Export features in Jalview format (again)
- includes graduated colourschemes
- </li>
- <li>
- <!-- JAL-2172,JAL-1722, JAL-2001-->More responsive when
- working with big alignments and lots of hidden columns
- </li>
- <li>
- <!-- JAL-2053-->Hidden column markers not always rendered
- at right of alignment window
- </li>
- <li>
- <!-- JAL-2067 -->Tidied up links in help file table of
- contents
- </li>
- <li>
- <!-- JAL-2072 -->Feature based tree calculation not shown
- for DNA alignments
- </li>
- <li>
- <!-- JAL-2075 -->Hidden columns ignored during feature
- based tree calculation
- </li>
- <li>
- <!-- JAL-2065 -->Alignment view stops updating when show
- unconserved enabled for group on alignment
- </li>
- <li>
- <!-- JAL-2086 -->Cannot insert gaps into sequence when
- set as reference
- </li>
- <li>
- <!-- JAL-2146 -->Alignment column in status incorrectly
- shown as "Sequence position" when mousing over
- annotation
- </li>
- <li>
- <!-- JAL-2099 -->Incorrect column numbers in ruler when
- hidden columns present
- </li>
- <li>
- <!-- JAL-1577 -->Colour by RNA Helices not enabled when
- user created annotation added to alignment
- </li>
- <li>
- <!-- JAL-1841 -->RNA Structure consensus only computed for
- '()' base pair annotation
- </li>
- <li>
- <!-- JAL-2215, JAL-1841 -->Enabling 'Ignore Gaps' results
- in zero scores for all base pairs in RNA Structure
- Consensus
- </li>
- <li>
- <!-- JAL-2174-->Extend selection with columns containing
- feature not working
- </li>
- <li>
- <!-- JAL-2275 -->Pfam format writer puts extra space at
- beginning of sequence
- </li>
- <li>
- <!-- JAL-1827 -->Incomplete sequence extracted from pdb
- entry 3a6s
- </li>
- <li>
- <!-- JAL-2238 -->Cannot create groups on an alignment from
- from a tree when t-coffee scores are shown
- </li>
- <li>
- <!-- JAL-1836,1967 -->Cannot import and view PDB
- structures with chains containing negative resnums (4q4h)
- </li>
- <li>
- <!-- JAL-1998 -->ArithmeticExceptions raised when parsing
- some structures
- </li>
- <li>
- <!-- JAL-1991, JAl-1952 -->'Empty' alignment blocks added
- to Clustal, PIR and PileUp output
- </li>
- <li>
- <!-- JAL-2008 -->Reordering sequence features that are
- not visible causes alignment window to repaint
- </li>
- <li>
- <!-- JAL-2006 -->Threshold sliders don't work in
- graduated colour and colour by annotation row for e-value
- scores associated with features and annotation rows
- </li>
- <li>
- <!-- JAL-1797 -->amino acid physicochemical conservation
- calculation should be case independent
- </li>
- <li>
- <!-- JAL-2173 -->Remove annotation also updates hidden
- columns
- </li>
- <li>
- <!-- JAL-2234 -->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)
- </li>
- <li>
- <!-- JAL-2065 -->Null pointer exceptions and redraw
- problems when reference sequence defined and 'show
- non-conserved' enabled
- </li>
- <li>
- <!-- JAL-1306 -->Quality and Conservation are now shown on
- load even when Consensus calculation is disabled
- </li>
- <li>
- <!-- JAL-1932 -->Remove right on penultimate column of
- alignment does nothing
- </li>
- </ul>
- <em>Application</em>
- <ul>
- <li>
- <!-- JAL-1552-->URLs and links can't be imported by
- drag'n'drop on OSX when launched via webstart (note - not
- yet fixed for El Capitan)
- </li>
- <li>
- <!-- JAL-1911-->Corrupt preferences for SVG, EPS & HTML
- output when running on non-gb/us i18n platforms
- </li>
- <li>
- <!-- JAL-1944 -->Error thrown when exporting a view with
- hidden sequences as flat-file alignment
- </li>
- <li>
- <!-- JAL-2030-->InstallAnywhere distribution fails when
- launching Chimera
- </li>
- <li>
- <!-- JAL-2080-->Jalview very slow to launch via webstart
- (also hotfix for 2.9.0b2)
- </li>
- <li>
- <!-- JAL-2085 -->Cannot save project when view has a
- reference sequence defined
- </li>
- <li>
- <!-- JAL-1011 -->Columns are suddenly selected in other
- alignments and views when revealing hidden columns
- </li>
- <li>
- <!-- JAL-1989 -->Hide columns not mirrored in complement
- view in a cDNA/Protein splitframe
- </li>
- <li>
- <!-- JAL-1369 -->Cannot save/restore representative
