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:
   * <ul>
   * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
   * <li>Lysine and Arginine (positive charge) blue</li>
   * <li>Cysteine - yellow</li>
   * <li>all others - white</li>
   * </ul>
   * 
   * @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<String, Color> 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<String> toShow);

}