+
+ /**
+ * Store selected annotation sort order for the view and repaint.
+ */
+ @Override
+ protected void sortAnnotations_actionPerformed()
+ {
+ this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
+ this.alignPanel.av
+ .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
+ alignPanel.paintAlignment(true);
+ }
+
+ /**
+ *
+ * @return alignment panels in this alignment frame
+ */
+ public List<? extends AlignmentViewPanel> getAlignPanels()
+ {
+ return alignPanels == null ? Arrays.asList(alignPanel)
+ : alignPanels;
+ }
+
+ /**
+ * Open a new alignment window, with the cDNA associated with this (protein)
+ * alignment, aligned as is the protein.
+ */
+ protected void viewAsCdna_actionPerformed()
+ {
+ // TODO no longer a menu action - refactor as required
+ final AlignmentI alignment = getViewport().getAlignment();
+ Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+ if (mappings == null)
+ {
+ return;
+ }
+ List<SequenceI> cdnaSeqs = new ArrayList<SequenceI>();
+ for (SequenceI aaSeq : alignment.getSequences()) {
+ for (AlignedCodonFrame acf : mappings) {
+ SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
+ if (dnaSeq != null)
+ {
+ /*
+ * There is a cDNA mapping for this protein sequence - add to new
+ * alignment. It will share the same dataset sequence as other mapped
+ * cDNA (no new mappings need to be created).
+ */
+ final Sequence newSeq = new Sequence(dnaSeq);
+ newSeq.setDatasetSequence(dnaSeq);
+ cdnaSeqs.add(newSeq);
+ }
+ }
+ }
+ if (cdnaSeqs.size() == 0)
+ {
+ // show a warning dialog no mapped cDNA
+ return;
+ }
+ AlignmentI cdna = new Alignment(cdnaSeqs.toArray(new SequenceI[cdnaSeqs
+ .size()]));
+ AlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ cdna.alignAs(alignment);
+ String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
+ + this.title;
+ Desktop.addInternalFrame(alignFrame, newtitle,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ /**
+ * Set visibility of dna/protein complement view (available when shown in a
+ * split frame).
+ *
+ * @param show
+ */
+ @Override
+ protected void showComplement_actionPerformed(boolean show)
+ {
+ SplitContainerI sf = getSplitViewContainer();
+ if (sf != null) {
+ sf.setComplementVisible(this, show);
+ }
+ }
+
+ public class ExportData
+ {
+ private AlignmentI alignment;
+
+ private String[] omitHidden;
+
+ private int[] startEnd;
+
+ private AlignExportSettings settings;
+
+ public ExportData(AlignmentI align, String[] ommit, int[] startEnd,
+ AlignExportSettings settings)
+ {
+ this.alignment = align;
+ this.omitHidden = ommit;
+ this.startEnd = startEnd;
+ this.settings = settings;
+ }
+
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ public void setAlignment(AlignmentI alignment)
+ {
+ this.alignment = alignment;
+ }
+
+ public String[] getOmitHidden()
+ {
+ return omitHidden;
+ }
+
+ public void setOmitHidden(String[] omitHidden)
+ {
+ this.omitHidden = omitHidden;
+ }
+
+ public int[] getStartEndPostions()
+ {
+ return startEnd;
+ }
+
+ public void setStartEndPostions(int[] startEnd)
+ {
+ this.startEnd = startEnd;
+ }
+
+ public AlignExportSettings getSettings()
+ {
+ return settings;
+ }
+
+ public void setSettings(AlignExportSettings settings)
+ {
+ this.settings = settings;
+ }
+ }
+