public List<String> getAttrList()
{
List<String> attributes = new ArrayList<>();
- String command = (isChimeraX ? "info " : "list") + "resattr";
+ String command = (isChimeraX ? "info " : "list ") + "resattr";
final List<String> reply = sendChimeraCommand(command, true);
if (reply != null)
{
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
return colourMap;
}
+ /**
+ * Returns the lowest model number used by the structure viewer
+ *
+ * @return
+ */
protected static int getModelStartNo()
{
return 0;
* @param endPos
* @param chain
*/
- protected static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
+ protected static final void addAtomSpecRange(
+ Map<Object, AtomSpecModel> map,
Object value, int model, int startPos, int endPos, String chain)
{
/*
* @param files
* @param seqs
* @param viewPanel
- * @param isChimeraX
* @return
*/
- public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
+ @Override
+ public String[] setAttributesForFeatures(
StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel, boolean isChimeraX)
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, viewPanel, isChimeraX);
-
- List<String> commands = buildSetAttributeCommands(featureMap,
- isChimeraX);
+ ssm, files, seqs, viewPanel);
- StructureMappingcommandSet cs = new StructureMappingcommandSet(
- ChimeraCommands.class, null,
- commands.toArray(new String[commands.size()]));
+ List<String> commands = buildSetAttributeCommands(featureMap);
- return cs;
+ return commands.toArray(new String[commands.size()]);
}
/**
* @param files
* @param seqs
* @param viewPanel
- * @param isChimeraX
* @return
*/
protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel, boolean isChimeraX)
+ AlignmentViewPanel viewPanel)
{
Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
AlignmentI alignment = viewPanel.getAlignment();
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- final int modelNumber = pdbfnum + (isChimeraX ? 1 : 0);
+ final int modelNumber = pdbfnum + getModelStartNo();
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
if (mapping == null || mapping.length < 1)
*
* <pre>
* <blockquote> setattr r <featureName> " " #modelnumber:range.chain
- * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
* </blockquote>
* </pre>
*
* @param featureMap
- * @param isChimeraX
* @return
*/
- protected static List<String> buildSetAttributeCommands(
- Map<String, Map<Object, AtomSpecModel>> featureMap,
- boolean isChimeraX)
+ protected List<String> buildSetAttributeCommands(
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<>();
for (String featureType : featureMap.keySet())
* Put values in single quotes, encoding any embedded single quotes
*/
AtomSpecModel atomSpecModel = values.get(value);
- StringBuilder sb = new StringBuilder(128);
- sb.append("setattr");
- if (isChimeraX)
- {
- sb.append(" ").append(atomSpecModel.getAtomSpecX());
- }
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
- sb.append(" res ").append(attributeName).append(" '")
- .append(featureValue).append("' ");
- if (isChimeraX)
- {
- sb.append(" create true");
- }
- else
- {
- sb.append(atomSpecModel.getAtomSpec());
- }
- commands.add(sb.toString());
+ String cmd = getSetAttributeCommand(attributeName, featureValue,
+ atomSpecModel);
+ commands.add(cmd);
}
}
}
/**
+ * Returns a viewer command to set the given residue attribute value on
+ * residues specified by the AtomSpecModel, for example
+ *
+ * <pre>
+ * setatr res jv_chain 'primary' #1:12-34,48-55.B
+ * </pre>
+ *
+ * @param attributeName
+ * @param attributeValue
+ * @param atomSpecModel
+ * @return
+ */
+ protected String getSetAttributeCommand(String attributeName,
+ String attributeValue,
+ AtomSpecModel atomSpecModel)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("setattr res ").append(attributeName).append(" '")
+ .append(attributeValue).append("' ");
+ sb.append(atomSpecModel.getAtomSpec());
+ return sb.toString();
+ }
+
+ /**
* 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
- *
- * <pre>
- * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
- * </pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
*/
protected static String makeAttributeName(String featureType)
{
import jalview.gui.Desktop;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
import jalview.util.Comparison;
*/
public class ChimeraXCommands extends ChimeraCommands
{
- public static final String NAMESPACE_PREFIX = "jv_";
-
private static final String CMD_COLOUR_BY_CHARGE = "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow";
/**
* Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
- * builds a Chimera format atom spec
+ * builds a ChimeraX format atom spec
*
* @param modelAndChainRanges
*/
}
/**
- * Helper method to add one contiguous range to the AtomSpec model for the given
- * value (creating the model if necessary). As used by Jalview, {@code value} is
- * <ul>
- * <li>a colour, when building a 'colour structure by sequence' command</li>
- * <li>a feature value, when building a 'set Chimera attributes from features'
- * command</li>
- * </ul>
- *
- * @param map
- * @param value
- * @param model
- * @param startPos
- * @param endPos
- * @param chain
- */
- protected static void addAtomSpecRange(Map<Object, AtomSpecModel> map,
- Object value, int model, int startPos, int endPos, String chain)
- {
- /*
- * Get/initialize map of data for the colour
- */
- AtomSpecModel atomSpec = map.get(value);
- if (atomSpec == null)
- {
- atomSpec = new AtomSpecModel();
- map.put(value, atomSpec);
- }
-
- atomSpec.addRange(model, startPos, endPos, chain);
- }
-
- /**
- * 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
- * @param seqs
- * @param viewPanel
- * @return
- */
- public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
- {
- Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, viewPanel);
-
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- StructureMappingcommandSet cs = new StructureMappingcommandSet(
- ChimeraXCommands.class, null,
- commands.toArray(new String[commands.size()]));
-
- return cs;
- }
-
- /**
* <pre>
* Helper method to build a map of
* { featureType, { feature value, AtomSpecModel } }
}
/**
- * Traverse the map of features/values/models/chains/positions to construct a
- * list of 'setattr' commands (one per distinct feature type and value).
