* - a group defined on sequences in the alignment held by the view
*/
void addSequenceGroup(SequenceGroup sequenceGroup);
+
+ /**
+ * Creates an empty Conservation annotation and adds it to the alignment
+ */
+ void initConservation();
+
+ /**
+ * Creates an empty Quality annotation and adds it to the alignment
+ */
+ void initQuality();
+
+ /**
+ * Creates an empty Consensus annotation and adds it to the alignment
+ */
+ void initConsensus();
+
+ /**
+ * Creates an empty Occupancy annotation and adds it to the alignment
+ */
+ void initOccupancy();
+
+ /**
+ * Creates an empty RNA Structure annotation and adds it to the alignment
+ */
+ void initRNAStructure();
}
}
}
+ /**
+ * Answers a (possibly empty) iterable list of those annotations in the supplied
+ * list whose reference sequence, calcId or label matches the supplied
+ * parameters. Null parameter values are ignored.
+ *
+ * @param list
+ * @param seq
+ * @param calcId
+ * @param label
+ * @return
+ */
public static Iterable<AlignmentAnnotation> findAnnotations(
Iterable<AlignmentAnnotation> list, SequenceI seq, String calcId,
String label)
{
-
- ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
+ List<AlignmentAnnotation> aa = new ArrayList<>();
for (AlignmentAnnotation ann : list)
{
- if ((calcId == null || (ann.getCalcId() != null
- && ann.getCalcId().equals(calcId)))
- && (seq == null || (ann.sequenceRef != null
- && ann.sequenceRef == seq))
- && (label == null
- || (ann.label != null && ann.label.equals(label))))
+ if ((calcId == null || calcId.equals(ann.getCalcId()))
+ && (seq == null || seq == ann.sequenceRef)
+ && (label == null || label.equals(ann.label)))
{
aa.add(ann);
}
return false;
}
+ /**
+ * Returns a (possibly empty) iterable set of annotations in the given list
+ * whose calcId matches the given value (which may not be null)
+ *
+ * @param list
+ * @param calcId
+ * @return
+ */
public static Iterable<AlignmentAnnotation> findAnnotation(
List<AlignmentAnnotation> list, String calcId)
{
scaleLeft.setVisible(av.getWrapAlignment());
scaleRight.setVisible(av.getWrapAlignment());
annotationPanelMenuItem.setState(av.isShowAnnotation());
+
/*
* Show/hide annotations only enabled if annotation panel is shown
*/
showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
showSequenceLogo.setSelected(av.isShowSequenceLogo());
normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
+ buildAutoAnnotationMenu(av);
ColourMenuHelper.setColourSelected(colourMenu,
av.getGlobalColourScheme());
}
/**
+ * Adds menu items for the Autocalculated Annotation sub-menu
+ *
+ * @param av
+ */
+ void buildAutoAnnotationMenu(AlignViewport av)
+ {
+ autoAnnMenu.removeAll();
+ autoAnnMenu.add(showAutoFirst);
+ autoAnnMenu.add(showAutoLast);
+ autoAnnMenu.addSeparator();
+ autoAnnMenu.add(applyAutoAnnotationSettings);
+ autoAnnMenu.add(showConsensusHistogram);
+ autoAnnMenu.add(showSequenceLogo);
+ autoAnnMenu.add(normaliseSequenceLogo);
+ autoAnnMenu.addSeparator();
+
+ /*
+ * add options to reinstate any deleted auto-calculated annotations
+ */
+ boolean hasConservation = false;
+ boolean hasQuality = false;
+ boolean hasConsensus = false;
+ boolean hasOccupancy = false;
+ boolean hasRnaStruct = false;
+ AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+ if (anns == null)
+ {
+ return;
+ }
+ for (int i = 0; i < anns.length; i++)
+ {
+ if (anns[i].autoCalculated)
+ {
+ // TODO JAL-3485 should let these strings be constants instead
+ if ("Conservation".equals(anns[i].label))
+ {
+ hasConservation = true;
+ }
+ else if ("Quality".equals(anns[i].label))
+ {
+ hasQuality = true;
+ }
+ else if ("Consensus".equals(anns[i].label))
+ {
+ hasConsensus = true;
+ }
+ else if ("Occupancy".equals(anns[i].label))
+ {
+ hasOccupancy = true;
+ }
+ else if ("StrucConsensus".equals(anns[i].label))
+ {
+ hasRnaStruct = true;
+ }
+ }
+ }
+ boolean added = false;
+
+ /*
+ * a shareable action to refresh stuff; NB action listeners
+ * get run in reverse order to that in which they are added!
