/*
 * 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.pymol;

import static org.testng.Assert.assertEquals;

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

import org.testng.annotations.Test;

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

public class PymolCommandsTest
{

  @Test(groups = { "Functional" })
  public void testColourBySequence()
  {

    Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
    PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
    PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
    PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
    PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
    PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
    PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
    PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
    PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
    PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");

    // Colours should appear in the Pymol command in the order in which
    // they were added; within colour, by model, by chain, ranges in start order
    List<StructureCommandI> commands = new PymolCommands()
            .colourBySequence(map);
    assertEquals(commands.size(), 3);
    assertEquals(commands.get(0).toString(),
            "color(0x0000ff,0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/)");
    assertEquals(commands.get(1).toString(), "color(0xffff00,1//A/3-5+8/)");
    assertEquals(
            commands.get(2).toString(), "color(0xff0000,0//A/3-9/)");
  }

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

  }

  @Test(groups = { "Functional" })
  public void testSuperposeStructures()
  {
    StructureCommandsI testee = new PymolCommands();
    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");
    List<StructureCommandI> commands = testee.superposeStructures(ref,
            toAlign);
    assertEquals(commands.size(), 2);
    String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
    String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
    String refSpec = "1//A/12-14/ 1//B/18+22-23/";
    String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
    String expected1 = String.format("super(%s,%s)", refSpecCA,
            toAlignSpecCA);
    String expected2 = String.format("show(cartoon,%s %s)", refSpec,
            toAlignSpec);
    assertEquals(commands.get(0).toString(), expected1);
    assertEquals(commands.get(1).toString(), expected2);
  }

  @Test(groups = "Functional")
  public void testGetAtomSpec_alphaOnly()
  {
    StructureCommandsI testee = new PymolCommands();
    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");
    model.addRange("1", 8, 8, "A");
    assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
    model.addRange("1", 5, 7, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "1//A/2-4+8/CA 1//B/5-7/CA");
    model.addRange("1", 3, 5, "A");
    assertEquals(testee.getAtomSpec(model, true),
            "1//A/2-5+8/CA 1//B/5-7/CA");
    model.addRange("0", 1, 4, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
    model.addRange("0", 5, 9, "C");
    assertEquals(testee.getAtomSpec(model, true),
            "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
    model.addRange("1", 8, 10, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
    model.addRange("1", 8, 9, "B");
    assertEquals(testee.getAtomSpec(model, true),
            "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
    model.addRange("0", 3, 10, "C"); // subsumes 5-9
    assertEquals(testee.getAtomSpec(model, true),
            "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
    model.addRange("5", 25, 35, " ");
    assertEquals(testee.getAtomSpec(model, true),
            "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
  }

  @Test(groups = "Functional")
  public void testGetModelStartNo()
  {
    StructureCommandsI testee = new PymolCommands();
    assertEquals(testee.getModelStartNo(), 0);
  }

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

  @Test(groups = "Functional")
  public void testShowBackbone()
  {
    PymolCommands testee = new PymolCommands();
    List<StructureCommandI> cmds = testee.showBackbone();
    assertEquals(cmds.size(), 2);
    assertEquals(cmds.get(0).toString(), "hide(everything)");
    assertEquals(cmds.get(1).toString(), "show(ribbon)");
  }

  @Test(groups = "Functional")
  public void testColourByCharge()
  {
    PymolCommands testee = new PymolCommands();
    List<StructureCommandI> cmds = testee.colourByCharge();
    assertEquals(cmds.size(), 4);
    assertEquals(cmds.get(0).toString(), "color(white,*)");
    assertEquals(cmds.get(1).toString(), "color(red,resn ASP resn GLU)");
    assertEquals(cmds.get(2).toString(), "color(blue,resn LYS resn ARG)");
    assertEquals(cmds.get(3).toString(), "color(yellow,resn CYS)");
  }

  @Test(groups = "Functional")
  public void testOpenCommandFile()
  {
    PymolCommands testee = new PymolCommands();
    assertEquals(testee.openCommandFile("commands.pml").toString(),
            "run(commands.pml)");
  }

  @Test(groups = "Functional")
  public void testSaveSession()
  {
    PymolCommands testee = new PymolCommands();
    assertEquals(testee.saveSession("somewhere.pse").toString(),
            "save(somewhere.pse)");
  }

  @Test(groups = "Functional")
  public void testColourByChain()
  {
    PymolCommands testee = new PymolCommands();
    assertEquals(testee.colourByChain().toString(), "spectrum(chain)");
  }

  @Test(groups = "Functional")
  public void testGetColourCommand()
  {
    PymolCommands testee = new PymolCommands();
    assertEquals(
            testee.getColourCommand("something", Color.MAGENTA).toString(),
            "color(0xff00ff,something)");
  }
}