package jalview.structure;
import jalview.api.AlignmentViewPanel;
import jalview.api.SequenceRenderer;
import jalview.datamodel.SequenceI;
import java.awt.Color;
import java.util.List;
import java.util.Map;
/**
* Methods that generate commands that can be sent to a molecular structure
* viewer program (e.g. Jmol, Chimera, ChimeraX)
*
* @author gmcarstairs
*
*/
public interface StructureCommandsI
{
/**
* Returns the command to colour by chain
*
* @return
*/
String colourByChain();
/**
* Returns the command to colour residues using a charge-based scheme:
*
* - Aspartic acid and Glutamic acid (negative charge) red
* - Lysine and Arginine (positive charge) blue
* - Cysteine - yellow
* - all others - white
*
*
* @return
*/
String colourByCharge();
/**
* Returns the command to colour residues with the colours provided in the
* map, one per three letter residue code
*
* @param colours
* @return
*/
String colourByResidues(Map colours);
/**
* Returns the command to set the background colour of the structure viewer
*
* @param col
* @return
*/
String setBackgroundColour(Color col);
/**
* Returns commands to colour mapped residues of structures according to
* Jalview's colouring (including feature colouring if applied)
*
* @param structureSelectionManager
* @param files
* @param seqs
* @param sr
* @param alignmentv
* @return
*/
String[] colourBySequence(
StructureSelectionManager structureSelectionManager,
String[] files, SequenceI[][] seqs, SequenceRenderer sr,
AlignmentViewPanel alignmentv);
/**
* Returns a command to centre the display in the structure viewer
*
* @return
*/
String focusView();
/**
* Returns a command to show only the selected chains. The items in the input
* list should be formatted as "modelno:chainid".
*
* @param toShow
* @return
*/
String showChains(List toShow);
}