X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=a16ea68b94d1774ef5af3239b0be085239c1ec20;hb=83d955d73ec9236ce46af494fc4242909763bbc5;hp=5d4b910304561e36be6d540bbe36f03505fb4542;hpb=a3b4ec9805c4cee4c2dbe2a4c98913ee9c189c6b;p=jalview.git diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 5d4b910..a16ea68 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,19 +20,16 @@ */ package jalview.gui; -import jalview.api.structures.JalviewStructureDisplayI; 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.ext.jmol.JalviewJmolBinding; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.gui.StructureViewer.ViewerType; import jalview.io.AppletFormatAdapter; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; -import jalview.jbgui.GStructureViewer; import jalview.schemes.BuriedColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.HelixColourScheme; @@ -42,12 +39,12 @@ import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.ZappoColourScheme; +import jalview.structures.models.AAStructureBindingModel; import jalview.util.MessageManager; import jalview.util.Platform; import java.awt.BorderLayout; import java.awt.Color; -import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.Graphics; @@ -60,9 +57,8 @@ 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.Enumeration; import java.util.Vector; import javax.swing.JCheckBoxMenuItem; @@ -78,9 +74,7 @@ import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; -public class AppJmol extends GStructureViewer implements Runnable, - ViewSetProvider, JalviewStructureDisplayI - +public class AppJmol extends StructureViewerBase { AppJmolBinding jmb; @@ -90,43 +84,8 @@ public class AppJmol extends GStructureViewer implements Runnable, RenderPanel renderPanel; - AlignmentPanel ap; - - Vector atomsPicked = new Vector(); - private boolean addingStructures = false; - /** - * - * @param file - * @param id - * @param seq - * @param ap - * @param loadStatus - * @param bounds - * @deprecated defaults to AppJmol(String[] files, ... , viewid); - */ - @Deprecated - public AppJmol(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds) - { - this(file, id, seq, ap, loadStatus, bounds, null); - } - - /** - * @deprecated - */ - @Deprecated - public AppJmol(String file, String id, SequenceI[] seq, - AlignmentPanel ap, String loadStatus, Rectangle bounds, - String viewid) - { - this(new String[] - { file }, new String[] - { id }, new SequenceI[][] - { seq }, ap, true, true, false, loadStatus, bounds, viewid); - } - ViewSelectionMenu seqColourBy; /** @@ -156,9 +115,9 @@ public class AppJmol extends GStructureViewer implements Runnable, PDBEntry[] pdbentrys = new PDBEntry[files.length]; for (int i = 0; i < pdbentrys.length; i++) { - PDBEntry pdbentry = new PDBEntry(); - pdbentry.setFile(files[i]); - pdbentry.setId(ids[i]); + // PDBEntry pdbentry = new PDBEntry(files[i], ids[i]); + PDBEntry pdbentry = new PDBEntry(ids[i], null, PDBEntry.Type.PDB, + files[i]); pdbentrys[i] = pdbentry; } // / TODO: check if protocol is needed to be set, and if chains are @@ -176,26 +135,27 @@ public class AppJmol extends GStructureViewer implements Runnable, { jmb.setColourBySequence(false); seqColour.setSelected(false); - jmolColour.setSelected(true); + viewerColour.setSelected(true); } - if (usetoColour) + else if (usetoColour) { useAlignmentPanelForColourbyseq(ap); jmb.setColourBySequence(true); seqColour.setSelected(true); - jmolColour.setSelected(false); + viewerColour.setSelected(false); } this.setBounds(bounds); initMenus(); - viewId = viewid; + setViewId(viewid); // jalview.gui.Desktop.addInternalFrame(this, "Loading File", // bounds.width,bounds.height); this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); initJmol(loadStatus); // pdbentry, seq, JBPCHECK! @@ -205,7 +165,7 @@ public class AppJmol extends GStructureViewer implements Runnable, private void initMenus() { seqColour.setSelected(jmb.isColourBySequence()); - jmolColour.setSelected(!jmb.isColourBySequence()); + viewerColour.setSelected(!jmb.isColourBySequence()); if (_colourwith == null) { _colourwith = new Vector(); @@ -251,8 +211,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } }); handler.itemStateChanged(null); - jmolActionMenu.add(alpanels); - jmolActionMenu.addMenuListener(new MenuListener() + viewerActionMenu.add(alpanels); + viewerActionMenu.addMenuListener(new MenuListener() { @Override @@ -303,16 +263,21 @@ public class AppJmol extends