X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=ffb963991333283fcbf0ea83997de3477e93df9a;hb=f831ddf7f52d6c4a1918e87d94877b22bd322648;hp=a1846bc75695384dbd950a69c3353da00dda744e;hpb=e1767448d422ab26a6920bae2173804eda662e31;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index a1846bc..ffb9639 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -21,26 +21,15 @@ package jalview.gui; import jalview.bin.Cache; -import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentI; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.StructureViewer.ViewerType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.schemes.BuriedColourScheme; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.HelixColourScheme; -import jalview.schemes.HydrophobicColourScheme; -import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.StrandColourScheme; -import jalview.schemes.TaylorColourScheme; -import jalview.schemes.TurnColourScheme; -import jalview.schemes.ZappoColourScheme; 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.BorderLayout; import java.awt.Color; @@ -49,34 +38,29 @@ import java.awt.Font; import java.awt.Graphics; import java.awt.Rectangle; import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.awt.event.ItemEvent; -import java.awt.event.ItemListener; -import java.io.BufferedReader; import java.io.File; -import java.io.FileOutputStream; -import java.io.FileReader; -import java.io.IOException; -import java.io.PrintWriter; import java.util.ArrayList; import java.util.List; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JSplitPane; +import javax.swing.SwingUtilities; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; -import javax.swing.event.MenuEvent; -import javax.swing.event.MenuListener; public class AppJmol extends StructureViewerBase { + // ms to wait for Jmol to load files + private static final int JMOL_LOAD_TIMEOUT = 20000; + + private static final String SPACE = " "; + + private static final String BACKSLASH = "\""; + AppJmolBinding jmb; JPanel scriptWindow; @@ -85,8 +69,6 @@ public class AppJmol extends StructureViewerBase RenderPanel renderPanel; - ViewSelectionMenu seqColourBy; - /** * * @param files @@ -122,7 +104,7 @@ public class AppJmol extends StructureViewerBase // / TODO: check if protocol is needed to be set, and if chains are // autodiscovered. jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), - pdbentrys, seqs, null, null); + pdbentrys, seqs, null); jmb.setLoadingFromArchive(true); addAlignmentPanel(ap); @@ -130,6 +112,7 @@ public class AppJmol extends StructureViewerBase { useAlignmentPanelForSuperposition(ap); } + initMenus(); if (leaveColouringToJmol || !usetoColour) { jmb.setColourBySequence(false); @@ -144,7 +127,6 @@ public class AppJmol extends StructureViewerBase viewerColour.setSelected(false); } this.setBounds(bounds); - initMenus(); setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); @@ -158,84 +140,19 @@ public class AppJmol extends StructureViewerBase } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! - } - private void initMenus() + @Override + protected void initMenus() { - seqColour.setSelected(jmb.isColourBySequence()); - viewerColour.setSelected(!jmb.isColourBySequence()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (_alignwith == null) - { - _alignwith = new Vector(); - } - - seqColourBy = new ViewSelectionMenu( - MessageManager.getString("label.colour_by"), this, _colourwith, - new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - if (!seqColour.isSelected()) - { - seqColour.doClick(); - } - else - { - // update the jmol display now. - seqColour_actionPerformed(null); - } - } - }); - viewMenu.add(seqColourBy); - final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu( - MessageManager.getString("label.superpose_with"), this, - _alignwith, handler = new ItemListener() - { - - @Override - public void itemStateChanged(ItemEvent e) - { - alignStructs.setEnabled(_alignwith.size() > 0); - alignStructs.setToolTipText(MessageManager - .formatMessage( - "label.align_structures_using_linked_alignment_views", - new String[] { new Integer(_alignwith - .size()).toString() })); - } - }); - handler.itemStateChanged(null); - viewerActionMenu.add(alpanels); - viewerActionMenu.addMenuListener(new MenuListener() - { + super.initMenus(); - @Override - public void menuSelected(MenuEvent e) - { - handler.itemStateChanged(null); - } - - @Override - public void menuDeselected(MenuEvent e) - { - // TODO Auto-generated method stub - - } - - @Override - public void menuCanceled(MenuEvent e) - { - // TODO