- sequence from project when only one sequence is
- represented
- </li>
- <li>
- <!-- JAL-2002 -->Disabled 'Best Uniprot Coverage' option
- in Structure Chooser
- </li>
- <li>
- <!-- JAL-2215 -->Modifying 'Ignore Gaps' on consensus or
- structure consensus didn't refresh annotation panel
- </li>
- <li>
- <!-- JAL-1962 -->View mapping in structure view shows
- mappings between sequence and all chains in a PDB file
- </li>
- <li>
- <!-- JAL-2102, JAL-2101, JAL-2102, -->PDB and Uniprot FTS
- dialogs format columns correctly, don't display array
- data, sort columns according to type
- </li>
- <li>
- <!-- JAL-1975 -->Export complete shown after destination
- file chooser is cancelled during an image export
- </li>
- <li>
- <!-- JAL-2025 -->Error when querying PDB Service with
- sequence name containing special characters
- </li>
- <li>
- <!-- JAL-2024 -->Manual PDB structure querying should be
- case insensitive
- </li>
- <li>
- <!-- JAL-2104 -->Large tooltips with broken HTML
- formatting don't wrap
- </li>
- <li>
- <!-- JAL-1128 -->Figures exported from wrapped view are
- truncated so L looks like I in consensus annotation
- </li>
- <li>
- <!-- JAL-2003 -->Export features should only export the
- currently displayed features for the current selection or
- view
- </li>
- <li>
- <!-- JAL-2036 -->Enable 'Get Cross-References' in menu
- after fetching cross-references, and restoring from
- project
- </li>
- <li>
- <!-- JAL-2032 -->Mouseover of a copy of a sequence is not
- followed in the structure viewer
- </li>
- <li>
- <!-- JAL-2163 -->Titles for individual alignments in
- splitframe not restored from project
- </li>
- <li>
- <!-- JAL-2145 -->missing autocalculated annotation at
- trailing end of protein alignment in transcript/product
- splitview when pad-gaps not enabled by default
- </li>
- <li>
- <!-- JAL-1797 -->amino acid physicochemical conservation
- is case dependent
- </li>
- <li>
- <!-- JAL-1448 -->RSS reader doesn't stay hidden after last
- article has been read (reopened issue due to
- internationalisation problems)
- </li>
- <li>
- <!-- JAL-1960 -->Only offer PDB structures in structure
- viewer based on sequence name, PDB and UniProt
- cross-references
- </li>
-
- <li>
- <!-- JAL-1976 -->No progress bar shown during export of
- alignment as HTML
- </li>
- <li>
- <!-- JAL-2213 -->Structures not always superimposed after
- multiple structures are shown for one or more sequences.
- </li>
- <li>
- <!-- JAL-1370 -->Reference sequence characters should not
- be replaced with '.' when 'Show unconserved' format option
- is enabled.
- </li>
- <li>
- <!-- JAL-1823 -->Cannot specify chain code when entering
- specific PDB id for sequence
- </li>
- <li>
- <!-- JAL-1944 -->File->Export->.. as doesn't work when
- 'Export hidden sequences' is enabled, but 'export hidden
- columns' is disabled.
- </li>
- <li>
- <!--JAL-2026-->Best Quality option in structure chooser
- selects lowest rather than highest resolution structures
- for each sequence
- </li>
- <li>
- <!-- JAL-1887 -->Incorrect start and end reported for PDB
- to sequence mapping in 'View Mappings' report
- </li>
- <li>
- <!-- JAL-2284 -->Unable to read old Jalview projects that
- contain non-XML data added after Jalvew wrote project.
- </li>
- <li>
- <!-- JAL-2118 -->Newly created annotation row reorders
- after clicking on it to create new annotation for a
- column.
- </li>
- <li>
- <!-- JAL-1980 -->Null Pointer Exception raised when
- pressing Add on an orphaned cut'n'paste window.
- </li>
- <!-- may exclude, this is an external service stability issue JAL-1941
- -- > RNA 3D structure not added via DSSR service</li> -->
- </ul>
- <em>Applet</em>
- <ul>
- <li>
- <!-- JAL-2151 -->Incorrect columns are selected when
- hidden columns present before start of sequence
- </li>
- <li>
- <!-- JAL-1986 -->Missing dependencies on applet pages
- (JSON jars)
- </li>
- <li>
- <!-- JAL-1947 -->Overview pixel size changes when
- sequences are hidden in applet
- </li>
- <li>
- <!-- JAL-1996 -->Updated instructions for applet
- deployment on examples pages.
