/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.viewmodel.seqfeatures;
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.Iterator;
import java.util.List;
import java.util.Map;
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
{
/*
* a data bean to hold one row of feature settings from the gui
*/
public static class FeatureSettingsBean
{
public final String featureType;
public final FeatureColourI featureColour;
public final FeatureMatcherSetI filter;
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
*/
protected float transparency = 1.0f;
/*
* colour scheme for each feature type
*/
protected Map featureColours = new ConcurrentHashMap<>();
/*
* visibility flag for each feature group
*/
protected Map featureGroups = new ConcurrentHashMap<>();
/*
* filters for each feature type
*/
protected Map featureFilters = new HashMap<>();
protected String[] renderOrder;
Map featureOrder = null;
protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
this);
protected AlignViewportI av;
@Override
public AlignViewportI getViewport()
{
return av;
}
public FeatureRendererSettings getSettings()
{
return new FeatureRendererSettings(this);
}
public void transferSettings(FeatureRendererSettings fr)
{
this.renderOrder = fr.renderOrder;
this.featureGroups = fr.featureGroups;
this.featureColours = fr.featureColours;
this.transparency = fr.transparency;
this.featureOrder = fr.featureOrder;
}
/**
* update from another feature renderer
*
* @param fr
* settings to copy
*/
public void transferSettings(jalview.api.FeatureRenderer _fr)
{
FeatureRenderer fr = (FeatureRenderer) _fr;
FeatureRendererSettings frs = new FeatureRendererSettings(fr);
this.renderOrder = frs.renderOrder;
this.featureGroups = frs.featureGroups;
this.featureColours = frs.featureColours;
this.featureFilters = frs.featureFilters;
this.transparency = frs.transparency;
this.featureOrder = frs.featureOrder;
if (av != null && av != fr.getViewport())
{
// copy over the displayed feature settings
if (_fr.getFeaturesDisplayed() != null)
{
FeaturesDisplayedI fd = getFeaturesDisplayed();
if (fd == null)
{
setFeaturesDisplayedFrom(_fr.getFeaturesDisplayed());
}
else
{
synchronized (fd)
{
fd.clear();
for (String type : _fr.getFeaturesDisplayed()
.getVisibleFeatures())
{
fd.setVisible(type);
}
}
}
}
}
}
public void setFeaturesDisplayedFrom(FeaturesDisplayedI featuresDisplayed)
{
av.setFeaturesDisplayed(new FeaturesDisplayed(featuresDisplayed));
}
@Override
public void setVisible(String featureType)
{
FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
if (fdi == null)
{
av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
}
if (!fdi.isRegistered(featureType))
{
pushFeatureType(Arrays.asList(new String[] { featureType }));
}
fdi.setVisible(featureType);
}
@Override
public void setAllVisible(List featureTypes)
{
FeaturesDisplayedI fdi = av.getFeaturesDisplayed();
if (fdi == null)
{
av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
}
List nft = new ArrayList<>();
for (String featureType : featureTypes)
{
if (!fdi.isRegistered(featureType))
{
nft.add(featureType);
}
}
if (nft.size() > 0)
{
pushFeatureType(nft);
}
fdi.setAllVisible(featureTypes);
}
/**
* push a set of new types onto the render order stack. Note - this is a
* direct mechanism rather than the one employed in updateRenderOrder
*
* @param types
*/
private void pushFeatureType(List types)
{
int ts = types.size();
String neworder[] = new String[(renderOrder == null ? 0
: renderOrder.length) + ts];
types.toArray(neworder);
if (renderOrder != null)
{
System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
}
renderOrder = neworder;
}
protected Map minmax = new Hashtable<>();
public Map getMinMax()
{
return minmax;
}
/**
* normalise a score against the max/min bounds for the feature type.
*
* @param sequenceFeature
* @return byte[] { signed, normalised signed (-127 to 127) or unsigned
* (0-255) value.
*/
protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
{
float[] mm = minmax.get(sequenceFeature.type)[0];
final byte[] r = new byte[] { 0, (byte) 255 };
if (mm != null)
{
if (r[0] != 0 || mm[0] < 0.0)
{
r[0] = 1;
r[1] = (byte) ((int) 128.0
+ 127.0 * (sequenceFeature.score / mm[1]));
}
else
{
r[1] = (byte) ((int) 255.0 * (sequenceFeature.score / mm[1]));
}
}
return r;
}
boolean newFeatureAdded = false;
boolean findingFeatures = false;
protected boolean updateFeatures()
{
if (av.getFeaturesDisplayed() == null || renderOrder == null
|| newFeatureAdded)
{
findAllFeatures();
if (av.getFeaturesDisplayed().getVisibleFeatureCount() < 1)
{
return false;
}
}
// TODO: decide if we should check for the visible feature count first
return true;
}
/**
* search the alignment for all new features, give them a colour and display
* them. Then fires a PropertyChangeEvent on the changeSupport object.