GStructureViewer implements Runnable, "label.pdb_entry_is_already_displayed", new String[] { pdbentry.getId() }), MessageManager.formatMessage( "label.map_sequences_to_visible_window", new String[] - { pdbentry.getId() }), JOptionPane.YES_NO_OPTION); + { pdbentry.getId() }), + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) + { + return; + } if (option == JOptionPane.YES_OPTION) { // TODO : Fix multiple seq to one chain issue here. ap.getStructureSelectionManager().setMapping(seq, chains, alreadyMapped, AppletFormatAdapter.FILE); - if (ap.seqPanel.seqCanvas.fr != null) + if (ap.getSeqPanel().seqCanvas.fr != null) { - ap.seqPanel.seqCanvas.fr.featuresAdded(); + ap.getSeqPanel().seqCanvas.fr.featuresAdded(); ap.paintAlignment(true); } @@ -327,15 +292,16 @@ public class AppJmol extends GStructureViewer implements Runnable, final AppJmol topJmol = ((AppJmol) frames[i]); // JBPNOTE: this looks like a binding routine, rather than a gui // routine - for (int pe = 0; pe < topJmol.jmb.pdbentry.length; pe++) + for (int pe = 0; pe < topJmol.jmb.getPdbCount(); pe++) { - if (topJmol.jmb.pdbentry[pe].getFile().equals(alreadyMapped)) + if (topJmol.jmb.getPdbEntry(pe).getFile() + .equals(alreadyMapped)) { topJmol.jmb.addSequence(pe, seq); topJmol.addAlignmentPanel(ap); // add it to the set used for colouring topJmol.useAlignmentPanelForColourbyseq(ap); - topJmol.buildJmolActionMenu(); + topJmol.buildActionMenu(); ap.getStructureSelectionManager() .sequenceColoursChanged(ap); break; @@ -347,32 +313,30 @@ public class AppJmol extends GStructureViewer implements Runnable, return; } } - // ///////////////////////////////// - // Check if there are other Jmol views involving this alignment - // and prompt user about adding this molecule to one of them - Vector existingViews = getJmolsFor(ap); - if (existingViews.size() > 0) + + /* + * Check if there are other Jmol views involving this alignment and prompt + * user about adding this molecule to one of them + */ + for (AppJmol topJmol : getJmolsFor(ap)) { - Enumeration jm = existingViews.elements(); - while (jm.hasMoreElements()) + // TODO: highlight topJmol in view somehow + int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + MessageManager.formatMessage("label.add_pdbentry_to_view", + new String[] + { pdbentry.getId(), topJmol.getTitle() }), + MessageManager + .getString("label.align_to_existing_structure_view"), + JOptionPane.YES_NO_CANCEL_OPTION); + if (option == JOptionPane.CANCEL_OPTION) { - AppJmol topJmol = (AppJmol) jm.nextElement(); - // TODO: highlight topJmol in view somehow - int option = JOptionPane - .showInternalConfirmDialog( - Desktop.desktop, - MessageManager.formatMessage( - "label.add_pdbentry_to_view", new String[] - { pdbentry.getId(), topJmol.getTitle() }), - MessageManager - .getString("label.align_to_existing_structure_view"), - JOptionPane.YES_NO_OPTION); - if (option == JOptionPane.YES_OPTION) - { - topJmol.useAlignmentPanelForSuperposition(ap); - topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } + return; + } + if (option == JOptionPane.YES_OPTION) + { + topJmol.useAlignmentPanelForSuperposition(ap); + topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); + return; } } // ///////////////////////////////// @@ -405,9 +369,10 @@ public class AppJmol extends GStructureViewer implements Runnable, } this.addInternalFrameListener(new InternalFrameAdapter() { + @Override public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -427,133 +392,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } /** - * list of sequenceSet ids associated with the view - */ - ArrayList _aps = new ArrayList(); - - public AlignmentPanel[] getAllAlignmentPanels() - { - AlignmentPanel[] t, list = new AlignmentPanel[0]; - for (String setid : _aps) - { - AlignmentPanel[] panels = PaintRefresher.getAssociatedPanels(setid); - if (panels != null) - { - t = new AlignmentPanel[list.length + panels.length]; - System.arraycopy(list, 0, t, 0, list.length); - System.arraycopy(panels, 0, t, list.length, panels.length); - list = t; - } - } - - return list; - } - - /** - * list of alignment panels to use for superposition - */ - Vector _alignwith = new Vector(); - - /** - * list of alignment panels that are used for colouring structures by aligned - * sequences - */ - Vector _colourwith = new Vector(); - - /** - * set the primary alignmentPanel reference and add another alignPanel to the - * list of ones to use for colouring and aligning - * - * @param nap - */ - public void addAlignmentPanel(AlignmentPanel nap) - { - if (ap == null) - { - ap = nap; - } - if (!