+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * 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;
* 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;
/**
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);
* alignment
* @param alignFrame
*/
- protected void addStructure(final PDBEntry pdbentry, final SequenceI[] seqs, final String[] chains,
+ protected void addStructure(final PDBEntry pdbentry,
+ final SequenceI[] seqs, final String[] chains,
final boolean align, final IProgressIndicator alignFrame)
{
if (pdbentry.getFile() == null)
try
{
Thread.sleep(100 + ((int) Math.random() * 100));
-
+
} catch (Exception e)
{
}
* @param view
* @return YES, NO or CANCEL JOptionPane code
*/
- protected int chooseAlignStructureToViewer(String pdbId, StructureViewerBase view)
+ 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
+ new Object[] { pdbId, view.getTitle() }),
+ MessageManager
.getString("label.align_to_existing_structure_view"),
JOptionPane.YES_NO_CANCEL_OPTION);
return option;
// NO_OPTION - offer the next viewer if any
}
}
-
+
/*
* nothing offered and selected
*/
/*
* create the mappings
*/
- apanel.getStructureSelectionManager().setMapping(seq, chains, pdbFilename,
- AppletFormatAdapter.FILE);
-
+ apanel.getStructureSelectionManager().setMapping(seq, chains,
+ pdbFilename, AppletFormatAdapter.FILE);
+
/*
* alert the FeatureRenderer to show new (PDB RESNUM) features
*/
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
apanel.paintAlignment(true);
}
-
+
/*
* add the sequences to any other viewers (of the same type) for this pdb
* file
*/
viewer.useAlignmentPanelForColourbyseq(apanel);
viewer.buildActionMenu();
- apanel.getStructureSelectionManager().sequenceColoursChanged(apanel);
+ apanel.getStructureSelectionManager().sequenceColoursChanged(
+ apanel);
break;
}
}
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);
+ 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;