X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=55d5f8c5fb67b7772ad1cc7194db01d26b7419c7;hp=bd1cc88ef1df6d3c5f81978b13beaa956f2fdc9b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hpb=06e3a52df5af8243cdb67c023c8ddd834711ad36 diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index bd1cc88..55d5f8c 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -27,7 +27,6 @@ import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; import jalview.gui.StructureViewer.ViewerType; -import jalview.io.AppletFormatAdapter; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.schemes.BuriedColourScheme; @@ -59,6 +58,8 @@ 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; @@ -84,8 +85,6 @@ public class AppJmol extends StructureViewerBase RenderPanel renderPanel; - private boolean addingStructures = false; - ViewSelectionMenu seqColourBy; /** @@ -175,7 +174,8 @@ public class AppJmol extends StructureViewerBase _alignwith = new Vector(); } - seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith, + seqColourBy = new ViewSelectionMenu( + MessageManager.getString("label.colour_by"), this, _colourwith, new ItemListener() { @@ -195,7 +195,8 @@ public class AppJmol extends StructureViewerBase }); viewMenu.add(seqColourBy); final ItemListener handler; - JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this, + JMenu alpanels = new ViewSelectionMenu( + MessageManager.getString("label.superpose_with"), this, _alignwith, handler = new ItemListener() { @@ -206,8 +207,8 @@ public class AppJmol extends StructureViewerBase alignStructs.setToolTipText(MessageManager .formatMessage( "label.align_structures_using_linked_alignment_views", - new String[] - { new Integer(_alignwith.size()).toString() })); + new String[] { new Integer(_alignwith + .size()).toString() })); } }); handler.itemStateChanged(null); @@ -251,98 +252,39 @@ public class AppJmol extends StructureViewerBase final AlignmentPanel ap) { progressBar = ap.alignFrame; - // //////////////////////////////// - // Is the pdb file already loaded? - String alreadyMapped = ap.getStructureSelectionManager() - .alreadyMappedToFile(pdbentry.getId()); + String pdbId = pdbentry.getId(); - if (alreadyMapped != null) + /* + * If the PDB file is already loaded, the user may just choose to add to an + * existing viewer (or cancel) + */ + if (addAlreadyLoadedFile(seq, chains, ap, pdbId)) { - int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop, - MessageManager.formatMessage( - "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_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.getSeqPanel().seqCanvas.fr != null) - { - ap.getSeqPanel().seqCanvas.fr.featuresAdded(); - ap.paintAlignment(true); - } - - // Now this AppJmol is mapped to new sequences. We must add them to - // the exisiting array - JInternalFrame[] frames = Desktop.instance.getAllFrames(); - - for (int i = 0; i < frames.length; i++) - { - if (frames[i] instanceof AppJmol) - { - 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.getPdbCount(); pe++) - { - 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.buildActionMenu(); - ap.getStructureSelectionManager() - .sequenceColoursChanged(ap); - break; - } - } - } - } - - return; - } + return; } /* * 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)) + if (addToExistingViewer(pdbentry, seq, chains, ap, pdbId)) { - // 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) - { - return; - } - if (option == JOptionPane.YES_OPTION) - { - topJmol.useAlignmentPanelForSuperposition(ap); - topJmol.addStructure(pdbentry, seq, chains, true, ap.alignFrame); - return; - } + return; } - // ///////////////////////////////// - openNewJmol(ap, new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }); + + /* + * If the options above are declined or do not apply, open a new viewer + */ + 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, @@ -392,78 +334,23 @@ public class AppJmol extends StructureViewerBase } /** - * pdb retrieval thread. + * Returns a list of any Jmol viewers. The list is restricted to those linked + * to the given alignment panel if it is not null. */ - private Thread worker = null; - - /** - * add a new structure (with associated sequences and chains) to this viewer, - * retrieving it if necessary first. - * - * @param pdbentry - * @param seq - * @param chains - * @param alignFrame - * @param align - * if true, new structure(s) will be align using associated alignment - */ - private void addStructure(final PDBEntry pdbentry, final SequenceI[] seq, - final String[] chains, final boolean b, - final IProgressIndicator alignFrame) - { - if (pdbentry.getFile() == null) - { - if (worker != null && worker.isAlive()) - { - // a retrieval is in progress, wait around and add ourselves to the - // queue. - new Thread(new Runnable() - { - public void run() - { - while (worker != null && worker.isAlive() && _started) - { - try - { - Thread.sleep(100 + ((int) Math.random() * 100)); - - } catch (Exception e) - { - } - - } - // and call ourselves again. - addStructure(pdbentry, seq, chains, b, alignFrame); - } - }).start(); - return; - } - } - // otherwise, start adding the structure. - jmb.addSequenceAndChain(new PDBEntry[] - { pdbentry }, new SequenceI[][] - { seq }, new String[][] - { chains }); - addingStructures = true; - _started = false; - alignAddedStructures = b; - progressBar = alignFrame; // visual indication happens on caller frame. - (worker = new Thread(this)).start(); - return; - } - - private Vector getJmolsFor(AlignmentPanel apanel) + @Override + protected List getViewersFor(AlignmentPanel apanel) { - Vector result = new Vector(); + List result = new ArrayList(); JInternalFrame[] frames = Desktop.instance.getAllFrames(); for (JInternalFrame frame : frames) { if (frame instanceof AppJmol) { - if (((AppJmol) frame).isLinkedWith(apanel)) + if (apanel == null + || ((StructureViewerBase) frame).isLinkedWith(apanel)) { - result.addElement((AppJmol) frame); + result.add((StructureViewerBase) frame); } } } @@ -547,8 +434,6 @@ public class AppJmol extends StructureViewerBase boolean allChainsSelected = false; - private boolean alignAddedStructures = false; - void centerViewer() { Vector toshow = new Vector(); @@ -568,8 +453,11 @@ public class AppJmol extends StructureViewerBase public void closeViewer(boolean closeExternalViewer) { - // JMol does not use an external viewer - jmb.closeViewer(); + // Jmol does not use an external viewer + if (jmb != null) + { + jmb.closeViewer(); + } setAlignmentPanel(null); _aps.clear(); _alignwith.clear(); @@ -579,11 +467,6 @@ public class AppJmol extends StructureViewerBase jmb = null; } - /** - * state flag for PDB retrieval thread - */ - private boolean _started = false; - public void run() { _started = true; @@ -607,7 +490,8 @@ public class AppJmol extends StructureViewerBase long hdl = pdbid.hashCode() - System.currentTimeMillis(); if (progressBar != null) { - progressBar.setProgressBar(MessageManager.formatMessage("status.fetching_pdb", new String[]{pdbid}), hdl); + progressBar.setProgressBar(MessageManager.formatMessage( + "status.fetching_pdb", new String[] { pdbid }), hdl); } try { @@ -622,7 +506,8 @@ public class AppJmol extends StructureViewerBase } if (progressBar != null) { - progressBar.setProgressBar(MessageManager.getString("label.state_completed"), hdl); + progressBar.setProgressBar( + MessageManager.getString("label.state_completed"), hdl); } if (pdbseq != null) { @@ -673,9 +558,8 @@ public class AppJmol extends StructureViewerBase JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", - new String[] - { errormsgs.toString() }), MessageManager - .getString("label.couldnt_load_file"), + new String[] { errormsgs.toString() }), + MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE); } @@ -742,7 +626,7 @@ public class AppJmol extends StructureViewerBase jmb.updateColours(ap); } // do superposition if asked to - if (alignAddedStructures) + if (Cache.getDefault("AUTOSUPERIMPOSE", true) && alignAddedStructures) { javax.swing.SwingUtilities.invokeLater(new Runnable() { @@ -793,8 +677,7 @@ public class AppJmol extends StructureViewerBase try { // TODO: cope with multiple PDB files in view - in = new BufferedReader(new FileReader( - jmb.getPdbFile()[0])); + in = new BufferedReader(new FileReader(jmb.getPdbFile()[0])); File outFile = chooser.getSelectedFile(); PrintWriter out = new PrintWriter(new FileOutputStream(outFile)); @@ -868,15 +751,14 @@ public class AppJmol extends StructureViewerBase if (type == jalview.util.ImageMaker.TYPE.PNG) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.PNG, - "Make PNG image from view", width, height, null, null); + jalview.util.ImageMaker.TYPE.PNG, "Make PNG image from view", + width, height, null, null); } else if (type == jalview.util.ImageMaker.TYPE.EPS) { im = new jalview.util.ImageMaker(this, - jalview.util.ImageMaker.TYPE.EPS, - "Make EPS file from view", width, height, null, - this.getTitle()); + jalview.util.ImageMaker.TYPE.EPS, "Make EPS file from view", + width, height, null, this.getTitle()); } else { @@ -1008,8 +890,9 @@ public class AppJmol extends StructureViewerBase @Override public void backGround_actionPerformed(ActionEvent actionEvent) { - java.awt.Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_backgroud_colour"), null); + java.awt.Color col = JColorChooser + .showDialog(this, MessageManager + .getString("label.select_backgroud_colour"), null); if (col != null) { jmb.setBackgroundColour(col); @@ -1228,4 +1111,10 @@ public class AppJmol extends StructureViewerBase return ViewerType.JMOL; } + @Override + protected AAStructureBindingModel getBindingModel() + { + return jmb; + } + }