<?xml version="1.0"?>
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	<id>https://beikolab.cs.dal.ca/gengis/?action=history&amp;feed=atom&amp;title=GenGIS_API_2.0.2</id>
	<title>GenGIS API 2.0.2 - Revision history</title>
	<link rel="self" type="application/atom+xml" href="https://beikolab.cs.dal.ca/gengis/?action=history&amp;feed=atom&amp;title=GenGIS_API_2.0.2"/>
	<link rel="alternate" type="text/html" href="https://beikolab.cs.dal.ca/gengis/?title=GenGIS_API_2.0.2&amp;action=history"/>
	<updated>2026-06-24T14:17:41Z</updated>
	<subtitle>Revision history for this page on the wiki</subtitle>
	<generator>MediaWiki 1.34.0</generator>
	<entry>
		<id>https://beikolab.cs.dal.ca/gengis/?title=GenGIS_API_2.0.2&amp;diff=1732&amp;oldid=prev</id>
		<title>Timothy at 18:43, 17 July 2012</title>
		<link rel="alternate" type="text/html" href="https://beikolab.cs.dal.ca/gengis/?title=GenGIS_API_2.0.2&amp;diff=1732&amp;oldid=prev"/>
		<updated>2012-07-17T18:43:37Z</updated>

		<summary type="html">&lt;p&gt;&lt;/p&gt;
&lt;table class=&quot;diff diff-contentalign-left&quot; data-mw=&quot;interface&quot;&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;col class=&quot;diff-marker&quot; /&gt;
				&lt;col class=&quot;diff-content&quot; /&gt;
				&lt;tr class=&quot;diff-title&quot; lang=&quot;en&quot;&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;← Older revision&lt;/td&gt;
				&lt;td colspan=&quot;2&quot; style=&quot;background-color: #fff; color: #222; text-align: center;&quot;&gt;Revision as of 18:43, 17 July 2012&lt;/td&gt;
				&lt;/tr&gt;&lt;tr&gt;&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot; id=&quot;mw-diff-left-l253&quot; &gt;Line 253:&lt;/td&gt;
&lt;td colspan=&quot;2&quot; class=&quot;diff-lineno&quot;&gt;Line 253:&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* GetGeoTreeView() - Get geophylogeny associated with this layer.&lt;/div&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;* GetGeoTreeView() - Get geophylogeny associated with this layer.&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td colspan=&quot;2&quot;&gt; &lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt;+&lt;/td&gt;&lt;td style=&quot;color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;&lt;ins style=&quot;font-weight: bold; text-decoration: none;&quot;&gt;* IsActive() - Get active state of layer.&lt;/ins&gt;&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;= Location Set Layer class =&lt;/div&gt;&lt;/td&gt;&lt;td class=&#039;diff-marker&#039;&gt; &lt;/td&gt;&lt;td style=&quot;background-color: #f8f9fa; color: #222; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;&quot;&gt;&lt;div&gt;= Location Set Layer class =&lt;/div&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;/table&gt;</summary>
		<author><name>Timothy</name></author>
		
	</entry>
	<entry>
		<id>https://beikolab.cs.dal.ca/gengis/?title=GenGIS_API_2.0.2&amp;diff=1731&amp;oldid=prev</id>
		<title>Timothy: New page: = Global objects =  * study - provides access to the Study Layer class * layerTree - provides access to the Layer Tree Controller class * viewport - provides access to the Viewport class *...</title>
		<link rel="alternate" type="text/html" href="https://beikolab.cs.dal.ca/gengis/?title=GenGIS_API_2.0.2&amp;diff=1731&amp;oldid=prev"/>
		<updated>2012-07-16T15:49:58Z</updated>

		<summary type="html">&lt;p&gt;New page: = Global objects =  * study - provides access to the Study Layer class * layerTree - provides access to the Layer Tree Controller class * viewport - provides access to the Viewport class *...&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;= Global objects =&lt;br /&gt;
&lt;br /&gt;
* study - provides access to the Study Layer class&lt;br /&gt;
* layerTree - provides access to the Layer Tree Controller class&lt;br /&gt;
* viewport - provides access to the Viewport class&lt;br /&gt;
* camera - provides access to the Camera class&lt;br /&gt;
* mainWindow - provides access to the Main Window class&lt;br /&gt;
* graphics - provides access to the Graphics class&lt;br /&gt;
* colourMapManager - provides access to the Colour Map Manager class&lt;br /&gt;
&lt;br /&gt;
= Global functions =&lt;br /&gt;
&lt;br /&gt;
* SafeYield() - Yields control to pending messages in the windowing system.&lt;br /&gt;
&lt;br /&gt;
= Main Window class =&lt;br /&gt;
&lt;br /&gt;
* GetPointer() - Get pointer to GenGIS window.&lt;br /&gt;
* SetSidePanelVisibility() - Set visibility of side panel.&lt;br /&gt;
