Difference between revisions of "GenGIS API"

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* GetAltitude - Get altitude (y-position) of light.
 
* GetAltitude - Get altitude (y-position) of light.
SetAltitude - Set altitude (y-position) of light.
+
* SetAltitude - Set altitude (y-position) of light.
SetGlobalAmbient - Set strength of global ambient light.
+
* SetGlobalAmbient - Set strength of global ambient light.
GetGlobalAmbient - Get strength of global ambient light.
+
* GetGlobalAmbient - Get strength of global ambient light.
GetPositionX - Get x-position of light.
+
* GetPositionX - Get x-position of light.
SetPositionX - Set x-position of light.
+
* SetPositionX - Set x-position of light.
GetPositionY - Get y-position of light.
+
* GetPositionY - Get y-position of light.
SetPositionY - Set y-position of light.
+
* SetPositionY - Set y-position of light.
GetPositionZ - Get z-position of light.
+
* GetPositionZ - Get z-position of light.
SetPositionZ - Set z-position of light.
+
* SetPositionZ - Set z-position of light.
  
 
= GeoTreeView class =
 
= GeoTreeView class =
  
SetGeographicAxisAngle - Set geographic layout line to the specified angle.
+
* SetGeographicAxisAngle - Set geographic layout line to the specified angle.
ProjectTree - Project tree to specified leaf nodes.
+
* ProjectTree - Project tree to specified leaf nodes.
RestoreTree - Restore original tree.
+
* RestoreTree - Restore original tree.
SetLayout - Set layout of geophylogeny.
+
* SetLayout - Set layout of geophylogeny.
GetLayout - Get layout of geophylogeny.
+
* GetLayout - Get layout of geophylogeny.
GetLayoutLineVisibility - Get visibility of geographic layout line.
+
* GetLayoutLineVisibility - Get visibility of geographic layout line.
SetLayoutLineVisibility - Set visibility of geographic layout line.
+
* SetLayoutLineVisibility - Set visibility of geographic layout line.
GetLayoutLine - Get geographic layout line.
+
* GetLayoutLine - Get geographic layout line.
SetLayoutLine - Set geographic layout line.
+
* SetLayoutLine - Set geographic layout line.
IsLayoutLine - Check if a layout line has been assigned to the tree.
+
* 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.
+
* IsGeographicAxis - Check if a non-linear geographic axis has been assigned to the tree.
GetGeographicAxisVisibility - Get visibility of non-linear geographic axis.
+
* GetGeographicAxisVisibility - Get visibility of non-linear geographic axis.
SetGeographicAxisVisibility - Set visibility of non-linear geographic axis.
+
* SetGeographicAxisVisibility - Set visibility of non-linear geographic axis.
GetLeafNodeSize - Get size of leaf nodes.
+
* GetLeafNodeSize - Get size of leaf nodes.
SetLeafNodeSize - Set size of leaf nodes.
+
* SetLeafNodeSize - Set size of leaf nodes.
GetInternalNodeSize - Get size of internal nodes.
+
* GetInternalNodeSize - Get size of internal nodes.
SetInternalNodeSize - Set size of internal nodes.
+
* SetInternalNodeSize - Set size of internal nodes.
GetLineThickness - Get thickness of tree branches.
+
* GetLineThickness - Get thickness of tree branches.
SetLineThickness - Set thickness of tree branches.
+
* SetLineThickness - Set thickness of tree branches.
GetOrientation - Get orientation of tree.
+
* GetOrientation - Get orientation of tree.
SetOrientation - Set orientation of tree.
+
* SetOrientation - Set orientation of tree.
GetHeight - Get height of tree.
+
* GetHeight - Get height of tree.
SetHeight - Set height of tree.
+
* SetHeight - Set height of tree.
GetColour - Get default colour for tree.
+
* GetColour - Get default colour for tree.
SetColour - Set default colour for tree.
+
* SetColour - Set default colour for tree.
GetOptimizeTopology - Check if optimal tree layout is being calcualte.
+
* GetOptimizeTopology - Check if optimal tree layout is being calcualte.
SetOptimizeTopology - Set flag indicating if optimal tree layout should be calculate.
+
* SetOptimizeTopology - Set flag indicating if optimal tree layout should be calculate.
GetLabelVisibility - Get visibility of leaf labels.
+
* GetLabelVisibility - Get visibility of leaf labels.
SetLabelVisibility - Set visibility of leaf labels.
+
* SetLabelVisibility - Set visibility of leaf labels.
GetFontSize - Get font size for leaf labels.
+
* GetFontSize - Get font size for leaf labels.
SetFontSize - Set font size for leaf labels.
+
* SetFontSize - Set font size for leaf labels.
GetFontColour - Get font colour for leaf labels.
+
* GetFontColour - Get font colour for leaf labels.
SetFontColour - Set font colour for leaf labels.
+
* SetFontColour - Set font colour for leaf labels.
Set3dInternalDropLineStyle - Set internal drop line style for 3D tree.
+
* Set3dInternalDropLineStyle - Set internal drop line style for 3D tree.
Get3dInternalDropLineStyle - Get 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.
+
