X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FStructureViewerBase.java;h=a0b199bb3431a2106aab331c51addd8a9e64d497;hb=0a2ec403c08a1747b7e876f00f468867f8329d36;hp=6dd7d502467bba44e8e9a5c3fa587cf0dc5deea1;hpb=9c1a9d682a2664d525bfd0f38bae861292dc3921;p=jalview.git diff --git a/src/jalview/gui/StructureViewerBase.java b/src/jalview/gui/StructureViewerBase.java index 6dd7d50..a0b199b 100644 --- a/src/jalview/gui/StructureViewerBase.java +++ b/src/jalview/gui/StructureViewerBase.java @@ -20,23 +20,6 @@ */ package jalview.gui; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.PDBEntry; -import jalview.datamodel.SequenceI; -import jalview.gui.StructureViewer.ViewerType; -import jalview.gui.ViewSelectionMenu.ViewSetProvider; -import jalview.io.DataSourceType; -import jalview.io.JalviewFileChooser; -import jalview.io.JalviewFileView; -import jalview.jbgui.GStructureViewer; -import jalview.schemes.ColourSchemeI; -import jalview.schemes.ColourSchemes; -import jalview.structure.StructureMapping; -import jalview.structures.models.AAStructureBindingModel; -import jalview.util.MessageManager; - import java.awt.Color; import java.awt.Component; import java.awt.event.ActionEvent; @@ -56,13 +39,32 @@ import java.util.Vector; import javax.swing.ButtonGroup; import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; import javax.swing.JMenu; import javax.swing.JMenuItem; import javax.swing.JRadioButtonMenuItem; import javax.swing.event.MenuEvent; import javax.swing.event.MenuListener; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.JalviewColourChooser.ColourChooserListener; +import jalview.gui.StructureViewer.ViewerType; +import jalview.gui.ViewSelectionMenu.ViewSetProvider; +import jalview.io.DataSourceType; +import jalview.io.JalviewFileChooser; +import jalview.io.JalviewFileView; +import jalview.jbgui.GStructureViewer; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.ColourSchemes; +import jalview.structure.StructureMapping; +import jalview.structures.models.AAStructureBindingModel; +import jalview.util.BrowserLauncher; +import jalview.util.MessageManager; +import jalview.ws.dbsources.Pdb; + /** * Base class with common functionality for JMol, Chimera or other structure * viewers. @@ -197,8 +199,6 @@ public abstract class StructureViewerBase extends GStructureViewer this.viewId = viewId; } - public abstract String getStateInfo(); - protected void buildActionMenu() { if (_alignwith == null) @@ -678,7 +678,10 @@ public abstract class StructureViewerBase extends GStructureViewer }); viewerColour = new JRadioButtonMenuItem(); - // text is set in overrides of this method + viewerColour + .setText(MessageManager.getString("label.colour_with_viewer")); + viewerColour.setToolTipText(MessageManager + .getString("label.let_viewer_manage_structure_colours")); viewerColour.setName(ViewerColour.ByViewer.name()); viewerColour.setSelected(!binding.isColourBySequence()); @@ -704,7 +707,7 @@ public abstract class StructureViewerBase extends GStructureViewer } else { - // update the Chimera display now. + // update the viewer display now. seqColour_actionPerformed(); } } @@ -716,10 +719,18 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void itemStateChanged(ItemEvent e) { - alignStructs.setEnabled(!_alignwith.isEmpty()); - alignStructs.setToolTipText(MessageManager.formatMessage( - "label.align_structures_using_linked_alignment_views", - _alignwith.size())); + if (_alignwith.isEmpty()) + { + alignStructs.setEnabled(false); + alignStructs.setToolTipText(null); + } + else + { + alignStructs.setEnabled(true); + alignStructs.setToolTipText(MessageManager.formatMessage( + "label.align_structures_using_linked_alignment_views", + _alignwith.size())); + } } }; viewSelectionMenu = new ViewSelectionMenu( @@ -746,6 +757,10 @@ public abstract class StructureViewerBase extends GStructureViewer } }); + viewerActionMenu.setText(getViewerName()); + helpItem.setText(MessageManager.formatMessage("label.viewer_help", + getViewerName())); + buildColourMenu(); } @@ -790,16 +805,23 @@ public abstract class StructureViewerBase extends GStructureViewer return reply; } + /** + * Opens a colour chooser dialog, and applies the chosen colour to the + * background of the structure viewer + */ @Override public void