Auto-generated method stub + viewerActionMenu = new JMenu(MessageManager.getString("label.jmol")); - } - }); + viewerColour + .setText(MessageManager.getString("label.colour_with_jmol")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_jmol_manage_structure_colours")); } IProgressIndicator progressBar = null; @@ -278,23 +195,15 @@ public class AppJmol extends StructureViewerBase openNewJmol(ap, new PDBEntry[] { pdbentry }, new SequenceI[][] { seq }); } - /** - * Answers true if this viewer already involves the given PDB ID - */ - @Override - protected boolean hasPdbId(String pdbId) - { - return jmb.hasPdbId(pdbId); - } - private void openNewJmol(AlignmentPanel ap, PDBEntry[] pdbentrys, SequenceI[][] seqs) { progressBar = ap.alignFrame; jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(), - pdbentrys, seqs, null, null); + pdbentrys, seqs, null); addAlignmentPanel(ap); useAlignmentPanelForColourbyseq(ap); + if (pdbentrys.length > 1) { alignAddedStructures = true; @@ -303,12 +212,10 @@ public class AppJmol extends StructureViewerBase jmb.setColourBySequence(true); setSize(400, 400); // probably should be a configurable/dynamic default here initMenus(); - worker = null; - { - addingStructures = false; - worker = new Thread(this); - worker.start(); - } + addingStructures = false; + worker = new Thread(this); + worker.start(); + this.addInternalFrameListener(new InternalFrameAdapter() { @Override @@ -375,8 +282,8 @@ public class AppJmol extends StructureViewerBase scriptWindow.setVisible(false); } - jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, - null); + jmb.allocateViewer(renderPanel, true, "", null, null, "", + scriptWindow, null); // jmb.newJmolPopup("Jmol"); if (command == null) { @@ -387,57 +294,12 @@ public class AppJmol extends StructureViewerBase jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) - { - chainMenu.removeAll(); - if (chains == null) - { - return; - } - JMenuItem menuItem = new JMenuItem( - MessageManager.getString("label.all")); - menuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent evt) - { - allChainsSelected = true; - for (int i = 0; i < chainMenu.getItemCount(); i++) - { - if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) - { - ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); - } - } - centerViewer(); - allChainsSelected = false; - } - }); - - chainMenu.add(menuItem); - for (String chain : chains) - { - menuItem = new JCheckBoxMenuItem(chain, true); - menuItem.addItemListener(new ItemListener() - { - @Override - public void itemStateChanged(ItemEvent evt) - { - if (!allChainsSelected) - { - centerViewer(); - } - } - }); - - chainMenu.add(menuItem); - } - } boolean allChainsSelected = false; - void centerViewer() + @Override + void showSelectedChains() { Vector toshow = new Vector(); for (int i = 0; i < chainMenu.getItemCount(); i++) @@ -475,15 +337,168 @@ public class AppJmol extends StructureViewerBase public void run() { _started = true; + try + { + List files = fetchPdbFiles(); + if (files.size() > 0) + { + showFilesInViewer(files); + } + } finally + { + _started = false; + worker = null; + } + } + + /** + * Either adds the given files to a structure viewer or opens a new viewer to + * show them + * + * @param files + * list of absolute paths to structure files + */ + void showFilesInViewer(List files) + { + long lastnotify = jmb.getLoadNotifiesHandled(); + StringBuilder fileList = new StringBuilder(); + for (String s : files) + { + fileList.append(SPACE).append(BACKSLASH) + .append(Platform.escapeString(s)).append(BACKSLASH); + } + String filesString = fileList.toString(); + + if (!addingStructures) + { + try + { + initJmol("load FILES " + filesString); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("When trying to open the Jmol viewer!", oomerror); + Cache.log.debug("File locations are " + filesString); + } catch (Exception ex) + { + Cache.log.error("Couldn't open Jmol viewer!", ex); + } + } + else + { + StringBuilder cmd = new StringBuilder(); + cmd.append("loadingJalviewdata=true\nload APPEND "); + cmd.append(filesString); + cmd.append("\nloadingJalviewdata=null"); + final String command = cmd.toString(); + lastnotify = jmb.getLoadNotifiesHandled(); + + try + { + jmb.evalStateCommand(command); + } catch (OutOfMemoryError oomerror) + { + new OOMWarning("When trying to add structures to the Jmol viewer!", + oomerror); + Cache.log.debug("File locations are " + filesString); + } catch (Exception ex) + { + Cache.log.error("Couldn't add files to Jmol viewer!", ex); + } + } + + // need to wait around until script has finished + int waitMax = JMOL_LOAD_TIMEOUT; + int waitFor = 35; + int waitTotal = 0; + while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() + : !(jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb + .getPdbFile().length == files.size())) + { + try + { + Cache.log.debug("Waiting around for jmb notify."); + Thread.sleep(waitFor); + waitTotal += waitFor; + } catch (Exception e) + { + } + if (waitTotal > waitMax) + { + System.err + .println("Timed out waiting for Jmol to load files after " + + waitTotal + "ms"); +// System.err.println("finished: " + jmb.isFinishedInit() +// + "; loaded: " + Arrays.toString(jmb.getPdbFile()) +// + "; files: " + files.toString()); + jmb.getPdbFile(); + break; + } + } + + // refresh the sequence colours for the new structure(s) + for (AlignmentPanel ap : _colourwith) + { + jmb.updateColours(ap); + } + // do superposition if asked to + if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) + { + alignAddedStructures(); + } + addingStructures = false; + } + + /** + * Queues a thread to align structures with Jalview alignments + */ + void alignAddedStructures() + { + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + @Override + public void run() + { + if (jmb.viewer.isScriptExecuting()) + { + SwingUtilities.invokeLater(this); + try + { + Thread.sleep(5); + } catch (InterruptedException q) + { + } + return; + } + else + { + alignStructs_withAllAlignPanels(); + } + } + }); + alignAddedStructures = false; + } + + /** + * Retrieves and saves as file any modelled PDB entries for which we do not + * already have a file saved. Returns a list of absolute paths to structure + * files which were either retrieved, or already stored but not modelled in + * the structure viewer (i.e. files to add to the viewer display). + * + * @return + */ + List fetchPdbFiles() + { + // todo - record which pdbids were successfully imported. + StringBuilder errormsgs = new StringBuilder(); + + List files = new ArrayList(); String pdbid = ""; - // todo - record which pdbids were successfuly imported. - StringBuffer errormsgs = new StringBuffer(), files = new StringBuffer(); try { - String[] curfiles = jmb.getPdbFile(); // files currently in viewer + String[] filesInViewer = jmb.getPdbFile(); // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) - jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); + Pdb pdbclient = new Pdb(); for (int pi = 0; pi < jmb.getPdbCount(); pi++) { String file = jmb.getPdbEntry(pi).getFile(); @@ -507,12 +522,15 @@ public class AppJmol extends StructureViewerBase } catch (Exception ex) { ex.printStackTrace(); - errormsgs.append("'" + pdbid + "'"); - } - if (progressBar != null) + errormsgs.append("'").append(pdbid).append("'"); + } finally { - progressBar.setProgressBar( - MessageManager.getString("label.state_completed"), hdl); + if (progressBar != null) + { + progressBar.setProgressBar( + MessageManager.getString("label.state_completed"), + hdl); + } } if (pdbseq != null) { @@ -521,22 +539,21 @@ public class AppJmol extends StructureViewerBase file = new File(pdbseq.getSequenceAt(0).getAllPDBEntries() .elementAt(0).getFile()).getAbsolutePath(); jmb.getPdbEntry(pi).setFile(file); - - files.append(" \"" + Platform.escapeString(file) + "\""); + files.add(file); } else { - errormsgs.append("'" + pdbid + "' "); + errormsgs.append("'").append(pdbid).append("' "); } } else { - if (curfiles != null && curfiles.length > 0) + if (filesInViewer != null && filesInViewer.length > 0) { addingStructures = true; // already files loaded. - for (int c = 0; c < curfiles.length; c++) + for (int c = 0; c < filesInViewer.length; c++) { - if (curfiles[c].equals(file)) + if (filesInViewer[c].equals(file)) { file = null; break; @@ -545,7 +562,7 @@ public class AppJmol extends StructureViewerBase } if (file != null) { - files.append(" \"" + Platform.escapeString(file) + "\""); + files.add(file); } } } @@ -555,184 +572,18 @@ public class AppJmol extends StructureViewerBase } catch (Exception ex) { ex.printStackTrace(); - errormsgs.append("When retrieving pdbfiles : current was: '" + pdbid - + "'"); + errormsgs.append("When retrieving pdbfiles : current was: '") + .append(pdbid).append("'"); } if (errormsgs.length() > 0) { - - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[] { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); - - } - long lastnotify = jmb.getLoadNotifiesHandled(); - if (files.length() > 0) - { - if (!addingStructures) - { - - try - { - initJmol("load FILES " + files.toString()); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning("When trying to open the Jmol viewer!", oomerror); - Cache.log.debug("File locations are " + files); - } catch (Exception ex) - { - Cache.log.error("Couldn't open Jmol viewer!", ex); - } - } - else - { - StringBuffer cmd = new StringBuffer(); - cmd.append("loadingJalviewdata=true\nload APPEND "); - cmd.append(files.toString()); - cmd.append("\nloadingJalviewdata=null"); - final String command = cmd.toString(); - cmd = null; - lastnotify = jmb.getLoadNotifiesHandled(); - - try - { - jmb.evalStateCommand(command); - } catch (OutOfMemoryError oomerror) - { - new OOMWarning( - "When trying to add structures to the Jmol viewer!", - oomerror); - Cache.log.debug("File locations are " + files); - } catch (Exception ex) - { - Cache.log.error("Couldn't add files to Jmol viewer!", ex); - } - } - - // need to wait around until script has finished - while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() - : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb - .getPdbFile().length != jmb.getPdbCount())) - { - try - { - Cache.log.debug("Waiting around for jmb notify."); - Thread.sleep(35); - } catch (Exception e) - { - } - } - - // refresh the sequence colours for the new structure(s) - for (AlignmentPanel ap : _colourwith) - { - jmb.updateColours(ap); - } - // do superposition if asked to - if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) - { - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - @Override - public void run() - { - if (jmb.viewer.isScriptExecuting()) - { - javax.swing.SwingUtilities.invokeLater(this); - try - { - Thread.sleep(5); - } catch (InterruptedException q) - { - } - ; - return; - } - else - { - alignStructs_withAllAlignPanels(); - } - } - }); - alignAddedStructures = false; - } - addingStructures = false; - - } - _started = false; - worker = null; - } - - @Override - public void pdbFile_actionPerformed(ActionEvent actionEvent) - { - JalviewFileChooser chooser = new JalviewFileChooser( - jalview.bin.Cache.getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file")); - chooser.setToolTipText(MessageManager.getString("action.save")); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - BufferedReader in = null; - try - { - // TODO: cope with multiple PDB files in view - in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); - File outFile = chooser.getSelectedFile(); - - PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); - String data; - while ((data = in.readLine()) != null) - { - if (!(data.indexOf("
") > -1 || data.indexOf("
") > -1)) - { - out.println(data); - } - } - out.close(); - } catch (Exception ex) - { - ex.printStackTrace(); - } finally - { - if (in != null) - { - try - { - in.close(); - } catch (IOException e) - { - // ignore - } - } - } + JvOptionPane.ERROR_MESSAGE); } - } - - @Override - public void viewMapping_actionPerformed(ActionEvent actionEvent) - { - jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); - try - { - cap.appendText(jmb.printMappings()); - } catch (OutOfMemoryError e) - { - new OOMWarning( - "composing sequence-structure alignments for display in text box.", - e); - cap.dispose(); - return; - } - jalview.gui.Desktop.addInternalFrame(cap, - MessageManager.getString("label.pdb_sequence_mapping"), 550, - 600); + return files; } @Override @@ -782,135 +633,11 @@ public class AppJmol extends StructureViewerBase } @Override - public void viewerColour_actionPerformed(ActionEvent actionEvent) - { - if (viewerColour.isSelected()) - { - // disable automatic sequence colouring. - jmb.setColourBySequence(false); - } - } - - @Override - public void seqColour_actionPerformed(ActionEvent actionEvent) - { - jmb.setColourBySequence(seqColour.isSelected()); - if (_colourwith == null) - { - _colourwith = new Vector(); - } - if (jmb.isColourBySequence()) - { - if (!jmb.isLoadingFromArchive()) - { - if (_colourwith.size() == 0 && getAlignmentPanel() != null) - { - // Make the currently displayed alignment panel the associated view - _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); - } - } - // Set the colour using the current view for the associated alignframe - for (AlignmentPanel ap : _colourwith) - { - jmb.colourBySequence(ap); - } - } - } - - @Override - public void chainColour_actionPerformed(ActionEvent actionEvent) - { - chainColour.setSelected(true); - jmb.colourByChain(); - } - - @Override - public void chargeColour_actionPerformed(ActionEvent actionEvent) - { - chargeColour.setSelected(true); - jmb.colourByCharge(); - } - - @Override - public void