- </li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.9.0b2">2.9.0b2</a><br />
- <em>16/10/2015</em></strong>
- </div>
- </td>
- <td><em>General</em>
- <ul>
- <li>Time stamps for signed Jalview application and applet
- jars</li>
- </ul></td>
- <td>
- <div align="left">
- <em>Application</em>
- <ul>
- <li>Duplicate group consensus and conservation rows
- shown when tree is partitioned</li>
- <li>Erratic behaviour when tree partitions made with
- multiple cDNA/Protein split views</li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td width="60" nowrap>
- <div align="center">
- <strong><a name="Jalview.2.9.0b1">2.9.0b1</a><br />
- <em>8/10/2015</em></strong>
- </div>
- </td>
- <td><em>General</em>
- <ul>
- <li>Updated Spanish translations of localized text for
- 2.9</li>
- </ul> <em>Application</em>
- <ul>
- <!-- <li>cDNA/Protein splitframe window geometry preserved in Jalview projects</li>-->
- <li>Signed OSX InstallAnywhere installer<br></li>
- <li>Support for per-sequence based annotations in BioJSON</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Split frame example added to applet examples page</li>
- </ul> <em>Build and Deployment</em>
- <ul>
- <li>
- <!-- JAL-1888 -->New ant target for running Jalview's test
- suite
- </li>
- </ul></td>
- <td>
- <div align="left">
- <em>General</em>
- <ul>
- <li>Mapping of cDNA to protein in split frames
- incorrect when sequence start > 1</li>
- <li>Broken images in filter column by annotation dialog
- documentation</li>
- <li>Feature colours not parsed from features file</li>
- <li>Exceptions and incomplete link URLs recovered when
- loading a features file containing HTML tags in feature
- description</li>
-
- </ul>
- <em>Application</em>
- <ul>
- <li>Annotations corrupted after BioJS export and
- reimport</li>
- <li>Incorrect sequence limits after Fetch DB References
- with 'trim retrieved sequences'</li>
- <li>Incorrect warning about deleting all data when
- deleting selected columns</li>
- <li>Patch to build system for shipping properly signed
- JNLP templates for webstart launch</li>
- <li>EMBL-PDBe fetcher/viewer dialogs do not offer
- unreleased structures for download or viewing</li>
- <li>Tab/space/return keystroke operation of EMBL-PDBe
- fetcher/viewer dialogs works correctly</li>
- <li>Disabled 'minimise' button on Jalview windows
- running on OSX to workaround redraw hang bug</li>
- <li>Split cDNA/Protein view position and geometry not
- recovered from jalview project</li>
- <li>Initial enabled/disabled state of annotation menu
- sorter 'show autocalculated first/last' corresponds to
- alignment view</li>
- <li>Restoring of Clustal, RNA Helices and T-Coffee
- color schemes from BioJSON</li>
- </ul>
- <em>Applet</em>
- <ul>
- <li>Reorder sequences mirrored in cDNA/Protein split
- frame</li>
- <li>Applet with Jmol examples not loading correctly</li>
- </ul>
- </div>
- </td>
- </tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.9">2.9</a><br /> <em>10/9/2015</em></strong>
- </div></td>
- <td><em>General</em>
- <ul>
- <li>Linked visualisation and analysis of DNA and Protein
- alignments:
- <ul>
- <li>Translated cDNA alignments shown as split protein
- and DNA alignment views</li>
- <li>Codon consensus annotation for linked protein and
- cDNA alignment views</li>
- <li>Link cDNA or Protein product sequences by loading
- them onto Protein or cDNA alignments</li>
- <li>Reconstruct linked cDNA alignment from aligned
- protein sequences</li>
- </ul>
- </li>
- <li>Jmol integration updated to Jmol v14.2.14</li>
- <li>Import and export of Jalview alignment views as <a
- href="features/bioJsonFormat.html">BioJSON</a></li>
- <li>New alignment annotation file statements for
- reference sequences and marking hidden columns</li>
- <li>Reference sequence based alignment shading to
- highlight variation</li>
- <li>Select or hide columns according to alignment
- annotation</li>
- <li>Find option for locating sequences by description</li>
- <li>Conserved physicochemical properties shown in amino
- acid conservation row</li>
- <li>Alignments can be sorted by number of RNA helices</li>
- </ul> <em>Application</em>
- <ul>
- <li>New cDNA/Protein analysis capabilities
- <ul>
- <li>Get Cross-References should open a Split Frame
- view with cDNA/Protein</li>
- <li>Detect when nucleotide sequences and protein
- sequences are placed in the same alignment</li>
- <li>Split cDNA/Protein views are saved in Jalview
- projects</li>
- </ul>
- </li>
-
- <li>Use REST API to talk to Chimera</li>
- <li>Selected regions in Chimera are highlighted in linked
- Jalview windows</li>
-
- <li>VARNA RNA viewer updated to v3.93</li>
- <li>VARNA views are saved in Jalview Projects</li>
- <li>Pseudoknots displayed as Jalview RNA annotation can
- be shown in VARNA</li>
-
- <li>Make groups for selection uses marked columns as well
- as the active selected region</li>
-
- <li>Calculate UPGMA and NJ trees using sequence feature
- similarity</li>
- <li>New Export options
- <ul>
- <li>New Export Settings dialog to control hidden
- region export in flat file generation</li>
-
- <li>Export alignment views for display with the <a
- href="http://msa.biojs.net/">BioJS MSAViewer</a></li>
-
- <li>Export scrollable SVG in HTML page</li>
- <li>Optional embedding of BioJSON data when exporting
- alignment figures to HTML</li>
- </li>
- <li>3D structure retrieval and display
- <ul>
- <li>Free text and structured queries with the PDBe
- Search API</li>
- <li>PDBe Search API based discovery and selection of
- PDB structures for a sequence set</li>
- </ul>
- </li>
-
- <li>JPred4 employed for protein secondary structure
- predictions</li>
- <li>Hide Insertions menu option to hide unaligned columns
- for one or a group of sequences</li>
- <li>Automatically hide insertions in alignments imported
- from the JPred4 web server</li>