- * <p>
- * The format of each command is
- *
- * <pre>
- * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
- * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
- * </blockquote>
- * </pre>
- *
- * @param featureMap
- * @return
- */
- protected static List<String> buildSetAttributeCommands(
- Map<String, Map<Object, AtomSpecModel>> featureMap)
- {
- List<String> commands = new ArrayList<>();
- for (String featureType : featureMap.keySet())
- {
- String attributeName = makeAttributeName(featureType);
-
- /*
- * clear down existing attributes for this feature
- */
- // 'problem' - sets attribute to None on all residues - overkill?
- // commands.add("~setattr r " + attributeName + " :*");
-
- Map<Object, AtomSpecModel> values = featureMap.get(featureType);
- for (Object value : values.keySet())
- {
- /*
- * for each distinct value recorded for this feature type,
- * add a command to set the attribute on the mapped residues
- * Put values in single quotes, encoding any embedded single quotes
- */
- StringBuilder sb = new StringBuilder(128);
- String featureValue = value.toString();
- featureValue = featureValue.replaceAll("\\'", "'");
- sb.append("setattr r ").append(attributeName).append(" '")
- .append(featureValue).append("' ");
- sb.append(values.get(value).getAtomSpec());
- commands.add(sb.toString());
- }
- }
-
- 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.
return "view";
}
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ protected static int getModelStartNo()
+ {
+ return 1;
+ }
+
+ /**
+ * Returns a viewer command to set the given residue attribute value on
+ * residues specified by the AtomSpecModel, for example
+ *
+ * <pre>
+ * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
+ * </pre>
+ *
+ * @param attributeName
+ * @param attributeValue
+ * @param atomSpecModel
+ * @return
+ */
+ @Override
+ protected String getSetAttributeCommand(String attributeName,
+ String attributeValue, AtomSpecModel atomSpecModel)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ sb.append("setattr ").append(atomSpecModel.getAtomSpecX());
+ sb.append(" res ").append(attributeName).append(" '")
+ .append(attributeValue).append("'");
+ sb.append(" create true");
+ return sb.toString();
+ }
+
}
import jalview.httpserver.AbstractRequestHandler;
import jalview.io.DataSourceType;
import jalview.structure.AtomSpec;
-import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
/*
* Map of ChimeraModel objects keyed by PDB full local file name
*/
- private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
+ protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
String lastHighlightCommand;
if (!alreadyOpen)
{
chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
- if (chimeraManager.isChimeraX())
- {
- /*
- * ChimeraX hack: force chimera model name to pdbId
- */
- int modelNumber = chimeraMaps.size() + 1;
- String command = "setattr #" + modelNumber + " models name "
- + pe.getId();
- executeCommand(command, false);
- modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
- modelNumber, 0));
- }
- else
- {
- /*
- * Chimera: query for actual models and find the one with
- * matching model name - set in viewer.openModel()
- */
- List<ChimeraModel> newList = chimeraManager.getModelList();
- // JAL-1728 newList.removeAll(oldList) does not work
- for (ChimeraModel cm : newList)
- {
- if (cm.getModelName().equals(pe.getId()))
- {
- modelsToMap.add(cm);
- }
- }
- }
+ addChimeraModel(pe, modelsToMap);
}
chimeraMaps.put(file, modelsToMap);
}
/**
+ * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
+ * name matching PDB id
+ *
+ * @param pe
+ * @param modelsToMap
+ */
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> modelsToMap)
+ {
+ /*
+ * Chimera: query for actual models and find the one with
+ * matching model name - already set in viewer.openModel()
+ */
+ List<ChimeraModel> newList = chimeraManager.getModelList();
+ // JAL-1728 newList.removeAll(oldList) does not work
+ for (ChimeraModel cm : newList)
+ {
+ if (cm.getModelName().equals(pe.getId()))
+ {
+ modelsToMap.add(cm);
+ }
+ }
+ }
+
+ /**
* Constructor
*
* @param ssm
return true;
}
- boolean launched = chimeraManager.launchChimera(
- StructureManager.getChimeraPaths(chimeraManager.isChimeraX()));
+ boolean launched = chimeraManager.launchChimera(getChimeraPaths());
if (launched)
{
startChimeraProcessMonitor();
}
/**
+ * Returns a list of candidate paths to the Chimera program executable
+ *
+ * @return
+ */
