*/
package jalview.viewmodel.seqfeatures;
-import jalview.api.AlignViewportI;
-import jalview.api.FeatureColourI;
-import jalview.api.FeaturesDisplayedI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeatures;
-import jalview.renderer.seqfeatures.FeatureRenderer;
-import jalview.schemes.FeatureColour;
-import jalview.util.ColorUtils;
-import jalview.util.matcher.KeyedMatcherSetI;
-
import java.awt.Color;
import java.beans.PropertyChangeListener;
import java.beans.PropertyChangeSupport;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
+import jalview.api.AlignViewportI;
+import jalview.api.FeatureColourI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SearchResultMatchI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
+import jalview.util.Platform;
+
public abstract class FeatureRendererModel
implements jalview.api.FeatureRenderer
{
/*
- * column indices of fields in Feature Settings table
- * todo: transfer valuers as data beans instead of Object[][]
+ * a data bean to hold one row of feature settings from the gui
*/
- public static final int TYPE_COLUMN = 0;
+ public static class FeatureSettingsBean
+ {
+ public final String featureType;
- public static final int COLOUR_COLUMN = 1;
+ public final FeatureColourI featureColour;
- public static final int FILTER_COLUMN = 2;
+ public final FeatureMatcherSetI filter;
- public static final int SHOW_COLUMN = 3;
+ public final Boolean show;
+
+ public FeatureSettingsBean(String type, FeatureColourI colour,
+ FeatureMatcherSetI theFilter, Boolean isShown)
+ {
+ featureType = type;
+ featureColour = colour;
+ filter = theFilter;
+ show = isShown;
+ }
+ }
/*
* global transparency for feature
/*
* filters for each feature type
*/
- protected Map<String, KeyedMatcherSetI> featureFilters = new HashMap<>();
+ protected Map<String, FeatureMatcherSetI> featureFilters = new HashMap<>();
protected String[] renderOrder;
Map<String, Float> featureOrder = null;
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
-
protected AlignViewportI av;
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+
@Override
public AlignViewportI getViewport()
{
{
firing = Boolean.TRUE;
findAllFeatures(true); // add all new features as visible
- changeSupport.firePropertyChange("changeSupport", null, null);
+ notifyFeaturesChanged();
firing = Boolean.FALSE;
}
}
}
@Override
+ public void notifyFeaturesChanged()
+ {
+ changeSupport.firePropertyChange("changeSupport", null, null);
+ }
+
+ @Override
public List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column)
{
/*
visibleTypes);
/*
- * include features unless their feature group is not displayed, or
- * they are hidden (have no colour) based on a filter or colour threshold
+ * include features unless they are hidden (have no colour), based on
+ * feature group visibility, or a filter or colour threshold
*/
for (SequenceFeature sf : features)
{
- if (!featureGroupNotShown(sf) && getColour(sf) != null)
+ if (getColour(sf) != null)
{
result.add(sf);
}
* @param type
* @return
*/
- protected boolean showFeatureOfType(String type)
+ public boolean showFeatureOfType(String type)
{
return type == null ? false : (av.getFeaturesDisplayed() == null ? true
: av.getFeaturesDisplayed().isVisible(type));
{
featureOrder = new Hashtable<>();
}
- featureOrder.put(type, new Float(position));
+ featureOrder.put(type, Float.valueOf(position));
return position;
}
* Replace current ordering with new ordering
*
* @param data
- * { String(Type), Colour(Type), Boolean(Displayed) }
+ * an array of { Type, Colour, Filter, Boolean }
* @return true if any visible features have been reordered, else false
*/
- public boolean setFeaturePriority(Object[][] data)
+ public boolean setFeaturePriority(FeatureSettingsBean[] data)
{
return setFeaturePriority(data, true);
}
/**
- * Sets the priority order for features, with the highest priority (displayed
- * on top) at the start of the data array
+ * Sets the priority order for features, with the highest priority (displayed on
+ * top) at the start of the data array
*
* @param data
- * { String(Type), Colour(Type), Boolean(Displayed) }
+ * an array of { Type, Colour, Filter, Boolean }
* @param visibleNew
* when true current featureDisplay list will be cleared
- * @return true if any visible features have been reordered or recoloured,
- * else false (i.e. no need to repaint)
+ * @return true if any visible features have been reordered or recoloured, else
+ * false (i.e. no need to repaint)
*/
- public boolean setFeaturePriority(Object[][] data, boolean visibleNew)
+ public boolean setFeaturePriority(FeatureSettingsBean[] data,
+ boolean visibleNew)
{
/*
* note visible feature ordering and colours before update
{
for (int i = 0; i < data.length; i++)
{
- String type = data[i][TYPE_COLUMN].toString();
- setColour(type, (FeatureColourI) data[i][COLOUR_COLUMN]);