* SetConsoleVisibility() - Set visibility of console.&lt;br /&gt;
* OpenMapFile() - Open map file.&lt;br /&gt;
* OpenLocationsFile() - Open location file.&lt;br /&gt;
* OpenSequenceFile() - Open sequence file.&lt;br /&gt;
* OpenTreeFile() - Open tree file.&lt;br /&gt;
* GetExeDir() - Get directory of GenGIS executable.&lt;br /&gt;
* Quit() - Exit GenGIS.&lt;br /&gt;
* Write() - Write text to the GenGIS console and the log file.&lt;br /&gt;
* Warning() - Write warning message to the GenGIS console and the log file.&lt;br /&gt;
* Error() - Write error message to the GenGIS console and the log file.&lt;br /&gt;
* Yield() - Yield control to main window for event processing.&lt;br /&gt;
&lt;br /&gt;
= Graphics class =&lt;br /&gt;
&lt;br /&gt;
* AddLine() - Add line to viewport.&lt;br /&gt;
* RemoveLine() - Remove line with a given id.&lt;br /&gt;
* ClearLines() - Clear all custom lines in viewport.&lt;br /&gt;
* AddMarker() - Add marker to Viewport.&lt;br /&gt;
* RemoveMarker() - Remove marker with a given id.&lt;br /&gt;
* ClearMarkers() - Clear all custom markers in viewport.&lt;br /&gt;
* AddCylinder() - Add cylinder to viewport.&lt;br /&gt;
* RemoveCylinder() - Remove cylinder with a given id.&lt;br /&gt;
* ClearCylinders() - Clear all custom cylinders in viewport.&lt;br /&gt;
* AddLabel() - Add label to viewport.&lt;br /&gt;
* RemoveLabel() - Remove label with a given id.&lt;br /&gt;
* ClearLabels() - Clear all custom labels in Viewport.&lt;br /&gt;
&lt;br /&gt;
= Camera class =&lt;br /&gt;
&lt;br /&gt;
* SetPosition() - Set position of camera.&lt;br /&gt;
* GetPosition() - Get current position of camera.&lt;br /&gt;
* SetHeight() - Set height of camera above terrain.&lt;br /&gt;
* GetHeight() - Get height of camera above terrain.&lt;br /&gt;
* SetPitch() - Set pitch of camera.&lt;br /&gt;
* GetPitch() - Get pitch of camera.&lt;br /&gt;
* SetYaw() - Set yaw of camera.&lt;br /&gt;
* GetYaw() - Get yaw of camera.&lt;br /&gt;
* ZoomDelta() - Change zoom (height) of camera by specified percentage.&lt;br /&gt;
* TranslateDelta() - Translate position of camera by specified amount.&lt;br /&gt;
* PitchDelta() - Change pitch of camera by specified amount.&lt;br /&gt;
* YawDelta() - Change yaw of camera by specified amount.&lt;br /&gt;
* ResetView() - Set camera to default position.&lt;br /&gt;
* TopView() - Set camera to provide a top &amp;#039;orthographic&amp;#039; view of the terrain&lt;br /&gt;
* GetMapExtentsZoom() - Get zoom (height) of camera required to view entire map.&lt;br /&gt;
* GetWindowHeight() - Get height of the viewport.&lt;br /&gt;
* GetWindowWidth() - Get width of the viewport.&lt;br /&gt;
&lt;br /&gt;
= Map Controller class =&lt;br /&gt;
&lt;br /&gt;
* GetProjectionExtents() - Get lower, left and upper, right corners of map after projection.&lt;br /&gt;
* GetWidth() - Get width of terrain.&lt;br /&gt;
* GetHeight() - Get height of terrain.&lt;br /&gt;
* IsWireFrame() - Determine if terrain is being rendered as a wireframe.&lt;br /&gt;
* SetWireFrame() - Set whether terrain should be rendered as a wireframe (True) or with texturing (False).&lt;br /&gt;
* GetElevation() - Get elevation at specified grid point.&lt;br /&gt;
* GetExaggeratedElevation() - Get exaggerated elevation at specified grid point.&lt;br /&gt;
* GetElevationMap() - Flag indicating if terrain contains elevation information.&lt;br /&gt;
* GetMinElevation() - Get minimum elevation.&lt;br /&gt;
* GetMaxElevation() - Get maximum elevation.&lt;br /&gt;
* ProjectToTerrain() - Project screen coodinates onto terrain. &lt;br /&gt;
* ProjectToScreen() - Project 3D world coordinates to screen coordinates.&lt;br /&gt;
* GeoToGrid() - Convert geographic coordinates to grid coordinates.&lt;br /&gt;
* LatLongToGrid() - Convert lat/long coordinates to grid coordinates.&lt;br /&gt;
* GridToGeo() - Convert grid coordinates to geographic coordinates.&lt;br /&gt;
&lt;br /&gt;
= Layer Tree Controller class =&lt;br /&gt;
&lt;br /&gt;
* GetName() - Get name of specified layer.&lt;br /&gt;
* GetDescription() - Get description of specified layer.&lt;br /&gt;
* SetDescription() - Set description of specified layer.&lt;br /&gt;
* GetAuthours() - Get authours of specified layer.&lt;br /&gt;
* SetAuthours() - Set authours of specified layer.&lt;br /&gt;
* GetPath() - Get path to file of specified layer.&lt;br /&gt;
* GetFilename() - Get filename of specified layer.&lt;br /&gt;
* SetVisible() - Set visibility of specified layer.&lt;br /&gt;