+ protected List<String> getChimeraPaths()
+ {
+ return StructureManager.getChimeraPaths(false);
+ }
+
+ /**
* Answers true if the Chimera process is still running, false if ended or not
* started.
*
* Chimera: https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
* ChimeraX: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
*/
- String command = isChimeraX() ? "save session " : "save ";
- List<String> reply = chimeraManager.sendChimeraCommand(command + filepath,
- true);
+ String command = getSaveSessionCommand(filepath);
+ List<String> reply = chimeraManager.sendChimeraCommand(command, true);
if (reply.contains("Session written"))
{
return true;
}
/**
+ * Returns the command to save the viewer session to the given file path
+ *
+ * @param filepath
+ * @return
+ */
+ protected String getSaveSessionCommand(String filepath)
+ {
+ return "save " + filepath;
+ }
+
+ /**
* Ask Chimera to open a session file. Returns true if successful, else false.
* The filename must have a .py (Chimera) or .cxs (ChimeraX) extension for
* this command to work.
return 0;
}
- StructureMappingcommandSet commandSet = ChimeraCommands
- .getSetAttributeCommandsForFeatures(getSsm(), files,
- getSequence(), avp, chimeraManager.isChimeraX());
- String[] commands = commandSet.commands;
+ String[] commands = getCommandGenerator()
+ .setAttributesForFeatures(getSsm(), files, getSequence(), avp);
if (commands.length > 10)
{
sendCommandsByFile(commands);
*/
protected void sendCommandsByFile(String[] commands)
{
- boolean toChimeraX = chimeraManager.isChimeraX();
try
{
- File tmp = File.createTempFile("chim", toChimeraX ? ".cxc" : ".com");
+ File tmp = File.createTempFile("chim", getCommandFileExtension());
tmp.deleteOnExit();
PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
for (String command : commands)
out.flush();
out.close();
String path = tmp.getAbsolutePath();
- String command = "open " + (toChimeraX ? "" : "cmd:") + path;
+ String command = getOpenCommandFileCommand(path);
sendAsynchronousCommand(command, null);
} catch (IOException e)
{
}
/**
+ * Returns the command for the structure viewer to open a file of commands at
+ * the given file path
+ *
+ * @param path
+ * @return
+ */
+ protected String getOpenCommandFileCommand(String path)
+ {
+ return "open cmd:" + path;
+ }
+
+ /**
+ * Returns the file extension required for a file of commands to be read by
+ * the structure viewer
+ * @return
+ */
+ protected String getCommandFileExtension()
+ {
+ return ".com";
+ }
+
+ /**
* Get Chimera residues which have the named attribute, find the mapped
* positions in the Jalview sequence(s), and set as sequence features
*
return atts;
}
- public boolean isChimeraX()
+ /**
+ * Returns the file extension to use for a saved viewer session file
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
+ {
+ return ".py";
+ }
+
+ public String getHelpURL()
{
- return chimeraManager.isChimeraX();
+ return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
}
}
/**
* Send a command to Chimera to create residue attributes for Jalview features
* <p>
- * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
* <p>
- * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
*/
protected void sendFeaturesToChimera()
{
{
try
{
- String url = jmb.isChimeraX()
- ? "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html"
- : "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+ String url = jmb.getHelpURL();
BrowserLauncher.openURL(url);
} catch (IOException ex)
{
{
if (pathUsed == null)
{
- String suffix = jmb.isChimeraX() ? ".cxs" : ".py";
+ String suffix = jmb.getSessionFileExtension();
File tempFile = File.createTempFile("chimera", suffix);
tempFile.deleteOnExit();
pathUsed = tempFile.getPath();
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import java.util.List;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
super(chimeraViewFrame, ssm, pdbentry, sequenceIs, protocol);
}
+ @Override
+ protected List<String> getChimeraPaths()
+ {
+ return StructureManager.getChimeraPaths(true);
+ }
+
+ @Override
+ protected void addChimeraModel(PDBEntry pe,
+ List<ChimeraModel> modelsToMap)
+ {
+ /*
+ * ChimeraX hack: force chimera model name to pdbId here
+ */
+ int modelNumber = chimeraMaps.size() + 1;
+ String command = "setattr #" + modelNumber + " models name "
+ + pe.getId();
+ executeCommand(command, false);
+ modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
+ modelNumber, 0));
+ }
+
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ @Override
