+ new FileLoader().LoadFile(this, file, DataSourceType.FILE, format,
+ async);
+ }
+
+ public void addFile(File file)
+ {
+ addFile(file, null);
+ }
+
+ /**
+ * Show a dialog with the option to open and link (cDNA <-> protein) as a new
+ * alignment, either as a standalone alignment or in a split frame. Returns
+ * true if the new alignment was opened, false if not, because the user
+ * declined the offer.
+ *
+ * @param al
+ * @param title
+ */
+ protected void 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_split_window?"));
+ final AlignViewport us = this;
+
+ /*
+ * options No, Split Window, New Window correspond to
+ * dialog responses 0, 1, 2 (even though JOptionPane shows them
+ * in reverse order)
+ */
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop)
+ .setResponseHandler(0, () -> {
+ addDataToAlignment(al);
+ }).setResponseHandler(1, () -> {
+ us.openLinkedAlignmentAs(al, title, true);
+ }).setResponseHandler(2, () -> {
+ us.openLinkedAlignmentAs(al, title, false);
+ });
+ dialog.showDialog(question,
+ MessageManager.getString("label.open_split_window"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+
+ protected void openLinkedAlignmentAs(AlignmentI al, String title,
+ boolean newWindowOrSplitPane)
+ {
+ /*
+ * Identify protein and dna alignments. Make a copy of this one if opening
+ * in a new split pane.
+ */
+ AlignmentI thisAlignment = newWindowOrSplitPane
+ ? new Alignment(getAlignment())
+ : getAlignment();
+ AlignmentI protein = al.isNucleotide() ? thisAlignment : al;
+ final AlignmentI cdna = al.isNucleotide() ? al : thisAlignment;
+
+ /*
+ * Map sequences. At least one should get mapped as we have already passed
+ * the test for 'mappability'. Any mappings made will be added to the
+ * protein alignment. Note creating dataset sequences on the new alignment
+ * is a pre-requisite for building mappings.
+ */
+ al.setDataset(null);
+ AlignmentUtils.mapProteinAlignmentToCdna(protein, cdna);
+
+ /*
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
+ */
+ AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ newAlignFrame.setTitle(title);
+ newAlignFrame.setStatus(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(DataSourceType.PASTE))
+ // {
+ // alignFrame.setFileName(file, format);
+ // }
+
+ if (!newWindowOrSplitPane)
+ {
+ Desktop.addInternalFrame(newAlignFrame, title,
+ AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ try
+ {
+ newAlignFrame.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
+ {
+ }
+
+ if (newWindowOrSplitPane)
+ {
+ al.alignAs(thisAlignment);
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
+ }
+ }
+
+ /**
+ * Helper method to open a new SplitFrame holding linked dna and protein
+ * alignments.
+ *
+ * @param newAlignFrame
+ * containing a new alignment to be shown
+ * @param complement
+ * cdna/protein complement alignment to show in the other split half
+ * @return the protein alignment in the split frame
+ */
+ protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
+ AlignmentI complement)
+ {
+ /*
+ * Make a new frame with a copy of the alignment we are adding to. If this
+ * is protein, the mappings to cDNA will be registered with
+ * StructureSelectionManager as a side-effect.
+ */
+ AlignFrame copyMe = new AlignFrame(complement, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ copyMe.setTitle(getAlignPanel().alignFrame.getTitle());
+
+ AlignmentI al = newAlignFrame.viewport.getAlignment();
+ final AlignFrame proteinFrame = al.isNucleotide() ? copyMe
+ : newAlignFrame;
+ final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame : copyMe;
+ cdnaFrame.setVisible(true);
+ proteinFrame.setVisible(true);
+ String linkedTitle = MessageManager
+ .getString("label.linked_view_title");
+
+ /*
+ * Open in split pane. DNA sequence above, protein below.
+ */
+ JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+ Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
+
+ return proteinFrame.viewport.getAlignment();
+ }
+
+ public AnnotationColumnChooser getAnnotationColumnSelectionState()
+ {
+ return annotationColumnSelectionState;
+ }
+
+ public void setAnnotationColumnSelectionState(
+ AnnotationColumnChooser currentAnnotationColumnSelectionState)
+ {
+ this.annotationColumnSelectionState = currentAnnotationColumnSelectionState;
+ }
+
+ @Override
+ public void setIdWidth(int i)
+ {
+ super.setIdWidth(i);
+ AlignmentPanel ap = getAlignPanel();
+ if (ap != null)
+ {
+ // modify GUI elements to reflect geometry change
+ Dimension idw = ap.getIdPanel().getIdCanvas().getPreferredSize();
+ idw.width = i;
+ ap.getIdPanel().getIdCanvas().setPreferredSize(idw);
+ }
+ }
+
+ public Rectangle getExplodedGeometry()
+ {
+ return explodedGeometry;
+ }
+
+ public void setExplodedGeometry(Rectangle explodedPosition)
+ {
+ this.explodedGeometry = explodedPosition;
+ }
+
+ public boolean isGatherViewsHere()
+ {
+ return gatherViewsHere;
+ }
+
+ public void setGatherViewsHere(boolean gatherViewsHere)
+ {
+ this.gatherViewsHere = gatherViewsHere;
+ }
+
+ /**
+ * If this viewport has a (Protein/cDNA) complement, then scroll the
+ * complementary alignment to match this one.
+ */
+ public void scrollComplementaryAlignment()
+ {
+ /*
+ * Populate a SearchResults object with the mapped location to scroll to. If
+ * there is no complement, or it is not following highlights, or no mapping
+ * is found, the result will be empty.
+ */
+ SearchResultsI sr = new SearchResults();
+ int verticalOffset = findComplementScrollTarget(sr);
+ if (!sr.isEmpty())
+ {
+ // TODO would like next line without cast but needs more refactoring...
+ final AlignmentPanel complementPanel = ((AlignViewport) getCodingComplement())
+ .getAlignPanel();
+ complementPanel.setToScrollComplementPanel(false);
+ complementPanel.scrollToCentre(sr, verticalOffset);
+ complementPanel.setToScrollComplementPanel(true);
+ }
+ }
+
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ if (!af.isClosed())