*/
package jalview.structures.models;
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ResidueProperties;
import jalview.structure.AtomSpec;
import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
-import jalview.structure.StructureCommandsI.SuperposeData;
import jalview.structure.StructureListener;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.SwingUtilities;
-
/**
*
* A base class to hold common function for protein structure model binding.
extends SequenceStructureBindingModel
implements StructureListener, StructureSelectionManagerProvider
{
+ /**
+ * Data bean class to simplify parameterisation in superposeStructures
+ */
+ public static class SuperposeData
+ {
+ public String filename;
+
+ public String pdbId;
+
+ public String chain = "";
+
+ public boolean isRna;
+
+ /*
+ * The pdb residue number (if any) mapped to columns of the alignment
+ */
+ public int[] pdbResNo; // or use SparseIntArray?
+
+ public String modelId;
+
+ /**
+ * Constructor
+ *
+ * @param width
+ * width of alignment (number of columns that may potentially
+ * participate in superposition)
+ * @param model
+ * structure viewer model number
+ */
+ public SuperposeData(int width, String model)
+ {
+ pdbResNo = new int[width];
+ modelId = model;
+ }
+ }
+
private static final int MIN_POS_TO_SUPERPOSE = 4;
private static final String COLOURING_STRUCTURES = MessageManager
private boolean finishedInit = false;
/**
- * current set of model filenames loaded in the Jmol instance
+ * current set of model filenames loaded in the viewer
*/
protected String[] modelFileNames = null;
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- BitSet matched, SuperposeData[] structures)
+ BitSet matched, AAStructureBindingModel.SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getStructureFiles();
}
}
- SuperposeData[] structures = new SuperposeData[files.length];
+ AAStructureBindingModel.SuperposeData[] structures = new AAStructureBindingModel.SuperposeData[files.length];
for (int f = 0; f < files.length; f++)
{
- structures[f] = new SuperposeData(width,
- f + commandGenerator.getModelStartNo());
+ structures[f] = new AAStructureBindingModel.SuperposeData(width,
+ getModelIdForFile(files[f]));
}
/*
* Show all as backbone before doing superposition(s)
* (residues used for matching will be shown as ribbon)
*/
- executeCommand(commandGenerator.showBackbone(), false);
+ // todo better way to ensure synchronous than setting getReply true!!
+ executeCommands(commandGenerator.showBackbone(), true, null);
/*
* superpose each (other) structure to the reference in turn
if (i != refStructure)
{
AtomSpecModel atomSpec = getAtomSpec(structures[i], matched);
- String commands = commandGenerator.superposeStructures(refAtoms,
- atomSpec);
- List<String> replies = executeCommands(true, commands);
+ List<StructureCommandI> commands = commandGenerator
+ .superposeStructures(refAtoms, atomSpec);
+ List<String> replies = executeCommands(commands, true, null);
for (String reply : replies)
{
// return this error (Chimera only) to the user
return error;
}
- private AtomSpecModel getAtomSpec(SuperposeData superposeData,
+ private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData,
BitSet matched)
{
AtomSpecModel model = new AtomSpecModel();
while (nextColumnMatch != -1)
{
int pdbResNum = superposeData.pdbResNo[nextColumnMatch];
- model.addRange(superposeData.modelNo, pdbResNum, pdbResNum,
+ model.addRange(superposeData.modelId, pdbResNum, pdbResNum,
superposeData.chain);
nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
}
{
colourBySequence = false;
- executeCommand(commandGenerator.colourByCharge(), false,
+ executeCommands(commandGenerator.colourByCharge(), false,
COLOURING_STRUCTURES);
}
/*
* pass to the command constructor, and send the command
*/
- String cmd = commandGenerator.colourByResidues(colours);
- executeCommand(cmd, false, COLOURING_STRUCTURES);
+ List<StructureCommandI> cmd = commandGenerator
+ .colourByResidues(colours);
+ executeCommands(cmd, false, COLOURING_STRUCTURES);
}
public void setBackgroundColour(Color col)
{
- String cmd = commandGenerator.setBackgroundColour(col);
+ StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
executeCommand(cmd, false, null);
}
* @param msg
* @return
*/
- private List<String> executeCommand(String cmd, boolean getReply,
- String msg)
+ private List<String> executeCommand(StructureCommandI cmd,
+ boolean getReply, String msg)
{
if (getReply)
{
- return executeSynchronous(cmd, msg, getReply);
+ /*
+ * synchronous (same thread) execution so reply can be returned
+ */
+ final JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+ try
+ {
+ return executeCommand(cmd, getReply);
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
}
else
{
- executeAsynchronous(cmd, msg);
+ /*
+ * asynchronous (new thread) execution if no reply needed
+ */
+ final JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ executeCommand(cmd, false);
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ }
+ }
+ });
return null;
}
}
/**
- * Sends the command in the current thread. If a message is supplied, this is
- * shown before the thread is started, and removed when it completes. May
- * return a reply to the command if requested.