* Set3dLeafDropLineStyle - Set leaf drop line style for 3D trees.
Get3dLeafDropLineStyle - Get leaf drop line style for 3D tree.
+
* Get3dLeafDropLineStyle - Get leaf drop line style for 3D tree.
SetGeographyLineOffsetPercentage - Set offset of geography line (in percentage of layout line length).
+
* SetGeographyLineOffsetPercentage - Set offset of geography line (in percentage of layout line length).
GetGeographyLineOffsetPercentage - Get 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).
+
* 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.
+
* SetSpreadGeographyPts - Set flag indicating if locations should be spread out evenly along the geography line.
SetLeafNodeBorderSize - Set border size for leaf nodes.
+
* SetLeafNodeBorderSize - Set border size for leaf nodes.
GetLeafNodeBorderSize - Get border size for leaf nodes.
+
* GetLeafNodeBorderSize - Get border size for leaf nodes.
SetInternalNodeBorderSize - Set border size for internal nodes.
+
* SetInternalNodeBorderSize - Set border size for internal nodes.
GetInternalNodeBorderSize - Get border size for internal nodes.
+
* GetInternalNodeBorderSize - Get border size for internal nodes.
SetGeoPtsBorderSize - Set border size for geographic points along geography line.
+
* SetGeoPtsBorderSize - Set border size for geographic points along geography line.
GetGeoPtsBorderSize - Get 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.
+
* SetBranchBorderSize - Set border size for tree branches.
GetBranchBorderSize - Get border size for tree branches.
+
* GetBranchBorderSize - Get border size for tree branches.
SetLocationLineBorderSize - Set border size for location lines.
+
* SetLocationLineBorderSize - Set border size for location lines.
GetLocationLineBorderSize - Get border size for location lines.
+
* GetLocationLineBorderSize - Get border size for location lines.
SetCorrelationLineBorderSize - Set border size for correlation lines.
+
* SetCorrelationLineBorderSize - Set border size for correlation lines.
GetCorrelationLineBorderSize - Get border size for correlation lines.
+
* GetCorrelationLineBorderSize - Get border size for correlation lines.
SetLeafNodeBorderColour - Set colour of leaf node borders.
+
* SetLeafNodeBorderColour - Set colour of leaf node borders.
GetLeafNodeBorderColour - Get colour of leaf node borders.
+
* GetLeafNodeBorderColour - Get colour of leaf node borders.
SetInternalNodeBorderColour - Set colour of internal node borders.
+
* SetInternalNodeBorderColour - Set colour of internal node borders.
GetInternalNodeBorderColour - Get colour of internal node borders.
+
* GetInternalNodeBorderColour - Get colour of internal node borders.
SetGeoPtsBorderColour - Set colour of geographic point borders.
+
* SetGeoPtsBorderColour - Set colour of geographic point borders.
GetGeoPtsBorderColour - Get colour og geographic point borders.
+
* GetGeoPtsBorderColour - Get colour og geographic point borders.
SetLocationLineBorderColour - Set colour of location line borders.
+
* SetLocationLineBorderColour - Set colour of location line borders.
GetLocationLineBorderColour - Get colour of location line borders.
+
* GetLocationLineBorderColour - Get colour of location line borders.
SetCorrelationLineBorderColour - Set colour of correlation line borders.
+
* SetCorrelationLineBorderColour - Set colour of correlation line borders.
GetCorrelationLineBorderColour - Get colour of correlation line borders.
+
* GetCorrelationLineBorderColour - Get colour of correlation line borders.
SetBranchBorderColour - Set colour of branch borders.
+
* SetBranchBorderColour - Set colour of branch borders.
GetBranchBorderColour - Get colour of branch borders.
+
* GetBranchBorderColour - Get colour of branch borders.
SetTreeColourStyle - Set colouring method for tree.
+
* SetTreeColourStyle - Set colouring method for tree.
GetTreeColourStyle - Get colouring method for tree.
+
* GetTreeColourStyle - Get colouring method for tree.
SetReverseOrderGeographicPts - Set whether geographic points should be reversed.
+
* SetReverseOrderGeographicPts - Set whether geographic points should be reversed.
GetReverseOrderGeographicPts - Check if geographic points are being reversed.
+
* GetReverseOrderGeographicPts - Check if geographic points are being reversed.
GetNumberOfNodes - Get total number of nodes.
+
* GetNumberOfNodes - Get total number of nodes.
GetNumberOfLeaves - Get number of leaf nodes.
+
* GetNumberOfLeaves - Get number of leaf nodes.
GetDepthOfTree - Get maximum depth of tree.
+
* GetDepthOfTree - Get maximum depth of tree.
IsMultifurcating - Check if tree is multifurcating.
+
* IsMultifurcating - Check if tree is multifurcating.
GetLeafNames - Get names of leaves.
+
* GetLeafNames - Get names of leaves.
SignificanceTest - Perform Monte Carlo significance test.
+
* SignificanceTest - Perform Monte Carlo significance test.
  
