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GenoViz Changelog

What's new in GenoViz 8.5.2

Jan 21, 2016
  • Disable ability to store empty passwords on dataproviders (IGBF-1060)
  • Improve error handling around data provider credentials (IGBF-1051)
  • Clearing data set fails when refreshing QL server on genomes with many contigs (IGBF-1061)
  • Symloaders not handling non-bed formats properly (IGBF-1059)
  • Insertion glyph not shown correctly (IGBF-1057)
  • Protannot paxml not recalled correctly (IGBF-1001)
  • Do not allow user to set Max Cache size lower than the current cache size (IGBF-1019)
  • Exception generated when trying to install an updatable plugin (IGBF-1043)
  • Exception generated when trying to install an updatable plugin (IGBF-1018)
  • Race condition vulnerability in bottom tabholder (IGBF-1056)

New in GenoViz 8.5.1 (Jan 21, 2016)

  • Remote Wig File loading fails (IGBF-1046)

New in GenoViz 8.5.0 (Jan 21, 2016)

  • Introduced support for narrowPeak and broadPeak file formats (IGBF-1005)
  • Introduced a new caching system to improve performance and speed up data access of commonly accessed files (IGBF-442)
  • Introduced a App Manager created with JavaFx (IGBF-959)
  • Added a bundled JRE for the linux distribution (IGBF-1000)
  • Added support for a new index attribute to the quickload annots.xml file tag (IGBF-445)
  • Improved error handling of broken quickload servers (IGBF-808)
  • Introduced support for unsorted bed files (IGBF-1020)
  • Enable javafx file chooser in custom genome dialog (IGBF-795)
  • Make the "Save Password" checkbox checked by default (IGBF-802)
  • Implement weight for items under Tools menu (IGBF-841)
  • Refactor image export service to support plugins (IGBF-974)

New in GenoViz 8.4.4 (Jan 21, 2016)

  • High level zoom on large genes is causing lag if label set to "none" (IGBF-933)

New in GenoViz 8.4.3 (Jan 21, 2016)

  • IGB returns to default chromosome after removing any track. (local files only) (IGBF-915)
  • Remove checkboxes from bottom of plug-ins tab (IGBF-914)
  • Bookmark module activation fails if menu depth exceeds 4 levels (IGBF-903)
  • UriUtils does not properly handling http 500 response if initial validation returns 200 (IGBF-902)
  • "Customize..." action should open to the "Tracks" tab in Preferences (IGBF-882)
  • Restore JFileChooser and revert use of AWT FileDialog for Ubuntu (IGBF-872)
  • Allow .svg export always, even Whole Frame (IGBF-779)

New in GenoViz 8.4.2 (Aug 11, 2015)

  • A minor release which includes a variety of small bug fixes and user experience improvements. This release also introduces a new plugin to our "Optional" plugins repository: the ProtAnnot plugin. This plugin integrates a viewer which is designed to make it easy to see how alternative mRNA structures affect the various protein products encoded at a locus.
  • Improve user feedback when adding broken quickload sites (IGBF-808)
  • Local species.txt is parsed incorrectly (IGBF-796)
  • Spaces getting converted to " " in Data Sources table (IGBF-748)
  • Editing URL of secured quickoad sites causes strange behavior in IGB including the inability to remove a data source (IGBF-868)
  • Not selecting "Save Password" checkbox when adding two secured Quickoad sites causes too many popups to appear during a session (IGBF-866)
  • Working with multiple secure quickload sites causes authentication popup to trigger unexpectedly (IGBF-840)

New in GenoViz 8.3.4 (May 15, 2015)

  • Graph Track Operations Usability Enhancements (IGBF-635)
  • Remove parameter input option for what should be hardcoded Track "Operators" (IGBF-393)
  • Examine and fix the synonym error in the C. elegans genome (IGBF-538)
  • Change the text in the MM8 genome from "March" to "Feb" (IGBF-551)
  • Create a nested folder inside the IGB.zip distribution (IGBF-583)
  • Fix "select" and "selectfeature" scripting commands, and update "loadmode" documentation to reflect actual options available (IGBF-598)
  • Remove Track Operation text and punctuation in Graph tab (IGBF-606)
  • Bed Symloader does not properly parse bedDetail type when the number of columns is less than 14 (IGBF-619)
  • Remove Input parameter box for Sqrt Graph Track Operation (IGBF-643)
  • Change minimum requirement for Residue Search to 1 character (IGBF-644)
  • Subtract Track Operation Works Differently if Commas are used in the Value (IGBF-648)
  • Selecting "Make Track" in the Graph Thresholds Dialogue generates an exception (IGBF-610)

New in GenoViz 8.3.3 (May 15, 2015)

  • Data Sources become duplicated when re-enabling server or refreshing server (IGBF-498)

New in GenoViz 8.3.2 (Mar 31, 2015)

  • Today we released IGB 8.3.2, a minor release which includes bug fixes and some improvements, such as:
  • Add support for other FASTA file extensions (IGBF-414)
  • Open Custom Genome improvements (IGBF-479)
  • Refactor and simplify Open File feature (IGBF-377)
  • Update Bundled JRE to resolve intermittent crashes on Mac OS X (IGBF-380)
  • Add "delete all tracks" IGB scripting command) (IGBF-472)
  • Bed Parser Minor Improvements to resolve issues related to optional bin field (IGBF-512)
  • GFF3 Tooltip duplicates removed (IGBF-513)
  • Advanced Search Tab "Gene Name" column should be renamed to Title and mapped to correct property (IGBF-514)