zappoColour_actionPerformed(ActionEvent actionEvent) - { - zappoColour.setSelected(true); - jmb.setJalviewColourScheme(new ZappoColourScheme()); - } - - @Override - public void taylorColour_actionPerformed(ActionEvent actionEvent) - { - taylorColour.setSelected(true); - jmb.setJalviewColourScheme(new TaylorColourScheme()); - } - - @Override - public void hydroColour_actionPerformed(ActionEvent actionEvent) - { - hydroColour.setSelected(true); - jmb.setJalviewColourScheme(new HydrophobicColourScheme()); - } - - @Override - public void helixColour_actionPerformed(ActionEvent actionEvent) - { - helixColour.setSelected(true); - jmb.setJalviewColourScheme(new HelixColourScheme()); - } - - @Override - public void strandColour_actionPerformed(ActionEvent actionEvent) - { - strandColour.setSelected(true); - jmb.setJalviewColourScheme(new StrandColourScheme()); - } - - @Override - public void turnColour_actionPerformed(ActionEvent actionEvent) - { - turnColour.setSelected(true); - jmb.setJalviewColourScheme(new TurnColourScheme()); - } - - @Override - public void buriedColour_actionPerformed(ActionEvent actionEvent) - { - buriedColour.setSelected(true); - jmb.setJalviewColourScheme(new BuriedColourScheme()); - } - - @Override - public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent) - { - setJalviewColourScheme(new PurinePyrimidineColourScheme()); - } - - @Override - public void userColour_actionPerformed(ActionEvent actionEvent) - { - userColour.setSelected(true); - new UserDefinedColours(this, null); - } - - @Override - public void backGround_actionPerformed(ActionEvent actionEvent) - { - java.awt.Color col = JColorChooser - .showDialog(this, MessageManager - .getString("label.select_backgroud_colour"), null); - if (col != null) - { - jmb.setBackgroundColour(col); - } - } - - @Override public void showHelp_actionPerformed(ActionEvent actionEvent) { try { - jalview.util.BrowserLauncher + BrowserLauncher .openURL("http://jmol.sourceforge.net/docs/JmolUserGuide/"); } catch (Exception ex) { @@ -959,7 +686,7 @@ public class AppJmol extends StructureViewerBase { getSize(currentSize); - if (jmb != null && jmb.fileLoadingError != null) + if (jmb != null && jmb.hasFileLoadingError()) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1002,104 +729,6 @@ public class AppJmol extends StructureViewerBase } } - public void updateTitleAndMenus() - { - if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) - { - repaint(); - return; - } - setChainMenuItems(jmb.chainNames); - - this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) - { - viewerActionMenu.setVisible(true); - } - if (!jmb.isLoadingFromArchive()) - { - seqColour_actionPerformed(null); - } - } - - /* - * (non-Javadoc) - * - * @see - * jalview.jbgui.GStructureViewer#alignStructs_actionPerformed(java.awt.event - * .ActionEvent) - */ - @Override - protected void alignStructs_actionPerformed(ActionEvent actionEvent) - { - alignStructs_withAllAlignPanels(); - } - - private void alignStructs_withAllAlignPanels() - { - if (getAlignmentPanel() == null) - { - return; - } - ; - if (_alignwith.size() == 0) - { - _alignwith.add(getAlignmentPanel()); - } - ; - try - { - AlignmentI[] als = new Alignment[_alignwith.size()]; - ColumnSelection[] alc = new ColumnSelection[_alignwith.size()]; - int[] alm = new int[_alignwith.size()]; - int a = 0; - - for (AlignmentPanel ap : _alignwith) - { - als[a] = ap.av.getAlignment(); - alm[a] = -1; - alc[a++] = ap.av.getColumnSelection(); - } - jmb.superposeStructures(als, alm, alc); - } catch (Exception e) - { - StringBuffer sp = new StringBuffer(); - for (AlignmentPanel ap : _alignwith) - { - sp.append("'" + ap.alignFrame.getTitle() + "' "); - } - Cache.log.info("Couldn't align structures with the " + sp.toString() - + "associated alignment panels.", e); - - } - - } - - @Override - public void setJalviewColourScheme(ColourSchemeI ucs) - { - jmb.setJalviewColourScheme(ucs); - - } - - /** - * - * @param alignment - * @return first alignment panel displaying given alignment, or the default - * alignment panel - */ - public AlignmentPanel getAlignmentPanelFor(AlignmentI alignment) - { - for (AlignmentPanel ap : getAllAlignmentPanels()) - { - if (ap.av.getAlignment() == alignment) - { - return ap; - } - } - return getAlignmentPanel(); - } - @Override public AAStructureBindingModel getBinding() { @@ -1119,9 +748,8 @@ public class AppJmol extends StructureViewerBase } @Override - protected AAStructureBindingModel getBindingModel() + protected String getViewerName() { - return jmb; + return "Jmol"; } - }