 
= Layer class =
 
= Layer class =
  
GetId - Get id of layer
+
* GetId - Get id of layer
GetName - Get name of layer.
+
* GetName - Get name of layer.
SetName - Set name of layer.
+
* SetName - Set name of layer.
GetDescription - Get description of layer.
+
* GetDescription - Get description of layer.
SetDescription - Set description of layer.
+
* SetDescription - Set description of layer.
GetAuthours - Get authours of layer.
+
* GetAuthours - Get authours of layer.
SetAuthours - Set authours of layer.
+
* SetAuthours - Set authours of layer.
GetPath - Get path to layer file.
+
* GetPath - Get path to layer file.
GetFilename - Get filename of layer.
+
* GetFilename - Get filename of layer.
GetType - Get type of layer.
+
* GetType - Get type of layer.
  
 
= Study Layer class =
 
= Study Layer class =
  
GetNumMapLayers - Get number of map layers in this study.
+
* GetNumMapLayers - Get number of map layers in this study.
GetMapLayer - Get specified map layer.     
+
* GetMapLayer - Get specified map layer.     
GetAllMapLayers - Get all maps in study.
+
* GetAllMapLayers - Get all maps in study.
GetController - Get study controller.
+
* GetController - Get study controller.
  
 
= Study Controller class =
 
= Study Controller class =
  
GetDatum - Get datum used by study.
+
* GetDatum - Get datum used by study.
SetDatum - Set datum used by study (must be set before map is loaded).
+
* SetDatum - Set datum used by study (must be set before map is loaded).
GetProjection - Get projection used by study.
+
* GetProjection - Get projection used by study.
SetProjection - Set projection used by study (must be set before map is loaded).
+
* 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.
+
* IsGeographic - Flag indicating if data is in geographic (i.e. lat/long) coordinates.
  
 
= Map Layer class =
 
= Map Layer class =
  
GetNumLocationSetLayers - Get number of location set layers for this map.
+
* GetNumLocationSetLayers - Get number of location set layers for this map.
GetLocationSetLayer - Get specified location set layer.     
+
* GetLocationSetLayer - Get specified location set layer.     
GetAllLocationSetLayers - Get all location set layers.   
+
* GetAllLocationSetLayers - Get all location set layers.   
GetNumTreeLayers - Get number of tree layers for this map.
+
* GetNumTreeLayers - Get number of tree layers for this map.
GetTreeLayer - Get specified tree layer.
+
* GetTreeLayer - Get specified tree layer.
GetAllTreeLayers - Get all tree layers.   
+
* GetAllTreeLayers - Get all tree layers.   
GetController - Get map/terrain controller.
+
* GetController - Get map/terrain controller.
  
 
= Tree class =
 
= Tree class =
  
GetGeoTreeView - Get geophylogeny associated with this layer.
+
* GetGeoTreeView - Get geophylogeny associated with this layer.
  
