-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.util.BitSet;
-import java.util.Vector;
+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 jalview.bin.Cache;
+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.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 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;
-import org.jmol.popup.JmolPopup;
-
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
- private AppJmol appJmolWindow;
-
- public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
- appJmolWindow = appJmol;
+ super(sSm, pdbentry, sequenceIs, protocol);
+ setViewer(appJmol);
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
- {
- if (fr == null)
- {
- fr = new FeatureRenderer(appJmolWindow.ap);
- }
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
- }
-
- return fr;
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer()
- {
- return new SequenceRenderer(appJmolWindow.ap.av);
- }
-
public void sendConsoleEcho(String strEcho)
{
- if (appJmolWindow.scriptWindow != null)
+ if (console != null)
{
- appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+ console.sendConsoleEcho(strEcho);
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow != null && strStatus != null)
+ if (console != null && strStatus != null)
// && !strStatus.equals("Script completed"))
// should we squash the script completed string ?
{
- appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+ console.sendConsoleMessage(strStatus);
}
}
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.
}
}
@Override
public void refreshGUI()
{
- // appJmolWindow.repaint();
- appJmolWindow.updateTitleAndMenus();
- }
-
- public void updateColours(Object source)
- {
- AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+ if (getMappedStructureCount() == 0)
+ {
+ // too soon!
return;
-
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ }
+ // appJmolWindow.repaint();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JalviewStructureDisplayI theViewer = getViewer();
+ // invokes colourbySequence() via seqColour_ActionPerformed()
+ theViewer.updateTitleAndMenus();
+ ((JComponent) theViewer).revalidate();
+ }
+ });
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
- if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
- msWalltime);
+ // todo - script termination doesn't happen ?
+ // if (console != null)
+ // console.notifyScriptTermination(strStatus,
+ // 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 JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);
+ }
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ @Override
+ public void selectionChanged(BS arg0)
+ {
}
- /**
- * add structures and any known sequence associations
- *
- * @returns the pdb entries added to the current set.
- */
- private PDBEntry[] addSequenceAndChain(PDBEntry[] pdbe,
- SequenceI[][] seq, String[][] chns)
+ @Override
+ public void showConsole(boolean b)
{
- int pe = -1;
- Vector v = new Vector();
- Vector rtn = new Vector();
- for (int i = 0; i < pdbentry.length; i++)
- {
- v.addElement(pdbentry[i]);
- }
- for (int i = 0; i < pdbe.length; i++)
- {
- int r = v.indexOf(pdbe[i]);
- if (r == -1 || r >= pdbentry.length)
- {
- rtn.addElement(new int[]
- { v.size(), i });
- v.addElement(pdbe[i]);
- }
- else
- {
- // just make sure the sequence/chain entries are all up to date
- addSequenceAndChain(r, seq[i], chns[i]);
- }
- }
- pdbe = new PDBEntry[v.size()];
- v.copyInto(pdbe);
- pdbentry = pdbe;
- if (rtn.size() > 0)
- {
- // expand the tied seuqence[] and string[] arrays
- SequenceI[][] sqs = new SequenceI[pdbentry.length][];
- String[][] sch = new String[pdbentry.length][];
- System.arraycopy(sequence, 0, sqs, 0, sequence.length);
- System.arraycopy(chains, 0, sch, 0, this.chains.length);
- sequence = sqs;
- chains = sch;
- pdbe = new PDBEntry[rtn.size()];
- for (int r = 0; r < pdbe.length; r++)
- {
- int[] stri = ((int[]) rtn.elementAt(r));
- // record the pdb file as a new addition
- pdbe[r] = pdbentry[stri[0]];
- // and add the new sequence/chain entries
- addSequenceAndChain(stri[0], seq[stri[1]], chns[stri[1]]);
- }
- }
- else
- {
- pdbe = null;
- }
- return pdbe;
+ getViewer().showConsole(b);
}
- void addSequence(int pe, SequenceI[] seq)
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
{
- // add sequences to the pe'th pdbentry's seuqence set.
- addSequenceAndChain(pe, seq, null);
+ jmolViewer.setJmolCallbackListener(this);
+ // BH comment: can't do this yet [for JS only, or generally?]
