X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=2699db187e9f7b1ff113c4e8483627d348775c5e;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=ffa34f834f2c3fe96b063e7e22b85b6391cc80b2;hpb=cd8f0eb5083ecbb73bde4b87c45e0d4286998ab9;p=jalview.git diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java index ffa34f83..2699db1 100644 --- a/src/jalview/gui/AppJmolBinding.java +++ b/src/jalview/gui/AppJmolBinding.java @@ -20,53 +20,41 @@ */ 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.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; +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.Map; - -import org.jmol.api.JmolAppConsoleInterface; -import org.jmol.java.BS; -import org.openscience.jmol.app.jmolpanel.console.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.isShowSequenceFeatures()) - { - if (fr == null) - { - fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer(); - } - else - { - ap.updateFeatureRenderer(fr); - } - } - - return fr; + super(sSm, pdbentry, sequenceIs, protocol); + setViewer(appJmol); } @Override @@ -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); + Cache.error("Failed to launch Jmol-associated url " + url, e); // TODO: 2.6 : warn user if browser was not configured. } } @@ -111,34 +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(); } }); } @Override - public void updateColours(Object source) - { - AlignmentPanel ap = (AlignmentPanel) source; - // ignore events from panels not used to colour this view - if (!appJmolWindow.isUsedforcolourby(ap)) - { - return; - } - if (!isLoadingFromArchive()) - { - colourBySequence(ap); - } - } - - @Override public void notifyScriptTermination(String strStatus, int msWalltime) { // todo - script termination doesn't happen ? @@ -162,35 +142,28 @@ public class AppJmolBinding extends JalviewJmolBinding @Override public void selectionChanged(BS arg0) { - // TODO Auto-generated method stub - - } - - @Override - public void refreshPdbEntries() - { - // TODO Auto-generated method stub - } @Override public void showConsole(boolean b) { - appJmolWindow.showConsole(b); + getViewer().showConsole(b); } @Override protected JmolAppConsoleInterface createJmolConsole( Container consolePanel, String buttonsToShow) { - viewer.setJmolCallbackListener(this); - return new AppConsole(viewer, consolePanel, 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); } @Override protected void releaseUIResources() { - appJmolWindow = null; + setViewer(null); closeConsole(); } @@ -199,7 +172,7 @@ public class AppJmolBinding extends JalviewJmolBinding { if (svl instanceof SeqPanel) { - appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap); + getViewer().removeAlignmentPanel(((SeqPanel) svl).ap); } } @@ -210,9 +183,113 @@ public class AppJmolBinding extends JalviewJmolBinding return null; } - @Override - public JalviewStructureDisplayI getViewer() + @SuppressWarnings("unused") + public void cacheFiles(List files) { - return appJmolWindow; + if (files == null) + { + return; + } + for (File f : files) + { + Platform.cacheFileData(f); + } + } + + /** + * 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) + { + // 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) + { + 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; } + }