 
= Location Set Layer class =
 
= Location Set Layer class =
  
GetNumLocationLayers - Get number of location layers for this location set.
+
* GetNumLocationLayers - Get number of location layers for this location set.
GetLocationLayer - Get specified location layer.   
+
* GetLocationLayer - Get specified location layer.   
GetAllLocationLayers - Get all location layers.
+
* GetAllLocationLayers - Get all location layers.
GetAllActiveLocationLayers - Get all visible location layers.
+
* GetAllActiveLocationLayers - Get all visible location layers.
IsSequencesData - Check if there is sequence data associated with at least one location.
+
* IsSequencesData - Check if there is sequence data associated with at least one location.
GetController - Get location set controller.
+
* GetController - Get location set controller.
GetChartSet - Get set of charts associated with this location set.
+
* GetChartSet - Get set of charts associated with this location set.
  
 
= Location Set Controller class =
 
= Location Set Controller class =
  
SetLocationVisibilities - Propogate set visibility state to all locations.
+
* SetLocationVisibilities - Propogate set visibility state to all locations.
SetLocationColours - Propogate set colour state to all locations.
+
* SetLocationColours - Propogate set colour state to all locations.
SetLocationBorders - Propogate set border state to all locations.
+
* SetLocationBorders - Propogate set border state to all locations.
SetLocationSizes - Propogate set size state to all locations.
+
* SetLocationSizes - Propogate set size state to all locations.
SetLocationShapes - Propogate set shape state to all locations.
+
* SetLocationShapes - Propogate set shape state to all locations.
SetLocationLabels - Propogate specified label states to all locations.
+
* SetLocationLabels - Propogate specified label states to all locations.
SetColourField - Set field used to determine location colour.
+
* SetColourField - Set field used to determine location colour.
GetColourField - Get field used to determine location colour.
+
* GetColourField - Get field used to determine location colour.
SetColourMap - Set colour map associated with location set.
+
* SetColourMap - Set colour map associated with location set.
GetColourMap - Get 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.
+
* SetUniformColourFlag - Set flag indicating if all locations should have the same colour.
GetUniformColourFlag - Get 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.
+
* SetUniformColour - Set uniform colour.
GetUniformColour - Get uniform colour.
+
* GetUniformColour - Get uniform colour.
SetBorderSize - Set border size.
+
* SetBorderSize - Set border size.
GetBorderSize - Get border size..
+
* GetBorderSize - Get border size..
SetBorderColour - Set border colour.
+
* SetBorderColour - Set border colour.
GetBorderColour - Get border colour.
+
* GetBorderColour - Get border colour.
SetLocationSetVisibility - Set visibility of location set.
+
* SetLocationSetVisibility - Set visibility of location set.
GetLocationSetVisibility - Get visibility of location set.
+
* GetLocationSetVisibility - Get visibility of location set.
SetShapeField - Set field used to determine location shape.
+
* SetShapeField - Set field used to determine location shape.
GetShapeField - Get field used to determine location shape.
+
* GetShapeField - Get field used to determine location shape.
SetShapeMap - Set shape map associated with location set.
+
* SetShapeMap - Set shape map associated with location set.
GetShapeMap - Get 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.
+
* SetUniformShapeFlag - Set flag indicating if all locations should have the same shape.
GetUniformShapeFlag - Get 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.
+
* SetUniformShape - Set uniform shape.
GetUniformShape - Get uniform shape.
+
* GetUniformShape - Get uniform shape.
SetSizeField - Set field used to determine location size.
+
* SetSizeField - Set field used to determine location size.
GetSizeField - Get field used to determine location size.
+
* GetSizeField - Get field used to determine location size.
SetMinLocationSize - Set min location size.  
+
* SetMinLocationSize - Set min location size.  
GetMinLocationSize - Get min location size.  
+
* GetMinLocationSize - Get min location size.  
SetMaxLocationSize - Set max location size.  
+
* SetMaxLocationSize - Set max location size.  
GetMaxLocationSize - Get max location size.
+
* GetMaxLocationSize - Get max location size.
SetLabelField - Set field used to determine location label.
+
* SetLabelField - Set field used to determine location label.
GetLabelField - Get field used to determine location label.
+
* GetLabelField - Get field used to determine location label.
SetLabelColour - Set label colour.
+
* SetLabelColour - Set label colour.
GetLabelColour - Get label colour.
+
* GetLabelColour - Get label colour.
SetLabelSize - Set label size.
+
* SetLabelSize - Set label size.
GetLabelSize - Get label size.
+
* GetLabelSize - Get label size.
SetLabelPosition - Set label position.
+
* SetLabelPosition - Set label position.
GetLabelPosition - Get label position.
+
* GetLabelPosition - Get label position.
SetLabelStyle - Set label style.
+
* SetLabelStyle - Set label style.
GetLabelStyle - Get label style.
+
* GetLabelStyle - Get label style.
SetLabelVisibility - Set label visibility.
+
* SetLabelVisibility - Set label visibility.
GetLabelVisibility - Get label visibility.
+
* GetLabelVisibility - Get label visibility.
SetLabelBindToChart - Set flag indicating if label is bound to chart.
+
* SetLabelBindToChart - Set flag indicating if label is bound to chart.
GetLabelBindToChart - Get 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).
+
* GetMetadata - Get location metadata for the specified field (list of strings).
GetNumericMetadata - Get location metadata for the specified field (list of floats).
+
* GetNumericMetadata - Get location metadata for the specified field (list of floats).
GetMetadataFields - Get fields for location metadata.
+
* GetMetadataFields - Get fields for location metadata.
GetNumericMetadataFields - Get numeric fields for location metadata.
+
* GetNumericMetadataFields - Get numeric fields for location metadata.
AddMetadata - Add field to location metadata.
+
* AddMetadata - Add field to location metadata.
  
