/*
* 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 .
* 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 java.awt.Color;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
public class ChimeraCommandsTest
{
@Test(groups = { "Functional" })
public void testBuildColourCommands()
{
Map map = new LinkedHashMap();
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> featuresMap = new LinkedHashMap>();
Map featureValues = new HashMap();
/*
* start with just one feature/value...
*/
featuresMap.put("chain", featureValues);
ChimeraCommands.addRange(featureValues, "X", 0, 8, 20, "A");
List 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_");
}
}