GenGIS API 2.0.2

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
• camera - provides access to the Camera class
• mainWindow - provides access to the Main Window class
• graphics - provides access to the Graphics class
• colourMapManager - provides access to the Colour Map Manager class

Global functions

• SafeYield() - Yields control to pending messages in the windowing system.

Main Window class

• GetPointer() - Get pointer to GenGIS window.
• SetSidePanelVisibility() - Set visibility of side panel.
• SetConsoleVisibility() - Set visibility of console.
• OpenMapFile() - Open map file.
• OpenLocationsFile() - Open location file.
• OpenSequenceFile() - Open sequence file.
• OpenTreeFile() - Open tree file.
• GetExeDir() - Get directory of GenGIS executable.
• Quit() - Exit GenGIS.
• Write() - Write text to the GenGIS console and the log file.
• Warning() - Write warning message to the GenGIS console and the log file.
• Error() - Write error message to the GenGIS console and the log file.
• Yield() - Yield control to main window for event processing.

Graphics class

• AddLine() - Add line to viewport.
• RemoveLine() - Remove line with a given id.
• ClearLines() - Clear all custom lines in viewport.
• AddMarker() - Add marker to Viewport.
• RemoveMarker() - Remove marker with a given id.
• ClearMarkers() - Clear all custom markers in viewport.
• AddCylinder() - Add cylinder to viewport.
• RemoveCylinder() - Remove cylinder with a given id.
• ClearCylinders() - Clear all custom cylinders in viewport.
• AddLabel() - Add label to viewport.
• RemoveLabel() - Remove label with a given id.
• ClearLabels() - Clear all custom labels in Viewport.

Camera class

• SetPosition() - Set position of camera.
• GetPosition() - Get current position of camera.
• SetHeight() - Set height of camera above terrain.
• GetHeight() - Get height of camera above terrain.
• SetPitch() - Set pitch of camera.
• GetPitch() - Get pitch of camera.
• SetYaw() - Set yaw of camera.
• GetYaw() - Get yaw of camera.
• ZoomDelta() - Change zoom (height) of camera by specified percentage.
• TranslateDelta() - Translate position of camera by specified amount.
• PitchDelta() - Change pitch of camera by specified amount.
• YawDelta() - Change yaw of camera by specified amount.
• ResetView() - Set camera to default position.
• TopView() - Set camera to provide a top 'orthographic' view of the terrain
• GetMapExtentsZoom() - Get zoom (height) of camera required to view entire map.
• GetWindowHeight() - Get height of the viewport.
• GetWindowWidth() - Get width of the viewport.

Map Controller class

• GetProjectionExtents() - Get lower, left and upper, right corners of map after projection.
• GetWidth() - Get width of terrain.
• GetHeight() - Get height of terrain.
• IsWireFrame() - Determine if terrain is being rendered as a wireframe.
• SetWireFrame() - Set whether terrain should be rendered as a wireframe (True) or with texturing (False).
• GetElevation() - Get elevation at specified grid point.
• GetExaggeratedElevation() - Get exaggerated elevation at specified grid point.
• GetElevationMap() - Flag indicating if terrain contains elevation information.
• GetMinElevation() - Get minimum elevation.
• GetMaxElevation() - Get maximum elevation.
• ProjectToTerrain() - Project screen coodinates onto terrain.
• ProjectToScreen() - Project 3D world coordinates to screen coordinates.
• GeoToGrid() - Convert geographic coordinates to grid coordinates.
• LatLongToGrid() - Convert lat/long coordinates to grid coordinates.
• GridToGeo() - Convert grid coordinates to geographic coordinates.