+ * Execute one structure viewer command. If {@code getReply} is true, may
+ * optionally return one or more reply messages, else returns null.
*
* @param cmd
- * @param msg
* @param getReply
- * @return
*/
- private List<String> executeSynchronous(String cmd, String msg, boolean getReply)
+ protected abstract List<String> executeCommand(StructureCommandI cmd,
+ boolean getReply);
+
+ /**
+ * A helper method that converts list of commands to a vararg array
+ *
+ * @param commands
+ * @param getReply
+ * @param msg
+ */
+ private List<String> executeCommands(List<StructureCommandI> commands,
+ boolean getReply, String msg)
{
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
- try
- {
- return executeCommand(cmd, getReply);
- } finally
- {
- if (msg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
- }
+ return executeCommands(getReply, msg,
+ commands.toArray(new StructureCommandI[commands.size()]));
}
/**
- * Sends the command in a separate thread. If a message is supplied, this is
- * shown before the thread is started, and removed when it completes. No value
- * is returned.
+ * Executes one or more structure viewer commands. If a progress message is
+ * provided, it is shown first, and removed after all commands have been run.
*
- * @param cmd
+ * @param getReply
* @param msg
+ * @param commands
+ * @return
*/
- private void executeAsynchronous(String cmd, String msg)
+ protected List<String> executeCommands(boolean getReply, String msg,
+ StructureCommandI[] commands)
{
+ // todo: tidy this up
+
+ /*
+ * show progress message if specified
+ */
final JalviewStructureDisplayI theViewer = getViewer();
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
- SwingUtilities.invokeLater(new Runnable()
+ List<String> response = getReply ? new ArrayList<>() : null;
+ try
{
- @Override
- public void run()
+ for (StructureCommandI cmd : commands)
{
- try
- {
- executeCommand(cmd, false);
- } finally
+ List<String> replies = executeCommand(cmd, getReply, null);
+ if (getReply && replies != null)
{
- if (msg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
+ response.addAll(replies);
}
}
- });
- }
-
- protected abstract List<String> executeCommand(String command,
- boolean getReply);
-
- protected List<String> executeCommands(boolean getReply,
- String... commands)
- {
- // todo: tidy this up
- List<String> response = getReply ? new ArrayList<>() : null;
- for (String cmd : commands)
+ return response;
+ } finally
{
- List<String> replies = executeCommand(cmd, getReply);
- if (getReply && replies != null)
+ if (msg != null)
{
- response.addAll(replies);
+ theViewer.stopProgressBar(null, handle);
}
}
- return response;
}
/**
Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
sequence, sr, alignmentv);
- String[] colourBySequenceCommands = commandGenerator
+ List<StructureCommandI> colourBySequenceCommands = commandGenerator
.colourBySequence(colourMap);
- executeCommands(false, colourBySequenceCommands);
+ executeCommands(colourBySequenceCommands, false, null);
}
/**
*/
public void focusView()
{
- executeCommand(commandGenerator.focusView(), false);
+ executeCommand(commandGenerator.focusView(), false, null);
}
/**
if (tokens.length == 2)
{
String pdbFile = getFileForChain(chainId);
- int modelNo = getModelNoForFile(pdbFile);
- String model = modelNo == -1 ? "" : String.valueOf(modelNo);
+ String model = getModelIdForFile(pdbFile);
showThese.add(model + ":" + tokens[1]);
}
}
- executeCommand(commandGenerator.showChains(showThese), false);
+ executeCommands(commandGenerator.showChains(showThese), false, null);
}
/**
- * Answers the structure viewer's model number given a PDB file name. Returns
- * -1 if model number is not found.
+ * Answers the structure viewer's model id given a PDB file name. Returns an
+ * empty string if model id is not found.
