*/
package jalview.gui;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.AlignmentUtils.MappingResult;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.analysis.NJTree;
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.PDBEntry;
import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
import jalview.structure.VamsasSource;
+import jalview.util.MessageManager;
import jalview.viewmodel.AlignmentViewport;
import jalview.ws.params.AutoCalcSetting;
import java.util.ArrayList;
import java.util.Deque;
import java.util.Hashtable;
-import java.util.List;
+import java.util.Set;
import java.util.Vector;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+
/**
* DOCUMENT ME!
*
boolean showSeqFeaturesHeight;
+ /**
+ * Send the current selection to be broadcast to any selection listeners.
+ */
public void sendSelection()
{
jalview.structure.StructureSelectionManager
*/
@Override
public void mirrorCommand(CommandI command, boolean undo,
- StructureSelectionManager ssm)
+ StructureSelectionManager ssm, VamsasSource source)
{
/*
- * Only EditCommand is currently handled by listeners.
+ * ...work in progress... do nothing unless we are a 'complement' of the
+ * source May replace this with direct calls not via SSM.
*/
- if (!(command instanceof EditCommand))
+ if (source instanceof AlignViewportI
+ && ((AlignViewportI) source).getCodingComplement() == this)
+ {
+ // ok to continue;
+ }
+ else
{
return;
}
- EditCommand edit = (EditCommand) command;
- List<SequenceI> seqs = getAlignment().getSequences();
- EditCommand mappedCommand = ssm.mapEditCommand(edit, undo, seqs,
+ CommandI mappedCommand = ssm.mapCommand(command, undo, getAlignment(),
getGapCharacter());
- AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
- mappedCommand.performEdit(0, views);
- getAlignPanel().alignmentChanged();
+ if (mappedCommand != null)
+ {
+ AlignmentI[] views = getAlignPanel().alignFrame.getViewAlignments();
+ mappedCommand.doCommand(views);
+ getAlignPanel().alignmentChanged();
+ }
}
@Override
{
return this.redoList;
}
+
+ /**
+ * Add the sequences from the given alignment to this viewport. Optionally,
+ * may give the user the option to open a new frame, or split panel, with cDNA
+ * and protein linked.
+ *
+ * @param al
+ * @param title
+ */
+ public void addAlignment(AlignmentI al, String title)
+ {
+ // TODO: promote to AlignViewportI? applet CutAndPasteTransfer is different
+
+ // refactored from FileLoader / CutAndPasteTransfer / SequenceFetcher with
+ // this comment:
+ // TODO: create undo object for this JAL-1101
+
+ /*
+ * If one alignment is protein and one nucleotide, with at least one
+ * sequence name in common, offer to open a linked alignment.
+ */
+ if (getAlignment().isNucleotide() != al.isNucleotide())
+ {
+ final Set<String> sequenceNames = getAlignment().getSequenceNames();
+ sequenceNames.retainAll(al.getSequenceNames());
+ if (!sequenceNames.isEmpty()) // at least one sequence name in both
+ {
+ if (openLinkedAlignment(al, title))
+ {
+ return;
+ }
+ }
+ }
+
+ for (int i = 0; i < al.getHeight(); i++)
+ {
+ getAlignment().addSequence(al.getSequenceAt(i));
+ }
+ // TODO this call was done by SequenceFetcher but not FileLoader or
+ // CutAndPasteTransfer. Is it needed?
+ setEndSeq(getAlignment().getHeight());
+ firePropertyChange("alignment", null, getAlignment().getSequences());
+ }
+
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment. Returns true if the new alignment was opened, false if not,
+ * because the user declined the offer.
+ *
+ * @param title
+ */
+ protected boolean openLinkedAlignment(AlignmentI al, String title)
+ {
+ String[] options = new String[]
+ { MessageManager.getString("action.no"),
+ MessageManager.getString("label.split_window"),
+ MessageManager.getString("label.new_window"), };
+ final String question = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.open_linked_alignment?"));
+ int response = JOptionPane.showOptionDialog(Desktop.desktop, question,
+ MessageManager.getString("label.open_linked_alignment"),
+ JOptionPane.DEFAULT_OPTION, JOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+
+ if (response != 1 && response != 2)
+ {
+ return false;
+ }
+ final boolean openSplitPane = (response == 1);
+ final boolean openInNewWindow = (response == 2);
+
+ /*
+ * Create the AlignFrame first (which creates the new alignment's datasets),
+ * before attempting sequence mapping.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = openSplitPane ? new Alignment(getAlignment())
+ : getAlignment();
+ final AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ newAlignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new Object[]
+ { title }));
+
+ // TODO if we want this (e.g. to enable reload of the alignment from file),
+ // we will need to add parameters to the stack.
+ // if (!protocol.equals(AppletFormatAdapter.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (openInNewWindow)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /*
+ * Try to find mappings for at least one sequence.
+ */
+ MappingResult mapped = AlignmentUtils.mapProteinToCdna(protein, cdna);
+ final StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (mapped == MappingResult.Mapped)
+ {
+
+ /*
+ * Register the mappings (held on the protein alignment) with the
+ * StructureSelectionManager (for mouseover linking).
+ */
+ ssm.addMappings(protein.getCodonFrames());
+ }
+ else
+ {
+
+ /*
+ * No mapping possible - warn the user, but leave window open.
+ */
+ final String msg = JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.mapping_failed"));
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, msg,
+ MessageManager.getString("label.no_mappings"),
+ JOptionPane.WARNING_MESSAGE);
+ }
+
+ try
+ {
+ newAlignFrame.setMaximum(jalview.bin.Cache.getDefault(
+ "SHOW_FULLSCREEN",
+ false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (openSplitPane)
+ {
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ AlignFrame copyMe = new AlignFrame(thisAlignment,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(""); // TODO would like this AlignFrame.title here
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
+ : copyMe;
+ newAlignFrame.setTitle(title);
+
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * Set the frames to list for each other's edit and sort commands.
+ */
+ ssm.addCommandListener(cdnaFrame.getViewport());
+ ssm.addCommandListener(proteinFrame.getViewport());
+
+ /*
+ * cDNA view will mirror edits, selection, sorting, show/hide on protein
+ */
+ proteinFrame.getViewport().setCodingComplement(cdnaFrame.getViewport());
+ }
+
+ return true;
+ }
}
git://source.jalview.org / jalview.git / blobdiff