+ */
+ ActionListener refresher = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ alignPanel.adjustAnnotationHeight();
+ av.alignmentChanged(alignPanel);
+ buildAutoAnnotationMenu(av);
+ }
+ };
+
+ if (!av.isNucleotide())
+ {
+ if (!hasConservation)
+ {
+ JMenuItem mi = new JMenuItem("Conservation");
+ mi.addActionListener(refresher);
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.initConservation();
+ }
+ });
+ autoAnnMenu.add(mi);
+ added = true;
+ }
+ if (!hasQuality)
+ {
+ JMenuItem mi = new JMenuItem("Quality");
+ mi.addActionListener(refresher);
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.initQuality();
+ }
+ });
+ autoAnnMenu.add(mi);
+ added = true;
+ }
+ }
+ if (!hasConsensus)
+ {
+ JMenuItem mi = new JMenuItem("Consensus");
+ mi.addActionListener(refresher);
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.initConsensus();
+ }
+ });
+ autoAnnMenu.add(mi);
+ added = true;
+ }
+ if (!hasOccupancy)
+ {
+ JMenuItem mi = new JMenuItem("Occupancy");
+ mi.addActionListener(refresher);
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.initOccupancy();
+ }
+ });
+ autoAnnMenu.add(mi);
+ added = true;
+ }
+ if (!hasRnaStruct && av.isNucleotide()
+ && av.getAlignment().hasRNAStructure())
+ {
+ JMenuItem mi = new JMenuItem("Structure Consensus");
+ mi.addActionListener(refresher);
+ mi.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ av.initRNAStructure();
+ }
+ });
+ autoAnnMenu.add(mi);
+ added = true;
+ }
+
+ if (added)
+ {
+ autoAnnMenu.addSeparator();
+ }
+ autoAnnMenu.add(showGroupConservation);
+ autoAnnMenu.add(showGroupConsensus);
+ }
+
+ /**
* Set the enabled state of the 'Run Groovy' option in the Calculate menu
*
* @param b
{
aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
-
+ ap.alignFrame.setMenusForViewport();
ap.refresh(fullRepaint);
}
private SplitContainerI splitFrame;
+ protected JMenu autoAnnMenu;
+
+ protected JRadioButtonMenuItem showAutoFirst;
+
+ protected JRadioButtonMenuItem showAutoLast;
+
public GAlignFrame()
{
try
});
ButtonGroup buttonGroup = new ButtonGroup();
- final JRadioButtonMenuItem showAutoFirst = new JRadioButtonMenuItem(
+ showAutoFirst = new JRadioButtonMenuItem(
MessageManager.getString("label.show_first"));
- final JRadioButtonMenuItem showAutoLast = new JRadioButtonMenuItem(
+ showAutoLast = new JRadioButtonMenuItem(
MessageManager.getString("label.show_last"));
buttonGroup.add(showAutoFirst);
buttonGroup.add(showAutoLast);
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
- JMenu autoAnnMenu = new JMenu(
+ autoAnnMenu = new JMenu(
MessageManager.getString("label.autocalculated_annotation"));
JMenu exportImageMenu = new JMenu(
annotationsMenu.add(sortAnnBySequence);
annotationsMenu.add(sortAnnByLabel);
annotationsMenu.addSeparator();
- autoAnnMenu.add(showAutoFirst);
- autoAnnMenu.add(showAutoLast);
- autoAnnMenu.addSeparator();
- autoAnnMenu.add(applyAutoAnnotationSettings);
- autoAnnMenu.add(showConsensusHistogram);
- autoAnnMenu.add(showSequenceLogo);
- autoAnnMenu.add(normaliseSequenceLogo);
- autoAnnMenu.addSeparator();
- autoAnnMenu.add(showGroupConservation);
- autoAnnMenu.add(showGroupConsensus);
- annotationsMenu.add(autoAnnMenu);
+ annotationsMenu.add(autoAnnMenu); // autoAnnMenu is populated later
sort.add(sortIDMenuItem);
sort.add(sortLengthMenuItem);
{
if (!alignment.isNucleotide())
{
- initConservation();
- initQuality();
+ if (showConservation && conservation == null)
+ {
+ initConservation();
+ }
+ if (showQuality && quality == null)
+ {
+ initQuality();
+ }
}
else
{
- initRNAStructure();
+ if (showConsensus && alignment.hasRNAStructure()
+ && strucConsensus == null)
+ {
+ initRNAStructure();
+ }
+ }
+ if (showConsensus)
+ {
+ initConsensus();
+ }
+ if (showOccupancy)
+ {
+ initOccupancy();
}
- consensus = new AlignmentAnnotation("Consensus",