Layer Tree Controller class

• GetName() - Get name of specified layer.
• GetDescription() - Get description of specified layer.
• SetDescription() - Set description of specified layer.
• GetAuthours() - Get authours of specified layer.
• SetAuthours() - Set authours of specified layer.
• GetPath() - Get path to file of specified layer.
• GetFilename() - Get filename of specified layer.
• SetVisible() - Set visibility of specified layer.
• IsVisible() - Get visibility of specified layer.
• SetVisible() - Set visibility of specified layer.
• GetNumStudyLayers() - Get number of study layers.
• GetStudyLayer() - Get specified study layer.
• GetNumMapLayers() - Get number of map layers.
• GetMapLayer() - Get specified map layer.
• GetNumLocationSetLayers() - Get number of location set layers.
• GetLocationSetLayer() - Get specified location set layer.
• GetNumLocationLayers() - Get number of location layers.
• GetLocationLayer() - Get specified location layer.
• GetLocationLayers() - Get all location layers.
• GetNumSequenceLayers() - Get number of sequence layers.
• GetSequenceLayer() - Get specified sequence layer.
• GetSequenceLayers() - Get all sequence layers.
• GetNumTreeLayers() - Get number of tree layers.
• GetTreeLayer() - Get specified tree layer.

Viewport class

• Refresh() - Regenerate all graphical elements within the viewport.
• SaveImage() - Save image of viewport.
• GetWidth() - Width of viewport.
• GetHeight() - Height of viewport.
• SetBackgroundColour() - Set background colour of viewport.
• GetBackgroundColour() - Get background colour of viewport.
• GetLighting() - Get object controlling lighting in viewport.

Lighting class

• GetAltitude() - Get altitude (y-position) of light.
• SetAltitude() - Set altitude (y-position) of light.
• SetGlobalAmbient() - Set strength of global ambient light.
• GetGlobalAmbient() - Get strength of global ambient light.
• GetPositionX() - Get x-position of light.
• SetPositionX() - Set x-position of light.
• GetPositionY() - Get y-position of light.
• SetPositionY() - Set y-position of light.
• GetPositionZ() - Get z-position of light.
• SetPositionZ() - Set z-position of light.

