X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;fp=src%2Fjalview%2Fgui%2FAppJmol.java;h=06ce7cacba8132e8bc544d5282727a1cf0307af2;hb=8a43b8353b89a47002ef17c959ed61281fc4d826;hp=205c33bef0c8f7feb4a4f7d99519b21d0005261b;hpb=55bfdb07355198ae1a1a8b5e14933b4669113ca6;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 205c33b..06ce7ca 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -20,28 +20,15 @@ */ package jalview.gui; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.StructureViewer.ViewerType; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.BrowserLauncher; -import jalview.util.MessageManager; -import jalview.util.Platform; -import jalview.ws.dbsources.Pdb; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; -import java.awt.Rectangle; -import java.awt.event.ActionEvent; import java.io.File; import java.util.ArrayList; import java.util.List; +import java.util.Map; import javax.swing.JPanel; import javax.swing.JSplitPane; @@ -49,6 +36,23 @@ import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.datamodel.StructureViewerModel; +import jalview.datamodel.StructureViewerModel.StructureData; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.gui.StructureViewer.ViewerType; +import jalview.structure.StructureCommand; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.dbsources.Pdb; + public class AppJmol extends StructureViewerBase { // ms to wait for Jmol to load files @@ -85,48 +89,55 @@ public class AppJmol extends StructureViewerBase * @param bounds * @param viewid */ - public AppJmol(String[] files, String[] ids, SequenceI[][] seqs, - AlignmentPanel ap, boolean usetoColour, boolean useToAlign, - boolean leaveColouringToJmol, String loadStatus, Rectangle bounds, - String viewid) + public AppJmol(StructureViewerModel viewerModel, AlignmentPanel ap, + String sessionFile, String viewid) { - PDBEntry[] pdbentrys = new PDBEntry[files.length]; - for (int i = 0; i < pdbentrys.length; i++) + Map pdbData = viewerModel.getFileData(); + PDBEntry[] pdbentrys = new PDBEntry[pdbData.size()]; + SequenceI[][] seqs = new SequenceI[pdbData.size()][]; + int i = 0; + for (StructureData data : pdbData.values()) { - // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); - PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, - files[i]); + PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null, + PDBEntry.Type.PDB, data.getFilePath()); pdbentrys[i] = pdbentry; + List sequencesForPdb = data.getSeqList(); + seqs[i] = sequencesForPdb + .toArray(new SequenceI[sequencesForPdb.size()]); + i++; } - // / TODO: check if protocol is needed to be set, and if chains are + + // TODO: check if protocol is needed to be set, and if chains are // autodiscovered. jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); - if (useToAlign) + if (viewerModel.isAlignWithPanel()) { useAlignmentPanelForSuperposition(ap); } initMenus(); - if (leaveColouringToJmol || !usetoColour) + boolean useToColour = viewerModel.isColourWithAlignPanel(); + boolean leaveColouringToJmol = viewerModel.isColourByViewer(); + if (leaveColouringToJmol || !useToColour) { jmb.setColourBySequence(false); seqColour.setSelected(false); viewerColour.setSelected(true); } - else if (usetoColour) + else if (useToColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); viewerColour.setSelected(false); } - this.setBounds(bounds); + + this.setBounds(viewerModel.getX(), viewerModel.getY(), + viewerModel.getWidth(), viewerModel.getHeight()); setViewId(viewid); - // jalview.gui.Desktop.addInternalFrame(this, "Loading File", - // bounds.width,bounds.height); this.addInternalFrameListener(new InternalFrameAdapter() { @@ -137,7 +148,10 @@ public class AppJmol extends StructureViewerBase closeViewer(false); } }); - initJmol(loadStatus); // pdbentry, seq, JBPCHECK! + StringBuilder cmd = new StringBuilder(); + cmd.append("load FILES ").append(QUOTE) + .append(Platform.escapeBackslashes(sessionFile)).append(QUOTE); + initJmol(cmd.toString()); } @Override @@ -145,22 +159,12 @@ public class AppJmol extends StructureViewerBase { super.initMenus(); - viewerActionMenu.setText(MessageManager.getString("label.jmol")); - viewerColour .setText(MessageManager.getString("label.colour_with_jmol")); viewerColour.setToolTipText(MessageManager .getString("label.let_jmol_manage_structure_colours")); } - IProgressIndicator progressBar = null; - - @Override - protected IProgressIndicator getIProgressIndicator() - { - return progressBar; - } - /** * display a single PDB structure in a new Jmol view * @@ -172,7 +176,7 @@ public class AppJmol extends StructureViewerBase public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains, final AlignmentPanel ap) { - progressBar = ap.alignFrame; + setProgressIndicator(ap.alignFrame); openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry }, new SequenceI[][] @@ -183,14 +187,17 @@ public class AppJmol extends StructureViewerBase PDBEntry[] pdbentrys, SequenceI[][] seqs) { - progressBar = ap.alignFrame; + setProgressIndicator(ap.alignFrame); jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); alignAddedStructures = alignAdded; - useAlignmentPanelForSuperposition(ap); + if (pdbentrys.length > 1) + { + useAlignmentPanelForSuperposition(ap); + } jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here @@ -253,29 +260,12 @@ public class AppJmol extends StructureViewerBase { command = ""; } - jmb.evalStateCommand(command); - jmb.evalStateCommand("set hoverDelay=0.1"); + jmb.executeCommand(new StructureCommand(command), false); + jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false); jmb.setFinishedInit(true); } @Override - public void closeViewer(boolean