*
*/
protected void findAllFeatures()
{
synchronized (firing)
{
if (firing.equals(Boolean.FALSE))
{
firing = Boolean.TRUE;
findAllFeatures(true); // add all new features as visible
changeSupport.firePropertyChange("changeSupport", null, null);
firing = Boolean.FALSE;
}
}
}
@Override
public List findFeaturesAtColumn(SequenceI sequence, int column)
{
/*
* include features at the position provided their feature type is
* displayed, and feature group is null or marked for display
*/
List result = new ArrayList<>();
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
{
return result;
}
Set visibleFeatures = getFeaturesDisplayed()
.getVisibleFeatures();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
List features = sequence.findFeatures(column, column,
visibleTypes);
/*
* 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 (getColour(sf) != null)
{
result.add(sf);
}
}
return result;
}
/**
* Searches alignment for all features and updates colours
*
* @param newMadeVisible
* if true newly added feature types will be rendered immediately
* TODO: check to see if this method should actually be proxied so
* repaint events can be propagated by the renderer code
*/
@Override
public synchronized void findAllFeatures(boolean newMadeVisible)
{
newFeatureAdded = false;
if (findingFeatures)
{
newFeatureAdded = true;
return;
}
findingFeatures = true;
if (av.getFeaturesDisplayed() == null)
{
av.setFeaturesDisplayed(new FeaturesDisplayed());
}
FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
Set oldfeatures = new HashSet<>();
if (renderOrder != null)
{
for (int i = 0; i < renderOrder.length; i++)
{
if (renderOrder[i] != null)
{
oldfeatures.add(renderOrder[i]);
}
}
}
AlignmentI alignment = av.getAlignment();
List allfeatures = new ArrayList<>();
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI asq = alignment.getSequenceAt(i);
for (String group : asq.getFeatures().getFeatureGroups(true))
{
boolean groupDisplayed = true;
if (group != null)
{
if (featureGroups.containsKey(group))
{
groupDisplayed = featureGroups.get(group);
}
else
{
groupDisplayed = newMadeVisible;
featureGroups.put(group, groupDisplayed);
}
}
if (groupDisplayed)
{
Set types = asq.getFeatures().getFeatureTypesForGroups(
true, group);
for (String type : types)
{
if (!allfeatures.contains(type)) // or use HashSet and no test?
{
allfeatures.add(type);
}
updateMinMax(asq, type, true); // todo: for all features?
}
}
}
}
// uncomment to add new features in alphebetical order (but JAL-2575)
// Collections.sort(allfeatures, String.CASE_INSENSITIVE_ORDER);
if (newMadeVisible)
{
for (String type : allfeatures)
{
if (!oldfeatures.contains(type))
{
featuresDisplayed.setVisible(type);
setOrder(type, 0);
}
}
}
updateRenderOrder(allfeatures);
findingFeatures = false;
}
/**
* Updates the global (alignment) min and max values for a feature type from
* the score for a sequence, if the score is not NaN. Values are stored
* separately for positional and non-positional features.
*
* @param seq
* @param featureType
* @param positional
*/
protected void updateMinMax(SequenceI seq, String featureType,
boolean positional)
{
float min = seq.getFeatures().getMinimumScore(featureType, positional);
if (Float.isNaN(min))
{
return;
}
float max = seq.getFeatures().getMaximumScore(featureType, positional);
/*
* stored values are
* { {positionalMin, positionalMax}, {nonPositionalMin, nonPositionalMax} }
*/
if (minmax == null)
{
minmax = new Hashtable<>();
}
synchronized (minmax)
{
float[][] mm = minmax.get(featureType);
int index = positional ? 0 : 1;
if (mm == null)
{
mm = new float[][] { null, null };
minmax.put(featureType, mm);
}
if (mm[index] == null)
{
mm[index] = new float[] { min, max };
}
else
{
mm[index][0] = Math.min(mm[index][0], min);
mm[index][1] = Math.max(mm[index][1], max);
}
}
}
protected Boolean firing = Boolean.FALSE;
/**
* replaces the current renderOrder with the unordered features in
* allfeatures. The ordering of any types in both renderOrder and allfeatures
* is preserved, and all new feature types are rendered on top of the existing
* types, in the order given by getOrder or the order given in allFeatures.