- if (((Boolean) data[i][SHOW_COLUMN]).booleanValue())
+ String type = data[i].featureType;
+ setColour(type, data[i].featureColour);
+ if (data[i].show)
{
av_featuresdisplayed.setVisible(type);
}
}
if (newGroupsVisible)
{
- featureGroups.put(group, new Boolean(true));
+ featureGroups.put(group, Boolean.valueOf(true));
return true;
}
return false;
@Override
public void setGroupVisibility(String group, boolean visible)
{
- featureGroups.put(group, new Boolean(visible));
+ featureGroups.put(group, Boolean.valueOf(visible));
}
@Override
for (String gst : toset)
{
Boolean st = featureGroups.get(gst);
- featureGroups.put(gst, new Boolean(visible));
+ featureGroups.put(gst, Boolean.valueOf(visible));
if (st != null)
{
rdrw = rdrw || (visible != st.booleanValue());
* @param sequenceFeature
* @return
*/
- protected boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
+ public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
{
return featureGroups != null
&& sequenceFeature.featureGroup != null
*/
@Override
public List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
- int resNo)
+ int fromResNo, int toResNo)
{
List<SequenceFeature> result = new ArrayList<>();
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
* displayed, and feature group is null or the empty string
* or marked for display
*/
- Set<String> visibleFeatures = getFeaturesDisplayed()
- .getVisibleFeatures();
+ List<String> visibleFeatures = getDisplayedFeatureTypes();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
List<SequenceFeature> features = sequence.getFeatures().findFeatures(
- resNo, resNo, visibleTypes);
+ fromResNo, toResNo, visibleTypes);
for (SequenceFeature sf : features)
{
}
/**
- * Removes from the list of features any that duplicate the location of a
- * feature of the same type. Should be used only for features of the same,
- * simple, feature colour (which normally implies the same feature type). Does
- * not check visibility settings for feature type or feature group.
+ * Removes from the list of features any whose group is not shown, or that are
+ * visible and duplicate the location of a visible feature of the same type.
+ * Should be used only for features of the same, simple, feature colour (which
+ * normally implies the same feature type). No filtering is done if
+ * transparency, or any feature filters, are in force.
*
* @param features
*/
public void filterFeaturesForDisplay(List<SequenceFeature> features)
{
- if (features.isEmpty())
+ /*
+ * fudge: JalviewJS's IntervalStore lacks the sort method called :-(
+ */
+ if (Platform.isJS())
{
return;
}
+
+ /*
+ * don't remove 'redundant' features if
+ * - transparency is applied (feature count affects depth of feature colour)
+ * - filters are applied (not all features may be displayable)
+ */
+ if (features.isEmpty() || transparency != 1f
+ || !featureFilters.isEmpty())
+ {
+ return;
+ }
+
SequenceFeatures.sortFeatures(features, true);
SequenceFeature lastFeature = null;
while (it.hasNext())
{
SequenceFeature sf = it.next();
+ if (featureGroupNotShown(sf))
+ {
+ it.remove();
+ continue;
+ }
/*
* a feature is redundant for rendering purposes if it has the
* (checking type and isContactFeature as a fail-safe here, although
* currently they are guaranteed to match in this context)
*/
- if (lastFeature != null && sf.getBegin() == lastFeature.getBegin()
+ if (lastFeature != null
+ && sf.getBegin() == lastFeature.getBegin()
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
}
@Override
- public Map<String, KeyedMatcherSetI> getFeatureFilters()
+ public Map<String, FeatureMatcherSetI> getFeatureFilters()
{
- return new HashMap<>(featureFilters);
+ return featureFilters;
}
@Override
- public void setFeatureFilters(Map<String, KeyedMatcherSetI> filters)
+ public void setFeatureFilters(Map<String, FeatureMatcherSetI> filters)
{
featureFilters = filters;
}
@Override
- public KeyedMatcherSetI getFeatureFilter(String featureType)
+ public FeatureMatcherSetI getFeatureFilter(String featureType)
{
return featureFilters.get(featureType);
}
@Override
- public void setFeatureFilter(String featureType, KeyedMatcherSetI filter)
+ public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
{
if (filter == null || filter.isEmpty())
{
/**
* Answers the colour for the feature, or null if the feature is excluded by
- * feature type or group visibility, by filters, or by colour threshold
- * settings
+ * feature group visibility, by filters, or by colour threshold settings. This
+ * method does not take feature type visibility into account.
*
* @param sf
* @param fc
public Color getColor(SequenceFeature sf, FeatureColourI fc)
{
/*
- * is the feature type displayed?
- */
- if (!showFeatureOfType(sf.getType()))
- {
- return null;
- }
-
- /*
* is the feature group displayed?
