1 package jalview.structure;
3 import jalview.api.AlignmentViewPanel;
4 import jalview.api.SequenceRenderer;
5 import jalview.datamodel.SequenceI;
12 * Methods that generate commands that can be sent to a molecular structure
13 * viewer program (e.g. Jmol, Chimera, ChimeraX)
18 public interface StructureCommandsI
22 * Returns the command to colour by chain
26 String colourByChain();
29 * Returns the command to colour residues using a charge-based scheme:
31 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
32 * <li>Lysine and Arginine (positive charge) blue</li>
33 * <li>Cysteine - yellow</li>
34 * <li>all others - white</li>
39 String colourByCharge();
42 * Returns the command to colour residues with the colours provided in the
43 * map, one per three letter residue code
48 String colourByResidues(Map<String, Color> colours);
51 * Returns the command to set the background colour of the structure viewer
56 String setBackgroundColour(Color col);
59 * Returns commands to colour mapped residues of structures according to
60 * Jalview's colouring (including feature colouring if applied)
62 * @param structureSelectionManager
69 String[] colourBySequence(
70 StructureSelectionManager structureSelectionManager,
71 String[] files, SequenceI[][] seqs, SequenceRenderer sr,
72 AlignmentViewPanel alignmentv);
75 * Returns a command to centre the display in the structure viewer
82 * Returns a command to show only the selected chains. The items in the input
83 * list should be formatted as "modelno:chainid".
88 String showChains(List<String> toShow);
91 * Returns zero, one or more commands to set attributes on mapped residues in
92 * the structure viewer for any features present and displayed in Jalview
100 String[] setAttributesForFeatures(StructureSelectionManager ssm,
101 String[] files, SequenceI[][] sequence, AlignmentViewPanel avp);