*/
package jalview.gui;
-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.Vector;
-import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
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.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
private static final String SPACE = " ";
- private static final String BACKSLASH = "\"";
+ private static final String QUOTE = "\"";
AppJmolBinding jmb;
.getString("label.let_jmol_manage_structure_colours"));
}
- IProgressIndicator progressBar = null;
-
- @Override
- protected IProgressIndicator getIProgressIndicator()
- {
- return progressBar;
- }
/**
- * add a single PDB structure to a new or existing Jmol view
+ * display a single PDB structure in a new Jmol view
*
* @param pdbentry
* @param seq
public AppJmol(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
final AlignmentPanel ap)
{
- progressBar = ap.alignFrame;
- String pdbId = pdbentry.getId();
-
- /*
- * If the PDB file is already loaded, the user may just choose to add to an
- * existing viewer (or cancel)
- */
- if (addAlreadyLoadedFile(seq, chains, ap, pdbId))
- {
- return;
- }
+ setProgressIndicator(ap.alignFrame);
- /*
- * Check if there are other Jmol views involving this alignment and prompt
- * user about adding this molecule to one of them
- */
- if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId))
- {
- return;
- }
-
- /*
- * If the options above are declined or do not apply, open a new viewer
- */
- openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq });
+ openNewJmol(ap, alignAddedStructures, new PDBEntry[] { pdbentry },
+ new SequenceI[][]
+ { seq });
}
- private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys,
+ private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
+ 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;
if (pdbentrys.length > 1)
{
- alignAddedStructures = true;
useAlignmentPanelForSuperposition(ap);
}
+
jmb.setColourBySequence(true);
setSize(400, 400); // probably should be a configurable/dynamic default here
initMenus();
}
/**
- * create a new Jmol containing several structures superimposed using the
- * given alignPanel.
+ * create a new Jmol containing several structures optionally superimposed
+ * using the given alignPanel.
*
* @param ap
+ * @param alignAdded
+ * - true to superimpose
* @param pe
* @param seqs
*/
- public AppJmol(AlignmentPanel ap, PDBEntry[] pe, SequenceI[][] seqs)
+ public AppJmol(AlignmentPanel ap, boolean alignAdded, PDBEntry[] pe,
+ SequenceI[][] seqs)
{
- openNewJmol(ap, pe, seqs);
+ openNewJmol(ap, alignAdded, pe, seqs);
}
- /**
- * Returns a list of any Jmol viewers. The list is restricted to those linked
- * to the given alignment panel if it is not null.
- */
- @Override
- protected List<StructureViewerBase> getViewersFor(AlignmentPanel apanel)
- {
- List<StructureViewerBase> result = new ArrayList<>();
- JInternalFrame[] frames = Desktop.instance.getAllFrames();
-
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof AppJmol)
- {
- if (apanel == null
- || ((StructureViewerBase) frame).isLinkedWith(apanel))
- {
- result.add((StructureViewerBase) frame);
- }
- }
- }
- return result;
- }
void initJmol(String command)
{
{
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);
}
- boolean allChainsSelected = false;
-
- @Override
- void showSelectedChains()
- {
- Vector<String> toshow = new Vector<>();
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if (item.isSelected())
- {
- toshow.addElement(item.getText());
- }
- }
- }
- jmb.centerViewer(toshow);
- }
-
- @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()
{
StringBuilder fileList = new StringBuilder();
for (String s : files)
{
- fileList.append(SPACE).append(BACKSLASH)
- .append(Platform.escapeString(s)).append(BACKSLASH);
+ fileList.append(SPACE).append(QUOTE)
+ .append(Platform.escapeBackslashes(s)).append(QUOTE);
}
String filesString = fileList.toString();
} catch (Exception ex)
{
Cache.log.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
{
- 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;
}
}
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)
{
}
}
// refresh the sequence colours for the new structure(s)
- for (AlignmentPanel ap : _colourwith)
+ for (AlignmentViewPanel ap : _colourwith)
{
jmb.updateColours(ap);
}
// do superposition if asked to
- if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures)
+ if (alignAddedStructures)
{
alignAddedStructures();
}
@Override
public void run()
{
- if (jmb.viewer.isScriptExecuting())
+ if (jmb.jmolViewer.isScriptExecuting())
{
SwingUtilities.invokeLater(this);
try
}
else
{
- alignStructs_withAllAlignPanels();
+ alignStructsWithAllAlignPanels();
}
}
});
- alignAddedStructures = false;
+
}
/**
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();
- 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);
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)
{
addingStructures = true; // already files loaded.
for (int c = 0; c < filesInViewer.length; c++)
{
- if (filesInViewer[c].equals(file))
+ if (Platform.pathEquals(filesInViewer[c], file))
{
file = null;
break;
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)
}
}
}
- 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);
}
else
{
- jmb.viewer.renderScreenImage(g, currentSize.width,
+ jmb.jmolViewer.renderScreenImage(g, currentSize.width,
currentSize.height);
}
}
}
@Override
- public String getStateInfo()
- {
- return jmb == null ? null : jmb.viewer.getStateInfo();
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.JMOL;
git://source.jalview.org / jalview.git / blobdiff