/*
- * 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.
*
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.gui.StructureViewer.ViewerType;
import jalview.io.AppletFormatAdapter;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.HelixColourScheme;
import java.awt.BorderLayout;
import java.awt.Color;
-import java.awt.Component;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics;
import java.io.File;
import java.io.FileOutputStream;
import java.io.FileReader;
+import java.io.IOException;
import java.io.PrintWriter;
-import java.util.Enumeration;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
-public class AppJmol extends GStructureViewer implements Runnable,
- ViewSetProvider
-
+public class AppJmol extends StructureViewerBase
{
AppJmolBinding jmb;
RenderPanel renderPanel;
- AlignmentPanel ap;
-
- Vector atomsPicked = new Vector();
-
private boolean addingStructures = false;
- /**
- *
- * @param file
- * @param id
- * @param seq
- * @param ap
- * @param loadStatus
- * @param bounds
- * @deprecated defaults to AppJmol(String[] files, ... , viewid);
- */
- @Deprecated
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds)
- {
- this(file, id, seq, ap, loadStatus, bounds, null);
- }
-
- /**
- * @deprecated
- */
- @Deprecated
- public AppJmol(String file, String id, SequenceI[] seq,
- AlignmentPanel ap, String loadStatus, Rectangle bounds,
- String viewid)
- {
- this(new String[]
- { file }, new String[]
- { id }, new SequenceI[][]
- { seq }, ap, true, true, false, loadStatus, bounds, viewid);
- }
-
ViewSelectionMenu seqColourBy;
/**
PDBEntry[] pdbentrys = new PDBEntry[files.length];
for (int i = 0; i < pdbentrys.length; i++)
{
- PDBEntry pdbentry = new PDBEntry();
- pdbentry.setFile(files[i]);
- pdbentry.setId(ids[i]);
+ // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]);
+ PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB,
+ files[i]);
pdbentrys[i] = pdbentry;
}
// / TODO: check if protocol is needed to be set, and if chains are
seqColour.setSelected(false);
viewerColour.setSelected(true);
}
- if (usetoColour)
+ else if (usetoColour)
{
useAlignmentPanelForColourbyseq(ap);
jmb.setColourBySequence(true);
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
initJmol(loadStatus); // pdbentry, seq, JBPCHECK!
topJmol.addAlignmentPanel(ap);
// add it to the set used for colouring
topJmol.useAlignmentPanelForColourbyseq(ap);
- topJmol.buildJmolActionMenu();
+ topJmol.buildActionMenu();
ap.getStructureSelectionManager()
.sequenceColoursChanged(ap);
break;
return;
}
}
- // /////////////////////////////////
- // Check if there are other Jmol views involving this alignment
- // and prompt user about adding this molecule to one of them
- Vector existingViews = getJmolsFor(ap);
- if (existingViews.size() > 0)
+
+ /*
+ * Check if there are other Jmol views involving this alignment and prompt
+ * user about adding this molecule to one of them
+ */
+ for (AppJmol topJmol : getJmolsFor(ap))
{
- Enumeration jm = existingViews.elements();
- while (jm.hasMoreElements())
+ // TODO: highlight topJmol in view somehow
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
{
- AppJmol topJmol = (AppJmol) jm.nextElement();
- // TODO: highlight topJmol in view somehow
- int option = JOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager.formatMessage(
- "label.add_pdbentry_to_view", new String[]
- { pdbentry.getId(), topJmol.getTitle() }),
- MessageManager
- .getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_CANCEL_OPTION);
- if (option == JOptionPane.CANCEL_OPTION)
- {
- return;
- }
- if (option == JOptionPane.YES_OPTION)
- {
- topJmol.useAlignmentPanelForSuperposition(ap);
- topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
- return;
- }
+ return;
+ }
+ if (option == JOptionPane.YES_OPTION)
+ {
+ topJmol.useAlignmentPanelForSuperposition(ap);
+ topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame);