+ protected String getCommandFileExtension()
+ {
+ return ".cxc";
+ }
+
+ /**
+ * {@inheritDoc}
+ *
+ * @return
+ */
+ @Override
+ protected String getOpenCommandFileCommand(String path)
+ {
+ return "open " + path;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ protected String getSaveSessionCommand(String filepath)
+ {
+ return "save session " + filepath;
+ }
+
+ /**
+ * Returns the file extension to use for a saved viewer session file
+ *
+ * @return
+ */
+ @Override
+ public String getSessionFileExtension()
+ {
+ return ".cxs";
+ }
+
+ @Override
+ public String getHelpURL()
+ {
+ return "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html";
+ }
+
}
package jalview.structure;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.SequenceI;
+
/**
* A base class holding methods useful to all classes that implement commands
* for structure viewers
*/
public abstract class StructureCommandsBase implements StructureCommandsI
{
+
+ @Override
+ public String[] setAttributesForFeatures(StructureSelectionManager ssm,
+ String[] files, SequenceI[][] sequence, AlignmentViewPanel avp)
+ {
+ // default does nothing, override where this is implemented
+ return null;
+ }
}
*/
String showChains(List<String> toShow);
+ /**
+ * Returns zero, one or more commands to set attributes on mapped residues in
+ * the structure viewer for any features present and displayed in Jalview
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param avp
+ * @return
+ */
+ String[] setAttributesForFeatures(StructureSelectionManager ssm,
+ String[] files, SequenceI[][] sequence, AlignmentViewPanel avp);
+
}
colourBySequence(ap);
}
}
+
+ public StructureCommandsI getCommandGenerator()
+ {
+ return commandGenerator;
+ }
}
featuresMap.put("chain", featureValues);
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
- List<String> commands = ChimeraCommands
- .buildSetAttributeCommands(featuresMap, false);
+ ChimeraCommands commandGenerator = new ChimeraCommands();
+ List<String> commands = commandGenerator
+ .buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
/*
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
// same feature value, contiguous range
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
- false);
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
assertEquals(commands.get(0), "setattr res jv_chain 'X' #0:3-25.A");
ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
// same feature value and chain, different model
ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
- false);
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
assertEquals(1, commands.size());
assertEquals(commands.get(0),
"setattr res jv_chain 'X' #0:3-25.A,21-25.B|#1:26-30.A");
// same feature, different value
ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
- false);
+ commands = commandGenerator.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:
"A");
// feature names are sanitised to change non-alphanumeric to underscore
// feature values are sanitised to encode single quote characters
- commands = ChimeraCommands.buildSetAttributeCommands(featuresMap,
- false);
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
assertTrue(commands
.contains(
"setattr res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' #0:7-15.A"));
}
@Test(groups = { "Functional" })
- public void testGetColourBySequenceCommands_hiddenColumns()
+ public void testColourBySequence_hiddenColumns()
{
/*
* load these sequences, coloured by Strand propensity,
--- /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.SequenceRenderer;
+import jalview.schemes.JalviewColourScheme;
+import jalview.structure.StructureMapping;
+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.Test;
+
+public class ChimeraXCommandsTest
+{
+
+ @Test(groups = { "Functional" })
+ public void testBuildColourCommands()
+ {
+
+ Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 2, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 7, 7, "B");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 0, 9, 23, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 1, 1, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.blue, 1, 4, 7, "B");
+ ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 8, 8, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.yellow, 1, 3, 5, "A");
+ ChimeraCommands.addAtomSpecRange(map, Color.red, 0, 3, 5, "A");
+ ChimeraCommands.addAtomSpecRange(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 = new ChimeraXCommands().buildColourCommands(map).get(0);
