From 3aa65eeda9ad02a8237543eadd9808b86bd1e15b Mon Sep 17 00:00:00 2001 From: gmungoc Date: Thu, 8 Aug 2019 17:23:47 +0100 Subject: [PATCH] JAL-3390 improved Jmol colour by sequence command + tests + deprecations --- src/jalview/ext/jmol/JmolCommands.java | 31 ++--- test/jalview/ext/jmol/JmolCommandsTest.java | 200 ++++++++++++++++++++++++--- 2 files changed, 195 insertions(+), 36 deletions(-) diff --git a/src/jalview/ext/jmol/JmolCommands.java b/src/jalview/ext/jmol/JmolCommands.java index 512080a..f0949b8 100644 --- a/src/jalview/ext/jmol/JmolCommands.java +++ b/src/jalview/ext/jmol/JmolCommands.java @@ -33,7 +33,6 @@ import jalview.renderer.seqfeatures.FeatureColourFinder; import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; -import jalview.structures.models.AAStructureBindingModel; import java.awt.Color; import java.util.ArrayList; @@ -51,21 +50,18 @@ public class JmolCommands extends StructureCommands private static final String COMMA = ","; /** - * Jmol utility which constructs the commands to colour chains by the given - * alignment - * - * @returns Object[] { Object[] { , + * Get commands to colour structure by sequence * + * @param ssm + * @param files + * @param sequence + * @param sr + * @param viewPanel + * @return + * @deprecated only called by applet code + * @see #getColourBySequenceCommand(Map) */ - public static StructureMappingcommandSet[] getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - AAStructureBindingModel binding, AlignmentViewPanel viewPanel) - { - SequenceRenderer sr = binding.getSequenceRenderer(viewPanel); - SequenceI[][] sequence = binding.getSequence(); - return getColourBySequenceCommand(ssm, files, sequence, sr, viewPanel); - } - + @Deprecated public static StructureMappingcommandSet[] getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, SequenceI[][] sequence, SequenceRenderer sr, @@ -238,7 +234,7 @@ public class JmolCommands extends StructureCommands StringBuilder cmd = new StringBuilder(128); Color c = (Color) o; String atomSpec = getAtomSpec(map.get(o)); - cmd.append("select ").append(atomSpec).append(";color[") + cmd.append("color (").append(atomSpec).append(") [") .append(c.getRed()).append(COMMA).append(c.getGreen()) .append(COMMA).append(c.getBlue()).append("];"); cmds[i] = cmd.toString(); @@ -252,10 +248,13 @@ public class JmolCommands extends StructureCommands * Builds a Jmol syntax selection expression from the given model, for example * * 
-   * 61-64,70:A/1.1,12-25,41-44:B/1.1,12:A/2.1
+   * (61-64,70)&:A/1.1,(12-25,41-44)&:B/1.1,12:A/2.1
    * for model 1, chain A, residues 61-64 and 70, chain B residues 12-25 and 41-44, model 2 chain A residue 12
    *
* + * Note the brackets to group multiple residue ranges for the same chain + * (without bracketing, ranges would apply to all chains) + * * @param atomSpecModel * @return */ diff --git a/test/jalview/ext/jmol/JmolCommandsTest.java b/test/jalview/ext/jmol/JmolCommandsTest.java index f1cc820..e140fe1 100644 --- a/test/jalview/ext/jmol/JmolCommandsTest.java +++ b/test/jalview/ext/jmol/JmolCommandsTest.java @@ -23,27 +23,120 @@ package jalview.ext.jmol; import static org.testng.Assert.assertEquals; import static org.testng.Assert.assertTrue; +import jalview.api.AlignmentViewPanel; +import jalview.api.FeatureRenderer; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.ext.rbvi.chimera.AtomSpecModel; +import jalview.ext.rbvi.chimera.StructureCommands; import jalview.gui.AlignFrame; import jalview.gui.JvOptionPane; import jalview.gui.SequenceRenderer; +import jalview.schemes.ColourSchemeI; import jalview.schemes.JalviewColourScheme; +import jalview.structure.AtomSpec; import jalview.structure.StructureMapping; import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; +import jalview.structures.models.AAStructureBindingModel; +import java.awt.Color; import java.util.HashMap; +import java.util.List; +import java.util.Map; import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; +import junit.extensions.PA; + public class JmolCommandsTest { + private SequenceRenderer sr; + + private String[] files; + + private AAStructureBindingModel mockBinding = new AAStructureBindingModel( + null, null) + { + @Override + public void releaseReferences(Object svl) + { + } + + @Override + public