X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=34d930d73d15f74604b3978795d579b4befcdd70;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=c70380c997c48e963f87add8de6bdf2d43315e7f;hpb=c4ec878c9cb59fc40a88ed8ecdf5fda46f3de111;p=jalview.git diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java index c70380c..34d930d 100644 --- a/src/jalview/gui/AppJmolBinding.java +++ b/src/jalview/gui/AppJmolBinding.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,63 +20,50 @@ */ package jalview.gui; +import java.awt.Container; +import java.io.File; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +import javax.swing.JComponent; + +import org.jmol.api.JmolAppConsoleInterface; +import org.openscience.jmol.app.jmolpanel.console.AppConsole; + import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; +import jalview.api.structures.JalviewStructureDisplayI; +import jalview.bin.Console; +import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.ext.jmol.JalviewJmolBinding; +import jalview.io.DataSourceType; import jalview.structure.StructureSelectionManager; - -import java.awt.Container; -import java.util.BitSet; - -import org.jmol.api.JmolAppConsoleInterface; -import org.jmol.api.JmolViewer; -import org.jmol.popup.JmolPopup; -import org.openscience.jmol.app.jmolpanel.AppConsole; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.ws.dbsources.EBIAlfaFold; +import jalview.ws.dbsources.Pdb; +import jalview.ws.utils.UrlDownloadClient; +import javajs.util.BS; public class AppJmolBinding extends JalviewJmolBinding { - private AppJmol appJmolWindow; - - private FeatureRenderer fr = null; - public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, - PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains, - String protocol) + PDBEntry[] pdbentry, SequenceI[][] sequenceIs, + DataSourceType protocol) { - super(sSm, pdbentry, sequenceIs, chains, protocol); - appJmolWindow = appJmol; - } - - @Override - public FeatureRenderer getFeatureRenderer( - AlignmentViewPanel alignment) - { - AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel() - : (AlignmentPanel) alignment; - if (ap.av.showSequenceFeatures) - { - if (fr == null) - { - fr = ap.cloneFeatureRenderer(); - } - else - { - ap.updateFeatureRenderer(fr); - } - } - - return fr; + super(sSm, pdbentry, sequenceIs, protocol); + setViewer(appJmol); } @Override - public SequenceRenderer getSequenceRenderer( - AlignmentViewPanel alignment) + public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment) { return new SequenceRenderer(((AlignmentPanel) alignment).av); } + @Override public void sendConsoleEcho(String strEcho) { if (console != null) @@ -85,6 +72,7 @@ public class AppJmolBinding extends JalviewJmolBinding } } + @Override public void sendConsoleMessage(String strStatus) { if (console != null && strStatus != null) @@ -103,7 +91,7 @@ public class AppJmolBinding extends JalviewJmolBinding jalview.util.BrowserLauncher.openURL(url); } catch (Exception e) { - Cache.log.error("Failed to launch Jmol-associated url " + url, e); + Console.error("Failed to launch Jmol-associated url " + url, e); // TODO: 2.6 : warn user if browser was not configured. } } @@ -111,31 +99,26 @@ public class AppJmolBinding extends JalviewJmolBinding @Override public void refreshGUI() { + if (getMappedStructureCount() == 0) + { + // too soon! + return; + } // appJmolWindow.repaint(); javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { - appJmolWindow.updateTitleAndMenus(); - appJmolWindow.revalidate(); + JalviewStructureDisplayI theViewer = getViewer(); + // invokes colourbySequence() via seqColour_ActionPerformed() + theViewer.updateTitleAndMenus(); + ((JComponent) theViewer).revalidate(); } }); } - public void updateColours(Object source) - { - AlignmentPanel ap = (AlignmentPanel) source, topap; - // ignore events from panels not used to colour this view - if (!appJmolWindow.isUsedforcolourby(ap)) - { - return; - } - if (!isLoadingFromArchive()) - { - colourBySequence(ap.av.getShowSequenceFeatures(), ap); - } - } - + @Override public void notifyScriptTermination(String strStatus, int msWalltime) { // todo - script termination doesn't happen ? @@ -144,74 +127,169 @@ public class AppJmolBinding extends JalviewJmolBinding // msWalltime); } + @Override public void showUrl(String url) { showUrl(url, "jmol"); } - public void newJmolPopup(boolean translateLocale, String menuName, - boolean asPopup) + public void newJmolPopup(String menuName) { - jmolpopup = new JmolPopup(); - jmolpopup.initialize(viewer, translateLocale, menuName, asPopup); + // jmolpopup = new JmolAwtPopup(); + // jmolpopup.jpiInitialize((viewer), menuName); } - public void selectionChanged(BitSet arg0) + @Override + public void selectionChanged(BS arg0) { - // TODO Auto-generated method stub - } - public void refreshPdbEntries() + @Override + public void showConsole(boolean b) { - // TODO Auto-generated method stub + getViewer().showConsole(b); + } + @Override + protected JmolAppConsoleInterface createJmolConsole( + Container consolePanel, String buttonsToShow) + { + jmolViewer.setJmolCallbackListener(this); + // BH comment: can't do this yet [for JS only, or generally?] + return Platform.isJS() ? null + : new AppConsole(jmolViewer, consolePanel, buttonsToShow); } - public void showConsole(boolean b) + @Override + protected void releaseUIResources() { - appJmolWindow.showConsole(b); + setViewer(null); + closeConsole(); } - /** - * add the given sequences to the mapping scope for the given pdb file handle - * - * @param pdbFile - * - pdbFile identifier - * @param seq - * - set of sequences it can be mapped to - */ - public void addSequenceForStructFile(String pdbFile, SequenceI[] seq) + @Override + public void releaseReferences(Object svl) { - for (int pe = 0; pe < getPdbCount(); pe++) + if (svl instanceof SeqPanel) { - if (getPdbEntry(pe).getFile().equals(pdbFile)) - { - addSequence(pe, seq); - } + getViewer().removeAlignmentPanel(((SeqPanel) svl).ap); } } @Override - protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2, - Container consolePanel, String buttonsToShow) + public Map getJSpecViewProperty(String arg0) { - return new AppConsole(viewer, consolePanel, buttonsToShow); + // TODO Auto-generated method stub + return null; } - @Override - protected void releaseUIResources() + @SuppressWarnings("unused") + public void cacheFiles(List files) { - appJmolWindow = null; - closeConsole(); + if (files == null) + { + return; + } + for (File f : files) + { + Platform.cacheFileData(f); + } } - @Override - public void releaseReferences(Object svl) + /** + * Retrieves and saves as file any modelled PDB entries for which we do not + * already have a file saved. Returns a list of absolute paths to structure + * files which were either retrieved, or already stored but not modelled in + * the structure viewer (i.e. files to add to the viewer display). + * + * Currently only used by Jmol - similar but different code used for Chimera/X + * and Pymol so still need to refactor + * + * @param structureViewer + * UI proxy for the structure viewer + * @return list of absolute paths to structures retrieved that need to be + * added to the display + */ + public List fetchPdbFiles(StructureViewerBase structureViewer) { - if (svl instanceof SeqPanel) + // todo - record which pdbids were successfully imported. + StringBuilder errormsgs = new StringBuilder(); + + List files = new ArrayList<>(); + String pdbid = ""; + try + { + String[] filesInViewer = getStructureFiles(); + // TODO: replace with reference fetching/transfer code (validate PDBentry + // as a DBRef?) + + for (int pi = 0; pi < getPdbCount(); pi++) + { + PDBEntry strucEntry = getPdbEntry(pi); + + String file = strucEntry.getFile(); + if (file == null) + { + pdbid = strucEntry.getId(); + try{ + file = structureViewer.fetchPdbFile(strucEntry); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("Retrieving PDB id " + pdbid, oomerror); + } catch (Exception ex) + { + ex.printStackTrace(); + errormsgs.append("'").append(pdbid).append("'"); + } + if (file!=null) + { + // success + files.add(file); + } + else + { + errormsgs.append("'").append(pdbid).append("' "); + } + } + else + { + if (filesInViewer != null && filesInViewer.length > 0) + { + structureViewer.setAddingStructures(true); // already files loaded. + for (int c = 0; c < filesInViewer.length; c++) + { + if (Platform.pathEquals(filesInViewer[c], file)) + { + file = null; + break; + } + } + } + if (file != null) + { + files.add(file); + } + } + } + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("Retrieving PDB files: " + pdbid, oomerror); + } catch (Exception ex) { - appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap); + ex.printStackTrace(); + errormsgs.append("When retrieving pdbfiles : current was: '") + .append(pdbid).append("'"); } + if (errormsgs.length() > 0) + { + JvOptionPane.showInternalMessageDialog(Desktop.desktop, + MessageManager.formatMessage( + "label.pdb_entries_couldnt_be_retrieved", new String[] + { errormsgs.toString() }), + MessageManager.getString("label.couldnt_load_file"), + JvOptionPane.ERROR_MESSAGE); + } + return files; } + }