Revision History

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v2.4.1 (Current Release)

  • Improvement: Updated GBIF plugin to work with new API.
  • Improvement: Improved error handling for MG-RAST plugin.
  • Improvement: Added the option to save all images when using ShowSpread.
  • Improvement: Functional speedup to Gridding.
  • Improvement: Bug fixes in CCA plugin.

v2.4.0

  • New Feature: Tree splitting.
  • New Feature: Collapsible tree nodes.
  • New Feature: Sub-tree zooming.
  • New Feature: Uniform Discrete Colours.
  • Improvement: Fixed bug in gridding with ShowSpread.

v2.3.0

  • New Feature: ShowSpread plugin to explore data over a variables extents.
  • New Feature: Polygons to cluster data over the levels of a field.
  • Improvement: Python on Windows is now version 2.7
  • Improvement: Locations can now be toggled from the properties menu, and on right click.
  • Improvement: Location Set Show/Hide All on right click.
  • Fixed: Linear Regression no longer requires sequence data.
  • Improvement: Gridding can now use the count(Sum) of string fields.

v2.2.2

  • Fixed: Save errors for plugins.
  • Improvement: Adjusted frame size on OSX for some plugins.
  • Fixed: Spelling and titling problems.

v2.2.1

  • Improvement: Fixed data requirements for some plugins.
  • Improvement: Increased performance of Gridding.
  • New Feature: Added sequence downloads to MG-RAST.
  • Improvement: Cleaned up MG-RAST options.
  • Improvement: Added 'About' to Location Merge.
  • Improvement: WorldClim Query now supports user data.

v2.2.0

  • New Feature: WorldClim Data Query plugin.
  • New Feature: MG-RAST Query plugin.
  • New Feature: Location Gridding.
  • New Feature: Support for multiple location layers.
  • New Feature: Location Layer Merge.
  • Fixed: Linear Regression Plugin bugs.
  • Improvement: Latitude/Longitude only accept numeric values.
  • Fixed: Fixed crash when all Locations have uniform number of sequence layers.
  • New Feature: Removing location layers now generates a warning as removing individual locations can cause unexpected behaviour.

v2.1.1

  • New Feature: Global Biodiversity Information Facility (GBIF) Query plugin.
  • Improvement: Support for visualizing multiple location sets (plugins currently only access first location set).
  • Improvement: Updated welcome screen.
  • Fixed: Cannot see number of tree crossings in GenGIS toolbar after restoring a session.

v2.1.0

  • New Feature: Beta Diversity plugin.
  • New Feature: One or more than one Shapefiles can be loaded and visualized in GenGIS.
  • New Feature: One or more than one shapefiles can be loaded on a digital map file.
  • Improvement: Serialization works for a session containing shapefiles as well.
  • Fixed: The Status bar in GenGIS shows the correct position (lat/long or UTM) of mouse on viewport.

v2.0.2

  • New Feature: Beta Diversity plugin.
  • Improvement: For nonlinear geographic axes, a tabular report of all permutations is now provided.
  • Improvement: For nonlinear geographic axes, the optimal ordering which minimizes the total Euclidean distance of all location lines is displayed.
  • Improvement: Major enhancements to the Alpha Diversity and Alpha Diversity Visualizer plugins.
  • Improvement: Major enhancements to the Dissimilarity Matrix Viewer plugin.
  • Improvement: Interface for exporting screen captures as PNG images.
  • Improvement: GenGIS allows multiple tree files to be loaded at the same time.
  • Improvement: GenGIS supports sessions with multiple trees.
  • Improvement: Cross-Platform session file compatibility.
  • Fixed: GenGIS sporadically crashes when performing a significance test or a linear axes analysis when more than one tree is loaded.
  • Fixed: Error while extending the geographic axis after loading a session file
  • Fixed: GenGIS closes unexpectedly while removing the map layer.
  • Fixed: Erroneous order of labels in the Dissimilarity Matrix Viewer plugin.
  • Fixed: File chooser appears behind "Export as Image" dialog (MacOS X).
  • Fixed: GenGIS occasionally crashes while re-opening sessions (MacOS X).

v2.0.1

  • New feature: Snapping charts to tree nodes.
  • New feature: Restoring charts to default placement over locations.
  • New feature: Border of pie charts can now be set to reflect the colour of their associated location marker.
  • Improvement: "Hidden" line style for chart dropline.
  • Improvement: Rendering of multifurcating trees.
  • Fixed: Problems with colours in the Map and Location Set properties dialogs.
  • Fixed: Error while changing study properties.
  • Fixed: Charts not reappearing after opening session.
  • Fixed: Linear axes analysis reporting incorrect values if multiple locations had the same longitude position.
  • Fixed: Serialization failure when location sets were assigned a colour map.
  • Fixed: Incorrect plotting of x- and y-data values for the Linear Regression and Mantel plugins.
  • Fixed: Bar chart rendering under certain situations.

v2.0.0

  • Serialization (Save and Open sessions to/from GenGIS *.GGIS session files)
  • Python Plugins and Plugin Manager
  • Additional support for RPy2
  • Plots showing results of Monte Carlo permutation test
  • Comprehensive linear axes analysis for testing all possible linear axes
  • Show/Hide text under user interface buttons
  • Updated Legend Panels (Layers, Locations and Sequences)
  • Welcome Screen
  • Updated Help->About dialog
  • Updated documentation

v1.08

  • added support for generating high-resolution images
  • fixed issue that was causing OpenGL rendering to be performed in software under Windows Vista/7
  • added functionality for creating bar charts
  • abundance information specified in sequence files can now be used to create quantitative pie or bar charts
  • continuous colours assigned to location sites can now be propagated onto an attached tree
  • labels (which are slow to render) are now automatically hidden when interacting with the viewport in order to improve responsiveness
  • visual properties of trees have been improved by adding support for thick branches, optional borders, and independent control over the size of leaf and internal nodes
  • added support for optional border around location markers
  • all properties dialogs have been changed to a modeless, stay-on-top style in order to facilitate interactively changing properties
  • font used to render labels can now be set in the Settings->Font Settings dialog
  • slightly reduced loading time for all maps and significantly reduced required memory for 2D GeoTIFF maps
  • the maximum terrain resolution can now be set in the Studies Properties Dialog (this can be helpful on low memory systems)
  • double clicking on a chart now bring up the Locations Properties Dialog instead of the Location Set Properties dialog
  • minor UI design improvements to the majority of the layer dialog boxes

v1.07

  • changed licensing from Creative Commons Attribution - Share Alike 3.0 to GPL 3.0 or later
  • initial interface to MOA database
  • Locations tab now shows a legend indicating the marker assigned to each location site
  • location site labels can now be set to either 'billboard' or 'dynamic' style
  • added View->Widgets menu items to show or hide all widgets
  • modified layer names are now reflected in the layer tree control
  • removed menu items associated with creating and saving studies (this functionality is now scheduled for v2.0)
  • added functionality to remove custom labels (right-click popup menu)
  • layers can now only be hidden through the check boxes in the layer tree control (this ensures that the visibility of a layer is allows indicated by the check box)
  • fixed bug introduced in v1.06 that prevented moving labels
  • fixed bug causing location site labels to transition from a 'billboard' to 'dynamic' style when moved

v1.06

  • added support for 3 or 4-channel GeoTIFF images
  • improved handling of OpenGL textures to support high-resolution GeoTIFF images
  • significant improvements to rendering speed under Microsoft Windows Vista and 7 (and possibly XP and OSX although these rendered quickly before)
  • changed default projection to plate carrée (equirectangular) projection as it can properly handle all maps
  • more efficient handling of main memory and GPU memory
  • fixed visual artifacts in compass widget under Microsoft Windows Vista and 7
  • fixed (hopefully!) bug which occasionally caused a map to fail to appear when loaded
  • modified handling of log file so it works under Microsoft Windows Vista and 7
  • added additional log statements to help in debugging end users
  • fixed bug in Map Properties dialog which was preventing modification to a map's colour map

v1.05

  • major bug fixes to OSX version:
    • sequences can now be loaded
    • layers can now be selected/unselected
    • map level-of-detail is now set properly
    • numerous cosmetic improvements
  • implemented dialog which allows user to specify which sequences are active
  • update dataHelper class to provide functions for placing sequences in the active set
  • added tree popup menu item to allow the order of points to be reversed
  • minor bug fixes to tree projection code
  • various minor bug fixes

v1.04

  • modified colour pickers to improve their visual appearance under OSX
  • extended GenGIS Python API to allow modification of phylogenetic trees
  • added functionality to project trees onto a subset of taxa

v1.03

  • added general purpose, user labels
  • Several extensions to the GenGIS Python API:
    • functions to obtain the width and height of the OpenGL Viewport.
    • functions for manipulating pie charts
    • functions for drawing markers, lines, and labels
    • several minor additions
  • trees of high dimensionality (> 9) can not be optimally laid out for computational reasons, so a heuristic layout is used
  • fixed memory leak related to incorrect use of Font class
  • shape maps now save any user modifications
  • various minor bug fixes

v1.02

  • background colour of GenGIS Viewport can be set by user in Study Properties Dialog
  • improved rendering quality of labels
  • labels associated with location sites can now be interactively positioned
  • the contents of the GenGIS Viewport can now be saved as a PNG file using File->Save image as...
  • added Python function convertGeoCoord() which allows geographic coordinates to be converted into GenGIS Viewport coordinates
  • added Python function addLine() which allows a user defined line to be rendered in the GenGIS Viewport
  • added Python function openTree() which allows tree files to be loaded
  • extended movieHelper.py to include setCameraParam() function
  • added warning message regarding optimization of leaf nodes for trees with degree > 9
  • various minor bug fixes

v1.01

  • updated all Python scripts
  • various minor bug fixes
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