X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=f1f2d307d4014f0a1424017e5a84a470d0561c6b;hb=05e40b4dd4e216024024fb921d797917d74daa76;hp=05cfd5ad168d3535874e992c2641189ce935c8ab;hpb=2fb924ec0d110eb3ca6c3fb06efa27acd34b2750;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 05cfd5a..f1f2d30 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; @@ -47,6 +49,7 @@ 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; @@ -66,7 +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. * @@ -83,20 +86,20 @@ 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 +265,7 @@ public abstract class AAStructureBindingModel chains = newchains; return chainmaps > 0; } + public StructureSelectionManager getSsm() { return ssm; @@ -580,6 +584,7 @@ public abstract class AAStructureBindingModel } } } + @Override public abstract void highlightAtoms(List atoms); @@ -659,7 +664,8 @@ 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 +891,8 @@ 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 +900,8 @@ 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; } @@ -927,7 +933,7 @@ public abstract class AAStructureBindingModel 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; } @@ -939,7 +945,8 @@ 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 +983,8 @@ 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 +1015,7 @@ public abstract class AAStructureBindingModel { return; } - + /* * build a map of {Residue3LetterCode, Color} */ @@ -1035,34 +1042,72 @@ 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) { + 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 */ - 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 +1116,39 @@ 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 +1166,7 @@ public abstract class AAStructureBindingModel List colourBySequenceCommands = commandGenerator .colourBySequence(colourMap); - executeCommands(colourBySequenceCommands, false, null); + executeCommands(colourBySequenceCommands, false, COLOURING_STRUCTURES); } /** @@ -1171,7 +1174,7 @@ public abstract class AAStructureBindingModel */ public void focusView() { - executeCommand(commandGenerator.focusView(), false, null); + executeCommand(false, null, commandGenerator.focusView()); } /** @@ -1219,8 +1222,7 @@ 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 +1235,7 @@ public abstract class AAStructureBindingModel { return null; } - return ap.getAlignViewport().isShowSequenceFeatures() - ? ap.getFeatureRenderer() - : null; + return ap.getFeatureRenderer(); } protected void setStructureCommands(StructureCommandsI cmd) @@ -1290,40 +1290,6 @@ 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 +1322,17 @@ public abstract class AAStructureBindingModel AlignmentI al = viewport.getAlignment(); Map colourMap = new LinkedHashMap<>(); Color lastColour = null; - + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { final String modelId = getModelIdForFile(files[pdbfnum]); StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - + if (mapping == null || mapping.length < 1) { continue; } - + int startPos = -1, lastPos = -1; String lastChain = ""; for (int s = 0; s < sequence[pdbfnum].length; s++) @@ -1386,14 +1352,14 @@ public abstract class AAStructureBindingModel continue; } int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - + if (pos < 1 || pos == lastPos) { continue; } - + Color colour = sr.getResidueColour(seq, r, finder); - + /* * darker colour for hidden regions */ @@ -1401,9 +1367,9 @@ public abstract class AAStructureBindingModel { colour = Color.GRAY; } - + final String chain = mapping[m].getChain(); - + /* * Just keep incrementing the end position for this colour range * _unless_ colour, PDB model or chain has changed, or there is a @@ -1416,8 +1382,8 @@ public abstract class AAStructureBindingModel { if (startPos != -1) { - addAtomSpecRange(colourMap, lastColour, modelId, - startPos, lastPos, lastChain); + addAtomSpecRange(colourMap, lastColour, modelId, startPos, + lastPos, lastChain); } startPos = pos; } @@ -1469,8 +1435,9 @@ public abstract class AAStructureBindingModel } /** - * 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 + * 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 *