GeoTreeView class

• ProjectTree() - Project tree to specified leaf nodes.
• RestoreTree() - Restore original tree.
• SetLayout() - Set layout of geophylogeny.
• GetLayout() - Get layout of geophylogeny.
• GetLayoutLineVisibility() - Get visibility of geographic layout line.
• SetLayoutLineVisibility() - Set visibility of geographic layout line.
• GetLayoutLine() - Get geographic layout line.
• SetLayoutLine() - Set geographic layout line.
• IsLayoutLine() - Check if a layout line has been assigned to the tree.
• IsGeographicAxis() - Check if a non-linear geographic axis has been assigned to the tree.
• GetGeographicAxisVisibility() - Get visibility of non-linear geographic axis.
• SetGeographicAxisVisibility() - Set visibility of non-linear geographic axis.
• GetLeafNodeSize() - Get size of leaf nodes.
• SetLeafNodeSize() - Set size of leaf nodes.
• GetInternalNodeSize() - Get size of internal nodes.
• SetInternalNodeSize() - Set size of internal nodes.
• GetLineThickness() - Get thickness of tree branches.
• SetLineThickness() - Set thickness of tree branches.
• GetOrientation() - Get orientation of tree.
• SetOrientation() - Set orientation of tree.
• GetHeight() - Get height of tree.
• SetHeight() - Set height of tree.
• GetColour() - Get default colour for tree.
• SetColour() - Set default colour for tree.
• GetOptimizeTopology() - Check if optimal tree layout is being calcualte.
• SetOptimizeTopology() - Set flag indicating if optimal tree layout should be calculate.
• GetLabelVisibility() - Get visibility of leaf labels.
• SetLabelVisibility() - Set visibility of leaf labels.
• GetFontSize() - Get font size for leaf labels.
• SetFontSize() - Set font size for leaf labels.
• GetFontColour() - Get font colour for leaf labels.
• SetFontColour() - Set font colour for leaf labels.
• Set3dInternalDropLineStyle() - Set internal drop line style for 3D tree.
• Get3dInternalDropLineStyle() - Get internal drop line style for 3D tree.
• Set3dLeafDropLineStyle() - Set leaf drop line style for 3D trees.
• Get3dLeafDropLineStyle() - Get leaf drop line style for 3D tree.
• SetGeographyLineOffsetPercentage() - Set offset of geography line (in percentage of layout line length).
• GetGeographyLineOffsetPercentage() - Get offset of geography line (in percentage of layout line length).
• GetGeographyLineOffset() - Get offset of geography line (in world coordinates).
• SetSpreadGeographyPts() - Set flag indicating if locations should be spread out evenly along the geography line.
• SetLeafNodeBorderSize() - Set border size for leaf nodes.
• GetLeafNodeBorderSize() - Get border size for leaf nodes.
• SetInternalNodeBorderSize() - Set border size for internal nodes.
• GetInternalNodeBorderSize() - Get border size for internal nodes.
• SetGeoPtsBorderSize() - Set border size for geographic points along geography line.
• GetGeoPtsBorderSize() - Get border size for geographic points along geography line.
• SetBranchBorderSize() - Set border size for tree branches.
• GetBranchBorderSize() - Get border size for tree branches.
• SetLocationLineBorderSize() - Set border size for location lines.
• GetLocationLineBorderSize() - Get border size for location lines.
• SetCorrelationLineBorderSize() - Set border size for correlation lines.
• GetCorrelationLineBorderSize() - Get border size for correlation lines.
• SetLeafNodeBorderColour() - Set colour of leaf node borders.
• GetLeafNodeBorderColour() - Get colour of leaf node borders.
• SetInternalNodeBorderColour() - Set colour of internal node borders.
• GetInternalNodeBorderColour() - Get colour of internal node borders.
• SetGeoPtsBorderColour() - Set colour of geographic point borders.
• GetGeoPtsBorderColour() - Get colour og geographic point borders.
• SetLocationLineBorderColour() - Set colour of location line borders.
• GetLocationLineBorderColour() - Get colour of location line borders.
• SetCorrelationLineBorderColour() - Set colour of correlation line borders.
• GetCorrelationLineBorderColour() - Get colour of correlation line borders.
• SetBranchBorderColour() - Set colour of branch borders.
• GetBranchBorderColour() - Get colour of branch borders.
• SetTreeColourStyle() - Set colouring method for tree.
• GetTreeColourStyle() - Get colouring method for tree.
• SetReverseOrderGeographicPts() - Set whether geographic points should be reversed.
• GetReverseOrderGeographicPts() - Check if geographic points are being reversed.
• GetNumberOfNodes() - Get total number of nodes.
• GetNumberOfLeaves() - Get number of leaf nodes.
• GetDepthOfTree() - Get maximum depth of tree.
• IsMultifurcating() - Check if tree is multifurcating.
• GetLeafNames() - Get names of leaves.
• SignificanceTest() - Perform Monte Carlo significance test.
• GetNewickString() - Get Newick representation of tree.
• PerformLinearAxesAnalysisOnRootNode() - Calculate goodness-of-fit for all linear axes.
• SetGeographicAxisAngleOnRoot() - Set geographic layout line to the specified angle.

Layer class

• GetId() - Get id of layer
• GetName() - Get name of layer.
• SetName() - Set name of layer.
• GetDescription() - Get description of layer.
• SetDescription() - Set description of layer.
• GetAuthours() - Get authours of layer.
• SetAuthours() - Set authours of layer.
• GetPath() - Get path to layer file.
• GetFilename() - Get filename of layer.
• GetType() - Get type of layer.

Study Layer class

• GetNumMapLayers() - Get number of map layers in this study.
• GetMapLayer() - Get specified map layer.
• GetAllMapLayers() - Get all maps in study.
• GetController() - Get study controller.

Study Controller class

• GetDatum() - Get datum used by study.
• SetDatum() - Set datum used by study (must be set before map is loaded).
• GetProjection() - Get projection used by study.
• SetProjection() - Set projection used by study (must be set before map is loaded).
• IsGeographic() - Flag indicating if data is in geographic (i.e. lat/long) coordinates.

Map Layer class

• GetNumLocationSetLayers() - Get number of location set layers for this map.
• GetLocationSetLayer() - Get specified location set layer.
• GetAllLocationSetLayers() - Get all location set layers.
• GetNumTreeLayers() - Get number of tree layers for this map.
• GetTreeLayer() - Get specified tree layer.
• GetAllTreeLayers() - Get all tree layers.
• GetController() - Get map controller.

Tree Layer class

• GetGeoTreeView() - Get geophylogeny associated with this layer.