- <li>(Nearly) Native 'Quaqua' dialogs for browsing file
- system on OSX<br />LGPL libraries courtesy of <a
- href="http://www.randelshofer.ch/quaqua/">http://www.randelshofer.ch/quaqua/</a>
- </li>
- <li>changed 'View nucleotide structure' submenu to 'View
- VARNA 2D Structure'</li>
- <li>change "View protein structure" menu option to "3D
- Structure ..."</li>
-
- </ul> <em>Applet</em>
- <ul>
- <li>New layout for applet example pages</li>
- <li>New parameters to enable SplitFrame view
- (file2,enableSplitFrame, scaleProteinAsCdna)</li>
- <li>New example demonstrating linked viewing of cDNA and
- Protein alignments</li>
- </ul> <em>Development and deployment</em>
- <ul>
- <li>Java 1.7 minimum requirement for Jalview 2.9</li>
- <li>Include installation type and git revision in build
- properties and console log output</li>
- <li>Jalview Github organisation, and new github site for
- storing BioJsMSA Templates</li>
- <li>Jalview's unit tests now managed with TestNG</li>
- </ul></td>
- <td>
- <!-- <em>General</em>
- <ul>
- </ul> --> <!-- issues resolved --> <em>Application</em>
- <ul>
- <li>Escape should close any open find dialogs</li>
- <li>Typo in select-by-features status report</li>
- <li>Consensus RNA secondary secondary structure
- predictions are not highlighted in amber</li>
- <li>Missing gap character in v2.7 example file means
- alignment appears unaligned when pad-gaps is not enabled</li>
- <li>First switch to RNA Helices colouring doesn't colour
- associated structure views</li>
- <li>ID width preference option is greyed out when auto
- width checkbox not enabled</li>
- <li>Stopped a warning dialog from being shown when
- creating user defined colours</li>
- <li>'View Mapping' in structure viewer shows sequence
- mappings for just that viewer's sequences</li>
- <li>Workaround for superposing PDB files containing
- multiple models in Chimera</li>
- <li>Report sequence position in status bar when hovering
- over Jmol structure</li>
- <li>Cannot output gaps as '.' symbols with Selection ->
- output to text box</li>
- <li>Flat file exports of alignments with hidden columns
- have incorrect sequence start/end</li>
- <li>'Aligning' a second chain to a Chimera structure from
- Jalview fails</li>
- <li>Colour schemes applied to structure viewers don't
- work for nucleotide</li>
- <li>Loading/cut'n'pasting an empty or invalid file leads
- to a grey/invisible alignment window</li>
- <li>Exported Jpred annotation from a sequence region
- imports to different position</li>
- <li>Space at beginning of sequence feature tooltips shown
- on some platforms</li>
- <li>Chimera viewer 'View | Show Chain' menu is not
- populated</li>
- <li>'New View' fails with a Null Pointer Exception in
- console if Chimera has been opened</li>
- <li>Mouseover to Chimera not working</li>
- <li>Miscellaneous ENA XML feature qualifiers not
- retrieved</li>
- <li>NPE in annotation renderer after 'Extract Scores'</li>
- <li>If two structures in one Chimera window, mouseover of
- either sequence shows on first structure</li>
- <li>'Show annotations' options should not make
- non-positional annotations visible</li>
- <li>Subsequence secondary structure annotation not shown
- in right place after 'view flanking regions'</li>
- <li>File Save As type unset when current file format is
- unknown</li>
- <li>Save as '.jar' option removed for saving Jalview
- projects</li>
- <li>Colour by Sequence colouring in Chimera more
- responsive</li>
- <li>Cannot 'add reference annotation' for a sequence in
- several views on same alignment</li>
- <li>Cannot show linked products for EMBL / ENA records</li>
- <li>Jalview's tooltip wraps long texts containing no
- spaces</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Jmol to JalviewLite mouseover/link not working</li>
- <li>JalviewLite can't import sequences with ID
- descriptions containing angle brackets</li>
- </ul> <em>General</em>
- <ul>
- <li>Cannot export and reimport RNA secondary structure
- via jalview annotation file</li>
- <li>Random helix colour palette for colour by annotation
- with RNA secondary structure</li>
- <li>Mouseover to cDNA from STOP residue in protein
- translation doesn't work.</li>
- <li>hints when using the select by annotation dialog box</li>
- <li>Jmol alignment incorrect if PDB file has alternate CA
- positions</li>
- <li>FontChooser message dialog appears to hang after
- choosing 1pt font</li>
- <li>Peptide secondary structure incorrectly imported from
- annotation file when annotation display text includes 'e' or
- 'h'</li>
- <li>Cannot set colour of new feature type whilst creating
- new feature</li>
- <li>cDNA translation alignment should not be sequence
- order dependent</li>
- <li>'Show unconserved' doesn't work for lower case
- sequences</li>
- <li>Nucleotide ambiguity codes involving R not recognised</li>
- </ul> <em>Deployment and Documentation</em>
- <ul>
- <li>Applet example pages appear different to the rest of
- www.jalview.org</li>
- </ul> <em>Application Known issues</em>
- <ul>
- <li>Incomplete sequence extracted from PDB entry 3a6s</li>
- <li>Misleading message appears after trying to delete
- solid column.</li>
- <li>Jalview icon not shown in dock after InstallAnywhere
- version launches</li>
- <li>Fetching EMBL reference for an RNA sequence results
- fails with a sequence mismatch</li>
- <li>Corrupted or unreadable alignment display when
- scrolling alignment to right</li>
- <li>ArrayIndexOutOfBoundsException thrown when remove
- empty columns called on alignment with ragged gapped ends</li>
- <li>auto calculated alignment annotation rows do not get
- placed above or below non-autocalculated rows</li>
- <li>Jalview dekstop becomes sluggish at full screen in
- ultra-high resolution</li>
- <li>Cannot disable consensus calculation independently of
- quality and conservation</li>
