- * The syntax is: setattr r <attName> <attValue> <atomSpec> - *
- * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A + * Sends command(s) to the structure viewer to create residue attributes for + * visible Jalview features */ protected void sendFeaturesToChimera() { + // todo pull up? int count = jmb.sendFeaturesToViewer(getAlignmentPanel()); statusBar.setText( MessageManager.formatMessage("label.attributes_set", count)); @@ -321,7 +308,8 @@ public class ChimeraViewFrame extends StructureViewerBase if (!jmb.launchChimera()) { JvOptionPane.showMessageDialog(Desktop.desktop, - MessageManager.getString("label.chimera_failed"), + MessageManager.formatMessage("label.open_viewer_failed", + getViewerName()), MessageManager.getString("label.error_loading_file"), JvOptionPane.ERROR_MESSAGE); this.dispose(); @@ -342,50 +330,6 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * 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. - * - * @param closeChimera - * if true, close any linked Chimera process; if false, prompt first - */ - @Override - public void closeViewer(boolean closeChimera) - { - if (jmb != null && jmb.isChimeraRunning()) - { - if (!closeChimera) - { - String prompt = MessageManager - .formatMessage("label.confirm_close_chimera", new Object[] - { jmb.getViewerTitle(getViewerName(), false) }); - prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JvOptionPane.showConfirmDialog(this, prompt, - MessageManager.getString("label.close_viewer"), - JvOptionPane.YES_NO_CANCEL_OPTION); - /* - * abort closure if user hits escape or Cancel - */ - if (confirm == JvOptionPane.CANCEL_OPTION - || confirm == JvOptionPane.CLOSED_OPTION) - { - return; - } - closeChimera = confirm == JvOptionPane.YES_OPTION; - } - jmb.closeViewer(closeChimera); - } - 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; - dispose(); - } - - /** * Open any newly added PDB structures in Chimera, having first fetched data * from PDB (if not already saved). */ @@ -571,31 +515,10 @@ public class ChimeraViewFrame extends StructureViewerBase } @Override - public void eps_actionPerformed() - { - throw new Error(MessageManager - .getString("error.eps_generation_not_implemented")); - } - - @Override - public void png_actionPerformed() + public void makePDBImage(TYPE imageType) { - throw new Error(MessageManager - .getString("error.png_generation_not_implemented")); - } - - @Override - public void showHelp_actionPerformed() - { - try - { - String url = jmb.getHelpURL(); - BrowserLauncher.openURL(url); - } catch (IOException ex) - { - System.err - .println("Show Chimera help failed with: " + ex.getMessage()); - } + throw new UnsupportedOperationException( + "Image export for Chimera is not implemented"); } @Override @@ -604,77 +527,6 @@ 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.getSessionFileExtension(); - 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() {