Location Set Layer class

• GetNumLocationLayers() - Get number of location layers for this location set.
• GetLocationLayer() - Get specified location layer.
• GetAllLocationLayers() - Get all location layers.
• GetAllActiveLocationLayers() - Get all visible location layers.
• IsSequencesData() - Check if there is sequence data associated with at least one location.
• GetController() - Get location set controller.
• GetChartSet() - Get set of charts associated with this location set.

Location Set Controller class

• SetLocationVisibilities() - Propogate set visibility state to all locations.
• SetLocationColours() - Propogate set colour state to all locations.
• SetLocationBorders() - Propogate set border state to all locations.
• SetLocationSizes() - Propogate set size state to all locations.
• SetLocationShapes() - Propogate set shape state to all locations.
• SetLocationLabels() - Propogate specified label states to all locations.
• SetColourField() - Set field used to determine location colour.
• GetColourField() - Get field used to determine location colour.
• SetColourMap() - Set colour map associated with location set.
• GetColourMap() - Get colour map associated with location set.
• SetUniformColourFlag() - Set flag indicating if all locations should have the same colour.
• GetUniformColourFlag() - Get flag indicating if all locations should have the same colour.
• SetUniformColour() - Set uniform colour.
• GetUniformColour() - Get uniform colour.
• SetBorderSize() - Set border size.
• GetBorderSize() - Get border size..
• SetBorderColour() - Set border colour.
• GetBorderColour() - Get border colour.
• SetLocationSetVisibility() - Set visibility of location set.
• GetLocationSetVisibility() - Get visibility of location set.
• SetShapeField() - Set field used to determine location shape.
• GetShapeField() - Get field used to determine location shape.
• SetShapeMap() - Set shape map associated with location set.
• GetShapeMap() - Get shape map associated with location set.
• SetUniformShapeFlag() - Set flag indicating if all locations should have the same shape.
• GetUniformShapeFlag() - Get flag indicating if all locations should have the same shape.
• SetUniformShape() - Set uniform shape.
• GetUniformShape() - Get uniform shape.
• SetSizeField() - Set field used to determine location size.
• GetSizeField() - Get field used to determine location size.
• SetMinLocationSize() - Set min location size.
• GetMinLocationSize() - Get min location size.
• SetMaxLocationSize() - Set max location size.
• GetMaxLocationSize() - Get max location size.
• SetLabelField() - Set field used to determine location label.
• GetLabelField() - Get field used to determine location label.
• SetLabelColour() - Set label colour.
• GetLabelColour() - Get label colour.
• SetLabelSize() - Set label size.
• GetLabelSize() - Get label size.
• SetLabelPosition() - Set label position.
• GetLabelPosition() - Get label position.
• SetLabelStyle() - Set label style.
• GetLabelStyle() - Get label style.
• SetLabelVisibility() - Set label visibility.
• GetLabelVisibility() - Get label visibility.
• SetLabelBindToChart() - Set flag indicating if label is bound to chart.
• GetLabelBindToChart() - Get flag indicating if label is bound to chart.
• GetMetadata() - Get location metadata for the specified field (list of strings).
• GetNumericMetadata() - Get location metadata for the specified field (list of floats).
• GetMetadataFields() - Get fields for location metadata.
• GetNumericMetadataFields() - Get numeric fields for location metadata.
• AddMetadata() - Add field to location metadata.

Location Layer class

• GetNumSequenceLayers() - Get number of sequence layers for this location.
• GetSequenceLayer() - Get specified sequence layer.
• GetAllSequenceLayers() - Get all sequence layers.
• GetAllActiveSequenceLayers() - Get all active sequence layers.
• GetController() - Get location controller.

Location Controller class

• GetId() - Get id of location.
• GetNorthing() - Get north or latitudinal position of location.
• GetEasting() - Get east or longitudinal position of location.
• GetLatitude() - Get north or latitudinal position of location.
• GetLongitude() - Get east or longitudinal position of location.
• GetData() - Get metadata associated with location.
• GetProjection() - Get projected coordinates of location.
• GetPosition() - Get grid coordinates of location.
• SetColour() - Set colour of location marker.
• GetColour() - Get colour of location marker.
• SetSize() - Set size of location marker.
• GetSize() - Get size of location marker.
• SetShape() - Set shape of location marker.
• GetShape() - Get shape of location marker.
• SetBorderSize() - Set border size of location marker.
• GetBorderSize() - Get border size of location marker.
• SetActive() - Set active state of location marker.
• IsActive() - Check if location is active.
• SetRenderingOrder() - Set rendering order of location marker.
• GetRenderingOrder() - Get rendering order of location marker.
• AddData() - Add metadata to location.

Sequence Layer class

• GetController() - Get sequence controller.

Sequence Controller class

• GetSequenceId() - Get id of sequence.
• GetSiteId() - Get id of site where sequence was sampled.
• IsActive() - Check if sequence is active.
• SetActive() - Set active state of sequence.
• GetData() - Get metadata associated with sequence.
• GetMetadataFields() - Get metadata fields.
• GetNumericMetadataFields() - Get numeric fields for sequences.

Chart Set View class

• GetChart() - Get specified chart.
• SetLayoutLine() - Set layout line for chart set.
• IsLayoutLine() - Check if a layout line has been specified for the chart set.
• GetLayoutLineVisibility() - Get visibility of layout line.
• SetLayoutLineVisibility() - Set visibility of layout line.
• SetLayout() - Set layout style.
• GetLayout() - Get layout style.
• UpdateCharts() - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).

Chart View class

• GetVisibility() - Get visibility of chart.
• SetVisibility() - Set visibility of chart.
• GetDepth() - Get depth of chart (controls rendering order).
• SetDepth() - Set depth of chart (controls rendering order).
• GetWidth() - Get width or diameter of chart.
• SetWidth() - Set width or diameter of chart.
• GetHeight() - Get height of chart.
• SetHeight() - Set height of chart.
• GetBorderSize() - Get border size of chart.
• SetBorderSize() - Set border size of chart.
• GetWedgeBorders() - Get wedge border size.
• SetWedgeBorders() - Set wedge border size.
• GetSizeProportionalToSeq() - Get flag indicating if chart size should be proportional to sequence count.
• SetSizeProportionalToSeq() - Set flag indicating if chart size should be proportional to sequence count.
• GetMinSize() - Get minimum allowed size of chart.
• SetMinSize() - Set minimum allowed size of chart.
• GetMaxSize() - Get maximum allowed size of chart.
• SetMaxSize() - Set maximum allowed size of chart.
• GetAdjustedSize() - Get adjusted chart size based on number of sequences.
• SetNormalizedNumSeq() - Set normalized number of sequences for this chart.
• SetField() - Set field used to create chart.
• GetField() - Get field used to create chart.
• GetNames() - Get name of all category.
• GetPercentage() - Get percentage of sequences assigned to the specified category.
• SetChartType() - Set type of chart to generate.
• GetChartType() - Get type of chart to generate.
• SetAssignToOther() - Set proportion for which a category will be assigned to the 'Other' category.
• GetAssignToOther() - Get proportion for which a category will be assigned to the 'Other' category.
• SetCentre() - Set centre of chart.
• GetCentre() - Get centre of chart.
• GetLocationPos() - Get position of associated location.
• SetScreenPos() - Set position of chart in screen coordinates.
• GetScreenPos() - Get position of chart in screen coordinates.
• SetLabelBindToChart() - Set flag indicating if labels should be bound to charts.
• GetLabelBindToChart() - Get flag indicating if labels should be bound to charts.
• SetLabel() - Set chart label.
• GetLabel() - Get chart label.
• UpdateChart() - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).

Visual Label class

• GetText() - Get text of label.
• GetColour() - Get colour of label font.
• GetSize() - Get size of label font.
• GetVisibility() - Get visibility of label.
• GetGridPosition() - Get grid coordinates of label.
• GetScreenPosition() - Get screen coordinates of label.
• GetRotateLabel() - Get flag indicating if text should be rotated onto the plane.
• GetRotateZ() - Get flag indicating if text should rotate to remain horizontal.
• GetRenderingStyle() - Get rendering style of label.
• SetText() - Set text of label.
• SetColour() - Set colour of label font.
• SetSize() - Set size of label font.
• SetVisibility() - Set visibility of label.
• SetGridPosition() - Set grid position of label.
• SetScreenPosition() - Set screen position of label.
• SetRenderingStyle() - Set rendering style of label.

