Details
Description
The Sequence ID colours are set in the following routine:
jalview.{applet}gui.IDCanvas.drawIDStrings(..).
These methods get the sequence ID colour from jalview.{applet}gui.AlignViewport.getSequenceColour(SequenceI) - which is a simple hash lookup to retrieve a colour.
This is currently used in just one way for sequence group based ID colouring. The jalview.datamodel.SequenceGroup object specifies a single ID colour that is examined and applied for each group member in the AlignViewport.updateSequenceIdColours() method.
If the T-Coffee colourscheme is selected, it should shade the sequence IDs according to the overall score. The easiest route to achieve this may be to extend the colourscheme interface with a new method: 'getSequenceIdColour(SequenceI)'. This would then get called in the .updateSequenceIdColours() loop to get the colour for each sequence according to the applied colourscheme.
Note: its important that the existing group idColour is given priority if it is set, because a number of web services used this feature to shade sequence IDs in this manner.
jalview.{applet}gui.IDCanvas.drawIDStrings(..).
These methods get the sequence ID colour from jalview.{applet}gui.AlignViewport.getSequenceColour(SequenceI) - which is a simple hash lookup to retrieve a colour.
This is currently used in just one way for sequence group based ID colouring. The jalview.datamodel.SequenceGroup object specifies a single ID colour that is examined and applied for each group member in the AlignViewport.updateSequenceIdColours() method.
If the T-Coffee colourscheme is selected, it should shade the sequence IDs according to the overall score. The easiest route to achieve this may be to extend the colourscheme interface with a new method: 'getSequenceIdColour(SequenceI)'. This would then get called in the .updateSequenceIdColours() loop to get the colour for each sequence according to the applied colourscheme.
Note: its important that the existing group idColour is given priority if it is set, because a number of web services used this feature to shade sequence IDs in this manner.