* IsVisible() - Get visibility of specified layer.&lt;br /&gt;
* SetVisible() - Set visibility of specified layer.&lt;br /&gt;
* GetNumStudyLayers() - Get number of study layers.&lt;br /&gt;
* GetStudyLayer() - Get specified study layer.&lt;br /&gt;
* GetNumMapLayers() - Get number of map layers.&lt;br /&gt;
* GetMapLayer() - Get specified map layer.&lt;br /&gt;
* GetNumLocationSetLayers() - Get number of location set layers.&lt;br /&gt;
* GetLocationSetLayer() - Get specified location set layer.&lt;br /&gt;
* GetNumLocationLayers() - Get number of location layers.&lt;br /&gt;
* GetLocationLayer() - Get specified location layer.&lt;br /&gt;
* GetLocationLayers() - Get all location layers.&lt;br /&gt;
* GetNumSequenceLayers() - Get number of sequence layers.&lt;br /&gt;
* GetSequenceLayer() - Get specified sequence layer.&lt;br /&gt;
* GetSequenceLayers() - Get all sequence layers.&lt;br /&gt;
* GetNumTreeLayers() - Get number of tree layers.&lt;br /&gt;
* GetTreeLayer() - Get specified tree layer.&lt;br /&gt;
&lt;br /&gt;
= Viewport class =&lt;br /&gt;
&lt;br /&gt;
* Refresh() - Regenerate all graphical elements within the viewport.&lt;br /&gt;
* SaveImage() - Save image of viewport.&lt;br /&gt;
* GetWidth() - Width of viewport.&lt;br /&gt;
* GetHeight() - Height of viewport.&lt;br /&gt;
* SetBackgroundColour() - Set background colour of viewport.&lt;br /&gt;
* GetBackgroundColour() - Get background colour of viewport.&lt;br /&gt;
* GetLighting() - Get object controlling lighting in viewport.&lt;br /&gt;
&lt;br /&gt;
= Lighting class =&lt;br /&gt;
&lt;br /&gt;
* GetAltitude() - Get altitude (y-position) of light.&lt;br /&gt;
* SetAltitude() - Set altitude (y-position) of light.&lt;br /&gt;
* SetGlobalAmbient() - Set strength of global ambient light.&lt;br /&gt;
* GetGlobalAmbient() - Get strength of global ambient light.&lt;br /&gt;
* GetPositionX() - Get x-position of light.&lt;br /&gt;
* SetPositionX() - Set x-position of light.&lt;br /&gt;
* GetPositionY() - Get y-position of light.&lt;br /&gt;
* SetPositionY() - Set y-position of light.&lt;br /&gt;
* GetPositionZ() - Get z-position of light.&lt;br /&gt;
* SetPositionZ() - Set z-position of light.&lt;br /&gt;
&lt;br /&gt;
= GeoTreeView class =&lt;br /&gt;
&lt;br /&gt;
* ProjectTree() - Project tree to specified leaf nodes.&lt;br /&gt;
* RestoreTree() - Restore original tree.&lt;br /&gt;
* SetLayout() - Set layout of geophylogeny.&lt;br /&gt;
* GetLayout() - Get layout of geophylogeny.&lt;br /&gt;
* GetLayoutLineVisibility() - Get visibility of geographic layout line.&lt;br /&gt;
* SetLayoutLineVisibility() - Set visibility of geographic layout line.&lt;br /&gt;
* GetLayoutLine() - Get geographic layout line.&lt;br /&gt;
* SetLayoutLine() - Set geographic layout line.&lt;br /&gt;
* IsLayoutLine() - Check if a layout line has been assigned to the tree.&lt;br /&gt;
* IsGeographicAxis() - Check if a non-linear geographic axis has been assigned to the tree.&lt;br /&gt;
* GetGeographicAxisVisibility() - Get visibility of non-linear geographic axis.&lt;br /&gt;
* SetGeographicAxisVisibility() - Set visibility of non-linear geographic axis.&lt;br /&gt;
* GetLeafNodeSize() - Get size of leaf nodes.&lt;br /&gt;
* SetLeafNodeSize() - Set size of leaf nodes.&lt;br /&gt;
* GetInternalNodeSize() - Get size of internal nodes.&lt;br /&gt;
* SetInternalNodeSize() - Set size of internal nodes.&lt;br /&gt;
* GetLineThickness() - Get thickness of tree branches.&lt;br /&gt;
* SetLineThickness() - Set thickness of tree branches.&lt;br /&gt;
* GetOrientation() - Get orientation of tree.&lt;br /&gt;
* SetOrientation() - Set orientation of tree.&lt;br /&gt;
* GetHeight() - Get height of tree.&lt;br /&gt;
* SetHeight() - Set height of tree.&lt;br /&gt;
* GetColour() - Get default colour for tree.&lt;br /&gt;
* SetColour() - Set default colour for tree.&lt;br /&gt;
* GetOptimizeTopology() - Check if optimal tree layout is being calcualte.&lt;br /&gt;
* SetOptimizeTopology() - Set flag indicating if optimal tree layout should be calculate.&lt;br /&gt;
* GetLabelVisibility() - Get visibility of leaf labels.&lt;br /&gt;
* SetLabelVisibility() - Set visibility of leaf labels.&lt;br /&gt;
* GetFontSize() - Get font size for leaf labels.&lt;br /&gt;
* SetFontSize() - Set font size for leaf labels.&lt;br /&gt;
* GetFontColour() - Get font colour for leaf labels.&lt;br /&gt;
* SetFontColour() - Set font colour for leaf labels.&lt;br /&gt;
