From: gmungoc Date: Thu, 10 Nov 2016 13:01:23 +0000 (+0000) Subject: JAL-2295 additional tests, stronger sanitisation of attribute name X-Git-Tag: Release_2_11_0~62^2~63 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=fb315d08a73717eebc3d3a8832a9456fcef52484 JAL-2295 additional tests, stronger sanitisation of attribute name --- diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index a5ee933..9ef89fd 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -49,12 +49,18 @@ import MCview.PDBChain; public class ChimeraCommands { + private static final String NAMESPACE_PREFIX = "jv_"; + /** - * utility to construct the commands to colour chains by the given alignment - * for passing to Chimera - * - * @returns Object[] { Object[] { , + * Constructs Chimera commands to colour residues as per the Jalview alignment * + * @param ssm + * @param files + * @param sequence + * @param sr + * @param fr + * @param alignment + * @return */ public static StructureMappingcommandSet getColourBySequenceCommand( StructureSelectionManager ssm, String[] files, @@ -286,8 +292,9 @@ public class ChimeraCommands } /** - * Constructs and returns a set of Chimera commands to set attributes on - * residues corresponding to features in Jalview + * Constructs and returns Chimera commands to set attributes on residues + * corresponding to features in Jalview. Attribute names are the Jalview + * feature type, with a "jv_" prefix. * * @param ssm * @param files @@ -403,7 +410,7 @@ public class ChimeraCommands if (!mappedRanges.isEmpty()) { String value = sf.getDescription(); - if (value == null) + if (value == null || value.length() == 0) { value = type; } @@ -460,8 +467,7 @@ public class ChimeraCommands List commands = new ArrayList(); for (String featureType : featureMap.keySet()) { - String attributeName = "jv_" - + featureType.replace(" ", "_").replace("-", "_"); + String attributeName = makeAttributeName(featureType); /* * clear down existing attributes for this feature @@ -487,4 +493,38 @@ public class ChimeraCommands return commands; } + /** + * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied + * for a 'Jalview' namespace, and any non-alphanumeric character is converted + * to an underscore. + * + * @param featureType + * @return 
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+   *
+ */ + protected static String makeAttributeName(String featureType) + { + StringBuilder sb = new StringBuilder(); + if (featureType != null) + { + for (char c : featureType.toCharArray()) + { + sb.append(Character.isLetterOrDigit(c) ? c : '_'); + } + } + String attName = NAMESPACE_PREFIX + sb.toString(); + + /* + * Chimera treats an attribute name ending in 'color' as colour-valued; + * Jalview doesn't, so prevent this by appending an underscore + */ + if (attName.toUpperCase().endsWith("COLOR")) + { + attName += "_"; + } + + return attName; + } + } diff --git a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java index b534b4f..f24ff22 100644 --- a/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java +++ b/test/jalview/ext/rbvi/chimera/ChimeraCommandsTest.java @@ -20,10 +20,13 @@ */ package jalview.ext.rbvi.chimera; -import static org.testng.AssertJUnit.assertEquals; +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; @@ -49,7 +52,89 @@ public class ChimeraCommandsTest // they were added; within colour, by model, by chain, ranges in start order String command = ChimeraCommands.buildColourCommands(map).get(0); assertEquals( - "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", - command); + 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_"); } }