+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.AppletFormatAdapter;
+import jalview.jbgui.GStructureViewer;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+
import java.awt.Component;
import java.util.ArrayList;
import java.util.List;
import java.util.Vector;
import javax.swing.JMenuItem;
-
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.jbgui.GStructureViewer;
+import javax.swing.JOptionPane;
/**
* Base class with common functionality for JMol, Chimera or other structure
* list of sequenceSet ids associated with the view
*/
protected List<String> _aps = new ArrayList<String>();
+
/**
* list of alignment panels to use for superposition
*/
protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+
private String viewId = null;
+
private AlignmentPanel ap;
+ protected boolean alignAddedStructures = false;
+
+ protected boolean _started = false;
+
+ protected boolean addingStructures = false;
+
+ protected Thread worker = null;
+
/**
*
* @param ap2
public boolean isUsedforaligment(AlignmentPanel ap2)
{
-
+
return (_alignwith != null) && _alignwith.contains(ap2);
}
list = t;
}
}
-
+
return list;
}
}
}
- public void useAlignmentPanelForColourbyseq(AlignmentPanel nap, boolean enableColourBySeq)
+ public void useAlignmentPanelForColourbyseq(AlignmentPanel nap,
+ boolean enableColourBySeq)
{
useAlignmentPanelForColourbyseq(nap);
getBinding().setColourBySequence(enableColourBySeq);
}
public abstract ViewerType getViewerType();
+
+ protected abstract AAStructureBindingModel getBindingModel();
+
+ /**
+ * add a new structure (with associated sequences and chains) to this viewer,
+ * retrieving it if necessary first.
+ *
+ * @param pdbentry
+ * @param seqs
+ * @param chains
+ * @param align
+ * if true, new structure(s) will be aligned using associated
+ * alignment
+ * @param alignFrame
+ */
+ protected void addStructure(final PDBEntry pdbentry,
+ final SequenceI[] seqs, final String[] chains,
+ final boolean align, 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, seqs, chains, align, alignFrame);
+ }
+ }).start();
+ return;
+ }
+ }
+ // otherwise, start adding the structure.
+ getBindingModel().addSequenceAndChain(new PDBEntry[] { pdbentry },
+ new SequenceI[][] { seqs }, new String[][] { chains });
+ addingStructures = true;
+ _started = false;
+ alignAddedStructures = align;
+ worker = new Thread(this);
+ worker.start();
+ return;
+ }
+
+ /**
+ * Presents a dialog with the option to add an align a structure to an
+ * existing structure view
+ *
+ * @param pdbId
+ * @param view
+ * @return YES, NO or CANCEL JOptionPane code
+ */
+ protected int chooseAlignStructureToViewer(String pdbId,
+ StructureViewerBase view)
+ {
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage("label.add_pdbentry_to_view",
+ new Object[] { pdbId, view.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ return option;
+ }
+
+ protected abstract boolean hasPdbId(String pdbId);
+
+ protected abstract List<StructureViewerBase> getViewersFor(
+ AlignmentPanel alp);
+
+ /**
+ * Check for any existing views involving this alignment and give user the
+ * option to add and align this molecule to one of them
+ *
+ * @param pdbentry
+ * @param seq
+ * @param chains
+ * @param apanel
+ * @param pdbId
+ * @return true if user adds to a view, or cancels entirely, else false
+ */
+ protected boolean addToExistingViewer(PDBEntry pdbentry, SequenceI[] seq,
+ String[] chains, final AlignmentPanel apanel, String pdbId)
+ {
+ for (StructureViewerBase view : getViewersFor(apanel))
+ {
+ // TODO: highlight the view somehow
+ /*
+ * JAL-1742 exclude view with this structure already mapped (don't offer
+ * to align chain B to chain A of the same structure)
+ */
+ if (view.hasPdbId(pdbId))
+ {
+ continue;
+ }
+ int option = chooseAlignStructureToViewer(pdbId, view);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ return true;
+ }
+ else if (option == JOptionPane.YES_OPTION)
+ {
+ view.useAlignmentPanelForSuperposition(apanel);
+ view.addStructure(pdbentry, seq, chains, true, apanel.alignFrame);
+ return true;
+ }
+ else
+ {
+ // NO_OPTION - offer the next viewer if any
+ }
+ }
+
+ /*
+ * nothing offered and selected
+ */
+ return false;
+ }
+
+ /**
+ * Adds mappings for the given sequences to an already opened PDB structure,
+ * and updates any viewers that have the PDB file
+ *
+ * @param seq
+ * @param chains
+ * @param apanel
+ * @param pdbFilename
+ */
+ protected void addSequenceMappingsToStructure(SequenceI[] seq,
+ String[] chains, final AlignmentPanel apanel, String pdbFilename)
+ {
+ // TODO : Fix multiple seq to one chain issue here.
+ /*
+ * create the mappings
+ */
+ apanel.getStructureSelectionManager().setMapping(seq, chains,
+ pdbFilename, AppletFormatAdapter.FILE);
+
+ /*
+ * alert the FeatureRenderer to show new (PDB RESNUM) features
+ */
+ if (apanel.getSeqPanel().seqCanvas.fr != null)
+ {
+ apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
+ apanel.paintAlignment(true);
+ }
+
+ /*
+ * add the sequences to any other viewers (of the same type) for this pdb
+ * file
+ */
+ // JBPNOTE: this looks like a binding routine, rather than a gui routine
+ for (StructureViewerBase viewer : getViewersFor(null))
+ {
+ AAStructureBindingModel bindingModel = viewer.getBindingModel();
+ for (int pe = 0; pe < bindingModel.getPdbCount(); pe++)
+ {
+ if (bindingModel.getPdbEntry(pe).getFile().equals(pdbFilename))
+ {
+ bindingModel.addSequence(pe, seq);
+ viewer.addAlignmentPanel(apanel);
+ /*
+ * add it to the set of alignments used for colouring structure by
+ * sequence
+ */
+ viewer.useAlignmentPanelForColourbyseq(apanel);
+ viewer.buildActionMenu();
+ apanel.getStructureSelectionManager().sequenceColoursChanged(
+ apanel);
+ break;
+ }
+ }
+ }
+ }
+
+ /**
+ * Check if the PDB file is already loaded, if so offer to add it to the
+ * existing viewer
+ *
+ * @param seq
+ * @param chains
+ * @param apanel
+ * @param pdbId
+ * @return true if the user chooses to add to a viewer, or to cancel entirely
+ */
+ protected boolean addAlreadyLoadedFile(SequenceI[] seq, String[] chains,
+ final AlignmentPanel apanel, String pdbId)
+ {
+ boolean finished = false;
+ String alreadyMapped = apanel.getStructureSelectionManager()
+ .alreadyMappedToFile(pdbId);
+
+ if (alreadyMapped != null)
+ {
+ /*
+ * the PDB file is already loaded
+ */
+ int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed",
+ new Object[] { pdbId }), MessageManager
+ .formatMessage(
+ "label.map_sequences_to_visible_window",
+ new Object[] { pdbId }),
+ JOptionPane.YES_NO_CANCEL_OPTION);
+ if (option == JOptionPane.CANCEL_OPTION)
+ {
+ finished = true;
+ }
+ else if (option == JOptionPane.YES_OPTION)
+ {
+ addSequenceMappingsToStructure(seq, chains, apanel, alreadyMapped);
+ finished = true;
+ }
+ }
+ return finished;
+ }
}
git://source.jalview.org / jalview.git / blobdiff