* Set3dInternalDropLineStyle() - Set internal drop line style for 3D tree.&lt;br /&gt;
* Get3dInternalDropLineStyle() - Get internal drop line style for 3D tree.&lt;br /&gt;
* Set3dLeafDropLineStyle() - Set leaf drop line style for 3D trees.&lt;br /&gt;
* Get3dLeafDropLineStyle() - Get leaf drop line style for 3D tree.&lt;br /&gt;
* SetGeographyLineOffsetPercentage() - Set offset of geography line (in percentage of layout line length).&lt;br /&gt;
* GetGeographyLineOffsetPercentage() - Get offset of geography line (in percentage of layout line length).&lt;br /&gt;
* GetGeographyLineOffset() - Get offset of geography line (in world coordinates).&lt;br /&gt;
* SetSpreadGeographyPts() - Set flag indicating if locations should be spread out evenly along the geography line.&lt;br /&gt;
* SetLeafNodeBorderSize() - Set border size for leaf nodes.&lt;br /&gt;
* GetLeafNodeBorderSize() - Get border size for leaf nodes.&lt;br /&gt;
* SetInternalNodeBorderSize() - Set border size for internal nodes.&lt;br /&gt;
* GetInternalNodeBorderSize() - Get border size for internal nodes.&lt;br /&gt;
* SetGeoPtsBorderSize() - Set border size for geographic points along geography line.&lt;br /&gt;
* GetGeoPtsBorderSize() - Get border size for geographic points along geography line.&lt;br /&gt;
* SetBranchBorderSize() - Set border size for tree branches.&lt;br /&gt;
* GetBranchBorderSize() - Get border size for tree branches.&lt;br /&gt;
* SetLocationLineBorderSize() - Set border size for location lines.&lt;br /&gt;
* GetLocationLineBorderSize() - Get border size for location lines.&lt;br /&gt;
* SetCorrelationLineBorderSize() - Set border size for correlation lines.&lt;br /&gt;
* GetCorrelationLineBorderSize() - Get border size for correlation lines.&lt;br /&gt;
* SetLeafNodeBorderColour() - Set colour of leaf node borders.&lt;br /&gt;
* GetLeafNodeBorderColour() - Get colour of leaf node borders.&lt;br /&gt;
* SetInternalNodeBorderColour() - Set colour of internal node borders.&lt;br /&gt;
* GetInternalNodeBorderColour() - Get colour of internal node borders.&lt;br /&gt;
* SetGeoPtsBorderColour() - Set colour of geographic point borders.&lt;br /&gt;
* GetGeoPtsBorderColour() - Get colour og geographic point borders.&lt;br /&gt;
* SetLocationLineBorderColour() - Set colour of location line borders.&lt;br /&gt;
* GetLocationLineBorderColour() - Get colour of location line borders.&lt;br /&gt;
* SetCorrelationLineBorderColour() - Set colour of correlation line borders.&lt;br /&gt;
* GetCorrelationLineBorderColour() - Get colour of correlation line borders.&lt;br /&gt;
* SetBranchBorderColour() - Set colour of branch borders.&lt;br /&gt;
* GetBranchBorderColour() - Get colour of branch borders.&lt;br /&gt;
* SetTreeColourStyle() - Set colouring method for tree.&lt;br /&gt;
* GetTreeColourStyle() - Get colouring method for tree.&lt;br /&gt;
* SetReverseOrderGeographicPts() - Set whether geographic points should be reversed.&lt;br /&gt;
* GetReverseOrderGeographicPts() - Check if geographic points are being reversed.&lt;br /&gt;
* GetNumberOfNodes() - Get total number of nodes.&lt;br /&gt;
* GetNumberOfLeaves() - Get number of leaf nodes.&lt;br /&gt;
* GetDepthOfTree() - Get maximum depth of tree.&lt;br /&gt;
* IsMultifurcating() - Check if tree is multifurcating.&lt;br /&gt;
* GetLeafNames() - Get names of leaves.&lt;br /&gt;
* SignificanceTest() - Perform Monte Carlo significance test.&lt;br /&gt;
* GetNewickString() - Get Newick representation of tree.&lt;br /&gt;
* PerformLinearAxesAnalysisOnRootNode() - Calculate goodness-of-fit for all linear axes.&lt;br /&gt;
* SetGeographicAxisAngleOnRoot() - Set geographic layout line to the specified angle.&lt;br /&gt;
&lt;br /&gt;
= Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetId() - Get id of layer&lt;br /&gt;
* GetName() - Get name of layer.&lt;br /&gt;
* SetName() - Set name of layer.&lt;br /&gt;
* GetDescription() - Get description of layer.&lt;br /&gt;
* SetDescription() - Set description of layer.&lt;br /&gt;
* GetAuthours() - Get authours of layer.&lt;br /&gt;
* SetAuthours() - Set authours of layer.&lt;br /&gt;
* GetPath() - Get path to layer file.&lt;br /&gt;
* GetFilename() - Get filename of layer.&lt;br /&gt;
* GetType() - Get type of layer.&lt;br /&gt;
&lt;br /&gt;
= Study Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetNumMapLayers() - Get number of map layers in this study.&lt;br /&gt;
* GetMapLayer() - Get specified map layer.&lt;br /&gt;
