import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.gui.StructureViewer.ViewerType;
/**
* list of sequenceSet ids associated with the view
*/
- protected List<String> _aps = new ArrayList<String>();
+ protected List<String> _aps = new ArrayList<>();
/**
* list of alignment panels to use for superposition
*/
- protected Vector<AlignmentPanel> _alignwith = new Vector<AlignmentPanel>();
+ protected Vector<AlignmentPanel> _alignwith = new Vector<>();
/**
* list of alignment panels that are used for colouring structures by aligned
* sequences
*/
- protected Vector<AlignmentPanel> _colourwith = new Vector<AlignmentPanel>();
+ protected Vector<AlignmentPanel> _colourwith = new Vector<>();
private String viewId = null;
protected boolean allChainsSelected = false;
+ protected JMenu viewSelectionMenu;
+
/**
* Default constructor
*/
{
super();
}
+
/**
*
* @param ap2
{
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
if (_alignwith.size() == 0 && ap != null)
{
}
// otherwise, start adding the structure.
getBinding().addSequenceAndChain(new PDBEntry[] { pdbentry },
- new SequenceI[][] { seqs }, new String[][] { chains });
+ new SequenceI[][]
+ { seqs }, new String[][] { chains });
addingStructures = true;
_started = false;
alignAddedStructures = align;
{
int option = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
MessageManager.formatMessage("label.add_pdbentry_to_view",
- new Object[] { pdbId, view.getTitle() }),
+ new Object[]
+ { pdbId, view.getTitle() }),
MessageManager
.getString("label.align_to_existing_structure_view"),
JvOptionPane.YES_NO_CANCEL_OPTION);
if (apanel.getSeqPanel().seqCanvas.fr != null)
{
apanel.getSeqPanel().seqCanvas.fr.featuresAdded();
- apanel.paintAlignment(true);
+ // note - we don't do a refresh for structure here because we do it
+ // explicitly for all panels later on
+ apanel.paintAlignment(true, false);
}
/*
*/
viewer.useAlignmentPanelForColourbyseq(apanel);
viewer.buildActionMenu();
- apanel.getStructureSelectionManager().sequenceColoursChanged(
- apanel);
+ apanel.getStructureSelectionManager()
+ .sequenceColoursChanged(apanel);
break;
}
}
*/
int option = JvOptionPane.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 }),
+ "label.pdb_entry_is_already_displayed", new Object[]
+ { pdbId }),
+ MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new Object[]
+ { pdbId }),
JvOptionPane.YES_NO_CANCEL_OPTION);
if (option == JvOptionPane.CANCEL_OPTION)
{
public void changeColour_actionPerformed(String colourSchemeName)
{
AlignmentI al = getAlignmentPanel().av.getAlignment();
- ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(
- colourSchemeName, al, null);
+ ColourSchemeI cs = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, al, null);
getBinding().setJalviewColourScheme(cs);
}
if (_colourwith == null)
{
- _colourwith = new Vector<AlignmentPanel>();
+ _colourwith = new Vector<>();
}
if (_alignwith == null)
{
- _alignwith = new Vector<AlignmentPanel>();
+ _alignwith = new Vector<>();
}
ViewSelectionMenu seqColourBy = new ViewSelectionMenu(
@Override
public void itemStateChanged(ItemEvent e)
{
- alignStructs.setEnabled(_alignwith.size() > 0);
+ alignStructs.setEnabled(!_alignwith.isEmpty());
alignStructs.setToolTipText(MessageManager.formatMessage(
"label.align_structures_using_linked_alignment_views",
- new String[] { String.valueOf(_alignwith.size()) }));
+ _alignwith.size()));
}
};
- JMenu alpanels = new ViewSelectionMenu(
+ viewSelectionMenu = new ViewSelectionMenu(
MessageManager.getString("label.superpose_with"), this,
_alignwith, handler);
handler.itemStateChanged(null);
- viewerActionMenu.add(alpanels);
+ viewerActionMenu.add(viewSelectionMenu, 0);
viewerActionMenu.addMenuListener(new MenuListener()
{
@Override
}
@Override
- public void setJalviewColourScheme(ColourSchemeI cs) {
+ public void setJalviewColourScheme(ColourSchemeI cs)
+ {
getBinding().setJalviewColourScheme(cs);
}
+
+ /**
+ * Sends commands to the structure viewer to superimpose structures based on
+ * currently associated alignments. May optionally return an error message for
+ * the operation.