* Note. this operates directly on the featureOrder hash for efficiency. TODO:
* eliminate the float storage for computing/recalling the persistent ordering
* New Cability: updates min/max for colourscheme range if its dynamic
*
* @param allFeatures
*/
private void updateRenderOrder(List allFeatures)
{
List allfeatures = new ArrayList<>(allFeatures);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
boolean initOrders = (featureOrder == null);
int opos = 0;
if (oldRender != null && oldRender.length > 0)
{
for (int j = 0; j < oldRender.length; j++)
{
if (oldRender[j] != null)
{
if (initOrders)
{
setOrder(oldRender[j],
(1 - (1 + (float) j) / oldRender.length));
}
if (allfeatures.contains(oldRender[j]))
{
renderOrder[opos++] = oldRender[j]; // existing features always
// appear below new features
allfeatures.remove(oldRender[j]);
if (minmax != null)
{
float[][] mmrange = minmax.get(oldRender[j]);
if (mmrange != null)
{
FeatureColourI fc = featureColours.get(oldRender[j]);
if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
&& !fc.isColourByAttribute())
{
fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
}
}
}
}
}
}
if (allfeatures.size() == 0)
{
// no new features - leave order unchanged.
return;
}
int i = allfeatures.size() - 1;
int iSize = i;
boolean sort = false;
String[] newf = new String[allfeatures.size()];
float[] sortOrder = new float[allfeatures.size()];
for (String newfeat : allfeatures)
{
newf[i] = newfeat;
if (minmax != null)
{
// update from new features minmax if necessary
float[][] mmrange = minmax.get(newf[i]);
if (mmrange != null)
{
FeatureColourI fc = featureColours.get(newf[i]);
if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
&& !fc.isColourByAttribute())
{
fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
}
}
if (initOrders || !featureOrder.containsKey(newf[i]))
{
int denom = initOrders ? allfeatures.size() : featureOrder.size();
// new unordered feature - compute persistent ordering at head of
// existing features.
setOrder(newf[i], i / (float) denom);
}
// set order from newly found feature from persisted ordering.
sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
if (i < iSize)
{
// only sort if we need to
sort = sort || sortOrder[i] > sortOrder[i + 1];
}
i--;
}
if (iSize > 1 && sort)
{
jalview.util.QuickSort.sort(sortOrder, newf);
}
sortOrder = null;
System.arraycopy(newf, 0, renderOrder, opos, newf.length);
}
/**
* get a feature style object for the given type string. Creates a
* java.awt.Color for a featureType with no existing colourscheme.
*
* @param featureType
* @return
*/
@Override
public FeatureColourI getFeatureStyle(String featureType)
{
FeatureColourI fc = featureColours.get(featureType);
if (fc == null)
{
Color col = ColorUtils.createColourFromName(featureType);
fc = new FeatureColour(col);
featureColours.put(featureType, fc);
}
return fc;
}
@Override
public Color getColour(SequenceFeature feature)
{
FeatureColourI fc = getFeatureStyle(feature.getType());
return getColor(feature, fc);
}
/**
* Answers true if the feature type is currently selected to be displayed,
* else false
*
* @param type
* @return
*/
public boolean showFeatureOfType(String type)
{
return type == null ? false : (av.getFeaturesDisplayed() == null ? true
: av.getFeaturesDisplayed().isVisible(type));
}
@Override
public void setColour(String featureType, FeatureColourI col)
{
featureColours.put(featureType, col);
}
@Override
public void setTransparency(float value)
{
transparency = value;
}
@Override
public float getTransparency()
{
return transparency;
}
/**
* analogous to colour - store a normalized ordering for all feature types in
* this rendering context.
*
* @param type
* Feature type string
* @param position
* normalized priority - 0 means always appears on top, 1 means
* always last.