* GetAllMapLayers() - Get all maps in study.&lt;br /&gt;
* GetController() - Get study controller.&lt;br /&gt;
&lt;br /&gt;
= Study Controller class =&lt;br /&gt;
&lt;br /&gt;
* GetDatum() - Get datum used by study.&lt;br /&gt;
* SetDatum() - Set datum used by study (must be set before map is loaded).&lt;br /&gt;
* GetProjection() - Get projection used by study.&lt;br /&gt;
* SetProjection() - Set projection used by study (must be set before map is loaded).&lt;br /&gt;
* IsGeographic() - Flag indicating if data is in geographic (i.e. lat/long) coordinates.&lt;br /&gt;
&lt;br /&gt;
= Map Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetNumLocationSetLayers() - Get number of location set layers for this map.&lt;br /&gt;
* GetLocationSetLayer() - Get specified location set layer.&lt;br /&gt;
* GetAllLocationSetLayers() - Get all location set layers.&lt;br /&gt;
* GetNumTreeLayers() - Get number of tree layers for this map.&lt;br /&gt;
* GetTreeLayer() - Get specified tree layer.&lt;br /&gt;
* GetAllTreeLayers() - Get all tree layers.&lt;br /&gt;
* GetController() - Get map controller.&lt;br /&gt;
&lt;br /&gt;
= Tree Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetGeoTreeView() - Get geophylogeny associated with this layer.&lt;br /&gt;
&lt;br /&gt;
= Location Set Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetNumLocationLayers() - Get number of location layers for this location set.&lt;br /&gt;
* GetLocationLayer() - Get specified location layer.&lt;br /&gt;
* GetAllLocationLayers() - Get all location layers.&lt;br /&gt;
* GetAllActiveLocationLayers() - Get all visible location layers.&lt;br /&gt;
* IsSequencesData() - Check if there is sequence data associated with at least one location.&lt;br /&gt;
* GetController() - Get location set controller.&lt;br /&gt;
* GetChartSet() - Get set of charts associated with this location set.&lt;br /&gt;
&lt;br /&gt;
= Location Set Controller class =&lt;br /&gt;
&lt;br /&gt;
* SetLocationVisibilities() - Propogate set visibility state to all locations.&lt;br /&gt;
* SetLocationColours() - Propogate set colour state to all locations.&lt;br /&gt;
* SetLocationBorders() - Propogate set border state to all locations.&lt;br /&gt;
* SetLocationSizes() - Propogate set size state to all locations.&lt;br /&gt;
* SetLocationShapes() - Propogate set shape state to all locations.&lt;br /&gt;
* SetLocationLabels() - Propogate specified label states to all locations.&lt;br /&gt;
* SetColourField() - Set field used to determine location colour.&lt;br /&gt;
* GetColourField() - Get field used to determine location colour.&lt;br /&gt;
* SetColourMap() - Set colour map associated with location set.&lt;br /&gt;
* GetColourMap() - Get colour map associated with location set.&lt;br /&gt;
* SetUniformColourFlag() - Set flag indicating if all locations should have the same colour.&lt;br /&gt;
* GetUniformColourFlag() - Get flag indicating if all locations should have the same colour.&lt;br /&gt;
* SetUniformColour() - Set uniform colour.&lt;br /&gt;
* GetUniformColour() - Get uniform colour.&lt;br /&gt;
* SetBorderSize() - Set border size.&lt;br /&gt;
* GetBorderSize() - Get border size..&lt;br /&gt;
* SetBorderColour() - Set border colour.&lt;br /&gt;
* GetBorderColour() - Get border colour.&lt;br /&gt;
* SetLocationSetVisibility() - Set visibility of location set.&lt;br /&gt;
* GetLocationSetVisibility() - Get visibility of location set.&lt;br /&gt;
* SetShapeField() - Set field used to determine location shape.&lt;br /&gt;
* GetShapeField() - Get field used to determine location shape.&lt;br /&gt;
* SetShapeMap() - Set shape map associated with location set.&lt;br /&gt;
* GetShapeMap() - Get shape map associated with location set.&lt;br /&gt;
* SetUniformShapeFlag() - Set flag indicating if all locations should have the same shape.&lt;br /&gt;
* GetUniformShapeFlag() - Get flag indicating if all locations should have the same shape.&lt;br /&gt;
* SetUniformShape() - Set uniform shape.&lt;br /&gt;
* GetUniformShape() - Get uniform shape.&lt;br /&gt;
* SetSizeField() - Set field used to determine location size.&lt;br /&gt;
* GetSizeField() - Get field used to determine location size.&lt;br /&gt;
* SetMinLocationSize() - Set min location size.&lt;br /&gt;
* GetMinLocationSize() - Get min location size.&lt;br /&gt;
* SetMaxLocationSize() - Set max location size.&lt;br /&gt;
* GetMaxLocationSize() - Get max location size.&lt;br /&gt;
* SetLabelField() - Set field used to determine location label.&lt;br /&gt;