_aps.contains(nap.av.getSequenceSetId())) - { - _aps.add(nap.av.getSequenceSetId()); - } - } - - /** - * remove any references held to the given alignment panel - * - * @param nap - */ - public void removeAlignmentPanel(AlignmentPanel nap) - { - try - { - _alignwith.remove(nap); - _colourwith.remove(nap); - if (ap == nap) - { - ap = null; - for (AlignmentPanel aps : getAllAlignmentPanels()) - { - if (aps != nap) - { - ap = aps; - break; - } - } - } - } catch (Exception ex) - { - } - if (ap != null) - { - buildJmolActionMenu(); - } - } - - public void useAlignmentPanelForSuperposition(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_alignwith.contains(nap)) - { - _alignwith.add(nap); - } - } - - public void excludeAlignmentPanelForSuperposition(AlignmentPanel nap) - { - if (_alignwith.contains(nap)) - { - _alignwith.remove(nap); - } - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, - boolean enableColourBySeq) - { - useAlignmentPanelForColourbyseq(nap); - jmb.setColourBySequence(enableColourBySeq); - seqColour.setSelected(enableColourBySeq); - jmolColour.setSelected(!enableColourBySeq); - } - - public void useAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - addAlignmentPanel(nap); - if (!_colourwith.contains(nap)) - { - _colourwith.add(nap); - } - } - - public void excludeAlignmentPanelForColourbyseq(AlignmentPanel nap) - { - if (_colourwith.contains(nap)) - { - _colourwith.remove(nap); - } - } - - /** * pdb retrieval thread. */ private Thread worker = null; @@ -614,25 +452,22 @@ public class AppJmol extends GStructureViewer implements Runnable, return; } - private Vector getJmolsFor(AlignmentPanel ap2) + private Vector getJmolsFor(AlignmentPanel apanel) { - Vector otherJmols = new Vector(); - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array + Vector result = new Vector(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); - for (int i = 0; i < frames.length; i++) + for (JInternalFrame frame : frames) { - if (frames[i] instanceof AppJmol) + if (frame instanceof AppJmol) { - AppJmol topJmol = ((AppJmol) frames[i]); - if (topJmol.isLinkedWith(ap2)) + if (((AppJmol) frame).isLinkedWith(apanel)) { - otherJmols.addElement(topJmol); + result.addElement((AppJmol) frame); } } } - return otherJmols; + return result; } void initJmol(String command) @@ -652,10 +487,10 @@ public class AppJmol extends GStructureViewer implements Runnable, scriptWindow = new JPanel(bl); scriptWindow.setVisible(false); } - ; + jmb.allocateViewer(renderPanel, true, "", null, null, "", scriptWindow, null); - jmb.newJmolPopup(true, "Jmol", true); + // jmb.newJmolPopup("Jmol"); if (command == null) { command = ""; @@ -664,7 +499,7 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.setFinishedInit(true); } - void setChainMenuItems(Vector chains) + void setChainMenuItems(Vector chains) { chainMenu.removeAll(); if (chains == null) @@ -692,9 +527,9 @@ public class AppJmol extends GStructureViewer implements Runnable, chainMenu.add(menuItem); - for (int c = 0; c < chains.size(); c++) + for (String chain : chains) { - menuItem = new JCheckBoxMenuItem(chains.elementAt(c).toString(), true); + menuItem = new JCheckBoxMenuItem(chain, true); menuItem.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent evt) @@ -716,9 +551,7 @@ public class AppJmol extends GStructureViewer implements Runnable, void centerViewer() { - Vector toshow = new Vector(); - String lbl; - int mlength, p, mnum; + Vector toshow = new Vector(); for (int i = 0; i < chainMenu.getItemCount(); i++) { if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) @@ -733,10 +566,11 @@ public class AppJmol extends GStructureViewer implements Runnable, jmb.centerViewer(toshow); } - public void closeViewer() + public void closeViewer(boolean closeExternalViewer) { + // JMol does not use an external viewer jmb.closeViewer(); - ap = null; + setAlignmentPanel(null); _aps.clear(); _alignwith.clear(); _colourwith.clear(); @@ -762,14 +596,14 @@ public class AppJmol extends GStructureViewer implements Runnable, // TODO: replace with reference fetching/transfer code (validate PDBentry // as a DBRef?) jalview.ws.dbsources.Pdb pdbclient = new jalview.ws.dbsources.Pdb(); - for (int pi = 0; pi < jmb.pdbentry.length; pi++) + for (int pi = 0; pi < jmb.getPdbCount(); pi++) { - String file = jmb.pdbentry[pi].getFile(); + String file = jmb.getPdbEntry(pi).getFile(); if (file == null) { // retrieve the pdb and store it locally AlignmentI pdbseq = null; - pdbid = jmb.pdbentry[pi].getId(); + pdbid = jmb.getPdbEntry(pi).getId(); long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { @@ -777,8 +611,7 @@ public class AppJmol extends GStructureViewer implements Runnable, } try { - pdbseq = pdbclient.getSequenceRecords(pdbid = jmb.pdbentry[pi] - .getId()); + pdbseq = pdbclient.getSequenceRecords(pdbid); } catch (OutOfMemoryError oomerror) { new OOMWarning("Retrieving PDB id " + pdbid, oomerror); @@ -795,9 +628,9 @@ public class AppJmol extends GStructureViewer implements Runnable, { // just transfer the file name from the first sequence's first // PDBEntry - file = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); - jmb.pdbentry[pi].setFile(file); + file = new File(pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0).getFile()).getAbsolutePath(); + jmb.getPdbEntry(pi).setFile(file); files.append(" \"" + Platform.escapeString(file) + "\""); } @@ -891,8 +724,8 @@ public class AppJmol extends GStructureViewer implements Runnable, // need to wait around until script has finished while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled() - : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb - .getPdbFile().length != jmb.pdbentry.length)) + : (!jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb + .getPdbFile().length != jmb.getPdbCount())) { try { @@ -902,6 +735,7 @@ public class AppJmol extends GStructureViewer implements Runnable, { } } + // refresh the sequence colours for the new structure(s) for (AlignmentPanel ap : _colourwith) { @@ -927,6 +761,7 @@ public class AppJmol extends GStructureViewer implements Runnable, worker = null; } + @Override public void pdbFile_actionPerformed(ActionEvent actionEvent) { JalviewFileChooser chooser = new JalviewFileChooser( @@ -940,10 +775,11 @@ public class AppJmol extends GStructureViewer implements Runnable, if (value == JalviewFileChooser.APPROVE_OPTION) { + BufferedReader in = null; try { // TODO: cope with multiple PDB files in view - BufferedReader in = new BufferedReader(new FileReader( + in = new BufferedReader(new FileReader( jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); @@ -960,20 +796,29 @@ public class AppJmol extends GStructureViewer implements Runnable, } catch (Exception ex) { ex.printStackTrace(); + } finally + { + if (in != null) + { + try + { + in.close(); + } catch (IOException e) + { + // ignore + } + } } } } + @Override public void viewMapping_actionPerformed(ActionEvent actionEvent) { jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer(); try { - for (int pdbe = 0; pdbe < jmb.pdbentry.length; pdbe++) - { - cap.appendText(jmb.printMapping(jmb.pdbentry[pdbe].getFile())); - cap.appendText("\n"); - } + cap.appendText(jmb.printMappings()); } catch (OutOfMemoryError e) { new OOMWarning( @@ -987,23 +832,13 @@ public class AppJmol extends GStructureViewer implements Runnable, 600); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void eps_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.TYPE.EPS); } - /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! - */ + @Override public void png_actionPerformed(ActionEvent e) { makePDBImage(jalview.util.ImageMaker.TYPE.PNG); @@ -1039,21 +874,22 @@ public class AppJmol extends GStructureViewer implements Runnable, if (im.getGraphics() != null) { - Rectangle rect = new Rectangle(width, height); - jmb.viewer.renderScreenImage(im.getGraphics(), rect.getSize(), rect); + jmb.viewer.renderScreenImage(im.getGraphics(), width, height); im.writeImage(); } } - public void jmolColour_actionPerformed(ActionEvent actionEvent) + @Override + public void viewerColour_actionPerformed(ActionEvent actionEvent) { - if (jmolColour.isSelected()) + if (viewerColour.isSelected()) { // disable automatic sequence colouring. jmb.setColourBySequence(false); } } + @Override public void seqColour_actionPerformed(ActionEvent actionEvent) { jmb.setColourBySequence(seqColour.isSelected()); @@ -1065,85 +901,97 @@ public class AppJmol extends GStructureViewer implements Runnable, { if (!jmb.isLoadingFromArchive()) { - if (_colourwith.size() == 0 && ap != null) + if (_colourwith.size() == 0 && getAlignmentPanel() != null) { // Make the currently displayed alignment panel the associated view - _colourwith.add(ap.alignFrame.alignPanel); + _colourwith.add(getAlignmentPanel().alignFrame.alignPanel); } } // Set the colour using the current view for the associated alignframe for (AlignmentPanel ap : _colourwith) { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + 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, @@ -1154,7 +1002,8 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - public void jmolHelp_actionPerformed(ActionEvent actionEvent) + @Override + public void showHelp_actionPerformed(ActionEvent actionEvent) { try { @@ -1202,14 +1051,12 @@ public class AppJmol extends GStructureViewer implements Runnable, { final Dimension currentSize = new Dimension(); - final Rectangle rectClip = new Rectangle(); - + @Override public void paintComponent(Graphics g) { getSize(currentSize); - g.getClipBounds(rectClip); - if (jmb.fileLoadingError != null) + if (jmb != null && jmb.fileLoadingError != null) { g.setColor(Color.black); g.fillRect(0, 0, currentSize.width, currentSize.height); @@ -1219,15 +1066,15 @@ public class AppJmol extends GStructureViewer implements Runnable, + "...", 20, currentSize.height / 2); StringBuffer sb = new StringBuffer(); int lines = 0; - for (int e = 0; e < jmb.pdbentry.length; e++) + for (int e = 0; e < jmb.getPdbCount(); e++) { - sb.append(jmb.pdbentry[e].getId()); - if (e < jmb.pdbentry.length - 1) + sb.append(jmb.getPdbEntry(e).getId()); + if (e < jmb.getPdbCount() - 1) { sb.append(","); } - if (e == jmb.pdbentry.length - 1 || sb.length() > 20) + if (e == jmb.getPdbCount() - 1 || sb.length() > 20) { lines++; g.drawString(sb.toString(), 20, currentSize.height / 2 - lines @@ -1246,22 +1093,12 @@ public class AppJmol extends GStructureViewer implements Runnable, } else { - jmb.viewer.renderScreenImage(g, currentSize, rectClip); + jmb.viewer.renderScreenImage(g, currentSize.width, + currentSize.height); } } } - String viewId = null; - - public String getViewId() - { - if (viewId == null) - { - viewId = System.currentTimeMillis() + "." + this.hashCode(); - } - return viewId; - } - public void updateTitleAndMenus() { if (jmb.fileLoadingError != null && jmb.fileLoadingError.length() > 0) @@ -1272,9 +1109,9 @@ public class AppJmol extends GStructureViewer implements Runnable, setChainMenuItems(jmb.chainNames); this.setTitle(jmb.getViewerTitle()); - if (jmb.getPdbFile().length > 1 && jmb.sequence.length > 1) + if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) { - jmolActionMenu.setVisible(true); + viewerActionMenu.setVisible(true); } if (!jmb.isLoadingFromArchive()) { @@ -1282,27 +1119,6 @@ public class AppJmol extends GStructureViewer implements Runnable, } } - protected void buildJmolActionMenu() - { - if (_alignwith == null) - { - _alignwith = new Vector(); - } - if (_alignwith.size() == 0 && ap != null) - { - _alignwith.add(ap); - } - ; - for (Component c : jmolActionMenu.getMenuComponents()) - { - if (c != alignStructs) - { - jmolActionMenu.remove((JMenuItem) c); - } - } - final ItemListener handler; - } - /* * (non-Javadoc) * @@ -1318,14 +1134,14 @@ public class AppJmol extends GStructureViewer implements Runnable, private void alignStructs_withAllAlignPanels() { - if (ap == null) + if (getAlignmentPanel() == null) { return; } ; if (_alignwith.size() == 0) { - _alignwith.add(ap); + _alignwith.add(getAlignmentPanel()); } ; try @@ -1377,42 +1193,25 @@ public class AppJmol extends GStructureViewer implements Runnable, return ap; } } - return ap; - } - - /** - * - * @param ap2 - * @return true if this Jmol instance is linked with the given alignPanel - */ - public boolean isLinkedWith(AlignmentPanel ap2) - { - return _aps.contains(ap2.av.getSequenceSetId()); - } - - public boolean isUsedforaligment(AlignmentPanel ap2) - { - - return (_alignwith != null) && _alignwith.contains(ap2); + return getAlignmentPanel(); } - public boolean isUsedforcolourby(AlignmentPanel ap2) + @Override + public AAStructureBindingModel getBinding() { - return (_colourwith != null) && _colourwith.contains(ap2); + return this.jmb; } - /** - * - * @return TRUE if the view is NOT being coloured by sequence associations. - */ - public boolean isColouredByJmol() + @Override + public String getStateInfo() { - return !jmb.isColourBySequence(); + return jmb == null ? null : jmb.viewer.getStateInfo(); } - public JalviewJmolBinding getBinding() + @Override + public ViewerType getViewerType() { - return jmb; + return ViewerType.JMOL; } }