import java.io.*;
-import java.awt.*;
import java.awt.event.*;
import javax.swing.*;
-import java.util.BitSet;
import jalview.datamodel.*;
import jalview.gui.*;
import jalview.io.*;
import jalview.schemes.*;
+import jalview.ws.ebi.EBIFetchClient;
-import org.jmol.api.*;
-import org.jmol.adapter.smarter.SmarterJmolAdapter;
-import org.jmol.util.Logger;
-import org.jmol.popup.*;
+import java.awt.BorderLayout;
public class PDBViewer
extends JInternalFrame implements Runnable
{
- PDBEntry pdb;
+
/**
* The associated sequence in an alignment
*/
- Sequence sequence;
PDBCanvas pdbcanvas;
+
+ PDBEntry pdbentry;
+ SequenceI[]seq;
+ String[]chains;
+ AlignmentPanel ap;
+ String protocol;
String tmpPDBFile;
- public PDBViewer(PDBEntry entry,
- Sequence seq,
- SeqCanvas seqcanvas)
+ public PDBViewer(PDBEntry pdbentry,
+ SequenceI[] seq,
+ String[] chains,
+ AlignmentPanel ap,
+ String protocol)
+
{
- /* try
+ this.pdbentry = pdbentry;
+ this.seq = seq;
+ this.chains = chains;
+ this.ap = ap;
+ this.protocol = protocol;
+
+ try
{
jbInit();
}
ex.printStackTrace();
}
- if (entry == null)
- {
- return;
- }
- pdb = entry;
- sequence = seq;
- pdbcanvas = new PDBCanvas(seqcanvas, sequence);
- if (pdb.getFile() != null)
+ StringBuffer title = new StringBuffer(seq[0].getName()
+ + ":"
+ + pdbentry.getFile());
+
+ pdbcanvas = new PDBCanvas();
+
+ setContentPane(pdbcanvas);
+
+ if (pdbentry.getFile() != null)
{
try
{
- tmpPDBFile = pdb.getFile();
+ tmpPDBFile = pdbentry.getFile();
PDBfile pdbfile = new PDBfile(tmpPDBFile,
jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
+
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
}
catch (java.io.IOException ex)
worker.start();
}
- public void run()
- {
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
- if (tmpPDBFile != null)
- {
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
- }
- else
- {
- throw new Exception("Empty result for WSDbFetch Query: " + query);
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
- }
- }
- setContentPane(pdbcanvas);
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
- if (pdb.getProperty() != null)
+ if (pdbentry.getProperty() != null)
{
- if (pdb.getProperty().get("method") != null)
+ if (pdbentry.getProperty().get("method") != null)
{
title.append(" Method: ");
- title.append(pdb.getProperty().get("method"));
+ title.append(pdbentry.getProperty().get("method"));
}
- if (pdb.getProperty().get("chains") != null)
+ if (pdbentry.getProperty().get("chains") != null)
{
title.append(" Chain:");
- title.append(pdb.getProperty().get("chains"));
+ title.append(pdbentry.getProperty().get("chains"));
}
}
- */
-
- Container contentPane = getContentPane();
- JmolPanel jmolPanel = new JmolPanel();
- contentPane.add(jmolPanel);
-
- JmolViewer viewer = jmolPanel.viewer;
-
-
- System.out.println(entry.getFile()+" "+entry.getId());
- viewer.openFile(entry.getFile());
-
-
- StringBuffer string = new StringBuffer();
-
- for(int i=0; i<seq.getLength(); i++)
- {
- Color col = seqcanvas.getSequenceRenderer().getResidueBoxColour(seq, i);
-
- string.append("select " + i + "B; color [" +
- col.getRed()+","
- +col.getGreen()+","
- +col.getBlue()+"]; ");
- }
- System.out.println(string);
-
- viewer.evalString(string.toString());
-
-
- String strError = viewer.getOpenFileError();
- if (strError != null)
- Logger.error(strError);
-
-
- // Desktop.addInternalFrame(this,
- // seq.getName() + ":1GAQ"
- // , 400, 400);
-
+ Desktop.addInternalFrame(this, title.toString(), 400, 400);
}
-
-
-
- static class JmolPanel
- extends JPanel implements JmolSelectionListener
- {
- JmolViewer viewer;
- JmolAdapter adapter;
- JmolPanel()
- {
- adapter = new SmarterJmolAdapter(null);
- viewer = org.jmol.viewer.Viewer.allocateViewer(this, adapter);
- viewer.addSelectionListener(this);
-
- MyStatusListener myStatusListener;
- myStatusListener = new MyStatusListener();
- viewer.setJmolStatusListener(myStatusListener);
-
- JFrame frame = new JFrame("script window");
- // scriptWindow = new ScriptWindow(viewer, frame);
-
- myStatusListener.jmolpopup = JmolPopup.newJmolPopup(viewer);
- }
- public ScriptWindow scriptWindow;
- class MyStatusListener implements JmolStatusListener
- {
-
- JmolPopup jmolpopup ;
-
-
- public String eval(String strEval) {
- return "# 'eval' is implemented only for the applet.";
- }
-
- public void createImage(String file, String type, int quality) {
- System.out.println("CREATE IMAGE");
- // ImageCreator c = new ImageCreator(viewer, status);
- // c.createImage(file, type, quality);
- }
-
- public void setCallbackFunction(String callbackType, String callbackFunction) {
- // applet only?
