/*
 * 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.gui.JvOptionPane;

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

import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;

public class ChimeraCommandsTest
{

  @BeforeClass(alwaysRun = true)
  public void setUpJvOptionPane()
  {
    JvOptionPane.setInteractiveMode(false);
    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  }

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

    Map<Object, AtomSpecModel> map = new LinkedHashMap<Object, AtomSpecModel>();
    ChimeraCommands.addRange(map, Color.blue, 0, 2, 5, "A");
    ChimeraCommands.addRange(map, Color.blue, 0, 7, 7, "B");
    ChimeraCommands.addRange(map, Color.blue, 0, 9, 23, "A");
    ChimeraCommands.addRange(map, Color.blue, 1, 1, 1, "A");
    ChimeraCommands.addRange(map, Color.blue, 1, 4, 7, "B");
    ChimeraCommands.addRange(map, Color.yellow, 1, 8, 8, "A");
    ChimeraCommands.addRange(map, Color.yellow, 1, 3, 5, "A");
    ChimeraCommands.addRange(map, Color.red, 0, 3, 5, "A");
    ChimeraCommands.addRange(map, Color.red, 0, 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 command = ChimeraCommands.buildColourCommands(map).get(0);
    assertEquals(
            command,
            "color #0000ff #0:2-5.A,9-23.A,7.B|#1:1.A,4-7.B; color #ffff00 #1:3-5.A,8.A; color #ff0000 #0:3-9.A");
  }

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

    /*
     * feature name gets a jv_ namespace prefix
     * feature value is quoted in case it contains spaces
     */
    assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:8-20.A");

    // add same feature value, overlapping range
    ChimeraCommands.addRange(featureValues, "X", 0, 3, 9, "A");
    // same feature value, contiguous range
    ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "A");
    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
    assertEquals(1, commands.size());
    assertEquals(commands.get(0), "setattr r jv_chain \"X\" #0:3-25.A");

    // same feature value and model, different chain
    ChimeraCommands.addRange(featureValues, "X", 0, 21, 25, "B");
    // same feature value and chain, different model
    ChimeraCommands.addRange(featureValues, "X", 1, 26, 30, "A");
    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
    assertEquals(1, commands.size());
    assertEquals(commands.get(0),
            "setattr r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A");

    // same feature, different value
    ChimeraCommands.addRange(featureValues, "Y", 0, 40, 50, "A");
    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
    assertEquals(2, commands.size());
    // commands are ordered by feature type but not by value
    // so use contains to test for the expected command:
    assertTrue(commands
            .contains("setattr r jv_chain \"X\" #0:3-25.A,21-25.B|#1:26-30.A"));
    assertTrue(commands.contains("setattr r jv_chain \"Y\" #0:40-50.A"));

    featuresMap.clear();
    featureValues.clear();
    featuresMap.put("side-chain binding!", featureValues);
    ChimeraCommands.addRange(featureValues, "metal ion!", 0, 7, 15, "A");
    // feature names are sanitised to change space or hyphen to underscore
    commands = ChimeraCommands.buildSetAttributeCommands(featuresMap);
    assertTrue(commands
            .contains("setattr r jv_side_chain_binding_ \"metal ion!\" #0:7-15.A"));
  }

  /**
   * Tests for the method that prefixes and sanitises a feature name so it can
   * be used as a valid, namespaced attribute name in Chimera
   */
  @Test(groups = { "Functional" })
  public void testMakeAttributeName()
  {
    assertEquals(ChimeraCommands.makeAttributeName(null), "jv_");
    assertEquals(ChimeraCommands.makeAttributeName(""), "jv_");
    assertEquals(ChimeraCommands.makeAttributeName("helix"), "jv_helix");
    assertEquals(ChimeraCommands.makeAttributeName("Hello World 24"),
            "jv_Hello_World_24");
    assertEquals(
            ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
            "jv__this_is_a_very__odd_name");
    // name ending in color gets underscore appended
    assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
            "jv_helixColor_");
  }
}