- MessageManager.getString("label.consensus_descr"),
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- initConsensus(consensus);
- initGapCounts();
initComplementConsensus();
}
return false;
}
+ @Override
+ public void initConsensus()
+ {
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ initConsensus(consensus);
+ }
+
private void initConsensus(AlignmentAnnotation aa)
{
- aa.hasText = true;
- aa.autoCalculated = true;
+ consensus = new AlignmentAnnotation("Consensus",
+ MessageManager.getString("label.consensus_descr"),
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
if (showConsensus)
{
- alignment.addAnnotation(aa);
+ alignment.addAnnotation(consensus);
}
}
- // these should be extracted from the view model - style and settings for
- // derived annotation
- private void initGapCounts()
+ @Override
+ public void initOccupancy()
{
- if (showOccupancy)
- {
- gapcounts = new AlignmentAnnotation("Occupancy",
- MessageManager.getString("label.occupancy_descr"),
- new Annotation[1], 0f, alignment.getHeight(),
- AlignmentAnnotation.BAR_GRAPH);
- gapcounts.hasText = true;
- gapcounts.autoCalculated = true;
- gapcounts.scaleColLabel = true;
- gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
+ gapcounts = new AlignmentAnnotation("Occupancy",
+ MessageManager.getString("label.occupancy_descr"),
+ new Annotation[1], 0f, alignment.getHeight(),
+ AlignmentAnnotation.BAR_GRAPH);
+ gapcounts.hasText = true;
+ gapcounts.autoCalculated = true;
+ gapcounts.scaleColLabel = true;
+ gapcounts.graph = AlignmentAnnotation.BAR_GRAPH;
- alignment.addAnnotation(gapcounts);
- }
+ alignment.addAnnotation(gapcounts);
}
- private void initConservation()
+ @Override
+ public void initConservation()
{
- if (showConservation)
- {
- if (conservation == null)
- {
- conservation = new AlignmentAnnotation("Conservation",
- MessageManager.formatMessage("label.conservation_descr",
- getConsPercGaps()),
- new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
- conservation.hasText = true;
- conservation.autoCalculated = true;
- alignment.addAnnotation(conservation);
- }
- }
+ conservation = new AlignmentAnnotation("Conservation",
+ MessageManager.formatMessage("label.conservation_descr",
+ getConsPercGaps()),
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ conservation.hasText = true;
+ conservation.autoCalculated = true;
+ alignment.addAnnotation(conservation);
}
- private void initQuality()
+ @Override
+ public void initQuality()
{
- if (showQuality)
- {
- if (quality == null)
- {
- quality = new AlignmentAnnotation("Quality",
- MessageManager.getString("label.quality_descr"),
- new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
- quality.hasText = true;
- quality.autoCalculated = true;
- alignment.addAnnotation(quality);
- }
- }
+ quality = new AlignmentAnnotation("Quality",
+ MessageManager.getString("label.quality_descr"),
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ quality.hasText = true;
+ quality.autoCalculated = true;
+ alignment.addAnnotation(quality);
}
- private void initRNAStructure()
+ @Override
+ public void initRNAStructure()
{
- if (alignment.hasRNAStructure() && strucConsensus == null)
- {
- strucConsensus = new AlignmentAnnotation("StrucConsensus",
- MessageManager.getString("label.strucconsensus_descr"),
- new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
- strucConsensus.hasText = true;
- strucConsensus.autoCalculated = true;
-
- if (showConsensus)
- {
- alignment.addAnnotation(strucConsensus);
- }
- }
+ strucConsensus = new AlignmentAnnotation("StrucConsensus",
+ MessageManager.getString("label.strucconsensus_descr"),
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ strucConsensus.hasText = true;
+ strucConsensus.autoCalculated = true;
+ alignment.addAnnotation(strucConsensus);
}
/*
git://source.jalview.org / jalview.git / commitdiff