*/
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.util.Locale;
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;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Console;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
+import jalview.fts.service.alphafold.AlphafoldRestClient;
+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;
+
public class AppJmol extends StructureViewerBase
{
// ms to wait for Jmol to load files
* @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<File, StructureData> 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<SequenceI> 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()
{
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
{
super.initMenus();
- viewerActionMenu.setText(MessageManager.getString("label.jmol"));
-
viewerColour
.setText(MessageManager.getString("label.colour_with_jmol"));
viewerColour.setToolTipText(MessageManager
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
{
command = "";
}
- jmb.executeCommand(command, false);
- jmb.executeCommand("set hoverDelay=0.1", false);
+ 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;
try
{
- List<String> files = fetchPdbFiles();
+ List<String> files = jmb.fetchPdbFiles(this);
if (files.size() > 0)
{
showFilesInViewer(files);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ Console.error("Couldn't open Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
}
else
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
{
new OOMWarning("When trying to add structures to the Jmol viewer!",
oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
+ return;
} catch (Exception ex)
{
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ Console.error("Couldn't add files to Jmol viewer!", ex);
+ ex.printStackTrace();
+ return;
}
}
{
try
{
- Cache.log.debug("Waiting around for jmb notify.");
- Thread.sleep(waitFor);
+ Console.debug("Waiting around for jmb notify.");
waitTotal += waitFor;
+
+ // Thread.sleep() throws an exception in JS
+ Thread.sleep(waitFor);
} catch (Exception e)
{
}
}
else
{
- alignStructs_withAllAlignPanels();
+ alignStructsWithAllAlignPanels();
}
}
});
}
/**
- * 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).
+ * 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)
*
- * @return
+ * @param type
*/
- List<String> fetchPdbFiles()
- {
- // todo - record which pdbids were successfully imported.
- StringBuilder errormsgs = new StringBuilder();
-
- List<String> files = new ArrayList<>();
- String pdbid = "";
- try
- {
- String[] filesInViewer = jmb.getStructureFiles();
- // TODO: replace with reference fetching/transfer code (validate PDBentry
- // as a DBRef?)
- Pdb pdbclient = new Pdb();
- for (int pi = 0; pi < jmb.getPdbCount(); pi++)
- {
- String file = jmb.getPdbEntry(pi).getFile();
- if (file == null)
- {
- // todo: extract block as method and pull up (also ChimeraViewFrame)
- // retrieve the pdb and store it locally
- AlignmentI pdbseq = null;
- pdbid = jmb.getPdbEntry(pi).getId();
- long hdl = pdbid.hashCode() - System.currentTimeMillis();
- setProgressMessage(MessageManager
- .formatMessage("status.fetching_pdb", new String[]
- { pdbid }), hdl);
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- errormsgs.append("'").append(pdbid).append("'");
- } finally
- {
- setProgressMessage(
- MessageManager.getString("label.state_completed"), hdl);
- }
- if (pdbseq != null)
- {
- // just transfer the file name from the first sequence's first
- // PDBEntry
- file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
- .elementAt(0).getFile()).getAbsolutePath();
- jmb.getPdbEntry(pi).setFile(file);
- files.add(file);
- }
- else
- {
- errormsgs.append("'").append(pdbid).append("' ");
- }
- }
- else
- {
- if (filesInViewer != null && filesInViewer.length > 0)
- {
- addingStructures = 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;
- }
-
- @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)
- {
- 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)
+ ImageWriterI writer = new ImageWriterI()
{
- jmb.jmolViewer.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(Locale.ROOT);
+ 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 String getStateInfo()
- {
- return jmb == null ? null : jmb.jmolViewer.getStateInfo();
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.JMOL;
git://source.jalview.org / jalview.git / blobdiff