 
= Location Layer class =
 
= Location Layer class =
  
GetNumSequenceLayers - Get number of sequence layers for this location.
+
* GetNumSequenceLayers - Get number of sequence layers for this location.
GetSequenceLayer - Get specified sequence layer.   
+
* GetSequenceLayer - Get specified sequence layer.   
GetAllSequenceLayers - Get all sequence layers.
+
* GetAllSequenceLayers - Get all sequence layers.
GetAllActiveSequenceLayers - Get all active sequence layers.
+
* GetAllActiveSequenceLayers - Get all active sequence layers.
GetController - Get location controller.
+
* GetController - Get location controller.
  
 
= Location Controller class =
 
= Location Controller class =
  
GetId - Get id of location.
+
* GetId - Get id of location.
GetNorthing - Get north or latitudinal position of location.
+
* GetNorthing - Get north or latitudinal position of location.
GetEasting - Get east or longitudinal position of location.
+
* GetEasting - Get east or longitudinal position of location.
GetLatitude - Get north or latitudinal position of location.
+
* GetLatitude - Get north or latitudinal position of location.
GetLongitude - Get east or longitudinal position of location.
+
* GetLongitude - Get east or longitudinal position of location.
GetData - Get metadata associated with location.
+
* GetData - Get metadata associated with location.
GetProjection - Get projected coordinates of location.
+
* GetProjection - Get projected coordinates of location.
GetPosition - Get grid coordinates of location.
+
* GetPosition - Get grid coordinates of location.
SetColour - Set colour of location marker.
+
* SetColour - Set colour of location marker.
GetColour - Get colour of location marker.
+
* GetColour - Get colour of location marker.
SetSize - Set size of location marker.
+
* SetSize - Set size of location marker.
GetSize - Get size of location marker.
+
* GetSize - Get size of location marker.
SetShape - Set shape of location marker.
+
* SetShape - Set shape of location marker.
GetShape - Get shape of location marker.
+
* GetShape - Get shape of location marker.
SetBorderSize - Set border size of location marker.
+
* SetBorderSize - Set border size of location marker.
GetBorderSize - Get border size of location marker.
+
* GetBorderSize - Get border size of location marker.
SetActive - Set active state of location marker.
+
* SetActive - Set active state of location marker.
IsActive - Check if location is active.
+
* IsActive - Check if location is active.
SetRenderingOrder - Set rendering order of location marker.
+
* SetRenderingOrder - Set rendering order of location marker.
GetRenderingOrder - Get rendering order of location marker.
+
* GetRenderingOrder - Get rendering order of location marker.
AddData - Add metadata to location.
+
* AddData - Add metadata to location.
  
 
= Sequence Layer class =
 
= Sequence Layer class =
  
GetController - Get sequence controller.
+
* GetController - Get sequence controller.
  
 
= Sequence Controller class =
 
= Sequence Controller class =
  
GetSequenceId - Get id of sequence.
+
* GetSequenceId - Get id of sequence.
GetSiteId - Get id of site where sequence was sampled.     
+
* GetSiteId - Get id of site where sequence was sampled.     
IsActive - Check if sequence is active.
+
* IsActive - Check if sequence is active.
SetActive - Set active state of sequence.
+
* SetActive - Set active state of sequence.
GetData - Get metadata associated with sequence.
+
* GetData - Get metadata associated with sequence.
GetMetadataFields - Get metadata fields.
+
* GetMetadataFields - Get metadata fields.
GetNumericMetadataFields - Get numeric fields for sequences.
+
* GetNumericMetadataFields - Get numeric fields for sequences.
  
 
= Chart Set View class =
 
= Chart Set View class =
  
GetChart - Get specified chart.
+
* GetChart - Get specified chart.
SetLayoutLine - Set layout line for chart set.
+
* SetLayoutLine - Set layout line for chart set.
IsLayoutLine - Check if a layout line has been specified for the chart set.
+
* IsLayoutLine - Check if a layout line has been specified for the chart set.
GetLayoutLineVisibility - Get visibility of layout line.
+
* GetLayoutLineVisibility - Get visibility of layout line.
SetLayoutLineVisibility - Set visibility of layout line.
+
* SetLayoutLineVisibility - Set visibility of layout line.
SetLayout - Set layout style.
+
* SetLayout - Set layout style.
GetLayout - Get layout style.
+
* GetLayout - Get layout style.
UpdateCharts - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).
+
* UpdateCharts - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).
  
 
= Chart View class =
 
= Chart View class =
  
GetVisibility - Get visibility of chart.
+
* GetVisibility - Get visibility of chart.
SetVisibility - Set visibility of chart.
+
* SetVisibility - Set visibility of chart.
GetDepth - Get depth of chart (controls rendering order).
+
* GetDepth - Get depth of chart (controls rendering order).
SetDepth - Set depth of chart (controls rendering order).
+
* SetDepth - Set depth of chart (controls rendering order).
GetWidth - Get width or diameter of chart.
+
* GetWidth - Get width or diameter of chart.
SetWidth - Set width or diameter of chart.
+
* SetWidth - Set width or diameter of chart.
GetHeight - Get height of chart.
+
* GetHeight - Get height of chart.
SetHeight - Set height of chart.
+
* SetHeight - Set height of chart.
GetBorderSize - Get border size of chart.
+
* GetBorderSize - Get border size of chart.
SetBorderSize - Set border size of chart.
+
* SetBorderSize - Set border size of chart.
GetWedgeBorders - Get wedge border size.
+
* GetWedgeBorders - Get wedge border size.
SetWedgeBorders - Set wedge border size.
+
* SetWedgeBorders - Set wedge border size.
GetSizeProportionalToSeq - Get flag indicating if chart size should be proportional to sequence count.
+
* 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.
+
* SetSizeProportionalToSeq - Set flag indicating if chart size should be proportional to sequence count.
GetMinSize - Get minimum allowed size of chart.
+
* GetMinSize - Get minimum allowed size of chart.
SetMinSize - Set minimum allowed size of chart.
+
* SetMinSize - Set minimum allowed size of chart.
GetMaxSize - Get maximum allowed size of chart.
+
* GetMaxSize - Get maximum allowed size of chart.
SetMaxSize - Set maximum allowed size of chart.
+
* SetMaxSize - Set maximum allowed size of chart.
GetAdjustedSize - Get adjusted chart size based on number of sequences.
+
* GetAdjustedSize - Get adjusted chart size based on number of sequences.
SetNormalizedNumSeq - Set normalized number of sequences for this chart.
+
* SetNormalizedNumSeq - Set normalized number of sequences for this chart.
SetField - Set field used to create chart.
+
* SetField - Set field used to create chart.
GetField - Get field used to create chart.
+
* GetField - Get field used to create chart.
GetNames - Get name of all category.
+
* GetNames - Get name of all category.
GetPercentage - Get percentage of sequences assigned to the specified category.
+
* GetPercentage - Get percentage of sequences assigned to the specified category.
SetChartType - Set type of chart to generate.
+
* SetChartType - Set type of chart to generate.
GetChartType - Get 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.
+
* 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.
+
* GetAssignToOther - Get proportion for which a category will be assigned to the 'Other' category.
SetCentre - Set centre of chart.
+
* SetCentre - Set centre of chart.
GetCentre - Get centre of chart.
+
* GetCentre - Get centre of chart.
GetLocationPos - Get position of associated location.
+
* GetLocationPos - Get position of associated location.
SetScreenPos - Set position of chart in screen coordinates.
+
* SetScreenPos - Set position of chart in screen coordinates.
GetScreenPos - Get 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.
+
* SetLabelBindToChart - Set flag indicating if labels should be bound to charts.
GetLabelBindToChart - Get flag indicating if labels should be bound to charts.
+
* GetLabelBindToChart - Get flag indicating if labels should be bound to charts.
SetLabel - Set chart label.
+
* SetLabel - Set chart label.
GetLabel - Get chart label.
+
* GetLabel - Get chart label.
UpdateChart - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).
+
* UpdateChart - Update chart to reflect any changes in the underlying data (e.g., changed active sequences).
  