closeExternalViewer) - { - // Jmol does not use an external viewer - if (jmb != null) - { - jmb.closeViewer(); - } - setAlignmentPanel(null); - _aps.clear(); - _alignwith.clear(); - _colourwith.clear(); - // TODO: check for memory leaks where instance isn't finalised because jmb - // holds a reference to the window - jmb = null; - } - - @Override public void run() { _started = true; @@ -323,6 +313,8 @@ public class AppJmol extends StructureViewerBase } catch (Exception ex) { Cache.log.error("Couldn't open Jmol viewer!", ex); + ex.printStackTrace(); + return; } } else @@ -331,20 +323,23 @@ public class AppJmol extends StructureViewerBase cmd.append("loadingJalviewdata=true\nload APPEND "); cmd.append(filesString); cmd.append("\nloadingJalviewdata=null"); - final String command = cmd.toString(); + final StructureCommand command = new StructureCommand(cmd.toString()); lastnotify = jmb.getLoadNotifiesHandled(); try { - jmb.evalStateCommand(command); + jmb.executeCommand(command, false); } catch (OutOfMemoryError oomerror) { new OOMWarning("When trying to add structures to the Jmol viewer!", oomerror); Cache.log.debug("File locations are " + filesString); + return; } catch (Exception ex) { Cache.log.error("Couldn't add files to Jmol viewer!", ex); + ex.printStackTrace(); + return; } } @@ -359,8 +354,10 @@ public class AppJmol extends StructureViewerBase try { Cache.log.debug("Waiting around for jmb notify."); - Thread.sleep(waitFor); waitTotal += waitFor; + + // Thread.sleep() throws an exception in JS + Thread.sleep(waitFor); } catch (Exception e) { } @@ -399,7 +396,7 @@ public class AppJmol extends StructureViewerBase @Override public void run() { - if (jmb.viewer.isScriptExecuting()) + if (jmb.jmolViewer.isScriptExecuting()) { SwingUtilities.invokeLater(this); try @@ -412,7 +409,7 @@ public class AppJmol extends StructureViewerBase } else { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } } }); @@ -450,12 +447,9 @@ public class AppJmol extends StructureViewerBase AlignmentI pdbseq = null; pdbid = jmb.getPdbEntry(pi).getId(); long hdl = pdbid.hashCode() - System.currentTimeMillis(); - if (progressBar != null) - { - progressBar.setProgressBar(MessageManager - .formatMessage("status.fetching_pdb", new String[] - { pdbid }), hdl); - } + setProgressMessage(MessageManager + .formatMessage("status.fetching_pdb", new String[] + { pdbid }), hdl); try { pdbseq = pdbclient.getSequenceRecords(pdbid); @@ -468,12 +462,8 @@ public class AppJmol extends StructureViewerBase errormsgs.append("'").append(pdbid).append("'"); } finally { - if (progressBar != null) - { - progressBar.setProgressBar( - MessageManager.getString("label.state_completed"), - hdl); - } + setProgressMessage( + MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { @@ -530,67 +520,48 @@ public class AppJmol extends StructureViewerBase return files; } + /** + * Outputs the Jmol viewer image as an image file, after prompting the user to + * choose a file and (for EPS) choice of Text or Lineart character rendering + * (unless a preference for this is set) + * + * @param type + */ @Override - public void eps_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.TYPE.EPS); - } - - @Override - public void png_actionPerformed(ActionEvent e) - { - makePDBImage(jalview.util.ImageMaker.TYPE.PNG); - } - - void makePDBImage(jalview.util.ImageMaker.TYPE type) + public void makePDBImage(ImageMaker.TYPE type) { int width = getWidth(); int height = getHeight(); - - jalview.util.ImageMaker im; - - if (type == jalview.util.ImageMaker.TYPE.PNG) + ImageWriterI writer = new ImageWriterI() { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", - width, height, null, null, null, 0, false); - } - else if (type == jalview.util.ImageMaker.TYPE.EPS) - { - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", - width, height, null, this.getTitle(), null, 0, false); - } - else - { - - im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.SVG, "Make SVG file from PCA", - width, height, null, this.getTitle(), null, 0, false); - } - - if (im.getGraphics() != null) - { - jmb.viewer.renderScreenImage(im.getGraphics(), width, height); - im.writeImage(); - } + @Override + public void exportImage(Graphics g) throws Exception + { + jmb.jmolViewer.renderScreenImage(g, width, height); + } + }; + String view = MessageManager.getString("action.view").toLowerCase(); + ImageExporter exporter = new ImageExporter(writer, + getProgressIndicator(), type, getTitle()); + exporter.doExport(null, this, width, height, view); } @Override - public void showHelp_actionPerformed(ActionEvent actionEvent) + public void showHelp_actionPerformed() { try { - BrowserLauncher - .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); + BrowserLauncher // BH 2018 + .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { + System.err.println("Show Jmol help failed with: " + ex.getMessage()); } } + @Override public void showConsole(boolean showConsole) { - if (showConsole) { if (splitPane == null) @@ -656,7 +627,7 @@ public class AppJmol extends StructureViewerBase } } } - else if (jmb == null || jmb.viewer == null || !jmb.isFinishedInit()) + else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -667,7 +638,7 @@ public class AppJmol extends StructureViewerBase } else { - jmb.viewer.renderScreenImage(g, currentSize.width, + jmb.jmolViewer.renderScreenImage(g, currentSize.width, currentSize.height); } } @@ -680,12 +651,6 @@ public class AppJmol extends StructureViewerBase } @Override - public String getStateInfo() - { - return jmb == null ? null : jmb.viewer.getStateInfo(); - } - - @Override public ViewerType getViewerType() { return ViewerType.JMOL;