/*
 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
 * Copyright (C) $$Year-Rel$$ The Jalview Authors
 * 
 * This file is part of Jalview.
 * 
 * Jalview is free software: you can redistribute it and/or
 * modify it under the terms of the GNU General Public License 
 * as published by the Free Software Foundation, either version 3
 * of the License, or (at your option) any later version.
 *  
 * Jalview is distributed in the hope that it will be useful, but 
 * WITHOUT ANY WARRANTY; without even the implied warranty 
 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
 * PURPOSE.  See the GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 * The Jalview Authors are detailed in the 'AUTHORS' file.
 */
package jalview.ext.rbvi.chimera;

import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;

import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsI;

import java.awt.Color;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;

import org.testng.annotations.Test;

public class ChimeraXCommandsTest
{
  @Test(groups = { "Functional" })
  public void testColourByCharge()
  {
    String cmd = new ChimeraXCommands().colourByCharge();
    assertEquals(cmd,
            "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
  }

  @Test(groups = { "Functional" })
  public void testColourByChain()
  {
    String cmd = new ChimeraXCommands().colourByChain();
    assertEquals(cmd, "rainbow chain");
  }

  @Test(groups = { "Functional" })
  public void testFocusView()
  {
    String cmd = new ChimeraXCommands().focusView();
    assertEquals(cmd, "view");
  }

  @Test(groups = { "Functional" })
  public void testColourBySequence()
  {
    Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
    ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 2, 5, "A");
    ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 7, 7, "B");
    ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 9, 23, "A");
    ChimeraCommands.addAtomSpecRange(map, Color.blue, 2, 1, 1, "A");
    ChimeraCommands.addAtomSpecRange(map, Color.blue, 2, 4, 7, "B");
    ChimeraCommands.addAtomSpecRange(map, Color.yellow, 2, 8, 8, "A");
    ChimeraCommands.addAtomSpecRange(map, Color.yellow, 2, 3, 5, "A");
    ChimeraCommands.addAtomSpecRange(map, Color.red, 1, 3, 5, "A");
    ChimeraCommands.addAtomSpecRange(map, Color.red, 1, 6, 9, "A");

    // Colours should appear in the Chimera command in the order in which
    // they were added; within colour, by model, by chain, ranges in start order
    String[] commands = new ChimeraXCommands().colourBySequence(map);
    assertEquals(commands.length, 1);
    assertEquals(
            commands[0],
            "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff; color #2/A:3-5,8 #ffff00; color #1/A:3-9 #ff0000");
  }

  @Test(groups = { "Functional" })
  public void testSetAttributes()
  {
    /*
     * make a map of { featureType, {featureValue, {residue range specification } } }
     */
    Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
    Map<Object, AtomSpecModel> featureValues = new HashMap<>();
    
    /*
     * start with just one feature/value...
     */
    featuresMap.put("chain", featureValues);
    ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
  
    ChimeraXCommands commandGenerator = new ChimeraXCommands();
    String[] commands = commandGenerator.setAttributes(featuresMap);
    assertEquals(commands.length, 1);

    /*
     * feature name gets a jv_ namespace prefix
     * feature value is quoted in case it contains spaces
     */
    assertEquals(commands[0],
            "setattr #0/A:8-20 res jv_chain 'X' create true");

    // add same feature value, overlapping range
    ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
    // same feature value, contiguous range
    ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
    commands = commandGenerator.setAttributes(featuresMap);
    assertEquals(commands.length, 1);
    assertEquals(commands[0],
            "setattr #0/A:3-25 res jv_chain 'X' create true");

    // same feature value and model, different chain
    ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
    // same feature value and chain, different model
    ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
    commands = commandGenerator.setAttributes(featuresMap);
    assertEquals(commands.length, 1);
    String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
    assertEquals(commands[0], expected1);

    // same feature, different value
    ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
    commands = commandGenerator.setAttributes(featuresMap);
    assertEquals(2, commands.length);
    // commands are ordered by feature type but not by value
    // so test for the expected command in either order
    assertTrue(
            commands[0].equals(expected1) || commands[1].equals(expected1));
    String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
    assertTrue(
            commands[0].equals(expected2) || commands[1].equals(expected2));

    featuresMap.clear();
    featureValues.clear();
    featuresMap.put("side-chain binding!", featureValues);
    ChimeraCommands.addAtomSpecRange(featureValues,
            "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", 0, 7, 15,
            "A");
    // feature names are sanitised to change non-alphanumeric to underscore
    // feature values are sanitised to encode single quote characters
    commands = commandGenerator.setAttributes(featuresMap);
    String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> &#39;ion!' create true";
    assertTrue(
            commands[0].equals(expected3) || commands[1].equals(expected3));
  }

  @Test(groups = { "Functional" })
  public void testSuperposeStructures()
  {
    StructureCommandsI testee = new ChimeraXCommands();
    AtomSpecModel ref = new AtomSpecModel();
    ref.addRange(1, 12, 14, "A");
    ref.addRange(1, 18, 18, "B");
    ref.addRange(1, 22, 23, "B");
    AtomSpecModel toAlign = new AtomSpecModel();
    toAlign.addRange(2, 15, 17, "B");
    toAlign.addRange(2, 20, 21, "B");
    toAlign.addRange(2, 22, 22, "C");
    String command = testee.superposeStructures(ref, toAlign);
    String refSpec = "#1/A:12-14/B:18,22-23";
    String toAlignSpec = "#2/B:15-17,20-21/C:22";

