GenGIS API

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.

Terrain Controller class

• 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

• SetGeographicAxisAngle - Set geographic layout line to the specified angle.
• 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 percentage of layout line length).
• 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.

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/terrain controller.

Tree 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).

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.