- <li>Mouseover highlighting between cDNA and protein can
- become sluggish with more than one splitframe shown</li>
- </ul> <em>Applet Known Issues</em>
- <ul>
- <li>Core PDB parsing code requires Jmol</li>
- <li>Sequence canvas panel goes white when alignment
- window is being resized</li>
-
- </ul>
- </td>
- </tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.8.2">2.8.2</a><br /> <em>3/12/2014</em></strong>
- </div></td>
- <td><em>General</em>
- <ul>
- <li>Updated Java code signing certificate donated by
- Certum.PL.</li>
- <li>Features and annotation preserved when performing
- pairwise alignment</li>
- <li>RNA pseudoknot annotation can be
- imported/exported/displayed</li>
- <li>'colour by annotation' can colour by RNA and
- protein secondary structure</li>
- <li>Warn user if 'Find' regular expression is invalid (<em>mentioned
- post-hoc with 2.9 release</em>)
- </li>
-
- </ul> <em>Application</em>
- <ul>
- <li>Extract and display secondary structure for sequences
- with 3D structures</li>
- <li>Support for parsing RNAML</li>
- <li>Annotations menu for layout
- <ul>
- <li>sort sequence annotation rows by alignment</li>
- <li>place sequence annotation above/below alignment
- annotation</li>
- </ul>
- <li>Output in Stockholm format</li>
- <li>Internationalisation: improved Spanish (es)
- translation</li>
- <li>Structure viewer preferences tab</li>
- <li>Disorder and Secondary Structure annotation tracks
- shared between alignments</li>
- <li>UCSF Chimera launch and linked highlighting from
- Jalview</li>
- <li>Show/hide all sequence associated annotation rows for
- all or current selection</li>
- <li>disorder and secondary structure predictions
- available as dataset annotation</li>
- <li>Per-sequence rna helices colouring</li>
-
-
- <li>Sequence database accessions imported when fetching
- alignments from Rfam</li>
- <li>update VARNA version to 3.91</li>
-
- <li>New groovy scripts for exporting aligned positions,
- conservation values, and calculating sum of pairs scores.</li>
- <li>Command line argument to set default JABAWS server</li>
- <li>include installation type in build properties and
- console log output</li>
- <li>Updated Jalview project format to preserve dataset
- annotation</li>
- </ul></td>
- <td>
- <!-- issues resolved --> <em>Application</em>
- <ul>
- <li>Distinguish alignment and sequence associated RNA
- structure in structure->view->VARNA</li>
- <li>Raise dialog box if user deletes all sequences in an
- alignment</li>
- <li>Pressing F1 results in documentation opening twice</li>
- <li>Sequence feature tooltip is wrapped</li>
- <li>Double click on sequence associated annotation
- selects only first column</li>
- <li>Redundancy removal doesn't result in unlinked
- leaves shown in tree</li>
- <li>Undos after several redundancy removals don't undo
- properly</li>
- <li>Hide sequence doesn't hide associated annotation</li>
- <li>User defined colours dialog box too big to fit on
- screen and buttons not visible</li>
- <li>author list isn't updated if already written to
- Jalview properties</li>
- <li>Popup menu won't open after retrieving sequence
- from database</li>
- <li>File open window for associate PDB doesn't open</li>
- <li>Left-then-right click on a sequence id opens a
- browser search window</li>
- <li>Cannot open sequence feature shading/sort popup menu
- in feature settings dialog</li>
- <li>better tooltip placement for some areas of Jalview
- desktop</li>
- <li>Allow addition of JABAWS Server which doesn't
- pass validation</li>
- <li>Web services parameters dialog box is too large to
- fit on screen</li>
- <li>Muscle nucleotide alignment preset obscured by
- tooltip</li>
- <li>JABAWS preset submenus don't contain newly
- defined user preset</li>
- <li>MSA web services warns user if they were launched
- with invalid input</li>
- <li>Jalview cannot contact DAS Registy when running on
- Java 8</li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1273'>JAL-1273</a>] -->
- 'Superpose with' submenu not shown when new view
- created
- </li>
-
- </ul> <!-- <em>Applet</em>
- <ul>
- </ul> <em>General</em>
- <ul>
- </ul>--> <em>Deployment and Documentation</em>
- <ul>
- <li>2G and 1G options in launchApp have no effect on
- memory allocation</li>
- <li>launchApp service doesn't automatically open
- www.jalview.org/examples/exampleFile.jar if no file is given</li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1511'>JAL-1511</a>] -->
- InstallAnywhere reports cannot find valid JVM when Java
- 1.7_055 is available
- </li>
- </ul> <em>Application Known issues</em>
- <ul>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-830'>JAL-830</a>] -->
- corrupted or unreadable alignment display when scrolling
- alignment to right
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1329'>JAL-1329</a>] -->
- retrieval fails but progress bar continues for DAS retrieval
- with large number of ID
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1486'>JAL-1486</a>] -->
- flatfile output of visible region has incorrect sequence
- start/end
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1487'>JAL-1487</a>] -->
- rna structure consensus doesn't update when secondary
- structure tracks are rearranged
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1591'>JAL-1591</a>] -->
- invalid rna structure positional highlighting does not
- highlight position of invalid base pairs
- </li>
- <li>
- <!-- <a href='http://issues.jalview.org/browse/JAL-1539'>JAL-1539</a>] -->
- out of memory errors are not raised when saving Jalview
- project from alignment window file menu
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1576'>JAL-1576</a>] -->
- Switching to RNA Helices colouring doesn't propagate to
- structures
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1577'>JAL-1577</a>] -->
- colour by RNA Helices not enabled when user created