New in GenoViz 8.3.1 (Feb 24, 2015)

  • Today we released IGB 8.3.1, a minor release which includes several bug fixes and small improvements:
  • Added Customize option back to track label context menu (IGBF-379)
  • Open File Diaolog modifications made for native look and feel (IGBF-377)
  • Search indexing problem with GFF file format vs. BED-detail (IGBF-23)
  • Moved igb-command-socket module into optional plugins (IGBF-417)
  • Genome load mode doesn’t indicate loading has happened for chromosomes for which there was no data (IGBF-378)
  • Set home as default location for Open File dialogs (IGBF-405)
  • Nothing appears above Annotations when labeling by "Title" (IGBF-387)

New in GenoViz 8.3.0 (Jan 23, 2015)

  • Create Native Installers (IGBF-347)
  • Improve current filter for paired data (IGBF-326)
  • Dragging a file over an icon in the toolbar generates a NullPointerException (IGBF-333)
  • Sliced View tab intron selection causing an error (IGBF-351)
  • Ensembl External Viewer is Not Using Current Genome Version after URL change (IGBF-354)
  • Remove "Accept Network Connections" popup when launching IGB on a Mac (IGBF-358)
  • Right-clicking on track label when no data has been loaded generates an exception (IGBF-346)
  • Fix and Organize Developer Plugins (IGBF-352)
  • Fix NPE in Merge Annotation Operator Development Plugin (IGBF-361)
  • Tooltips are not displaying on Windows;generates a "BadLocationException" (IGBF-336)
  • Bottom of tooltips box may be cutoff (IGBF-304)
  • Put "cigar", "mapq", and "id" in all caps in tooltips/selection info (IGBF-330)
  • Typing zero into Export Image size parameter box causes annoying question mark to appear (IGBF-252)
  • Remove "Do you want to run script" dialog (IGBF-273)
  • Hovering across gene models in HG16 prints harmless stacktrace, which should be a warning or silenced (IGBF-355)
  • Selecting the "Axis" option while Selecting Tracks under the Edit menu generates a null pointer exception (IGBF-357)

New in GenoViz 8.2.3 (Jan 10, 2015)

  • Resolves a small bug with IGB's cache system.
  • File name too long IOException from igbquickload server (IGBF-342)

New in GenoViz 8.2.1 (Dec 30, 2014)

  • Bam Flag Interpreter does not properly handle combinations of flag values (IGBF-321)
  • Misleading message after opening a Custom Genome (IGBF-306)
  • Reorganize the tooltip info for Paired-End data (IGBF-327)
  • Prevent "zoom in to see your data" popup when loading reference sequence (IGBF-318)
  • "Copy Bookmark URL" under the Bookmarks menu does not copy the URL for the selected bookmark (IGBF-311)
  • Disable "+/-" checkbox under the Annotation tab when "Show as Paired" is enabled (IGBF-320)

New in GenoViz 8.1.13 (Dec 11, 2014)

  • In preparation for our upcoming IGB 8.2 release, we have released a minor release with some minor bug fixed to our update notification system. With this notification system we will be able to notify users when we release IGB 8.2. This is important, because major releases cannot be pushed out silently, and require users to download a fresh copy of our software.
  • Patch bug in Notification System so it can be leveraged to notify user's of IGB 8.2 release (IGBF-282)

New in GenoViz 8.1.12 (Nov 27, 2014)

  • We have released a minor patch to ensure our blast functionality is not impacted by an upcoming NCBI blast URL change:
  • NCBI BLAST url is changing on Dec. 1, 2014

New in GenoViz 6.5 (Apr 8, 2011)

  • compiled with Java 6
  • enhanced data source preferences page
  • unification of "Pattern Search", "Name Search", and "Annotation Browser" tabs
  • added "Restriction sites" tab by default
  • auto-loading of features (if specified by DAS/2 server)
  • data provider hyperlinks and icons
  • feature hyperlinks and description tooltips
  • QuickLoad annots.xml file (similar to DAS/2)
  • GFF and BED parsing bugfixes
  • warnings for chromosome conflicts
  • assorted GUI enhancements and bugfixes

New in GenoViz 5.5 (Sep 10, 2009)

  • Incremental change: UI improvements, memory management, code cleanup. This is the last Java 5-compatible release; Java 5 will NOT be supported after this.
  • Image export (print to file) for many formats, such as:
  • PostScript, PDF, EMF, SVF, Flash SWF, as well as GIF, PNG, JPG and PPM.
  • Image export (print to file) for Sliced View.
  • Clearer and more robust "Add Server" page, including a fix for an Apple bug when saving server preferences.
  • New IGB icon and splash screen.
  • Major performance improvement in Heatmaps for mid- to large- size graphs.
  • More efficient Wiggle format representation, using an estimated ~30% less memory.
  • Several parser bug fixes.
  • Finite timeouts for remote resources (DAS servers, etc.)
  • Closing resource leaks.
  • Case sensitivity improvements for data sets.
  • Default shortcuts.
  • Additional unification for DAS/1.
  • New Genoviz FASTQ parser.

New in GenoViz 5.14 RC (Apr 22, 2009)

  • Updated xerces jar files to version 2.9.1.
  • Removed jetty.jar file. It is no longer needed.