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg) {
-
- }
-
- public void notifyFrameChanged(int frameNo) {
- // Note: twos-complement. To get actual frame number, use
- // Math.max(frameNo, -2 - frameNo)
- // -1 means all frames are now displayed
-
- boolean isAnimationRunning = (frameNo <= -2);
-
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo) {
- //System.out.println("notifyScriptStart:" + statusMessage + (additionalInfo == "" ? "" : additionalInfo));
- }
-
- public void sendConsoleEcho(String strEcho) {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
- }
-
- public void sendConsoleMessage(String strStatus) {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime) {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
- }
-
- public void handlePopupMenu(int x, int y) {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo) {
- // measurementTable.updateTables();
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo) {
-
- System.out.println("ATOM PICKED "+atomIndex+" "+strInfo);
- if (scriptWindow != null) {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo) {
-System.out.println("HOVER "+atomIndex+" "+strInfo);
- }
-
- public void sendSyncScript(String script, String appletName) {
- }
-
- public void showUrl(String url) {
- }
-
- public void showConsole(boolean showConsole) {
- System.out.println("SHOW CONSOLE" +(scriptWindow==null));
- if (scriptWindow == null)
- return;
- if (showConsole)
- scriptWindow.show();
- else
- scriptWindow.hide();
- }
-
- public float functionXY(String functionName, int x, int y) {
- return 0; // for user-defined isosurface functions (testing only -- bob hanson)
- }
-
- }
-
-
- class ScriptWindowAction extends AbstractAction {
-
- public ScriptWindowAction() {
- super("BLAH");
- }
-
- public void actionPerformed(ActionEvent e) {
- if (scriptWindow != null)
- scriptWindow.show();
- }
- }
-
- /**
- * Called when the selected atoms change
- * @param selection bit set giving selection of atom indexes
- */
- public void selectionChanged(BitSet selection)
- {
- System.out.println("SELECTION: "+selection);
- }
-
-
- public JmolSimpleViewer getViewer()
- {
- return viewer;
- }
-
- final Dimension currentSize = new Dimension();
- final Rectangle rectClip = new Rectangle();
-
- public void paint(Graphics g)
- {
-
- getSize(currentSize);
- g.getClipBounds(rectClip);
- viewer.renderScreenImage(g, currentSize, rectClip);
- }
- }
-
-
public void run()
{
try
{
EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
- if (tmpPDBFile != null)
- {
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
- }
- else
- {
- throw new Exception("Empty result for WSDbFetch Query: " + query);
- }
+ String query = "pdb:" + pdbentry.getId();
+ pdbentry.setFile(ebi.fetchDataAsFile(query, "default", "raw")
+ .getAbsolutePath());
+
+ if(pdbentry.getFile()!=null)
+ pdbcanvas.init(pdbentry, seq, chains, ap, protocol);
}
catch (Exception ex)
{
+ pdbcanvas.errorMessage = "Error retrieving file: "+pdbentry.getId();
ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
}
}
public void mapping_actionPerformed(ActionEvent e)
{
jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
- // Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+ Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
cap.setText(pdbcanvas.mappingDetails.toString());
}
pdbcanvas.setAllchainsVisible(allchains.getState());
}
- void showErrorMessage(String error)
- {
- // JOptionPane.showInternalMessageDialog(Desktop.desktop,
- // error, "PDB Viewer Error",
- // JOptionPane.WARNING_MESSAGE);
- }
public void zappo_actionPerformed(ActionEvent e)
{
{
if (e.getActionCommand().equals("User Defined..."))
{
- new UserDefinedColours(pdbcanvas, null);
+ // new UserDefinedColours(pdbcanvas, null);
}
else
{
git://source.jalview.org / jalview.git / blobdiff