*/
public float setOrder(String type, float position)
{
if (featureOrder == null)
{
featureOrder = new Hashtable<>();
}
featureOrder.put(type, Float.valueOf(position));
return position;
}
/**
* get the global priority (0 (top) to 1 (bottom))
*
* @param type
* @return [0,1] or -1 for a type without a priority
*/
public float getOrder(String type)
{
if (featureOrder != null)
{
if (featureOrder.containsKey(type))
{
return featureOrder.get(type).floatValue();
}
}
return -1;
}
@Override
public Map getFeatureColours()
{
return featureColours;
}
/**
* Replace current ordering with new ordering
*
* @param data
* an array of { Type, Colour, Filter, Boolean }
* @return true if any visible features have been reordered, else false
*/
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
*
* @param data
* 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)
*/
public boolean setFeaturePriority(FeatureSettingsBean[] data,
boolean visibleNew)
{
/*
* note visible feature ordering and colours before update
*/
List visibleFeatures = getDisplayedFeatureTypes();
Map visibleColours = new HashMap<>(
getFeatureColours());
FeaturesDisplayedI av_featuresdisplayed = null;
if (visibleNew)
{
if ((av_featuresdisplayed = av.getFeaturesDisplayed()) != null)
{
av.getFeaturesDisplayed().clear();
}
else
{
av.setFeaturesDisplayed(
av_featuresdisplayed = new FeaturesDisplayed());
}
}
else
{
av_featuresdisplayed = av.getFeaturesDisplayed();
}
if (data == null)
{
return false;
}
// The feature table will display high priority
// features at the top, but these are the ones
// we need to render last, so invert the data
renderOrder = new String[data.length];
if (data.length > 0)
{
for (int i = 0; i < data.length; i++)
{
String type = data[i].featureType;
setColour(type, data[i].featureColour);
if (data[i].show)
{
av_featuresdisplayed.setVisible(type);
}
renderOrder[data.length - i - 1] = type;
}
}
/*
* get the new visible ordering and return true if it has changed
* order or any colour has changed
*/
List reorderedVisibleFeatures = getDisplayedFeatureTypes();
if (!visibleFeatures.equals(reorderedVisibleFeatures))
{
/*
* the list of ordered visible features has changed
*/
return true;
}
/*
* return true if any feature colour has changed
*/
for (String feature : visibleFeatures)
{
if (visibleColours.get(feature) != getFeatureStyle(feature))
{
return true;
}
}
return false;
}
/**
* @param listener
* @see java.beans.PropertyChangeSupport#addPropertyChangeListener(java.beans.PropertyChangeListener)
*/
public void addPropertyChangeListener(PropertyChangeListener listener)
{
changeSupport.addPropertyChangeListener(listener);
}
/**
* @param listener
* @see java.beans.PropertyChangeSupport#removePropertyChangeListener(java.beans.PropertyChangeListener)
*/
public void removePropertyChangeListener(PropertyChangeListener listener)
{
changeSupport.removePropertyChangeListener(listener);
}
public Set getAllFeatureColours()
{
return featureColours.keySet();
}
public void clearRenderOrder()
{
renderOrder = null;
}
public boolean hasRenderOrder()
{
return renderOrder != null;
}
/**
* Returns feature types in ordering of rendering, where last means on top
*/
public List getRenderOrder()
{
if (renderOrder == null)
{
return Arrays.asList(new String[] {});
}
return Arrays.asList(renderOrder);
}
public int getFeatureGroupsSize()
{
return featureGroups != null ? 0 : featureGroups.size();
}
@Override
public List getFeatureGroups()
{
// conflict between applet and desktop - featureGroups returns the map in
// the desktop featureRenderer
return (featureGroups == null) ? Arrays.asList(new String[0])
: Arrays.asList(featureGroups.keySet().toArray(new String[0]));
}
public boolean checkGroupVisibility(String group,
boolean newGroupsVisible)
{
if (featureGroups == null)
{
// then an exception happens next..
}
if (featureGroups.containsKey(group))
{
return featureGroups.get(group).booleanValue();
}
if (newGroupsVisible)
{
featureGroups.put(group, Boolean.valueOf(true));
return true;
}
return false;
}
/**
* get visible or invisible groups
*
* @param visible
* true to return visible groups, false to return hidden ones.
* @return list of groups
*/
@Override
public List getGroups(boolean visible)
{
if (featureGroups != null)
{
List gp = new ArrayList<>();
for (String grp : featureGroups.keySet())
{
Boolean state = featureGroups.get(grp);
if (state.booleanValue() == visible)
{
gp.add(grp);
}
}
return gp;
}
return null;
}
@Override
public void setGroupVisibility(String group, boolean visible)
{
featureGroups.put(group, Boolean.valueOf(visible));
}
@Override
public void setGroupVisibility(List toset, boolean visible)
{
if (toset != null && toset.size() > 0 && featureGroups != null)
{
boolean rdrw = false;
for (String gst : toset)
{
Boolean st = featureGroups.get(gst);
featureGroups.put(gst, Boolean.valueOf(visible));
if (st != null)
{
rdrw = rdrw || (visible != st.booleanValue());
}
}
if (rdrw)
{
// set local flag indicating redraw needed ?