+ return;
}
}
// /////////////////////////////////
}
this.addInternalFrameListener(new InternalFrameAdapter()
{
+ @Override
public void internalFrameClosing(InternalFrameEvent internalFrameEvent)
{
- closeViewer();
+ closeViewer(false);
}
});
openNewJmol(ap, pe, seqs);
}
- public AlignmentPanel[] getAllAlignmentPanels()
- {
- AlignmentPanel[] t, list = new AlignmentPanel[0];
- for (String setid : _aps)
- {
- AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid);
- if (panels != null)
- {
- t = new AlignmentPanel[list.length + panels.length];
- System.arraycopy(list, 0, t, 0, list.length);
- System.arraycopy(panels, 0, t, list.length, panels.length);
- list = t;
- }
- }
-
- return list;
- }
-
- /**
- * set the primary alignmentPanel reference and add another alignPanel to the
- * list of ones to use for colouring and aligning
- *
- * @param nap
- */
- public void addAlignmentPanel(AlignmentPanel nap)
- {
- if (ap == null)
- {
- ap = nap;
- }
- if (!_aps.contains(nap.av.getSequenceSetId()))
- {
- _aps.add(nap.av.getSequenceSetId());
- }
- }
-
- /**
- * remove any references held to the given alignment panel
- *
- * @param nap
- */
- public void removeAlignmentPanel(AlignmentPanel nap)
- {
- try
- {
- _alignwith.remove(nap);
- _colourwith.remove(nap);
- if (ap == nap)
- {
- ap = null;
- for (AlignmentPanel aps : getAllAlignmentPanels())
- {
- if (aps != nap)
- {
- ap = aps;
- break;
- }
- }
- }
- } catch (Exception ex)
- {
- }
- if (ap != null)
- {
- buildJmolActionMenu();
- }
- }
-
- public void useAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_alignwith.contains(nap))
- {
- _alignwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap)
- {
- if (_alignwith.contains(nap))
- {
- _alignwith.remove(nap);
- }
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
- boolean enableColourBySeq)
- {
- useAlignmentPanelForColourbyseq(nap);
- jmb.setColourBySequence(enableColourBySeq);
- seqColour.setSelected(enableColourBySeq);
- viewerColour.setSelected(!enableColourBySeq);
- }
-
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- addAlignmentPanel(nap);
- if (!_colourwith.contains(nap))
- {
- _colourwith.add(nap);
- }
- }
-
- public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap)
- {
- if (_colourwith.contains(nap))
- {
- _colourwith.remove(nap);
- }
- }
-
/**
* pdb retrieval thread.
*/
return;
}
- private Vector getJmolsFor(AlignmentPanel apanel)
+ private Vector<AppJmol> getJmolsFor(AlignmentPanel apanel)
{
- Vector result = new Vector();
+ Vector<AppJmol> result = new Vector<AppJmol>();
JInternalFrame[] frames = Desktop.instance.getAllFrames();
for (JInternalFrame frame : frames)
{
if (frame instanceof AppJmol)
{
- if (((GStructureViewer) frame).isLinkedWith(apanel))
+ if (((AppJmol) frame).isLinkedWith(apanel))
{
- result.addElement(frame);
+ result.addElement((AppJmol) frame);
}
}
}
scriptWindow = new JPanel(bl);
scriptWindow.setVisible(false);
}
- ;
+
jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow,
null);
- jmb.newJmolPopup(true, "Jmol", true);
+ // jmb.newJmolPopup("Jmol");
if (command == null)
{
command = "";
jmb.setFinishedInit(true);
}
- void setChainMenuItems(Vector chains)
+ void setChainMenuItems(Vector<String> chains)
{
chainMenu.removeAll();
if (chains == null)
chainMenu.add(menuItem);
- for (int c = 0; c < chains.size(); c++)
+ for (String chain : chains)
{
- menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true);
+ menuItem = new JCheckBoxMenuItem(chain, true);
menuItem.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent evt)
void centerViewer()
{
- Vector toshow = new Vector();
- String lbl;
- int mlength, p, mnum;
+ Vector<String> toshow = new Vector<String>();
for (int i = 0; i < chainMenu.getItemCount(); i++)
{
if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
jmb.centerViewer(toshow);
}
- public void closeViewer()