 
= Visual Label class =
 
= Visual Label class =
  
GetText - Get text of label.
+
* GetText - Get text of label.
GetColour - Get colour of label font.
+
* GetColour - Get colour of label font.
GetSize - Get size of label font.
+
* GetSize - Get size of label font.
GetVisibility - Get visibility of label.
+
* GetVisibility - Get visibility of label.
GetGridPosition - Get grid coordinates of label.
+
* GetGridPosition - Get grid coordinates of label.
GetScreenPosition - Get screen coordinates of label.
+
* GetScreenPosition - Get screen coordinates of label.
GetRotateLabel - Get flag indicating if text should be rotated onto the plane.
+
* GetRotateLabel - Get flag indicating if text should be rotated onto the plane.
GetRotateZ - Get flag indicating if text should rotate to remain horizontal.
+
* GetRotateZ - Get flag indicating if text should rotate to remain horizontal.
GetRenderingStyle - Get rendering style of label.
+
* GetRenderingStyle - Get rendering style of label.
SetText - Set text of label.
+
* SetText - Set text of label.
SetColour - Set colour of label font.
+
* SetColour - Set colour of label font.
SetSize - Set size of label font.
+
* SetSize - Set size of label font.
SetVisibility - Set visibility of label.
+
* SetVisibility - Set visibility of label.
SetGridPosition - Set grid position of label.
+
* SetGridPosition - Set grid position of label.
SetScreenPosition - Set screen position of label.
+
* SetScreenPosition - Set screen position of label.
SetRenderingStyle - Set rendering style of label.
+
* SetRenderingStyle - Set rendering style of label.
  
 
= Visual Marker class =
 
= Visual Marker class =
  
GetPosition - Get position of marker.
+
* GetPosition - Get position of marker.
GetShape - Get shape of marker.
+
* GetShape - Get shape of marker.
GetRotation - Get rotation of marker.
+
* GetRotation - Get rotation of marker.
GetDepth - Get depth of marker.
+
* GetDepth - Get depth of marker.
GetRenderingStyle - Get rendering style of marker.
+
* GetRenderingStyle - Get rendering style of marker.
GetColour - Get colour of marker.
+
* GetColour - Get colour of marker.
GetSize - Get size of marker.
+
* GetSize - Get size of marker.
GetVisibility - Get visibility of marker.
+
* GetVisibility - Get visibility of marker.
GetRenderingOrder - Get rendering order of marker.
+
* GetRenderingOrder - Get rendering order of marker.
GetBorderSize - Get border size of marker.
+
* GetBorderSize - Get border size of marker.
SetPosition - Set position of marker.
+
* SetPosition - Set position of marker.
SetShape - Set shape of marker.
+
* SetShape - Set shape of marker.
SetRotation - Set rotation of marker.
+
* SetRotation - Set rotation of marker.
SetDepth - Set depth of marker.
+
* SetDepth - Set depth of marker.
SetRenderingStyle - Set rendering style of marker.
+
* SetRenderingStyle - Set rendering style of marker.
SetColour - Set colour of marker.
+
* SetColour - Set colour of marker.
SetSize - Set size of marker.
+
* SetSize - Set size of marker.
SetVisibility - Set visibility of marker.
+
* SetVisibility - Set visibility of marker.
SetRenderingOrder - Set rendering order of marker.
+
* SetRenderingOrder - Set rendering order of marker.
SetBorderSize - Set border size of marker.
+
* SetBorderSize - Set border size of marker.
  
