X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=5a7b4484cd728b78f51d21b0a6ef9dd7e735dcb0;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=f69a423b5c9ec962a5ee35d68247476173dab8a1;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git
diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index f69a423..5a7b448 100644
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -47,6 +47,7 @@ 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;
@@ -83,20 +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
*
@@ -262,6 +263,7 @@ public abstract class AAStructureBindingModel
chains = newchains;
return chainmaps > 0;
}
+
public StructureSelectionManager getSsm()
{
return ssm;
@@ -659,7 +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();
@@ -885,8 +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
@@ -894,8 +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;
}
@@ -939,7 +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();
@@ -976,8 +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());
}
/**
@@ -1008,7 +1012,7 @@ public abstract class AAStructureBindingModel
{
return;
}
-
+
/*
* build a map of {Residue3LetterCode, Color}
*/
@@ -1035,34 +1039,69 @@ public abstract class AAStructureBindingModel
public void setBackgroundColour(Color col)
{
StructureCommandI cmd = commandGenerator.setBackgroundColour(col);
- executeCommand(cmd, false, null);
+ executeCommand(false, null, cmd);
}
/**
- * 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.
+ * Execute one structure viewer command. If {@code getReply} is true, may
+ * optionally return one or more reply messages, else returns null.
*
* @param cmd
* @param getReply
+ */
+ protected abstract List executeCommand(StructureCommandI cmd,
+ boolean getReply);
+
+ /**
+ * Executes one or more structure viewer commands
+ *
+ * @param commands
+ * @param getReply
* @param msg
- * @return
*/
- private List executeCommand(StructureCommandI cmd,
+ protected List executeCommands(List commands,
boolean getReply, String msg)
{
+ return executeCommand(getReply, msg,
+ commands.toArray(new StructureCommandI[commands.size()]));
+ }
+
+ /**
+ * 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 cmds
+ * @return
+ */
+ protected List executeCommand(boolean getReply, String msg,
+ StructureCommandI... cmds)
+ {
+ JalviewStructureDisplayI theViewer = getViewer();
+ final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+
if (getReply)
{
/*
- * synchronous (same thread) execution so reply can be returned
+ * execute and wait for reply
*/
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
+ List response = new ArrayList<>();
try
{
- return executeCommand(cmd, getReply);
+ for (StructureCommandI cmd : cmds)
+ {
+ List replies = executeCommand(cmd, true);
+ if (replies != null)
+ {
+ response.addAll(replies);
+ }
+ }
+ return response;
} finally
{
if (msg != null)
@@ -1071,81 +1110,39 @@ public abstract class AAStructureBindingModel
}
}
}
- else
+
+ /*
+ * fire and forget
+ */
+ String threadName = msg == null ? "StructureCommand" : msg;
+ new Thread(new Runnable()
{
- /*
- * 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()
{
- @Override
- public void run()
+ try
{
- try
+ for (StructureCommandI cmd : cmds)
{
executeCommand(cmd, false);
- } finally
+ }
+ } finally
+ {
+ if (msg != null)
{
- if (msg != null)
+ SwingUtilities.invokeLater(new Runnable()
{
- theViewer.stopProgressBar(null, handle);
- }
+ @Override
+ public void run()
+ {
+ theViewer.stopProgressBar(null, handle);
+ }
+ });
}
}
- });
- return null;
- }
- }
-
- /**
- * Execute one structure viewer command. If {@code getReply} is true, may
- * optionally return one or more reply messages, else returns null.
- *
- * @param cmd
- * @param getReply
- */
- protected abstract List executeCommand(StructureCommandI cmd,
- boolean getReply);
-
- /**
- * 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 commands
- * @param getReply
- * @param msg
- */
- protected List executeCommands(List commands,
- boolean getReply, String msg)
- {
- /*
- * show progress message if specified
- */
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = msg == null ? 0 : theViewer.startProgressBar(msg);
-
- List response = getReply ? new ArrayList<>() : null;
- try
- {
- for (StructureCommandI cmd : commands)
- {
- List replies = executeCommand(cmd, getReply, null);
- if (getReply && replies != null)
- {
- response.addAll(replies);
- }
}
- return response;
- } finally
- {
- if (msg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
- }
+ }, threadName).start();
+ return null;
}
/**
@@ -1163,7 +1160,7 @@ public abstract class AAStructureBindingModel
List colourBySequenceCommands = commandGenerator
.colourBySequence(colourMap);
- executeCommands(colourBySequenceCommands, false, null);
+ executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES);
}
/**
@@ -1171,7 +1168,7 @@ public abstract class AAStructureBindingModel
*/
public void focusView()
{
- executeCommand(commandGenerator.focusView(), false, null);
+ executeCommand(false, null, commandGenerator.focusView());
}
/**
@@ -1219,8 +1216,7 @@ public abstract class AAStructureBindingModel
}
/**
- * Returns the FeatureRenderer for the given alignment view, or null if
- * feature display is turned off in the view.
+ * Returns the FeatureRenderer for the given alignment view
*
* @param avp
* @return
@@ -1233,9 +1229,7 @@ public abstract class AAStructureBindingModel
{
return null;
}
- return ap.getAlignViewport().isShowSequenceFeatures()
- ? ap.getFeatureRenderer()
- : null;
+ return ap.getFeatureRenderer();
}
protected void setStructureCommands(StructureCommandsI cmd)
@@ -1290,40 +1284,6 @@ public abstract class AAStructureBindingModel
protected abstract ViewerType getViewerType();
/**
- * Send a structure viewer command asynchronously in a new thread. If the
- * progress message is not null, display this message while the command is
- * executing.
- *
- * @param command
- * @param progressMsg
- */
- protected void sendAsynchronousCommand(StructureCommandI command,
- String progressMsg)
- {
- final JalviewStructureDisplayI theViewer = getViewer();
- final long handle = progressMsg == null ? 0
- : theViewer.startProgressBar(progressMsg);
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- try
- {
- executeCommand(command, false, null);
- } finally
- {
- if (progressMsg != null)
- {
- theViewer.stopProgressBar(null, handle);
- }
- }
- }
- });
-
- }
-
- /**
* Builds a data structure which records mapped structure residues for each
* colour. From this we can easily generate the viewer commands for colour by
* sequence. Constructs and returns a map of {@code Color} to
@@ -1356,17 +1316,17 @@ public abstract class AAStructureBindingModel
AlignmentI al = viewport.getAlignment();
Map