    /*
     * superposition arguments include AlphaCarbon restriction,
     * ribbon command does not
     */
    String expected = String.format(
            "align %s@CA|P toAtoms %s@CA|P; ribbon %s|%s; view",
            refSpec, toAlignSpec, refSpec, toAlignSpec);
    assertEquals(command, expected);
  }

  @Test(groups = "Functional")
  public void testGetAtomSpec()
  {
    StructureCommandsI testee = new ChimeraXCommands();
    AtomSpecModel model = new AtomSpecModel();
    assertEquals(testee.getAtomSpec(model, false), "");
    model.addRange(1, 2, 4, "A");
    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
    model.addRange(1, 8, 8, "A");
    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
    model.addRange(1, 5, 7, "B");
    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
    model.addRange(1, 3, 5, "A");
    assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
    model.addRange(0, 1, 4, "B");
    assertEquals(testee.getAtomSpec(model, false),
            "#0/B:1-4|#1/A:2-5,8/B:5-7");
    model.addRange(0, 5, 9, "C");
    assertEquals(testee.getAtomSpec(model, false),
            "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
    model.addRange(1, 8, 10, "B");
    assertEquals(testee.getAtomSpec(model, false),
            "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
    model.addRange(1, 8, 9, "B");
    assertEquals(testee.getAtomSpec(model, false),
            "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
    model.addRange(0, 3, 10, "C"); // subsumes 5-9
    assertEquals(testee.getAtomSpec(model, false),
            "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
    model.addRange(5, 25, 35, " ");
    assertEquals(testee.getAtomSpec(model, false),
            "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
  }

  @Test(groups = "Functional")
  public void testGetAtomSpec_alphaOnly()
  {
    StructureCommandsI testee = new ChimeraXCommands();
    AtomSpecModel model = new AtomSpecModel();
    assertEquals(testee.getAtomSpec(model, true), "");
    model.addRange(1, 2, 4, "A");
    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA|P");
    model.addRange(1, 8, 8, "A");
    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA|P");
    model.addRange(1, 5, 7, "B");
    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA|P");
    model.addRange(1, 3, 5, "A");
    assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA|P");
    model.addRange(0, 1, 4, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "#0/B:1-4@CA|P|#1/A:2-5,8/B:5-7@CA|P");
    model.addRange(0, 5, 9, "C");
    assertEquals(testee.getAtomSpec(model, true),
            "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-7@CA|P");
    model.addRange(1, 8, 10, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-10@CA|P");
    model.addRange(1, 8, 9, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "#0/B:1-4/C:5-9@CA|P|#1/A:2-5,8/B:5-10@CA|P");
    model.addRange(0, 3, 10, "C"); // subsumes 5-9
    assertEquals(testee.getAtomSpec(model, true),
            "#0/B:1-4/C:3-10@CA|P|#1/A:2-5,8/B:5-10@CA|P");
    model.addRange(5, 25, 35, " "); // empty chain code
    assertEquals(testee.getAtomSpec(model, true),
            "#0/B:1-4/C:3-10@CA|P|#1/A:2-5,8/B:5-10@CA|P|#5/:25-35@CA|P");
  }

  @Test(groups = "Functional")
  public void testGetModelStartNo()
  {
    StructureCommandsI testee = new ChimeraXCommands();
    assertEquals(testee.getModelStartNo(), 1);
  }

  @Test(groups = "Functional")
  public void testGetResidueSpec()
  {
    ChimeraCommands testee = new ChimeraXCommands();
    assertEquals(testee.getResidueSpec("ALA"), ":ALA");
  }

  @Test(groups = "Functional")
  public void testShowBackbone()
  {
    ChimeraCommands testee = new ChimeraXCommands();
    assertEquals(testee.showBackbone(), "~display all;show @CA|P pbonds");
  }

  @Test(groups = "Functional")
  public void testOpenCommandFile()
  {
    ChimeraCommands testee = new ChimeraXCommands();
    assertEquals(testee.openCommandFile("nowhere"), "open nowhere");
  }

  @Test(groups = "Functional")
  public void testSaveSession()
  {
    ChimeraCommands testee = new ChimeraXCommands();
    assertEquals(testee.saveSession("somewhere"), "save session somewhere");
  }

  @Test(groups = "Functional")
  public void testGetColourCommand()
  {
    ChimeraCommands testee = new ChimeraXCommands();
    assertEquals(testee.getColourCommand("something", Color.MAGENTA),
            "color something #ff00ff");
  }

  @Test(groups = "Functional")
  public void testSetAttribute()
  {
    ChimeraCommands testee = new ChimeraXCommands();
    AtomSpecModel model = new AtomSpecModel();
    model.addRange(1, 89, 92, "A");
    model.addRange(2, 12, 20, "B");
    model.addRange(2, 8, 9, "B");
    assertEquals(testee.setAttribute("phi", "27.3", model),
            "setattr #1/A:89-92|#2/B:8-9,12-20 res phi '27.3' create true");
  }
}