- annotation added to alignment
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1439'>JAL-1439</a>] -->
- Jalview icon not shown on dock in Mountain Lion/Webstart
- </li>
- </ul> <em>Applet Known Issues</em>
- <ul>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1394'>JAL-1394</a>] -->
- JalviewLite needs JmolApplet and VARNA-3.91 jar dependencies
- </li>
- <li>
- <!-- [<a href='http://issues.jalview.org/browse/JAL-1510'>JAL-1510</a>] -->
- Jalview and Jmol example not compatible with IE9
- </li>
-
- <li>Sort by annotation score doesn't reverse order
- when selected</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.8.1">2.8.1</a><br /> <em>4/6/2014</em></strong>
- </div></td>
- <td>
- <!-- New features --> <!-- For major releases, split into sections: Application | Applet | General | Deployment and Documentation -->
- <em>General</em>
- <ul>
- <li>Internationalisation of user interface (usually
- called i18n support) and translation for Spanish locale</li>
- <li>Define/Undefine group on current selection with
- Ctrl-G/Shift Ctrl-G</li>
- <li>Improved group creation/removal options in
- alignment/sequence Popup menu</li>
- <li>Sensible precision for symbol distribution
- percentages shown in logo tooltip.</li>
- <li>Annotation panel height set according to amount of
- annotation when alignment first opened</li>
- </ul> <em>Application</em>
- <ul>
- <li>Interactive consensus RNA secondary structure
- prediction VIENNA RNAAliFold JABA 2.1 service</li>
- <li>Select columns containing particular features from
- Feature Settings dialog</li>
- <li>View all 'representative' PDB structures for selected
- sequences</li>
- <li>Update Jalview project format:
- <ul>
- <li>New file extension for Jalview projects '.jvp'</li>
- <li>Preserve sequence and annotation dataset (to
- store secondary structure annotation,etc)</li>
- <li>Per group and alignment annotation and RNA helix
- colouring</li>
- </ul>
- </li>
- <li>New similarity measures for PCA and Tree calculation
- (PAM250)</li>
- <li>Experimental support for retrieval and viewing of
- flanking regions for an alignment</li>
- </ul>
- </td>
- <td>
- <!-- issues resolved --> <em>Application</em>
- <ul>
- <li>logo keeps spinning and status remains at queued or
- running after job is cancelled</li>
- <li>cannot export features from alignments imported from
- Jalview/VAMSAS projects</li>
- <li>Buggy slider for web service parameters that take
- float values</li>
- <li>Newly created RNA secondary structure line doesn't
- have 'display all symbols' flag set</li>
- <li>T-COFFEE alignment score shading scheme and other
- annotation shading not saved in Jalview project</li>
- <li>Local file cannot be loaded in freshly downloaded
- Jalview</li>
- <li>Jalview icon not shown on dock in Mountain
- Lion/Webstart</li>
- <li>Load file from desktop file browser fails</li>
- <li>Occasional NPE thrown when calculating large trees</li>
- <li>Cannot reorder or slide sequences after dragging an
- alignment onto desktop</li>
- <li>Colour by annotation dialog throws NPE after using
- 'extract scores' function</li>
- <li>Loading/cut'n'pasting an empty file leads to a grey
- alignment window</li>
- <li>Disorder thresholds rendered incorrectly after
- performing IUPred disorder prediction</li>
- <li>Multiple group annotated consensus rows shown when
- changing 'normalise logo' display setting</li>
- <li>Find shows blank dialog after 'finished searching' if
- nothing matches query</li>
- <li>Null Pointer Exceptions raised when sorting by
- feature with lots of groups<!-- possibly JAL-599 but commit 7c7a5a297e063d3892dd7e629bc317cdde837b81 associated with JAL-971 -->
- </li>
- <li>Errors in Jmol console when structures in alignment
- don't overlap <!-- JAL-1476 Work in progress - don't send junk to Jmol -->
- </li>
- <li>Not all working JABAWS services are shown in
- Jalview's menu</li>
- <li>JAVAWS version of Jalview fails to launch with
- 'invalid literal/length code'</li>
- <li>Annotation/RNA Helix colourschemes cannot be applied
- to alignment with groups (actually fixed in 2.8.0b1)</li>
- <li>RNA Helices and T-Coffee Scores available as default
- colourscheme</li>
-
- </ul> <em>Applet</em>
- <ul>
- <li>Remove group option is shown even when selection is
- not a group</li>
- <li>Apply to all groups ticked but colourscheme changes
- don't affect groups</li>
- <li>Documented RNA Helices and T-Coffee Scores as valid
- colourscheme name</li>
- <li>Annotation labels drawn on sequence IDs when
- Annotation panel is not displayed</li>
- <li>Increased font size for dropdown menus on OSX and
- embedded windows</li>
- </ul> <em>Other</em>
- <ul>
- <li>Consensus sequence for alignments/groups with a
- single sequence were not calculated</li>
- <li>annotation files that contain only groups imported as
- annotation and junk sequences</li>
- <li>Fasta files with sequences containing '*' incorrectly
- recognised as PFAM or BLC</li>
- <li>conservation/PID slider apply all groups option
- doesn't affect background (2.8.0b1)
- <li></li>
- <li>redundancy highlighting is erratic at 0% and 100%</li>
- <li>Remove gapped columns fails for sequences with ragged
- trailing gaps</li>
- <li>AMSA annotation row with leading spaces is not
- registered correctly on import</li>
- <li>Jalview crashes when selecting PCA analysis for
- certain alignments</li>
- <li>Opening the colour by annotation dialog for an
- existing annotation based 'use original colours'
- colourscheme loses original colours setting</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview.2.8.0b1">2.8.0b1</a><br />
- <em>30/1/2014</em></strong>
- </div></td>
- <td>
- <ul>
- <li>Trusted certificates for JalviewLite applet and
- Jalview Desktop application<br />Certificate was donated by
- <a href="https://www.certum.eu">Certum</a> to the Jalview
- open source project).
