import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.util.BrowserLauncher;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.Collections;
import java.util.List;
-import javax.swing.JCheckBoxMenuItem;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
import javax.swing.JMenuItem;
/**
* Send a command to Chimera to create residue attributes for Jalview features
* <p>
- * The syntax is: setattr r <attName> <attValue> <atomSpec>
+ * The syntax is: setattr r <attName> <attValue> <atomSpec>
* <p>
- * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
*/
protected void sendFeaturesToChimera()
{
SequenceI[][] seqs)
{
createProgressBar();
- jmb = new JalviewChimeraBindingModel(this,
- ap.getStructureSelectionManager(), pdbentrys, seqs, null);
+ jmb = newBindingModel(ap, pdbentrys, seqs);
addAlignmentPanel(ap);
useAlignmentPanelForColourbyseq(ap);
}
+ protected JalviewChimeraBindingModel newBindingModel(AlignmentPanel ap,
+ PDBEntry[] pdbentrys, SequenceI[][] seqs)
+ {
+ return new JalviewChimeraBindingModel(this,
+ ap.getStructureSelectionManager(), pdbentrys, seqs, null);
+ }
+
/**
* Create a new viewer from saved session state data including Chimera session
* file
}
/**
- * Show only the selected chain(s) in the viewer
- */
- @Override
- void showSelectedChains()
- {
- List<String> toshow = new ArrayList<>();
- for (int i = 0; i < chainMenu.getItemCount(); i++)
- {
- if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem)
- {
- JCheckBoxMenuItem item = (JCheckBoxMenuItem) chainMenu.getItem(i);
- if (item.isSelected())
- {
- toshow.add(item.getText());
- }
- }
- }
- jmb.showChains(toshow);
- }
-
- /**
* Close down this instance of Jalview's Chimera viewer, giving the user the
* option to close the associated Chimera window (process). They may wish to
* keep it open until they have had an opportunity to save any work.
pdb = jmb.getSsm().setMapping(jmb.getSequence()[pos],
jmb.getChains()[pos], pe.getFile(), protocol,
getProgressIndicator());
- stashFoundChains(pdb, pe.getFile());
+ jmb.stashFoundChains(pdb, pe.getFile());
} catch (OutOfMemoryError oomerror)
{
@Override
public void run()
{
- alignStructs_withAllAlignPanels();
+ alignStructsWithAllAlignPanels();
}
}).start();
}
worker = null;
}
- /**
- * Fetch PDB data and save to a local file. Returns the full path to the file,
- * or null if fetch fails. TODO: refactor to common with Jmol ? duplication
- *
- * @param processingEntry
- * @return
- * @throws Exception
- */
-
- private void stashFoundChains(StructureFile pdb, String file)
- {
- for (int i = 0; i < pdb.getChains().size(); i++)
- {
- String chid = new String(
- pdb.getId() + ":" + pdb.getChains().elementAt(i).id);
- jmb.getChainNames().add(chid);
- jmb.getChainFile().put(chid, file);
- }
- }
-
- private String fetchPdbFile(PDBEntry processingEntry) throws Exception
- {
- String filePath = null;
- Pdb pdbclient = new Pdb();
- AlignmentI pdbseq = null;
- String pdbid = processingEntry.getId();
- long handle = System.currentTimeMillis()
- + Thread.currentThread().hashCode();
-
- /*
- * Write 'fetching PDB' progress on AlignFrame as we are not yet visible
- */
- String msg = MessageManager.formatMessage("status.fetching_pdb",
- new Object[]
- { pdbid });
- getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
- // long hdl = startProgressBar(MessageManager.formatMessage(
- // "status.fetching_pdb", new Object[]
- // { pdbid }));
- try
- {
- pdbseq = pdbclient.getSequenceRecords(pdbid);
- } catch (OutOfMemoryError oomerror)
- {
- new OOMWarning("Retrieving PDB id " + pdbid, oomerror);
- } finally
- {
- msg = pdbid + " " + MessageManager.getString("label.state_completed");
- getAlignmentPanel().alignFrame.setProgressBar(msg, handle);
- // stopProgressBar(msg, hdl);
- }
- /*
- * If PDB data were saved and are not invalid (empty alignment), return the
- * file path.
- */
- if (pdbseq != null && pdbseq.getHeight() > 0)
- {
- // just use the file name from the first sequence's first PDBEntry
- filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries()
- .elementAt(0).getFile()).getAbsolutePath();
- processingEntry.setFile(filePath);
- }
- return filePath;
- }
-
@Override
- public void eps_actionPerformed(ActionEvent e)
+ public void eps_actionPerformed()
{
throw new Error(MessageManager
.getString("error.eps_generation_not_implemented"));
}
@Override
- public void png_actionPerformed(ActionEvent e)
+ public void png_actionPerformed()
{
throw new Error(MessageManager
.getString("error.png_generation_not_implemented"));
}
@Override
- public void showHelp_actionPerformed(ActionEvent actionEvent)
+ public void showHelp_actionPerformed()
{
try
{
- String url = jmb.isChimeraX()
- ? "http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html"
- : "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
+ String url = jmb.getHelpURL();
BrowserLauncher.openURL(url);
} catch (IOException ex)
{
return jmb;
}
- /**
- * Ask Chimera to save its session to the designated file path, or to a
- * temporary file if the path is null. Returns the file path if successful,
- * else null.
- *
- * @param filepath
- * @see getStateInfo
- */
- protected String saveSession(String filepath)
- {
- String pathUsed = filepath;
- try
- {
- if (pathUsed == null)
- {
- String suffix = jmb.isChimeraX() ? ".cxs" : ".py";
- File tempFile = File.createTempFile("chimera", suffix);
- tempFile.deleteOnExit();
- pathUsed = tempFile.getPath();
- }
- boolean result = jmb.saveSession(pathUsed);
- if (result)
- {
- this.chimeraSessionFile = pathUsed;
- return pathUsed;
- }
- } catch (IOException e)
- {
- }
- return null;
- }
-
- /**
- * Returns a string representing the state of the Chimera session. This is
- * done by requesting Chimera to save its session to a temporary file, then
- * reading the file contents. Returns an empty string on any error.
- */
- @Override
- public String getStateInfo()
- {
- String sessionFile = saveSession(null);
- if (sessionFile == null)
- {
- return "";
- }
- InputStream is = null;
- try
- {
- File f = new File(sessionFile);
- byte[] bytes = new byte[(int) f.length()];
- is = new FileInputStream(sessionFile);
- is.read(bytes);
- return new String(bytes);
- } catch (IOException e)
- {
- return "";
- } finally
- {
- if (is != null)
- {
- try
- {
- is.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
-
@Override
protected void fitToWindow_actionPerformed()
{
{
return "Chimera";
}
-
- /**
- * Sends commands to align structures according to associated alignment(s).
- *
- * @return
- */
- @Override
- protected String alignStructs_withAllAlignPanels()
- {
- String reply = super.alignStructs_withAllAlignPanels();
- if (reply != null)
- {
- statusBar.setText("Superposition failed: " + reply);
- }
- return reply;
- }
}
git://source.jalview.org / jalview.git / blobdiff