X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=0d6a216e54078410f21b702f16f4ccb91d295bca;hb=1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b;hp=22876a4e59199fd6be4786e5689819a53f919ac1;hpb=f2511dd2e8e37b8e999e924f8a53d150377b21b5;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 22876a4..0d6a216 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -23,7 +23,6 @@ package jalview.gui; 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; @@ -34,7 +33,6 @@ 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.event.ActionEvent; import java.awt.event.ActionListener; @@ -48,7 +46,6 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import javax.swing.JCheckBoxMenuItem; import javax.swing.JInternalFrame; import javax.swing.JMenu; import javax.swing.JMenuItem; @@ -165,9 +162,9 @@ public class ChimeraViewFrame extends StructureViewerBase /** * Send a command to Chimera to create residue attributes for Jalview features *

- * The syntax is: setattr r + * The syntax is: setattr r <attName> <attValue> <atomSpec> *

- * 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() { @@ -209,8 +206,7 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqs) { createProgressBar(); - jmb = new JalviewChimeraBindingModel(this, - ap.getStructureSelectionManager(), pdbentrys, seqs, null); + jmb = newBindingModel(ap, pdbentrys, seqs); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); @@ -238,6 +234,13 @@ public class ChimeraViewFrame extends StructureViewerBase } + 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 @@ -339,27 +342,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * Show only the selected chain(s) in the viewer - */ - @Override - void showSelectedChains() - { - List 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. @@ -532,7 +514,7 @@ public class ChimeraViewFrame extends StructureViewerBase 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) { @@ -578,7 +560,7 @@ public class ChimeraViewFrame extends StructureViewerBase @Override public void run() { - alignStructs_withAllAlignPanels(); + alignStructsWithAllAlignPanels(); } }).start(); } @@ -588,93 +570,26 @@ public class ChimeraViewFrame extends StructureViewerBase 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) { @@ -689,77 +604,6 @@ public class ChimeraViewFrame extends StructureViewerBase 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() { @@ -777,20 +621,4 @@ public class ChimeraViewFrame extends StructureViewerBase { 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; - } }