- </li>
- <li>Jalview SRS links replaced by UniProt and EBI-search</li>
- <li>Output in Stockholm format</li>
- <li>Allow import of data from gzipped files</li>
- <li>Export/import group and sequence associated line
- graph thresholds</li>
- <li>Nucleotide substitution matrix that supports RNA and
- ambiguity codes</li>
- <li>Allow disorder predictions to be made on the current
- selection (or visible selection) in the same way that JPred
- works</li>
- <li>Groovy scripting for headless Jalview operation</li>
- </ul> <em>Other improvements</em>
- <ul>
- <li>Upgrade desktop installer to InstallAnywhere 2013</li>
- <li>COMBINE statement uses current SEQUENCE_REF and
- GROUP_REF scope to group annotation rows</li>
- <li>Support '' style escaping of quotes in Newick
- files</li>
- <li>Group options for JABAWS service by command line name</li>
- <li>Empty tooltip shown for JABA service options with a
- link but no description</li>
- <li>Select primary source when selecting authority in
- database fetcher GUI</li>
- <li>Add .mfa to FASTA file extensions recognised by
- Jalview</li>
- <li>Annotation label tooltip text wrap</li>
- </ul>
- </td>
- <td>
- <ul>
- <li>Slow scrolling when lots of annotation rows are
- displayed</li>
- <li>Lots of NPE (and slowness) after creating RNA
- secondary structure annotation line</li>
- <li>Sequence database accessions not imported when
- fetching alignments from Rfam</li>
- <li>Incorrect SHMR submission for sequences with
- identical IDs</li>
- <li>View all structures does not always superpose
- structures</li>
- <li>Option widgets in service parameters not updated to
- reflect user or preset settings</li>
- <li>Null pointer exceptions for some services without
- presets or adjustable parameters</li>
- <li>Discover PDB IDs entry in structure menu doesn't
- discover PDB xRefs</li>
- <li>Exception encountered while trying to retrieve
- features with DAS</li>
- <li>Lowest value in annotation row isn't coloured
- when colour by annotation (per sequence) is coloured</li>
- <li>Keyboard mode P jumps to start of gapped region when
- residue follows a gap</li>
- <li>Jalview appears to hang importing an alignment with
- Wrap as default or after enabling Wrap</li>
- <li>'Right click to add annotations' message
- shown in wrap mode when no annotations present</li>
- <li>Disorder predictions fail with NPE if no automatic
- annotation already exists on alignment</li>
- <li>oninit javascript function should be called after
- initialisation completes</li>
- <li>Remove redundancy after disorder prediction corrupts
- alignment window display</li>
- <li>Example annotation file in documentation is invalid</li>
- <li>Grouped line graph annotation rows are not exported
- to annotation file</li>
- <li>Multi-harmony analysis cannot be run when only two
- groups created</li>
- <li>Cannot create multiple groups of line graphs with
- several 'combine' statements in annotation file</li>
- <li>Pressing return several times causes Number Format
- exceptions in keyboard mode</li>
- <li>Multi-harmony (SHMMR) method doesn't submit
- correct partitions for input data</li>
- <li>Translation from DNA to Amino Acids fails</li>
- <li>Jalview fail to load newick tree with quoted label</li>
- <li>--headless flag isn't understood</li>
- <li>ClassCastException when generating EPS in headless
- mode</li>
- <li>Adjusting sequence-associated shading threshold only
- changes one row's threshold</li>
- <li>Preferences and Feature settings panel panel
- doesn't open</li>
- <li>hide consensus histogram also hides conservation and
- quality histograms</li>
- </ul>
- </td>
- </tr>
- <tr>
- <td><div align="center">
- <strong><a name="Jalview2.8">2.8</a></strong><br /> <em>12/11/2012</em>
- </div></td>
- <td><em>Application</em>
- <ul>
- <li>Support for JABAWS 2.0 Services (AACon alignment
- conservation, protein disorder and Clustal Omega)</li>
- <li>JABAWS server status indicator in Web Services
- preferences</li>
- <li>VARNA (http://varna.lri.fr) viewer for RNA structures
- in Jalview alignment window</li>
- <li>Updated Jalview build and deploy framework for OSX
- mountain lion, windows 7, and 8</li>
- <li>Nucleotide substitution matrix for PCA that supports
- RNA and ambiguity codes</li>
-
- <li>Improved sequence database retrieval GUI</li>
- <li>Support fetching and database reference look up
- against multiple DAS sources (Fetch all from in 'fetch db
- refs')</li>
- <li>Jalview project improvements
- <ul>
- <li>Store and retrieve the 'belowAlignment'
- flag for annotation</li>
- <li>calcId attribute to group annotation rows on the
- alignment</li>
- <li>Store AACon calculation settings for a view in
- Jalview project</li>
-
- </ul>
- </li>
- <li>horizontal scrolling gesture support</li>
- <li>Visual progress indicator when PCA calculation is
- running</li>
- <li>Simpler JABA web services menus</li>
- <li>visual indication that web service results are still
- being retrieved from server</li>
- <li>Serialise the dialogs that are shown when Jalview
- starts up for first time</li>
- <li>Jalview user agent string for interacting with HTTP
- services</li>
- <li>DAS 1.6 and DAS 2.0 source support using new JDAS