 
= Visual Line class =
 
= Visual Line class =
  
GetColour - Get colour of line.
+
* GetColour - Get colour of line.
GetThickness - Get thickness of line.
+
* GetThickness - Get thickness of line.
GetVisibility - Get visibility of line.
+
* GetVisibility - Get visibility of line.
GetLineStyle - Get style of line.
+
* GetLineStyle - Get style of line.
GetStartPt - Get start point of line.
+
* GetStartPt - Get start point of line.
GetEndPt - Get end point of line.
+
* GetEndPt - Get end point of line.
SetColour - Set colour of line.
+
* SetColour - Set colour of line.
SetThickness - Set thickness of line.
+
* SetThickness - Set thickness of line.
SetVisibility - Set visibility of line.
+
* SetVisibility - Set visibility of line.
SetLineStyle - Set style of line.
+
* SetLineStyle - Set style of line.
SetStartPt - Set start point of line.
+
* SetStartPt - Set start point of line.
SetEndPt - Set end point of line.
+
* SetEndPt - Set end point of line.
GetLine - Get line.
+
* GetLine - Get line.
SetLine - Set line.
+
* SetLine - Set line.
GetDepth - Get depth of line (determines rendering order).
+
* GetDepth - Get depth of line (determines rendering order).
SetDepth - Set depth of line (determines rendering order).
+
* SetDepth - Set depth of line (determines rendering order).
  
 
= Colour class =
 
= Colour class =
  
GetRed - Get red channel.
+
* GetRed - Get red channel.
SetRed - Set red channel.
+
* SetRed - Set red channel.
GetGreen - Get green channel.
+
* GetGreen - Get green channel.
SetGreen - Set green channel.
+
* SetGreen - Set green channel.
GetBlue - Get blue channel.
+
* GetBlue - Get blue channel.
SetBlue - Set blue channel.
+
* SetBlue - Set blue channel.
GetAlpha - Get alpha channel.
+
* GetAlpha - Get alpha channel.
SetAlpha - Set alpha channel.
+
* SetAlpha - Set alpha channel.
SetRGBA - Set new colour.
+
* SetRGBA - Set new colour.
  
 
= Colour Map Base class =
 
= Colour Map Base class =
  
GetColour - Get colour at specified index.
+
* GetColour - Get colour at specified index.
GetInterpolatedColour - Interpolate colour from colour map.
+
* GetInterpolatedColour - Interpolate colour from colour map.
GetName - Get name of colour map.
+
* GetName - Get name of colour map.
GetExtendedName - Get name of colour map with either 'Continuous:' or 'Discrete:' prefixed to it.
+
* GetExtendedName - Get name of colour map with either 'Continuous:' or 'Discrete:' prefixed to it.
GetSize - Get size of colour map.
+
* GetSize - Get size of colour map.
GetType - Get type of colour map.
+
* GetType - Get type of colour map.
  
 
= Discrete Colour Map class =
 
= Discrete Colour Map class =
  
GetColourMap - Get colour map with the provided name.
+
* GetColourMap - Get colour map with the provided name.
GetColourMapNames - Get name of all colour maps.
+
* GetColourMapNames - Get name of all colour maps.
GetColourMapDiscreteNames - Get name of all discrete colour maps.
+
* GetColourMapDiscreteNames - Get name of all discrete colour maps.
GetColourMapContinuousNames - Get name of all continuous colour maps.
+
* GetColourMapContinuousNames - Get name of all continuous colour maps.
  
 
= Point3D class =
 
= Point3D class =
  
Length - Distance from origin to point.
+
* Length - Distance from origin to point.
SquaredLength - Squared distance from origin to point.
+
* SquaredLength - Squared distance from origin to point.
Offset - Create new point offset by the specified amount.
+
* Offset - Create new point offset by the specified amount.
Normalize - Normalize point (vector) to unit length.
+
* Normalize - Normalize point (vector) to unit length.
Cross - Calculate cross product between two points (vectors).
+
* Cross - Calculate cross product between two points (vectors).
Dot - Calculate dot product between two points (vectors).
+
* Dot - Calculate dot product between two points (vectors).
Angle - Calculate angle between two points (vectors).
+
* Angle - Calculate angle between two points (vectors).
  
 
= GeoCoord class =
 
= GeoCoord class =
  
easting - Get easting or longitudinal position of location.
+
* easting - Get easting or longitudinal position of location.
northing - Get northing or latitudinal position of location.
+
* northing - Get northing or latitudinal position of location.
longitude - Get easting or longitudinal position of location.
+
* longitude - Get easting or longitudinal position of location.
latitude - Get northing or latitudinal position of location.
+
* latitude - Get northing or latitudinal position of location.
  
 
= Line3D class =
 
= Line3D class =
  
Offset - New line offset by the specified amount.
+
* Offset - New line offset by the specified amount.
start - Start point of line.
+
* start - Start point of line.
end - End point of line.
+
* end - End point of line.
startId - General purpose label associated with start point.
+
* startId - General purpose label associated with start point.
endId - General purpose label associated with end point.
+
* endId - General purpose label associated with end point.

Revision as of 19:22, 26 March 2012

Contents

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.