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.