* GetLabelField() - Get field used to determine location label.&lt;br /&gt;
* SetLabelColour() - Set label colour.&lt;br /&gt;
* GetLabelColour() - Get label colour.&lt;br /&gt;
* SetLabelSize() - Set label size.&lt;br /&gt;
* GetLabelSize() - Get label size.&lt;br /&gt;
* SetLabelPosition() - Set label position.&lt;br /&gt;
* GetLabelPosition() - Get label position.&lt;br /&gt;
* SetLabelStyle() - Set label style.&lt;br /&gt;
* GetLabelStyle() - Get label style.&lt;br /&gt;
* SetLabelVisibility() - Set label visibility.&lt;br /&gt;
* GetLabelVisibility() - Get label visibility.&lt;br /&gt;
* SetLabelBindToChart() - Set flag indicating if label is bound to chart.&lt;br /&gt;
* GetLabelBindToChart() - Get flag indicating if label is bound to chart.&lt;br /&gt;
* GetMetadata() - Get location metadata for the specified field (list of strings).&lt;br /&gt;
* GetNumericMetadata() - Get location metadata for the specified field (list of floats).&lt;br /&gt;
* GetMetadataFields() - Get fields for location metadata.&lt;br /&gt;
* GetNumericMetadataFields() - Get numeric fields for location metadata.&lt;br /&gt;
* AddMetadata() - Add field to location metadata.&lt;br /&gt;
&lt;br /&gt;
= Location Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetNumSequenceLayers() - Get number of sequence layers for this location.&lt;br /&gt;
* GetSequenceLayer() - Get specified sequence layer.&lt;br /&gt;
* GetAllSequenceLayers() - Get all sequence layers.&lt;br /&gt;
* GetAllActiveSequenceLayers() - Get all active sequence layers.&lt;br /&gt;
* GetController() - Get location controller.&lt;br /&gt;
&lt;br /&gt;
= Location Controller class =&lt;br /&gt;
&lt;br /&gt;
* GetId() - Get id of location.&lt;br /&gt;
* GetNorthing() - Get north or latitudinal position of location.&lt;br /&gt;
* GetEasting() - Get east or longitudinal position of location.&lt;br /&gt;
* GetLatitude() - Get north or latitudinal position of location.&lt;br /&gt;
* GetLongitude() - Get east or longitudinal position of location.&lt;br /&gt;
* GetData() - Get metadata associated with location.&lt;br /&gt;
* GetProjection() - Get projected coordinates of location.&lt;br /&gt;
* GetPosition() - Get grid coordinates of location.&lt;br /&gt;
* SetColour() - Set colour of location marker.&lt;br /&gt;
* GetColour() - Get colour of location marker.&lt;br /&gt;
* SetSize() - Set size of location marker.&lt;br /&gt;
* GetSize() - Get size of location marker.&lt;br /&gt;
* SetShape() - Set shape of location marker.&lt;br /&gt;
* GetShape() - Get shape of location marker.&lt;br /&gt;
* SetBorderSize() - Set border size of location marker.&lt;br /&gt;
* GetBorderSize() - Get border size of location marker.&lt;br /&gt;
* SetActive() - Set active state of location marker.&lt;br /&gt;
* IsActive() - Check if location is active.&lt;br /&gt;
* SetRenderingOrder() - Set rendering order of location marker.&lt;br /&gt;
* GetRenderingOrder() - Get rendering order of location marker.&lt;br /&gt;
* AddData() - Add metadata to location.&lt;br /&gt;
&lt;br /&gt;
= Sequence Layer class =&lt;br /&gt;
&lt;br /&gt;
* GetController() - Get sequence controller.&lt;br /&gt;
&lt;br /&gt;
= Sequence Controller class =&lt;br /&gt;
&lt;br /&gt;
* GetSequenceId() - Get id of sequence.&lt;br /&gt;
* GetSiteId() - Get id of site where sequence was sampled.&lt;br /&gt;
* IsActive() - Check if sequence is active.&lt;br /&gt;
* SetActive() - Set active state of sequence.&lt;br /&gt;
* GetData() - Get metadata associated with sequence.&lt;br /&gt;
* GetMetadataFields() - Get metadata fields.&lt;br /&gt;
* GetNumericMetadataFields() - Get numeric fields for sequences.&lt;br /&gt;
&lt;br /&gt;
= Chart Set View class =&lt;br /&gt;
&lt;br /&gt;
* GetChart() - Get specified chart.&lt;br /&gt;
* SetLayoutLine() - Set layout line for chart set.&lt;br /&gt;
* IsLayoutLine() - Check if a layout line has been specified for the chart set.&lt;br /&gt;
* GetLayoutLineVisibility() - Get visibility of layout line.&lt;br /&gt;
* SetLayoutLineVisibility() - Set visibility of layout line.&lt;br /&gt;
* SetLayout() - Set layout style.&lt;br /&gt;
* GetLayout() - Get layout style.&lt;br /&gt;
* UpdateCharts() - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).&lt;br /&gt;
&lt;br /&gt;
= Chart View class =&lt;br /&gt;
&lt;br /&gt;
* GetVisibility() - Get visibility of chart.&lt;br /&gt;
* SetVisibility() - Set visibility of chart.&lt;br /&gt;