- client library</li>
- <li>Examples directory and Groovy library included in
- InstallAnywhere distribution</li>
- </ul> <em>Applet</em>
- <ul>
- <li>RNA alignment and secondary structure annotation
- visualization applet example</li>
- </ul> <em>General</em>
- <ul>
- <li>Normalise option for consensus sequence logo</li>
- <li>Reset button in PCA window to return dimensions to
- defaults</li>
- <li>Allow seqspace or Jalview variant of alignment PCA
- calculation</li>
- <li>PCA with either nucleic acid and protein substitution
- matrices
- <li>Allow windows containing HTML reports to be exported
- in HTML</li>
- <li>Interactive display and editing of RNA secondary
- structure contacts</li>
- <li>RNA Helix Alignment Colouring</li>
- <li>RNA base pair logo consensus</li>
- <li>Parse sequence associated secondary structure
- information in Stockholm files</li>
- <li>HTML Export database accessions and annotation
- information presented in tooltip for sequences</li>
- <li>Import secondary structure from LOCARNA clustalw
- style RNA alignment files</li>
- <li>import and visualise T-COFFEE quality scores for an
- alignment</li>
- <li>'colour by annotation' per sequence option to
- shade each sequence according to its associated alignment
- annotation</li>
- <li>New Jalview Logo</li>
- </ul> <em>Documentation and Development</em>
- <ul>
- <li>documentation for score matrices used in Jalview</li>
- <li>New Website!</li>
- </ul></td>
- <td><em>Application</em>
- <ul>
- <li>PDB, Unprot and EMBL (ENA) databases retrieved via
- wsdbfetch REST service</li>
- <li>Stop windows being moved outside desktop on OSX</li>
- <li>Filetype associations not installed for webstart
- launch</li>
- <li>Jalview does not always retrieve progress of a JABAWS
- job execution in full once it is complete</li>
- <li>revise SHMR RSBS definition to ensure alignment is
- uploaded via ali_file parameter</li>
- <li>Jalview 2.7 is incompatible with Jmol-12.2.2</li>
- <li>View all structures superposed fails with exception</li>
- <li>Jnet job queues forever if a very short sequence is
- submitted for prediction</li>
- <li>Cut and paste menu not opened when mouse clicked on
- desktop window</li>
- <li>Putting fractional value into integer text box in
- alignment parameter dialog causes Jalview to hang</li>
- <li>Structure view highlighting doesn't work on
- windows 7</li>
- <li>View all structures fails with exception shown in
- structure view</li>
- <li>Characters in filename associated with PDBEntry not
- escaped in a platform independent way</li>
- <li>Jalview desktop fails to launch with exception when
- using proxy</li>
- <li>Tree calculation reports 'you must have 2 or more
- sequences selected' when selection is empty</li>
- <li>Jalview desktop fails to launch with jar signature
- failure when java web start temporary file caching is
- disabled</li>
- <li>DAS Sequence retrieval with range qualification
- results in sequence xref which includes range qualification</li>
- <li>Errors during processing of command line arguments
- cause progress bar (JAL-898) to be removed</li>
- <li>Replace comma for semi-colon option not disabled for
- DAS sources in sequence fetcher</li>
- <li>Cannot close news reader when JABAWS server warning
- dialog is shown</li>
- <li>Option widgets not updated to reflect user settings</li>
- <li>Edited sequence not submitted to web service</li>
- <li>Jalview 2.7 Webstart does not launch on mountain lion</li>
- <li>InstallAnywhere installer doesn't unpack and run
- on OSX Mountain Lion</li>
- <li>Annotation panel not given a scroll bar when
- sequences with alignment annotation are pasted into the
- alignment</li>
- <li>Sequence associated annotation rows not associated
- when loaded from Jalview project</li>
- <li>Browser launch fails with NPE on java 1.7</li>
- <li>JABAWS alignment marked as finished when job was
- cancelled or job failed due to invalid input</li>
- <li>NPE with v2.7 example when clicking on Tree
- associated with all views</li>
- <li>Exceptions when copy/paste sequences with grouped
- annotation rows to new window</li>
- </ul> <em>Applet</em>
- <ul>
- <li>Sequence features are momentarily displayed before
- they are hidden using hidefeaturegroups applet parameter</li>
- <li>loading features via javascript API automatically
- enables feature display</li>
- <li>scrollToColumnIn javascript API method doesn't
- work</li>
- </ul> <em>General</em>
- <ul>
- <li>Redundancy removal fails for rna alignment</li>
- <li>PCA calculation fails when sequence has been selected
- and then deselected</li>
- <li>PCA window shows grey box when first opened on OSX</li>
- <li>Letters coloured pink in sequence logo when alignment
- coloured with clustalx</li>
- <li>Choosing fonts without letter symbols defined causes
- exceptions and redraw errors</li>
- <li>Initial PCA plot view is not same as manually
- reconfigured view</li>
- <li>Grouped annotation graph label has incorrect line
- colour</li>
- <li>Grouped annotation graph label display is corrupted
- for lots of labels</li>
- </ul>
- </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 Envision2
- 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