X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=336c6f84d1a1e9529a6715c1d93ba4298bae2cf6;hb=0b6e9403e96ee9f0d41211b2f90130ff850c4e98;hp=1afa15e7673a9a992a60d268311aef9e7d533b84;hpb=4ee3a368d2de9eaa050137f7d45cfac0c432ef53;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 1afa15e..336c6f8 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -20,6 +20,8 @@ */ package jalview.structures.models; +import java.util.Locale; + import java.awt.Color; import java.io.File; import java.io.IOException; @@ -39,7 +41,7 @@ import jalview.api.FeatureRenderer; import jalview.api.SequenceRenderer; import jalview.api.StructureSelectionManagerProvider; import jalview.api.structures.JalviewStructureDisplayI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.datamodel.AlignmentI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; @@ -57,7 +59,6 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.AtomSpec; import jalview.structure.AtomSpecModel; -import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsI; import jalview.structure.StructureListener; @@ -68,7 +69,7 @@ import jalview.util.MessageManager; /** * - * A base class to hold common function for protein structure model binding. + * A base class to hold common function for 3D structure model binding. * Initial version created by refactoring JMol and Chimera binding models, but * other structure viewers could in principle be accommodated in future. * @@ -90,6 +91,9 @@ public abstract class AAStructureBindingModel public String chain = ""; + /** + * is the mapped sequence not protein ? + */ public boolean isRna; /* @@ -166,6 +170,9 @@ public abstract class AAStructureBindingModel protected boolean colourBySequence = true; + /** + * true if all sequences appear to be nucleotide + */ private boolean nucleotide; private boolean finishedInit = false; @@ -583,6 +590,7 @@ public abstract class AAStructureBindingModel } } } + @Override public abstract void highlightAtoms(List atoms); @@ -714,7 +722,7 @@ public abstract class AAStructureBindingModel structures[pdbfnum].chain = chain; } structures[pdbfnum].pdbId = mapping.getPdbId(); - structures[pdbfnum].isRna = theSequence.getRNA() != null; + structures[pdbfnum].isRna = !theSequence.isProtein(); /* * move on to next pdb file (ignore sequences for other chains @@ -916,7 +924,8 @@ public abstract class AAStructureBindingModel */ // todo better way to ensure synchronous than setting getReply true!! executeCommands(commandGenerator.showBackbone(), true, null); - + + boolean isNucleotide = structures[refStructure].isRna; /* * superpose each (other) structure to the reference in turn */ @@ -926,12 +935,12 @@ public abstract class AAStructureBindingModel { AtomSpecModel atomSpec = getAtomSpec(structures[i], matched); List commands = commandGenerator - .superposeStructures(refAtoms, atomSpec); + .superposeStructures(refAtoms, atomSpec,isNucleotide); List replies = executeCommands(commands, true, null); for (String reply : replies) { // return this error (Chimera only) to the user - if (reply.toLowerCase().contains("unequal numbers of atoms")) + if (reply.toLowerCase(Locale.ROOT).contains("unequal numbers of atoms")) { error += "; " + reply; } @@ -981,8 +990,8 @@ 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()); } /** @@ -1040,34 +1049,72 @@ 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) { - final JalviewStructureDisplayI theViewer = getViewer(); + 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). WARNING: if you + * are sending commands that need to execute before later calls to + * executeCommand (e.g. mouseovers, which clean up after previous ones) then + * set getReply true to ensure that commands are not executed out of order. + * + * @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 */ + List response = new ArrayList<>(); try { - return executeCommand(cmd, true); + for (StructureCommandI cmd : cmds) + { + List replies = executeCommand(cmd, true); + if (replies != null) + { + response.addAll(replies); + } + } + return response; } finally { if (msg != null) @@ -1076,62 +1123,39 @@ 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 - */ - 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 - * - * @param commands - * @param getReply - * @param msg - */ - protected List executeCommands(List commands, - boolean getReply, String msg) - { - List response = getReply ? new ArrayList<>() : null; - for (StructureCommandI cmd : commands) - { - List replies = executeCommand(cmd, getReply, msg); - if (replies != null) - { - response.addAll(replies); } - } - return response; + }, threadName).start(); + return null; } /** @@ -1157,7 +1181,7 @@ public abstract class AAStructureBindingModel */ public void focusView() { - executeCommand(commandGenerator.focusView(), false, null); + executeCommand(false, null, commandGenerator.focusView()); } /** @@ -1205,8 +1229,7 @@ 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 @@ -1219,9 +1242,7 @@ public abstract class AAStructureBindingModel { return null; } - return ap.getAlignViewport().isShowSequenceFeatures() - ? ap.getFeatureRenderer() - : null; + return ap.getFeatureRenderer(); } protected void setStructureCommands(StructureCommandsI cmd) @@ -1276,40 +1297,6 @@ 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 @@ -1517,7 +1504,7 @@ public abstract class AAStructureBindingModel saveSession(f); } catch (IOException e) { - Cache.log.error(String.format("Error saving %s session: %s", prefix, + Console.error(String.format("Error saving %s session: %s", prefix, e.toString())); }