*/
if (featureGroupNotShown(sf))
*/
protected boolean featureMatchesFilters(SequenceFeature sf)
{
- KeyedMatcherSetI filter = featureFilters.get(sf.getType());
- // TODO temporary fudge for Score and Label
- return filter == null ? true
- : filter.matches(
- key -> "Label".equals(key[0]) ? sf.getDescription()
- : ("Score".equals(key[0])
- ? String.valueOf(sf.getScore())
- : sf.getValueAsString(key)));
+ FeatureMatcherSetI filter = featureFilters.get(sf.getType());
+ return filter == null ? true : filter.matches(sf);
+ }
+
+ /**
+ * Answers true unless the specified group is set to hidden. Defaults to true
+ * if group visibility is not set.
+ *
+ * @param group
+ * @return
+ */
+ public boolean isGroupVisible(String group)
+ {
+ if (!featureGroups.containsKey(group))
+ {
+ return true;
+ }
+ return featureGroups.get(group);
+ }
+
+ /**
+ * Orders features in render precedence (last in order is last to render, so
+ * displayed on top of other features)
+ *
+ * @param order
+ */
+ public void orderFeatures(Comparator<String> order)
+ {
+ Arrays.sort(renderOrder, order);
}
+ @Override
+ public MappedFeatures findComplementFeaturesAtResidue(
+ final SequenceI sequence, final int pos)
+ {
+ SequenceI ds = sequence.getDatasetSequence();
+ if (ds == null)
+ {
+ ds = sequence;
+ }
+ final char residue = ds.getCharAt(pos - ds.getStart());
+
+ List<SequenceFeature> found = new ArrayList<>();
+ List<AlignedCodonFrame> mappings = this.av.getAlignment()
+ .getCodonFrame(sequence);
+
+ /*
+ * fudge: if no mapping found, check the complementary alignment
+ * todo: only store in one place? StructureSelectionManager?
+ */
+ if (mappings.isEmpty())
+ {
+ mappings = this.av.getCodingComplement().getAlignment()
+ .getCodonFrame(sequence);
+ }
+
+ /*
+ * todo: direct lookup of CDS for peptide and vice-versa; for now,
+ * have to search through an unordered list of mappings for a candidate
+ */
+ SequenceToSequenceMapping mapping = null;
+ SequenceI mapFrom = null;
+
+ for (AlignedCodonFrame acf : mappings)
+ {
+ mapping = acf.getCoveringCodonMapping(ds);
+ if (mapping == null)
+ {
+ continue;
+ }
+ SearchResultsI sr = new SearchResults();
+ mapping.markMappedRegion(ds, pos, sr);
+ for (SearchResultMatchI match : sr.getResults())
+ {
+ int fromRes = match.getStart();
+ int toRes = match.getEnd();
+ mapFrom = match.getSequence();
+ List<SequenceFeature> fs = findFeaturesAtResidue(
+ mapFrom, fromRes, toRes);
+ for (SequenceFeature sf : fs)
+ {
+ if (!found.contains(sf))
+ {
+ found.add(sf);
+ }
+ }
+ }
+
+ /*
+ * just take the first mapped features we find
+ */
+ if (!found.isEmpty())
+ {
+ break;
+ }
+ }
+ if (found.isEmpty())
+ {
+ return null;
+ }
+
+ /*
+ * sort by renderorder (inefficiently but ok for small scale);
+ * NB this sorts 'on top' feature to end, for rendering
+ */
+ List<SequenceFeature> result = new ArrayList<>();
+ final int toAdd = found.size();
+ int added = 0;
+ for (String type : renderOrder)
+ {
+ for (SequenceFeature sf : found)
+ {
+ if (type.equals(sf.getType()))
+ {
+ result.add(sf);
+ added++;
+ }
+ if (added == toAdd)
+ {
+ break;
+ }
+ }
+ }
+
+ return new MappedFeatures(mapping.getMapping(), mapFrom, pos, residue, result);
+ }
+
+ @Override
+ public boolean isVisible(SequenceFeature feature)
+ {
+ if (feature == null)
+ {
+ return false;
+ }
+ if (getFeaturesDisplayed() == null
+ || !getFeaturesDisplayed().isVisible(feature.getType()))
+ {
+ return false;
+ }
+ if (featureGroupNotShown(feature))
+ {
+ return false;
+ }
+ FeatureColourI fc = featureColours.get(feature.getType());
+ if (fc != null && fc.isOutwithThreshold(feature))
+ {
+ return false;
+ }
+ if (!featureMatchesFilters(feature))
+ {
+ return false;
+ }
+ return true;
+ }
}
git://source.jalview.org / jalview.git / blobdiff