+ assertEquals(
+ command,
+ "color #0/A:2-5,9-23/B:7|#1/A:1/B:4-7 #0000ff; color #1/A:3-5,8 #ffff00; color #0/A:3-9 #ff0000");
+ }
+
+ @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.addAtomSpecRange(featureValues, "X", 0, 8, 20, "A");
+
+ ChimeraXCommands commandGenerator = new ChimeraXCommands();
+ List<String> commands = commandGenerator
+ .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 #0/A:8-20 res jv_chain 'X' create true");
+
+ // add same feature value, overlapping range
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 3, 9, "A");
+ // same feature value, contiguous range
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "A");
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
+ assertEquals(1, commands.size());
+ assertEquals(commands.get(0),
+ "setattr #0/A:3-25 res jv_chain 'X' create true");
+
+ // same feature value and model, different chain
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 0, 21, 25, "B");
+ // same feature value and chain, different model
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", 1, 26, 30, "A");
+ commands = commandGenerator.buildSetAttributeCommands(featuresMap);
+ assertEquals(1, commands.size());
+ assertEquals(commands.get(0),
+ "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true");
+
+ // same feature, different value
+ ChimeraCommands.addAtomSpecRange(featureValues, "Y", 0, 40, 50, "A");
+ commands = commandGenerator.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 #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true"));
+ assertTrue(commands
+ .contains("setattr #0/A:40-50 res jv_chain 'Y' create true"));
+
+ featuresMap.clear();
+ featureValues.clear();
+ featuresMap.put("side-chain binding!", featureValues);
+ ChimeraCommands.addAtomSpecRange(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 = commandGenerator.buildSetAttributeCommands(featuresMap);
+ assertTrue(commands.contains(
+ "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testColourBySequence_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 = new StructureSelectionManager();
+
+ /*
+ * 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);
+
+ String[] commands = new ChimeraXCommands()
+ .colourBySequence(ssm, files, seqs, sr, af.alignPanel);
+ assertEquals(1, commands.length);
+ String theCommand = commands[0];
+ // M colour is #82827d (see strand.html help page)
+ assertTrue(theCommand.contains("color #0/A:21|#1/B:21 #82827d"));// #0:21.A|#1:21.B"));
+ // H colour is #60609f
+ assertTrue(theCommand.contains("color #0/A:22 #60609f"));
+ // V colour is #ffff00
+ assertTrue(theCommand.contains("color #1/B:22 #ffff00"));
+ // hidden columns are Gray (128, 128, 128)
+ assertTrue(theCommand.contains("color #0/A:23-25|#1/B:23-25"));
+ // S and G are both coloured #4949b6
+ assertTrue(theCommand.contains("color #0/A:26-30|#1/B:26-30"));
+ }
+}
assertEquals(binding.getPdbCount(), 1);
/*
- * 'perform' menu action to copy visible features to
- * attributes in Chimera
+ * 'perform' menu action to copy Chimera attributes
+ * to features in Jalview
*/
// TODO rename and pull up method to binding interface
// once functionality is added for Jmol as well
binding.copyStructureAttributesToFeatures("phi", af.getViewport()
.getAlignPanel());
fr.setVisible("phi");
- List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54);
- assertEquals(fs.size(), 3);
- /*
- * order of returned features is not guaranteed
- */
- assertTrue("RESNUM".equals(fs.get(0).getType())
- || "RESNUM".equals(fs.get(1).getType())
- || "RESNUM".equals(fs.get(2).getType()));
+ List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54,
+ "phi");
+ assertEquals(fs.size(), 2);
assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54,
-131.0713f, "Chimera")));
assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54,
int res, String featureType)
{
String where = "at position " + res;
- List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res);
+ List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res,
+ featureType);
- assertEquals(fs.size(), 2, where);
- assertEquals(fs.get(0).getType(), "RESNUM", where);
- SequenceFeature sf = fs.get(1);
+ assertEquals(fs.size(), 1, where);
+ SequenceFeature sf = fs.get(0);
assertEquals(sf.getType(), featureType, where);
assertEquals(sf.getFeatureGroup(), "Chimera", where);
assertEquals(sf.getDescription(), "True", where);
git://source.jalview.org / jalview.git / commitdiff