* GetDepth() - Get depth of chart (controls rendering order).&lt;br /&gt;
* SetDepth() - Set depth of chart (controls rendering order).&lt;br /&gt;
* GetWidth() - Get width or diameter of chart.&lt;br /&gt;
* SetWidth() - Set width or diameter of chart.&lt;br /&gt;
* GetHeight() - Get height of chart.&lt;br /&gt;
* SetHeight() - Set height of chart.&lt;br /&gt;
* GetBorderSize() - Get border size of chart.&lt;br /&gt;
* SetBorderSize() - Set border size of chart.&lt;br /&gt;
* GetWedgeBorders() - Get wedge border size.&lt;br /&gt;
* SetWedgeBorders() - Set wedge border size.&lt;br /&gt;
* GetSizeProportionalToSeq() - Get flag indicating if chart size should be proportional to sequence count.&lt;br /&gt;
* SetSizeProportionalToSeq() - Set flag indicating if chart size should be proportional to sequence count.&lt;br /&gt;
* GetMinSize() - Get minimum allowed size of chart.&lt;br /&gt;
* SetMinSize() - Set minimum allowed size of chart.&lt;br /&gt;
* GetMaxSize() - Get maximum allowed size of chart.&lt;br /&gt;
* SetMaxSize() - Set maximum allowed size of chart.&lt;br /&gt;
* GetAdjustedSize() - Get adjusted chart size based on number of sequences.&lt;br /&gt;
* SetNormalizedNumSeq() - Set normalized number of sequences for this chart.&lt;br /&gt;
* SetField() - Set field used to create chart.&lt;br /&gt;
* GetField() - Get field used to create chart.&lt;br /&gt;
* GetNames() - Get name of all category.&lt;br /&gt;
* GetPercentage() - Get percentage of sequences assigned to the specified category.&lt;br /&gt;
* SetChartType() - Set type of chart to generate.&lt;br /&gt;
* GetChartType() - Get type of chart to generate.&lt;br /&gt;
* SetAssignToOther() - Set proportion for which a category will be assigned to the &amp;#039;Other&amp;#039; category.&lt;br /&gt;
* GetAssignToOther() - Get proportion for which a category will be assigned to the &amp;#039;Other&amp;#039; category.&lt;br /&gt;
* SetCentre() - Set centre of chart.&lt;br /&gt;
* GetCentre() - Get centre of chart.&lt;br /&gt;
* GetLocationPos() - Get position of associated location.&lt;br /&gt;
* SetScreenPos() - Set position of chart in screen coordinates.&lt;br /&gt;
* GetScreenPos() - Get position of chart in screen coordinates.&lt;br /&gt;
* SetLabelBindToChart() - Set flag indicating if labels should be bound to charts.&lt;br /&gt;
* GetLabelBindToChart() - Get flag indicating if labels should be bound to charts.&lt;br /&gt;
* SetLabel() - Set chart label.&lt;br /&gt;
* GetLabel() - Get chart label.&lt;br /&gt;
* UpdateChart() - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).&lt;br /&gt;
&lt;br /&gt;
= Visual Label class =&lt;br /&gt;
&lt;br /&gt;
* GetText() - Get text of label.&lt;br /&gt;
* GetColour() - Get colour of label font.&lt;br /&gt;
* GetSize() - Get size of label font.&lt;br /&gt;
* GetVisibility() - Get visibility of label.&lt;br /&gt;
* GetGridPosition() - Get grid coordinates of label.&lt;br /&gt;
* GetScreenPosition() - Get screen coordinates of label.&lt;br /&gt;
* GetRotateLabel() - Get flag indicating if text should be rotated onto the plane.&lt;br /&gt;
* GetRotateZ() - Get flag indicating if text should rotate to remain horizontal.&lt;br /&gt;
* GetRenderingStyle() - Get rendering style of label.&lt;br /&gt;
* SetText() - Set text of label.&lt;br /&gt;
* SetColour() - Set colour of label font.&lt;br /&gt;
* SetSize() - Set size of label font.&lt;br /&gt;
* SetVisibility() - Set visibility of label.&lt;br /&gt;
* SetGridPosition() - Set grid position of label.&lt;br /&gt;
* SetScreenPosition() - Set screen position of label.&lt;br /&gt;
* SetRenderingStyle() - Set rendering style of label.&lt;br /&gt;
&lt;br /&gt;
= Visual Marker class =&lt;br /&gt;
&lt;br /&gt;
* GetPosition() - Get position of marker.&lt;br /&gt;
* GetShape() - Get shape of marker.&lt;br /&gt;
* GetRotation() - Get rotation of marker.&lt;br /&gt;
* GetDepth() - Get depth of marker.&lt;br /&gt;
* GetRenderingStyle() - Get rendering style of marker.&lt;br /&gt;
* GetColour() - Get colour of marker.&lt;br /&gt;
* GetSize() - Get size of marker.&lt;br /&gt;
* GetVisibility() - Get visibility of marker.&lt;br /&gt;
* GetRenderingOrder() - Get rendering order of marker.&lt;br /&gt;
* GetBorderSize() - Get border size of marker.&lt;br /&gt;
* SetPosition() - Set position of marker.&lt;br /&gt;
* SetShape() - Set shape of marker.&lt;br /&gt;
* SetRotation() - Set rotation of marker.&lt;br /&gt;
* SetDepth() - Set depth of marker.&lt;br /&gt;