Visual Marker class

• GetPosition() - Get position of marker.
• GetShape() - Get shape of marker.
• GetRotation() - Get rotation of marker.
• GetDepth() - Get depth of marker.
• GetRenderingStyle() - Get rendering style of marker.
• GetColour() - Get colour of marker.
• GetSize() - Get size of marker.
• GetVisibility() - Get visibility of marker.
• GetRenderingOrder() - Get rendering order of marker.
• GetBorderSize() - Get border size of marker.
• SetPosition() - Set position of marker.
• SetShape() - Set shape of marker.
• SetRotation() - Set rotation of marker.
• SetDepth() - Set depth of marker.
• SetRenderingStyle() - Set rendering style of marker.
• SetColour() - Set colour of marker.
• SetSize() - Set size of marker.
• SetVisibility() - Set visibility of marker.
• SetRenderingOrder() - Set rendering order of marker.
• SetBorderSize() - Set border size of marker.

Visual Line class

• GetColour() - Get colour of line.
• GetThickness() - Get thickness of line.
• GetVisibility() - Get visibility of line.
• GetLineStyle() - Get style of line.
• GetStartPt() - Get start point of line.
• GetEndPt() - Get end point of line.
• SetColour() - Set colour of line.
• SetThickness() - Set thickness of line.
• SetVisibility() - Set visibility of line.
• SetLineStyle() - Set style of line.
• SetStartPt() - Set start point of line.
• SetEndPt() - Set end point of line.
• GetLine() - Get line.
• SetLine() - Set line.
• GetDepth() - Get depth of line (determines rendering order).
• SetDepth() - Set depth of line (determines rendering order).

Colour class

• GetRed() - Get red channel.
• SetRed() - Set red channel.
• GetGreen() - Get green channel.
• SetGreen() - Set green channel.
• GetBlue() - Get blue channel.
• SetBlue() - Set blue channel.
• GetAlpha() - Get alpha channel.
• SetAlpha() - Set alpha channel.
• SetRGBA() - Set new colour.

Colour Map Base class

• GetColour() - Get colour at specified index.
• GetInterpolatedColour() - Interpolate colour from colour map.
• GetName() - Get name of colour map.
• GetExtendedName() - Get name of colour map with either 'Continuous:' or 'Discrete:' prefixed to it.
• GetSize() - Get size of colour map.
• GetType() - Get type of colour map.

Discrete Colour Map class

• GetColourMap() - Get colour map with the provided name.
• GetColourMapNames() - Get name of all colour maps.
• GetColourMapDiscreteNames() - Get name of all discrete colour maps.
• GetColourMapContinuousNames() - Get name of all continuous colour maps.

Point3D class

• Length() - Distance from origin to point.
• SquaredLength() - Squared distance from origin to point.
• Offset() - Create new point offset by the specified amount.
• Normalize() - Normalize point (vector) to unit length.
• Cross() - Calculate cross product between two points (vectors).
• Dot() - Calculate dot product between two points (vectors).
• Angle() - Calculate angle between two points (vectors).
• x - Get x position of point.
• y - Get y position of point.
• z - Get z position of point.

GeoCoord class

• easting - Get easting or longitudinal position of location.
• northing - Get northing or latitudinal position of location.
• longitude - Get easting or longitudinal position of location.
• latitude - Get northing or latitudinal position of location.

Line3D class

• Offset() - New line offset by the specified amount.
• start - Start point of line.
• end - End point of line.
• startId - General purpose label associated with start point.
• endId - General purpose label associated with end point.

Box2D class

• x1 - Lower, left x-coordinate of box.
• y1 - Lower, left y-coordinate of box.
• dx - Width of bounding box.
• dy - Height of bounding box.

Linear Results class

• angle() - Angle of geographic layout line in degrees.
• numCrossings() - Number of crossings which occurs for this layout lines.