}
}
}
@Override
public Map getDisplayedFeatureCols()
{
Map fcols = new Hashtable<>();
if (getViewport().getFeaturesDisplayed() == null)
{
return fcols;
}
Set features = getViewport().getFeaturesDisplayed()
.getVisibleFeatures();
for (String feature : features)
{
fcols.put(feature, getFeatureStyle(feature));
}
return fcols;
}
@Override
public FeaturesDisplayedI getFeaturesDisplayed()
{
return av.getFeaturesDisplayed();
}
/**
* Returns a (possibly empty) list of visible feature types, in render order
* (last is on top)
*/
@Override
public List getDisplayedFeatureTypes()
{
List typ = getRenderOrder();
List displayed = new ArrayList<>();
FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
if (feature_disp != null)
{
synchronized (feature_disp)
{
for (String type : typ)
{
if (feature_disp.isVisible(type))
{
displayed.add(type);
}
}
}
}
return displayed;
}
@Override
public List getDisplayedFeatureGroups()
{
List _gps = new ArrayList<>();
for (String gp : getFeatureGroups())
{
if (checkGroupVisibility(gp, false))
{
_gps.add(gp);
}
}
return _gps;
}
/**
* Answers true if the feature belongs to a feature group which is not
* currently displayed, else false
*
* @param sequenceFeature
* @return
*/
public boolean featureGroupNotShown(final SequenceFeature sequenceFeature)
{
return featureGroups != null
&& sequenceFeature.featureGroup != null
&& sequenceFeature.featureGroup.length() != 0
&& featureGroups.containsKey(sequenceFeature.featureGroup)
&& !featureGroups.get(sequenceFeature.featureGroup)
.booleanValue();
}
/**
* {@inheritDoc}
*/
@Override
public List findFeaturesAtResidue(SequenceI sequence,
int fromResNo, int toResNo)
{
List result = new ArrayList<>();
if (!av.areFeaturesDisplayed() || getFeaturesDisplayed() == null)
{
return result;
}
/*
* include features at the position provided their feature type is
* displayed, and feature group is null or the empty string
* or marked for display
*/
List visibleFeatures = getDisplayedFeatureTypes();
String[] visibleTypes = visibleFeatures
.toArray(new String[visibleFeatures.size()]);
List features = sequence.getFeatures().findFeatures(
fromResNo, toResNo, visibleTypes);
for (SequenceFeature sf : features)
{
if (!featureGroupNotShown(sf) && getColour(sf) != null)
{
result.add(sf);
}
}
return result;
}
/**
* 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 features)
{
/*
* 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;
Iterator it = features.iterator();
while (it.hasNext())
{
SequenceFeature sf = it.next();
if (featureGroupNotShown(sf))
{
it.remove();
continue;
}
/*
* a feature is redundant for rendering purposes if it has the
* same extent as another (so would just redraw the same colour);
* (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()
&& sf.getEnd() == lastFeature.getEnd()
&& sf.isContactFeature() == lastFeature.isContactFeature()
&& sf.getType().equals(lastFeature.getType()))
{
it.remove();
}
lastFeature = sf;
}
}
@Override
public Map getFeatureFilters()
{
return featureFilters;
}
@Override
public void setFeatureFilters(Map filters)
{
featureFilters = filters;
}
@Override
public FeatureMatcherSetI getFeatureFilter(String featureType)
{
return featureFilters.get(featureType);
}
@Override
public void setFeatureFilter(String featureType, FeatureMatcherSetI filter)
{
if (filter == null || filter.isEmpty())
{
featureFilters.remove(featureType);
}
else
{
featureFilters.put(featureType, filter);
}
}
/**
* Answers the colour for the feature, or null if the feature is excluded by
* feature group visibility, by filters, or by colour threshold settings. This
* method does not take feature type visibility into account.
*
* @param sf
* @param fc
* @return
*/
public Color getColor(SequenceFeature sf, FeatureColourI fc)
{
/*
* is the feature group displayed?
*/
if (featureGroupNotShown(sf))
{
return null;
}
/*
* does the feature pass filters?
*/
if (!featureMatchesFilters(sf))
{
return null;
}
return fc.getColor(sf);
}
/**
* Answers true if there no are filters defined for the feature type, or this
* feature matches the filters. Answers false if the feature fails to match
* filters.
*
* @param sf
* @return
*/
protected boolean featureMatchesFilters(SequenceFeature sf)
{
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 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 found = new ArrayList<>();
List 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 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 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;
}
}