+ */
@Override
- protected void alignStructs_actionPerformed(ActionEvent actionEvent)
+ protected String alignStructs_actionPerformed(ActionEvent actionEvent)
{
- alignStructs_withAllAlignPanels();
+ return alignStructs_withAllAlignPanels();
}
- protected void alignStructs_withAllAlignPanels()
+
+ protected String alignStructs_withAllAlignPanels()
{
if (getAlignmentPanel() == null)
{
- return;
+ return null;
}
-
+
if (_alignwith.size() == 0)
{
_alignwith.add(getAlignmentPanel());
}
-
+
+ String reply = null;
try
{
AlignmentI[] als = new Alignment[_alignwith.size()];
- ColumnSelection[] alc = new ColumnSelection[_alignwith.size()];
+ HiddenColumns[] alc = new HiddenColumns[_alignwith.size()];
int[] alm = new int[_alignwith.size()];
int a = 0;
-
+
for (AlignmentPanel ap : _alignwith)
{
als[a] = ap.av.getAlignment();
alm[a] = -1;
- alc[a++] = ap.av.getColumnSelection();
+ alc[a++] = ap.av.getAlignment().getHiddenColumns();
+ }
+ reply = getBinding().superposeStructures(als, alm, alc);
+ if (reply != null)
+ {
+ String text = MessageManager
+ .formatMessage("error.superposition_failed", reply);
+ statusBar.setText(text);
}
- getBinding().superposeStructures(als, alm, alc);
} catch (Exception e)
{
StringBuffer sp = new StringBuffer();
Cache.log.info("Couldn't align structures with the " + sp.toString()
+ "associated alignment panels.", e);
}
+ return reply;
}
+
@Override
public void background_actionPerformed(ActionEvent actionEvent)
{
getBinding().setBackgroundColour(col);
}
}
+
@Override
public void viewerColour_actionPerformed(ActionEvent actionEvent)
{
getBinding().setColourBySequence(false);
}
}
+
@Override
public void chainColour_actionPerformed(ActionEvent actionEvent)
{
chainColour.setSelected(true);
getBinding().colourByChain();
}
+
@Override
public void chargeColour_actionPerformed(ActionEvent actionEvent)
{
chargeColour.setSelected(true);
getBinding().colourByCharge();
}
+
@Override
public void seqColour_actionPerformed(ActionEvent actionEvent)
{
binding.setColourBySequence(seqColour.isSelected());
if (_colourwith == null)
{
- _colourwith = new Vector<AlignmentPanel>();
+ _colourwith = new Vector<>();
}
if (binding.isColourBySequence())
{
}
}
}
+
@Override
public void pdbFile_actionPerformed(ActionEvent actionEvent)
{
JalviewFileChooser chooser = new JalviewFileChooser(
Cache.getProperty("LAST_DIRECTORY"));
-
+
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle(MessageManager.getString("label.save_pdb_file"));
chooser.setToolTipText(MessageManager.getString("action.save"));
-
+
int value = chooser.showSaveDialog(this);
-
+
if (value == JalviewFileChooser.APPROVE_OPTION)
{
BufferedReader in = null;
{
// TODO: cope with multiple PDB files in view
in = new BufferedReader(
- new FileReader(getBinding().getPdbFile()[0]));
+ new FileReader(getBinding().getStructureFiles()[0]));
File outFile = chooser.getSelectedFile();
-
+
PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
String data;
while ((data = in.readLine()) != null)
}
}
}
+
@Override
public void viewMapping_actionPerformed(ActionEvent actionEvent)
{
}
protected abstract String getViewerName();
+
+ /**
+ * Configures the title and menu items of the viewer panel.
+ */
public void updateTitleAndMenus()
{
AAStructureBindingModel binding = getBinding();
return;
}
setChainMenuItems(binding.getChainNames());
-
+
this.setTitle(binding.getViewerTitle(getViewerName(), true));
- if (binding.getPdbFile().length > 1 && binding.getSequence().length > 1)
+
+ /*
+ * enable 'Superpose with' if more than one mapped structure
+ */
+ viewSelectionMenu.setEnabled(false);
+ if (getBinding().getStructureFiles().length > 1
+ && getBinding().getSequence().length > 1)
+ {
+ viewSelectionMenu.setEnabled(true);
+ }
+
+ /*
+ * Show action menu if it has any enabled items
+ */
+ viewerActionMenu.setVisible(false);
+ for (int i = 0; i < viewerActionMenu.getItemCount(); i++)
{
- viewerActionMenu.setVisible(true);
+ if (viewerActionMenu.getItem(i).isEnabled())
+ {
+ viewerActionMenu.setVisible(true);
+ break;
+ }
}
+
if (!binding.isLoadingFromArchive())
{
seqColour_actionPerformed(null);
git://source.jalview.org / jalview.git / blobdiff