X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=5a7b4484cd728b78f51d21b0a6ef9dd7e735dcb0;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=7899c40633f96ae5fc6294cddf2b7cbc9ae4140b;hpb=1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b;p=jalview.git
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 7899c40..5a7b448 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -42,8 +42,13 @@ import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.Desktop;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
@@ -79,20 +84,20 @@ public abstract class AAStructureBindingModel
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
*
@@ -171,6 +176,8 @@ public abstract class AAStructureBindingModel
public String fileLoadingError;
+ protected Thread externalViewerMonitor;
+
/**
* Constructor
*
@@ -256,6 +263,7 @@ public abstract class AAStructureBindingModel
chains = newchains;
return chainmaps > 0;
}
+
public StructureSelectionManager getSsm()
{
return ssm;
@@ -653,7 +661,8 @@ public abstract class AAStructureBindingModel
* @return
*/
protected int findSuperposableResidues(AlignmentI alignment,
- BitSet matched, AAStructureBindingModel.SuperposeData[] structures)
+ BitSet matched,
+ AAStructureBindingModel.SuperposeData[] structures)
{
int refStructure = -1;
String[] files = getStructureFiles();
@@ -879,8 +888,8 @@ public abstract class AAStructureBindingModel
* Calculate the superposable alignment columns ('matched'), and the
* corresponding structure residue positions (structures.pdbResNo)
*/
- int refStructure = findSuperposableResidues(alignment,
- matched, structures);
+ int refStructure = findSuperposableResidues(alignment, matched,
+ structures);
/*
* require at least 4 positions to be able to execute superposition
@@ -888,8 +897,8 @@ public abstract class AAStructureBindingModel
int nmatched = matched.cardinality();
if (nmatched < MIN_POS_TO_SUPERPOSE)
{
- String msg = MessageManager.formatMessage("label.insufficient_residues",
- nmatched);
+ String msg = MessageManager
+ .formatMessage("label.insufficient_residues", nmatched);
error += view.getViewName() + ": " + msg + "; ";
continue;
}
@@ -933,7 +942,8 @@ public abstract class AAStructureBindingModel
return error;
}
- private AtomSpecModel getAtomSpec(AAStructureBindingModel.SuperposeData superposeData,
+ private AtomSpecModel getAtomSpec(
+ AAStructureBindingModel.SuperposeData superposeData,
BitSet matched)
{
AtomSpecModel model = new AtomSpecModel();
@@ -970,8 +980,8 @@ public abstract class AAStructureBindingModel
// TODO: JAL-628 colour chains distinctly across all visible models
- executeCommand(commandGenerator.colourByChain(), false,
- COLOURING_STRUCTURES);
+ executeCommand(false, COLOURING_STRUCTURES,
+ commandGenerator.colourByChain());
}
/**
@@ -1002,7 +1012,7 @@ public abstract class AAStructureBindingModel
{
return;
}
-
+
/*
* build a map of {Residue3LetterCode, Color}
*/
@@ -1029,69 +1039,7 @@ public abstract class AAStructureBindingModel
public void setBackgroundColour(Color col)
{
StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
- executeCommand(cmd, false, null);
- }
-
- /**
- * Sends one command to the structure viewer. If {@code getReply} is true, the
- * command is sent synchronously, otherwise in a deferred thread.
- *
- * If a progress message is supplied, this is displayed before command
- * execution, and removed afterwards.
- *
- * @param cmd
- * @param getReply
- * @param msg
- * @return
- */
- private List executeCommand(StructureCommandI cmd,
- boolean getReply, String msg)
- {
- if (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
- {
- /*
- * 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;
- }
+ executeCommand(false, null, cmd);
}
/**
@@ -1105,84 +1053,114 @@ public abstract class AAStructureBindingModel
boolean getReply);
/**
- * A helper method that converts list of commands to a vararg array
+ * Executes one or more structure viewer commands
*
* @param commands
* @param getReply
* @param msg
*/
- private List executeCommands(List commands,
+ protected List executeCommands(List commands,
boolean getReply, String msg)
{
- return executeCommands(getReply, msg,
+ return executeCommand(getReply, msg,
commands.toArray(new StructureCommandI[commands.size()]));
}
/**
- * 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.
+ * Executes one or more structure viewer commands, optionally returning the
+ * reply, and optionally showing a status message while the command is being
+ * executed.
+ *
+ * If a reply is wanted, the execution is done synchronously (waits),
+ * otherwise it is done in a separate thread (doesn't wait).
*
* @param getReply
* @param msg
- * @param commands
+ * @param cmds
* @return
*/
- protected List executeCommands(boolean getReply, String msg,
- StructureCommandI[] commands)
+ protected List executeCommand(boolean getReply, String msg,
+ StructureCommandI... cmds)
{
- // todo: tidy this up
-
- /*
- * show progress message if specified
- */
- final JalviewStructureDisplayI theViewer = getViewer();
+ JalviewStructureDisplayI theViewer = getViewer();
final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
- List response = getReply ? new ArrayList<>() : null;
- try
+ if (getReply)
{
- for (StructureCommandI cmd : commands)
+ /*
+ * execute and wait for reply
+ */
+ List response = new ArrayList<>();
+ try
{
- List replies = executeCommand(cmd, getReply, null);
- if (getReply && replies != null)
+ for (StructureCommandI cmd : cmds)
{
- response.addAll(replies);
+ List replies = executeCommand(cmd, true);
+ if (replies != null)
+ {
+ response.addAll(replies);
+ }
+ }
+ return response;
+ } finally
+ {
+ if (msg != null)
+ {
+ theViewer.stopProgressBar(null, handle);
}
}
- return response;
- } finally
+ }
+
+ /*
+ * fire and forget
+ */
+ String threadName = msg == null ? "StructureCommand" : msg;
+ new Thread(new Runnable()
{
- if (msg != null)
+ @Override
+ public void run()
{
- theViewer.stopProgressBar(null, handle);
+ try
+ {
+ for (StructureCommandI cmd : cmds)
+ {
+ executeCommand(cmd, false);
+ }
+ } finally
+ {
+ if (msg != null)
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ });
+ }
+ }
}
- }
+ }, threadName).start();
+ return null;
}
/**
- * colour any structures associated with sequences in the given alignment
- * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
- * if colourBySequence is enabled.
+ * Colours any structures associated with sequences in the given alignment as
+ * coloured in the alignment view, provided colourBySequence is enabled
*/
public void colourBySequence(AlignmentViewPanel alignmentv)
{
- if (!colourBySequence || !isLoadingFinished())
- {
- return;
- }
- if (getSsm() == null)
+ if (!colourBySequence || !isLoadingFinished() || getSsm() == null)
{
return;
}
- String[] files = getStructureFiles();
-
- SequenceRenderer sr = getSequenceRenderer(alignmentv);
- Map