*
* @param chainId
* @return
*/
- protected abstract int getModelNoForFile(String chainId);
+ protected abstract String getModelIdForFile(String chainId);
public boolean hasFileLoadingError()
{
* @param command
* @param progressMsg
*/
- protected void sendAsynchronousCommand(String command, String progressMsg)
+ protected void sendAsynchronousCommand(StructureCommandI command,
+ String progressMsg)
{
final JalviewStructureDisplayI theViewer = getViewer();
final long handle = progressMsg == null ? 0
{
try
{
- executeCommand(command, false);
+ executeCommand(command, false, null);
} finally
{
if (progressMsg != null)
* {@code AtomSpecModel}, where the atomspec model holds
*
* <pre>
- * Model numbers
+ * Model ids
* Chains
* Residue positions
* </pre>
for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
{
- final int modelNumber = pdbfnum + commandGenerator.getModelStartNo();
+ final String modelId = getModelIdForFile(files[pdbfnum]);
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
if (mapping == null || mapping.length < 1)
{
if (startPos != -1)
{
- addAtomSpecRange(colourMap, lastColour, modelNumber,
+ addAtomSpecRange(colourMap, lastColour, modelId,
startPos, lastPos, lastChain);
}
startPos = pos;
// final colour range
if (lastColour != null)
{
- addAtomSpecRange(colourMap, lastColour, modelNumber, startPos,
+ addAtomSpecRange(colourMap, lastColour, modelId, startPos,
lastPos, lastChain);
}
// break;
}
/**
+ * todo better refactoring (map lookup or similar to get viewer structure id)
+ *
+ * @param pdbfnum
+ * @param file
+ * @return
+ */
+ protected String getModelId(int pdbfnum, String file)
+ {
+ return String.valueOf(pdbfnum);
+ }
+
+ /**
+ * Saves chains, formatted as "pdbId:chainCode", and lookups from this to the
+ * full PDB file path
+ *
+ * @param pdb
+ * @param file
+ */
+ public void stashFoundChains(StructureFile pdb, String file)
+ {
+ for (int i = 0; i < pdb.getChains().size(); i++)
+ {
+ String chid = pdb.getId() + ":" + pdb.getChains().elementAt(i).id;
+ addChainFile(chid, file);
+ getChainNames().add(chid);
+ }
+ }
+
+ /**
* 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>
*/
public static final void addAtomSpecRange(Map<Object, AtomSpecModel> map,
Object value,
- int model, int startPos, int endPos, String chain)
+ String model, int startPos, int endPos, String chain)
{
/*
* Get/initialize map of data for the colour
atomSpec.addRange(model, startPos, endPos, chain);
}
+
+ /**
+ * Returns the file extension (including '.' separator) to use for a saved
+ * viewer session file. Default is to return null (not supported), override as
+ * required.
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
+ {
+ return null;
+ }
+
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file. Returns null and logs an error on any failure.
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ String prefix = getViewerType().toString();
+ String suffix = getSessionFileExtension();
+ File f = null;
+ try
+ {
+ f = File.createTempFile(prefix, suffix);
+ saveSession(f);
+ } catch (IOException e)
+ {
+ Cache.log.error(String.format("Error saving %s session: %s",
+ prefix, e.toString()));
+ }
+
+ return f;
+ }
+
+ /**
+ * Saves the structure viewer session to the given file
+ *
+ * @param f
+ */
+ protected void saveSession(File f)
+ {
+ StructureCommandI cmd = commandGenerator
+ .saveSession(f.getPath());
+ if (cmd != null)
+ {
+ executeCommand(cmd, false);
+ }
+ }
+
+ /**
+ * Returns true if the viewer is an external structure viewer for which the
+ * process is still alive, else false (for Jmol, or an external viewer which
+ * the user has independently closed)
+ *
+ * @return
+ */
+ public boolean isViewerRunning()
+ {
+ return false;
+ }
+
+ /**
+ * Closes Jalview's structure viewer panel and releases associated resources.
+ * If it is managing an external viewer program, and {@code forceClose} is
+ * true, also shuts down that program.
+ *
+ * @param forceClose
+ */
+ public void closeViewer(boolean forceClose)
+ {
+ getSsm().removeStructureViewerListener(this, this.getStructureFiles());
+ releaseUIResources();
+
+ // add external viewer shutdown in overrides
+ // todo - or can maybe pull up to here
+ }
}
git://source.jalview.org / jalview.git / blobdiff