void highlightAtoms(List atoms) + { + } + + @Override + public void setJalviewColourScheme(ColourSchemeI cs) + { + } + + @Override + public String superposeStructures(AlignmentI[] alignments, + int[] structureIndices, HiddenColumns[] hiddenCols) + { + return null; + } + + @Override + public void setBackgroundColour(Color col) + { + } + + @Override + protected String[] getColourBySequenceCommands(String[] files, + AlignmentViewPanel avp) + { + return null; + } + + @Override + public jalview.api.SequenceRenderer getSequenceRenderer( + AlignmentViewPanel alignment) + { + return sr; + } + + @Override + protected void colourBySequence(String[] colourBySequenceCommands) + { + } + + @Override + public void colourByChain() + { + } + + @Override + public void colourByCharge() + { + } + + @Override + public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment) + { + return null; + } + + @Override + public String[] getStructureFiles() + { + return files; + } + + @Override + public String getModelSpec(int model) + { + return "#" + String.valueOf(model); + } + }; @BeforeClass(alwaysRun = true) public void setUpJvOptionPane() @@ -52,26 +145,10 @@ public class JmolCommandsTest JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); } - @Test(groups = { "Functional" }) - public void testGetColourBySequenceCommand_noFeatures() - { - SequenceI seq1 = new Sequence("seq1", "MHRSQTRALK"); - SequenceI seq2 = new Sequence("seq2", "MRLEITQSGD"); - AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); - AlignFrame af = new AlignFrame(al, 800, 500); - SequenceRenderer sr = new SequenceRenderer(af.getViewport()); - SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; - String[] files = new String[] { "seq1.pdb", "seq2.pdb" }; - StructureSelectionManager ssm = new StructureSelectionManager(); - - // need some mappings! - - StructureMappingcommandSet[] commands = JmolCommands - .getColourBySequenceCommand(ssm, files, seqs, sr, - af.alignPanel); - } - - @Test(groups = { "Functional" }) + /** + * Test for the now deprecated version of getColourBySequenceCommand + */ + @Test(groups = { "Functional" }, enabled = false) public void testGetColourBySequenceCommands_hiddenColumns() { /* @@ -195,4 +272,87 @@ public class JmolCommandsTest assertEquals(JmolCommands.getAtomSpec(model), "1-4:B/1.1,(3-10)&:C/1.1,(2-5,8)&:A/2.1,(5-10)&:B/2.1,25-35:/6.1"); } + + @Test(groups = "Functional") + public void testGetColourBySequenceCommand_mapVersion() + { + /* + * load these sequences, coloured by Strand propensity, + * with columns 2-4 hidden (counting from 0) + */ + SequenceI seq1 = new Sequence("seq1", "MHRSQSSSGG"); + SequenceI seq2 = new Sequence("seq2", "MVRSNGGMSS"); + 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); + sr = new SequenceRenderer(af.getViewport()); + SequenceI[][] seqs = new SequenceI[][] { { seq1 }, { seq2 } }; + files = new String[] { "seq1.pdb", "seq2.pdb" }; + StructureSelectionManager ssm = new StructureSelectionManager(); + + /* + * map residues 1-10 to residues 21-30 (atoms 105-150) in structures + */ + HashMap 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); + + /* + * put data into the mock binding object + */ + PA.setValue(mockBinding, "ssm", ssm); + PA.setValue(mockBinding, "sequence", seqs); + + Map colourMap = StructureCommands + .buildColoursMap(mockBinding, af.alignPanel); + + String[] commands = JmolCommands.getColourBySequenceCommand(colourMap); + + assertEquals(commands.length, 5); + + /* + * verify selections and colours match Strand Propensity colour scheme + * (see strand.html help page for colours) + * + * M is #82827d == (130, 130, 125) at model 1 pos 21A, model 2 21B + */ + assertEquals(commands[0], + "color (21:A/1.1,(21,28)&:B/2.1) [130,130,125];"); + + /* + * H is #60609f == (96, 96, 159) + */ + assertEquals(commands[1], "color (22:A/1.1) [96,96,159];"); + + /* + * hidden columns are Gray (128, 128, 128) + */ + assertEquals(commands[2], + "color (23-25:A/1.1,23-25:B/2.1) [128,128,128];"); + + /* + * S and G are both coloured #4949b6 == (73, 73, 182) + */ + assertEquals(commands[3], + "color (26-30:A/1.1,(26-27,29-30)&:B/2.1) [73,73,182];"); + + /* + * V is ffff00 == (255, 255, 0) + */ + assertEquals(commands[4], "color (22:B/2.1) [255,255,0];"); + } } -- 1.7.10.2