background_actionPerformed() { - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_background_colour"), - null); - if (col != null) + String ttl = MessageManager.getString("label.select_background_colour"); + ColourChooserListener listener = new ColourChooserListener() { - getBinding().setBackgroundColour(col); - } + @Override + public void colourSelected(Color c) + { + getBinding().setBackgroundColour(c); + } + }; + JalviewColourChooser.showColourChooser(this, ttl, null, listener); } @Override @@ -857,6 +879,7 @@ public abstract class StructureViewerBase extends GStructureViewer @Override public void pdbFile_actionPerformed() { + // TODO: JAL-3048 not needed for Jalview-JS - save PDB file JalviewFileChooser chooser = new JalviewFileChooser( Cache.getProperty("LAST_DIRECTORY")); @@ -947,7 +970,7 @@ public abstract class StructureViewerBase extends GStructureViewer * enable 'Superpose with' if more than one mapped structure */ viewSelectionMenu.setEnabled(false); - if (getBinding().getStructureFiles().length > 1 + if (getBinding().getMappedStructureCount() > 1 && getBinding().getSequence().length > 1) { viewSelectionMenu.setEnabled(true); @@ -1087,4 +1110,136 @@ public abstract class StructureViewerBase extends GStructureViewer getBinding().showChains(toshow); } + /** + * Tries to fetch a PDB file and save to a temporary local file. Returns the + * saved file path if successful, or null if not. + * + * @param processingEntry + * @return + */ + protected String fetchPdbFile(PDBEntry processingEntry) + { + String filePath = null; + Pdb pdbclient = new Pdb(); + AlignmentI pdbseq = null; + String pdbid = processingEntry.getId(); + long handle = System.currentTimeMillis() + + Thread.currentThread().hashCode(); + + /* + * Write 'fetching PDB' progress on AlignFrame as we are not yet visible + */ + String msg = MessageManager.formatMessage("status.fetching_pdb", + new Object[] + { pdbid }); + getAlignmentPanel().alignFrame.setProgressBar(msg, handle); + // long hdl = startProgressBar(MessageManager.formatMessage( + // "status.fetching_pdb", new Object[] + // { pdbid })); + try + { + pdbseq = pdbclient.getSequenceRecords(pdbid); + } catch (Exception e) + { + System.err.println( + "Error retrieving PDB id " + pdbid + ": " + e.getMessage()); + } finally + { + msg = pdbid + " " + MessageManager.getString("label.state_completed"); + getAlignmentPanel().alignFrame.setProgressBar(msg, handle); + // stopProgressBar(msg, hdl); + } + /* + * If PDB data were saved and are not invalid (empty alignment), return the + * file path. + */ + if (pdbseq != null && pdbseq.getHeight() > 0) + { + // just use the file name from the first sequence's first PDBEntry + filePath = new File(pdbseq.getSequenceAt(0).getAllPDBEntries() + .elementAt(0).getFile()).getAbsolutePath(); + processingEntry.setFile(filePath); + } + return filePath; + } + + /** + * If supported, saves the state of the structure viewer to a temporary file + * and returns the file, else returns null + * + * @return + */ + public File saveSession() + { + // TODO: a wait loop to ensure the file is written fully before returning? + return getBinding() == null ? null : getBinding().saveSession(); + } + + /** + * 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 forceClose + * if true, close any linked Chimera process; if false, prompt first + */ + @Override + public void closeViewer(boolean forceClose) + { + AAStructureBindingModel binding = getBinding(); + if (binding != null && binding.isViewerRunning()) + { + if (!forceClose) + { + String viewerName = getViewerName(); + String prompt = MessageManager + .formatMessage("label.confirm_close_viewer", new Object[] + { binding.getViewerTitle(viewerName, false), viewerName }); + 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; + } + forceClose = confirm == JvOptionPane.YES_OPTION; + } + } + if (binding != null) + { + binding.closeViewer(forceClose); + } + 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(); + } + + @Override + public void showHelp_actionPerformed() + { + try + { + String url = getBinding().getHelpURL(); + if (url != null) + { + BrowserLauncher.openURL(url); + } + } catch (IOException ex) + { + System.err + .println("Show " + getViewerName() + " failed with: " + + ex.getMessage()); + } + } + }