+ return Platform.isJS() ? null
+ : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
- private void addSequenceAndChain(int pe, SequenceI[] seq, String[] tchain)
+ @Override
+ protected void releaseUIResources()
{
- if (pe < 0 || pe >= pdbentry.length)
- {
- throw new Error(
- "Implementation error - no corresponding pdbentry (for index "
- + pe + ") to add sequences mappings to");
- }
- final String nullChain = "TheNullChain";
- Vector s = new Vector();
- Vector c = new Vector();
- if (chains == null)
- {
- chains = new String[pdbentry.length][];
- }
- if (sequence[pe] != null)
- {
- for (int i = 0; i < sequence[pe].length; i++)
- {
- s.addElement(sequence[pe][i]);
- if (chains[pe] != null)
- {
- if (i < chains[pe].length)
- {
- c.addElement(chains[pe][i]);
- }
- else
- {
- c.addElement(nullChain);
- }
- }
- else
- {
- if (tchain != null && tchain.length > 0)
- {
- c.addElement(nullChain);
- }
- }
- }
- }
- for (int i = 0; i < seq.length; i++)
- {
- if (!s.contains(seq[i]))
- {
- s.addElement(seq[i]);
- if (tchain != null && i < tchain.length)
- {
- c.addElement(tchain[i] == null ? nullChain : tchain[i]);
- }
- }
- }
- SequenceI[] tmp = new SequenceI[s.size()];
- s.copyInto(tmp);
- sequence[pe] = tmp;
- if (c.size() > 0)
- {
- String[] tch = new String[c.size()];
- c.copyInto(tch);
- for (int i = 0; i < tch.length; i++)
- {
- if (tch[i] == nullChain)
- {
- tch[i] = null;
- }
- }
- chains[pe] = tch;
- }
- else
+ setViewer(null);
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ if (svl instanceof SeqPanel)
{
- chains[pe] = null;
+ getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
- public void selectionChanged(BitSet arg0)
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
{
// TODO Auto-generated method stub
-
+ return null;
}
- public void refreshPdbEntries()
+ @SuppressWarnings("unused")
+ public void cacheFiles(List<File> files)
{
- // TODO Auto-generated method stub
-
+ if (files == null)
+ {
+ return;
+ }
+ for (File f : files)
+ {
+ Platform.cacheFileData(f);
+ }
}
/**
- * add another pdb entry into the view, with associated sequences and chains
+ * 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).
*
- * @param pdbentry
- * @param seq
- * @param chains
- * @param align
- * if true, new structure(s) will be align using associated alignment
+ * 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 synchronized void addStructure(PDBEntry pdbentry, SequenceI[] seq,
- String[] chains, final boolean align)
+ public List<String> fetchPdbFiles(StructureViewerBase structureViewer)
{
- PDBEntry[] pe = addSequenceAndChain(new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains });
- if (pe != null)
+ // todo - record which pdbids were successfully imported.
+ StringBuilder errormsgs = new StringBuilder();
+
+ List<String> files = new ArrayList<>();
+ String pdbid = "";
+ try
{
- StringBuffer cmd = new StringBuffer();
- cmd.append("load APPEND");
- for (int p = 0; p < pe.length; p++)
- {
- cmd.append(" \"");
- cmd.append(pe[p].getFile());
- cmd.append("\"");
- }
- cmd.append("\n");
- final String command = cmd.toString();
- cmd = null;
- new Thread(new Runnable()
+ String[] filesInViewer = getStructureFiles();
+ // TODO: replace with reference fetching/transfer code (validate PDBentry
+ // as a DBRef?)
+
+ for (int pi = 0; pi < getPdbCount(); pi++)
{
- public void run()
+ PDBEntry strucEntry = getPdbEntry(pi);
+
+ String file = strucEntry.getFile();
+ if (file == null)
{
- evalStateCommand(command);
- if (align)
+ pdbid = strucEntry.getId();
+ try
+ {
+ file = structureViewer.fetchPdbFile(strucEntry);
+ } catch (OutOfMemoryError oomerror)
+ {
+ new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
+ } catch (Exception ex)
{
- // may need to wait around until script has finished
- while (viewer.isScriptExecuting())
+ 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++)
{
- try
- {
- Thread.sleep(20);
- } catch (Exception e)
+ if (Platform.pathEquals(filesInViewer[c], file))
{
+ file = null;
+ break;
}
- ;
}
- superposeStructures(appJmolWindow.ap.av.getAlignment(), -1, null);
+ }
+ if (file != null)
+ {
+ files.add(file);
}
}
- }).start();
+ }
+ } 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("'");
}
- }
-
- /**
- * 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)
- {
- for (int pe = 0; pe < pdbentry.length; pe++)
+ if (errormsgs.length() > 0)
{
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
+ 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;
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff