X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=fda4afb4da195e65b61f91aef66de14bded0f0c0;hb=5d59bb58f5bcecc6b240d125e13bbe1f1868f681;hp=4e313b5fecf619691875f825465479f140d3545b;hpb=0c5e8f8ba81b913c63b60d7670d66aca661ea4f5;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index 4e313b5..fda4afb 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.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. * @@ -20,31 +20,6 @@ */ 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.ext.rbvi.chimera.JalviewChimeraBinding; -import jalview.gui.Jalview2XML.ViewerData; -import jalview.io.AppletFormatAdapter; -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.MessageManager; -import jalview.util.Platform; -import jalview.ws.dbsources.Pdb; - import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import java.awt.event.ItemEvent; @@ -70,6 +45,30 @@ import javax.swing.event.InternalFrameEvent; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +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.rbvi.chimera.JalviewChimeraBinding; +import jalview.io.AppletFormatAdapter; +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.MessageManager; +import jalview.util.Platform; +import jalview.ws.dbsources.Pdb; + /** * GUI elements for handlnig an external chimera display * @@ -99,9 +98,11 @@ public class ChimeraViewFrame extends StructureViewerBase private Thread worker = null; /* - * Path to Chimera session file - set in saveSession() + * Path to Chimera session file. This is set when an open Jalview/Chimera + * session is saved, or on restore from a Jalview project (if it holds the + * filename of any saved Chimera sessions). */ - private String chimeraSessionFile = ""; + private String chimeraSessionFile = null; /** * Initialise menu options. @@ -311,17 +312,16 @@ public class ChimeraViewFrame 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() { public void internalFrameClosing(InternalFrameEvent internalFrameEvent) { - closeViewer(); + closeViewer(false); } }); @@ -343,20 +343,37 @@ public class ChimeraViewFrame extends StructureViewerBase } /** - * Create a new viewer from saved session state data. + * Create a new viewer from saved session state data including Chimera session + * file. * - * @param viewerData - * @param af + * @param chimeraSession + * + * @param alignPanel + * @param pdbArray + * @param seqsArray + * @param colourByChimera + * @param colourBySequence */ - public ChimeraViewFrame(ViewerData viewerData, AlignFrame af) + public ChimeraViewFrame(String chimeraSession, AlignmentPanel alignPanel, + PDBEntry[] pdbArray, + SequenceI[][] seqsArray, boolean colourByChimera, + boolean colourBySequence) { super(); - String chimeraSessionFile = viewerData.stateData; - openNewChimera(af.alignPanel, new PDBEntry[] - {}, new SequenceI[][] - {}); - initChimera("open " + chimeraSessionFile); - // TODO restore mappings + this.chimeraSessionFile = chimeraSession; + openNewChimera(alignPanel, pdbArray, seqsArray); + if (colourByChimera) + { + jmb.setColourBySequence(false); + seqColour.setSelected(false); + viewerColour.setSelected(true); + } + else if (colourBySequence) + { + jmb.setColourBySequence(true); + seqColour.setSelected(true); + viewerColour.setSelected(false); + } } /** @@ -433,19 +450,34 @@ public class ChimeraViewFrame extends StructureViewerBase return result; } - void initChimera(String command) + /** + * Launch Chimera. If we have a chimera session file name, send Chimera the + * command to open its saved session file. + */ + void initChimera() { jmb.setFinishedInit(false); - // TODO: consider waiting until the structure/view is fully loaded before - // displaying jalview.gui.Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true), getBounds().width, getBounds().height); - if (command == null) + + /* + * Pass an empty 'command' to launch Chimera + */ + jmb.evalStateCommand("", false); + + if (this.chimeraSessionFile != null) { - command = ""; + boolean opened = jmb.openSession(chimeraSessionFile); + if (!opened) + { + System.err + .println("An error occurred opening Chimera session file " + + chimeraSessionFile); + } } - jmb.evalStateCommand(command, false); jmb.setFinishedInit(true); + + jmb.startChimeraListener(); } void setChainMenuItems(List chainNames) @@ -515,19 +547,26 @@ 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 */ - public void closeViewer() + public void closeViewer(boolean closeChimera) { if (jmb.isChimeraRunning()) { - String prompt = MessageManager - .formatMessage("label.confirm_close_chimera", new Object[] - { jmb.getViewerTitle("Chimera", false) }); - prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JOptionPane.showConfirmDialog(this, prompt, - MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_OPTION); - jmb.closeViewer(confirm == JOptionPane.YES_OPTION); + if (!closeChimera) + { + String prompt = MessageManager.formatMessage( + "label.confirm_close_chimera", new Object[] + { jmb.getViewerTitle("Chimera", false) }); + prompt = JvSwingUtils.wrapTooltip(true, prompt); + int confirm = JOptionPane.showConfirmDialog(this, prompt, + MessageManager.getString("label.close_viewer"), + JOptionPane.YES_NO_OPTION); + closeChimera = confirm == JOptionPane.YES_OPTION; + } + jmb.closeViewer(closeChimera); } setAlignmentPanel(null); _aps.clear(); @@ -625,7 +664,7 @@ public class ChimeraViewFrame extends StructureViewerBase { try { - initChimera(""); + initChimera(); } catch (Exception ex) { Cache.log.error("Couldn't open Chimera viewer!", ex); @@ -746,8 +785,8 @@ public class ChimeraViewFrame extends StructureViewerBase if (pdbseq != null && pdbseq.getHeight() > 0) { // just use the file name from the first sequence's first PDBEntry - filePath = new File(((PDBEntry) pdbseq.getSequenceAt(0).getPDBId() - .elementAt(0)).getFile()).getAbsolutePath(); + filePath = new File(pdbseq.getSequenceAt(0).getPDBId() + .elementAt(0).getFile()).getAbsolutePath(); processingEntry.setFile(filePath); } return filePath; @@ -874,7 +913,7 @@ public class ChimeraViewFrame extends StructureViewerBase // Set the colour using the current view for the associated alignframe for (AlignmentPanel ap : _colourwith) { - jmb.colourBySequence(ap.av.showSequenceFeatures, ap); + jmb.colourBySequence(ap.av.isShowSequenceFeatures(), ap); } } } @@ -986,7 +1025,7 @@ public class ChimeraViewFrame extends StructureViewerBase repaint(); return; } - setChainMenuItems(jmb.chainNames); + setChainMenuItems(jmb.getChainNames()); this.setTitle(jmb.getViewerTitle("Chimera", true)); if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1)