+++ /dev/null
-/*
- * 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.datamodel.Alignment;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.JvOptionPane;
-import jalview.gui.SequenceRenderer;
-import jalview.schemes.JalviewColourScheme;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
-import jalview.structure.StructureSelectionManager;
-
-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<>();
- ChimeraCommands.addColourRange(map, Color.blue, 0, 2, 5, "A");
- ChimeraCommands.addColourRange(map, Color.blue, 0, 7, 7, "B");
- ChimeraCommands.addColourRange(map, Color.blue, 0, 9, 23, "A");
- ChimeraCommands.addColourRange(map, Color.blue, 1, 1, 1, "A");
- ChimeraCommands.addColourRange(map, Color.blue, 1, 4, 7, "B");
- ChimeraCommands.addColourRange(map, Color.yellow, 1, 8, 8, "A");
- ChimeraCommands.addColourRange(map, Color.yellow, 1, 3, 5, "A");
- ChimeraCommands.addColourRange(map, Color.red, 0, 3, 5, "A");
- ChimeraCommands.addColourRange(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<>();
- Map<Object, AtomSpecModel> featureValues = new HashMap<>();
-
- /*
- * start with just one feature/value...
- */
- featuresMap.put("chain", featureValues);
- ChimeraCommands.addColourRange(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.addColourRange(featureValues, "X", 0, 3, 9, "A");
- // same feature value, contiguous range
- ChimeraCommands.addColourRange(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.addColourRange(featureValues, "X", 0, 21, 25, "B");
- // same feature value and chain, different model
- ChimeraCommands.addColourRange(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.addColourRange(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.addColourRange(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 = ChimeraCommands.buildSetAttributeCommands(featuresMap);
- assertTrue(commands
- .contains("setattr r jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> '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_");
- }
-
- @Test(groups = { "Functional" })
- public void testGetColourBySequenceCommands_hiddenColumns()
- {
- /*
- * load these sequences, coloured by Strand propensity,
- * with columns 2-4 hidden
- */
- SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG");
- SequenceI seq2 = new Sequence("seq2", "MVRSNGGSSS");
- AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
- AlignFrame af = new AlignFrame(al, 800, 500);
- af.changeColour_actionPerformed(JalviewColourScheme.Strand.toString());
- ColumnSelection cs = new ColumnSelection();
- cs.addElement(2);
- cs.addElement(3);
- cs.addElement(4);
- af.getViewport().setColumnSelection(cs);
- af.hideSelColumns_actionPerformed(null);
- SequenceRenderer sr = new SequenceRenderer(af.getViewport());
- SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } };
- String[] files = new String[] { "seq1.pdb", "seq2.pdb" };
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(null);
-
- /*
- * map residues 1-10 to residues 21-30 (atoms 105-150) in structures
- */
- HashMap<Integer, int[]> map = new HashMap<>();
- for (int pos = 1; pos <= seq1.getLength(); pos++)
- {
- map.put(pos, new int[] { 20 + pos, 5 * (20 + pos) });
- }
- StructureMapping sm1 = new StructureMapping(seq1, "seq1.pdb", "pdb1",
- "A", map, null);
- ssm.addStructureMapping(sm1);
- StructureMapping sm2 = new StructureMapping(seq2, "seq2.pdb", "pdb2",
- "B", map, null);
- ssm.addStructureMapping(sm2);
-
- StructureMappingcommandSet[] commands = ChimeraCommands
- .getColourBySequenceCommand(ssm, files, seqs, sr, af.alignPanel);
- assertEquals(1, commands.length);
- assertEquals(1, commands[0].commands.length);
- String theCommand = commands[0].commands[0];
- // M colour is #82827d (see strand.html help page)
- assertTrue(theCommand.contains("color #82827d #0:21.A|#1:21.B"));
- // H colour is #60609f
- assertTrue(theCommand.contains("color #60609f #0:22.A"));
- // V colour is #ffff00
- assertTrue(theCommand.contains("color #ffff00 #1:22.B"));
- // hidden columns are Gray (128, 128, 128)
- assertTrue(theCommand.contains("color #808080 #0:23-25.A|#1:23-25.B"));
- // S and G are both coloured #4949b6
- assertTrue(theCommand.contains("color #4949b6 #0:26-30.A|#1:26-30.B"));
- }
-}
git://source.jalview.org / jalview.git / blobdiff