* SetRenderingStyle() - Set rendering style of marker.&lt;br /&gt;
* SetColour() - Set colour of marker.&lt;br /&gt;
* SetSize() - Set size of marker.&lt;br /&gt;
* SetVisibility() - Set visibility of marker.&lt;br /&gt;
* SetRenderingOrder() - Set rendering order of marker.&lt;br /&gt;
* SetBorderSize() - Set border size of marker.&lt;br /&gt;
&lt;br /&gt;
= Visual Line class =&lt;br /&gt;
&lt;br /&gt;
* GetColour() - Get colour of line.&lt;br /&gt;
* GetThickness() - Get thickness of line.&lt;br /&gt;
* GetVisibility() - Get visibility of line.&lt;br /&gt;
* GetLineStyle() - Get style of line.&lt;br /&gt;
* GetStartPt() - Get start point of line.&lt;br /&gt;
* GetEndPt() - Get end point of line.&lt;br /&gt;
* SetColour() - Set colour of line.&lt;br /&gt;
* SetThickness() - Set thickness of line.&lt;br /&gt;
* SetVisibility() - Set visibility of line.&lt;br /&gt;
* SetLineStyle() - Set style of line.&lt;br /&gt;
* SetStartPt() - Set start point of line.&lt;br /&gt;
* SetEndPt() - Set end point of line.&lt;br /&gt;
* GetLine() - Get line.&lt;br /&gt;
* SetLine() - Set line.&lt;br /&gt;
* GetDepth() - Get depth of line (determines rendering order).&lt;br /&gt;
* SetDepth() - Set depth of line (determines rendering order).&lt;br /&gt;
&lt;br /&gt;
= Colour class =&lt;br /&gt;
&lt;br /&gt;
* GetRed() - Get red channel.&lt;br /&gt;
* SetRed() - Set red channel.&lt;br /&gt;
* GetGreen() - Get green channel.&lt;br /&gt;
* SetGreen() - Set green channel.&lt;br /&gt;
* GetBlue() - Get blue channel.&lt;br /&gt;
* SetBlue() - Set blue channel.&lt;br /&gt;
* GetAlpha() - Get alpha channel.&lt;br /&gt;
* SetAlpha() - Set alpha channel.&lt;br /&gt;
* SetRGBA() - Set new colour.&lt;br /&gt;
&lt;br /&gt;
= Colour Map Base class =&lt;br /&gt;
&lt;br /&gt;
* GetColour() - Get colour at specified index.&lt;br /&gt;
* GetInterpolatedColour() - Interpolate colour from colour map.&lt;br /&gt;
* GetName() - Get name of colour map.&lt;br /&gt;
* GetExtendedName() - Get name of colour map with either &amp;#039;Continuous:&amp;#039; or &amp;#039;Discrete:&amp;#039; prefixed to it.&lt;br /&gt;
* GetSize() - Get size of colour map.&lt;br /&gt;
* GetType() - Get type of colour map.&lt;br /&gt;
&lt;br /&gt;
= Discrete Colour Map class =&lt;br /&gt;
&lt;br /&gt;
* GetColourMap() - Get colour map with the provided name.&lt;br /&gt;
* GetColourMapNames() - Get name of all colour maps.&lt;br /&gt;
* GetColourMapDiscreteNames() - Get name of all discrete colour maps.&lt;br /&gt;
* GetColourMapContinuousNames() - Get name of all continuous colour maps.&lt;br /&gt;
&lt;br /&gt;
= Point3D class =&lt;br /&gt;
&lt;br /&gt;
* Length() - Distance from origin to point.&lt;br /&gt;
* SquaredLength() - Squared distance from origin to point.&lt;br /&gt;
* Offset() - Create new point offset by the specified amount.&lt;br /&gt;
* Normalize() - Normalize point (vector) to unit length.&lt;br /&gt;
* Cross() - Calculate cross product between two points (vectors).&lt;br /&gt;
* Dot() - Calculate dot product between two points (vectors).&lt;br /&gt;
* Angle() - Calculate angle between two points (vectors).&lt;br /&gt;
* x - Get x position of point.&lt;br /&gt;
* y - Get y position of point.&lt;br /&gt;
* z - Get z position of point.&lt;br /&gt;
&lt;br /&gt;
= GeoCoord class =&lt;br /&gt;
&lt;br /&gt;
* easting - Get easting or longitudinal position of location.&lt;br /&gt;
* northing - Get northing or latitudinal position of location.&lt;br /&gt;
* longitude - Get easting or longitudinal position of location.&lt;br /&gt;
* latitude - Get northing or latitudinal position of location.&lt;br /&gt;
&lt;br /&gt;
= Line3D class =&lt;br /&gt;
&lt;br /&gt;
* Offset() - New line offset by the specified amount.&lt;br /&gt;
* start - Start point of line.&lt;br /&gt;
* end - End point of line.&lt;br /&gt;
* startId - General purpose label associated with start point.&lt;br /&gt;
* endId - General purpose label associated with end point.&lt;br /&gt;
&lt;br /&gt;
= Box2D class =&lt;br /&gt;
&lt;br /&gt;
* x1 - Lower, left x-coordinate of box.&lt;br /&gt;
* y1 - Lower, left y-coordinate of box.&lt;br /&gt;
* dx - Width of bounding box.&lt;br /&gt;
* dy - Height of bounding box.&lt;br /&gt;
&lt;br /&gt;
= Linear Results class =&lt;br /&gt;
&lt;br /&gt;
* angle() - Angle of geographic layout line in degrees.&lt;br /&gt;
* numCrossings() - Number of crossings which occurs for this layout lines.&lt;/div&gt;</summary>
		<author><name>Timothy</name></author>
		
	</entry>
</feed>