+ public void closeViewer(boolean closeExternalViewer)
{
+ // JMol does not use an external viewer
jmb.closeViewer();
- ap = null;
+ setAlignmentPanel(null);
_aps.clear();
_alignwith.clear();
_colourwith.clear();
}
try
{
- pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.getPdbEntry(
- pi)
- .getId());
+ pdbseq = pdbclient.getSequenceRecords(pdbid);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
{
// just transfer the file name from the first sequence's first
// PDBEntry
- file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId()
- .elementAt(0)).getFile()).getAbsolutePath();
+ file = new File(pdbseq.getSequenceAt(0).getPDBId()
+ .elementAt(0).getFile()).getAbsolutePath();
jmb.getPdbEntry(pi).setFile(file);
files.append(" \"" + Platform.escapeString(file) + "\"");
// need to wait around until script has finished
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
.getPdbFile().length != jmb.getPdbCount()))
{
try
{
}
}
+
// refresh the sequence colours for the new structure(s)
for (AlignmentPanel ap : _colourwith)
{
if (value == JalviewFileChooser.APPROVE_OPTION)
{
+ BufferedReader in = null;
try
{
// TODO: cope with multiple PDB files in view
- BufferedReader in = new BufferedReader(new FileReader(
+ in = new BufferedReader(new FileReader(
jmb.getPdbFile()[0]));
File outFile = chooser.getSelectedFile();
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (in != null)
+ {
+ try
+ {
+ in.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
}
}
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
try
{
- for (int pdbe = 0; pdbe < jmb.getPdbCount(); pdbe++)
- {
- cap.appendText(jmb.printMapping(jmb.getPdbEntry(pdbe).getFile()));
- cap.appendText("\n");
- }
+ cap.appendText(jmb.printMappings());
} catch (OutOfMemoryError e)
{
new OOMWarning(
if (im.getGraphics() != null)
{
- Rectangle rect = new Rectangle(width, height);
- jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect);
+ jmb.viewer.renderScreenImage(im.getGraphics(), width, height);
im.writeImage();
}
}
{
if (!jmb.isLoadingFromArchive())
{
- if (_colourwith.size() == 0 && ap != null)
+ if (_colourwith.size() == 0 && getAlignmentPanel() != null)
{
// Make the currently displayed alignment panel the associated view
- _colourwith.add(ap.alignFrame.alignPanel);
+ _colourwith.add(getAlignmentPanel().alignFrame.alignPanel);
}
}
// Set the colour using the current view for the associated alignframe
for (AlignmentPanel ap : _colourwith)
{
- jmb.colourBySequence(ap.av.showSequenceFeatures, ap);
+ jmb.colourBySequence(ap);
}
}
}
{
final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
+ @Override
public void paintComponent(Graphics g)
{
getSize(currentSize);
- g.getClipBounds(rectClip);
- if (jmb.fileLoadingError != null)
+ if (jmb != null && jmb.fileLoadingError != null)
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);
}
else
{
- jmb.viewer.renderScreenImage(g, currentSize, rectClip);
+ jmb.viewer.renderScreenImage(g, currentSize.width,
+ currentSize.height);
}
}
}
}
}
- protected void buildJmolActionMenu()
- {
- if (_alignwith == null)
- {
- _alignwith = new Vector<AlignmentPanel>();
- }
- if (_alignwith.size() == 0 && ap != null)
- {
- _alignwith.add(ap);
- }
- ;
- for (Component c : viewerActionMenu.getMenuComponents())
- {
- if (c != alignStructs)
- {
- viewerActionMenu.remove((JMenuItem) c);
- }
- }
- final ItemListener handler;
- }
-
/*
* (non-Javadoc)
*
private void alignStructs_withAllAlignPanels()
{
- if (ap == null)
+ if (getAlignmentPanel() == null)
{
return;
}
;
if (_alignwith.size() == 0)
{
- _alignwith.add(ap);
+ _alignwith.add(getAlignmentPanel());
}
;
try
return ap;
}
}
- return ap;
+ return getAlignmentPanel();
}
@Override
return jmb == null ? null : jmb.viewer.getStateInfo();
}
+ @Override
+ public ViewerType getViewerType()
+ {
+ return ViewerType.JMOL;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff