Difference between revisions of "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=== | ===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 <tt>convertGeoCoord()</tt> which allows geographic coordinates to be converted into GenGIS Viewport coordinates | ||
| + | * added Python function <tt>addLine()</tt> which allows a user defined line to be rendered in the GenGIS Viewport | ||
| + | * added Python function <tt>openTree()</tt> which allows tree files to be loaded | ||
| + | * extended ''movieHelper.py'' to include <tt>setCameraParam()</tt> function | ||
| + | * added warning message regarding optimization of leaf nodes for trees with degree > 9 | ||
| + | * various minor bug fixes | ||
===v1.01=== | ===v1.01=== | ||
| − | + | * updated all Python scripts | |
| − | + | * various minor bug fixes | |
Latest revision as of 19:08, 27 August 2015
Contents
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
