X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fviewmodel%2Fseqfeatures%2FFeatureRendererModel.java;h=e812ed58c594ad5c3e890ab872344351800f9869;hb=e57f77dc13f5a295cf49a403da05770a68a6e22b;hp=bcf808df4638265c09f3e9243232231dbce284df;hpb=70c81d16f9b2bbcfcfb1479954c1caebff8e08cc;p=jalview.git
diff --git a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
index bcf808d..e812ed5 100644
--- a/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
+++ b/src/jalview/viewmodel/seqfeatures/FeatureRendererModel.java
@@ -1,19 +1,33 @@
+/*
+ * 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 jalview.api.AlignViewportI;
-import jalview.api.FeaturesDisplayedI;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.renderer.seqfeatures.FeatureRenderer;
-import jalview.schemes.GraduatedColor;
-import jalview.viewmodel.AlignmentViewport;
-
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;
@@ -21,28 +35,81 @@ import java.util.Map;
import java.util.Set;
import java.util.concurrent.ConcurrentHashMap;
-public abstract class FeatureRendererModel implements
- jalview.api.FeatureRenderer
+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;
- protected Map featureColours = new ConcurrentHashMap();
+ /*
+ * colour scheme for each feature type
+ */
+ protected Map featureColours = new ConcurrentHashMap<>();
- protected Map featureGroups = new ConcurrentHashMap();
+ /*
+ * visibility flag for each feature group
+ */
+ protected Map featureGroups = new ConcurrentHashMap<>();
- protected Object currentColour;
+ /*
+ * filters for each feature type
+ */
+ protected Map featureFilters = new HashMap<>();
protected String[] renderOrder;
- protected PropertyChangeSupport changeSupport = new PropertyChangeSupport(
- this);
+ Map featureOrder = null;
- protected AlignmentViewport av;
+ protected AlignViewportI av;
+
+ private PropertyChangeSupport changeSupport = new PropertyChangeSupport(
+ this);
+ @Override
public AlignViewportI getViewport()
{
return av;
@@ -75,6 +142,7 @@ public abstract class FeatureRendererModel implements
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())
@@ -92,11 +160,10 @@ public abstract class FeatureRendererModel implements
synchronized (fd)
{
fd.clear();
- java.util.Iterator fdisp = _fr.getFeaturesDisplayed()
- .getVisibleFeatures();
- while (fdisp.hasNext())
+ for (String type : _fr.getFeaturesDisplayed()
+ .getVisibleFeatures())
{
- fd.setVisible(fdisp.next());
+ fd.setVisible(type);
}
}
}
@@ -119,8 +186,7 @@ public abstract class FeatureRendererModel implements
}
if (!fdi.isRegistered(featureType))
{
- pushFeatureType(Arrays.asList(new String[]
- { featureType }));
+ pushFeatureType(Arrays.asList(new String[] { featureType }));
}
fdi.setVisible(featureType);
}
@@ -133,7 +199,7 @@ public abstract class FeatureRendererModel implements
{
av.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
}
- List nft = new ArrayList();
+ List nft = new ArrayList<>();
for (String featureType : featureTypes)
{
if (!fdi.isRegistered(featureType))
@@ -163,15 +229,15 @@ public abstract class FeatureRendererModel implements
types.toArray(neworder);
if (renderOrder != null)
{
- System.arraycopy(neworder,0,neworder,renderOrder.length,ts);
+ System.arraycopy(neworder, 0, neworder, renderOrder.length, ts);
System.arraycopy(renderOrder, 0, neworder, 0, renderOrder.length);
}
renderOrder = neworder;
}
- protected Hashtable minmax = new Hashtable();
+ protected Map minmax = new Hashtable<>();
- public Hashtable getMinMax()
+ public Map getMinMax()
{
return minmax;
}
@@ -185,15 +251,15 @@ public abstract class FeatureRendererModel implements
*/
protected final byte[] normaliseScore(SequenceFeature sequenceFeature)
{
- float[] mm = ((float[][]) minmax.get(sequenceFeature.type))[0];
- final byte[] r = new byte[]
- { 0, (byte) 255 };
+ 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]));
+ r[1] = (byte) ((int) 128.0
+ + 127.0 * (sequenceFeature.score / mm[1]));
}
else
{
@@ -235,59 +301,58 @@ public abstract class FeatureRendererModel implements
{
firing = Boolean.TRUE;
findAllFeatures(true); // add all new features as visible
- changeSupport.firePropertyChange("changeSupport", null, null);
+ notifyFeaturesChanged();
firing = Boolean.FALSE;
}
}
}
@Override
- public List findFeaturesAtRes(SequenceI sequence, int res)
+ public void notifyFeaturesChanged()
{
- ArrayList tmp = new ArrayList();
- SequenceFeature[] features = sequence.getSequenceFeatures();
+ changeSupport.firePropertyChange("changeSupport", null, null);
+ }
- while (features == null && sequence.getDatasetSequence() != null)
+ @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)
{
- sequence = sequence.getDatasetSequence();
- features = sequence.getSequenceFeatures();
+ return result;
}
- if (features != null)
+ 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)
{
- for (int i = 0; i < features.length; i++)
+ if (getColour(sf) != null)
{
- if (!av.areFeaturesDisplayed()
- || !av.getFeaturesDisplayed().isVisible(
- features[i].getType()))
- {
- continue;
- }
-
- if (features[i].featureGroup != null
- && featureGroups != null
- && featureGroups.containsKey(features[i].featureGroup)
- && !featureGroups.get(features[i].featureGroup)
- .booleanValue())
- {
- continue;
- }
-
- if ((features[i].getBegin() <= res)
- && (features[i].getEnd() >= res))
- {
- tmp.add(features[i]);
- }
+ result.add(sf);
}
}
- return tmp;
+ return result;
}
/**
* Searches alignment for all features and updates colours
*
* @param newMadeVisible
- * if true newly added feature types will be rendered immediatly
+ * 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
*/
@@ -309,8 +374,7 @@ public abstract class FeatureRendererModel implements
}
FeaturesDisplayedI featuresDisplayed = av.getFeaturesDisplayed();
- ArrayList allfeatures = new ArrayList();
- ArrayList oldfeatures = new ArrayList();
+ Set oldfeatures = new HashSet<>();
if (renderOrder != null)
{
for (int i = 0; i < renderOrder.length; i++)
@@ -321,97 +385,111 @@ public abstract class FeatureRendererModel implements
}
}
}
- if (minmax == null)
- {
- minmax = new Hashtable();
- }
+
AlignmentI alignment = av.getAlignment();
+ List allfeatures = new ArrayList<>();
+
for (int i = 0; i < alignment.getHeight(); i++)
{
SequenceI asq = alignment.getSequenceAt(i);
- SequenceI dasq = asq.getDatasetSequence();
- SequenceFeature[] features = dasq != null ? dasq
- .getSequenceFeatures() : asq.getSequenceFeatures();
-
- if (features == null)
+ for (String group : asq.getFeatures().getFeatureGroups(true))
{
- continue;
- }
-
- int index = 0;
- while (index < features.length)
- {
- if (!featuresDisplayed.isRegistered(features[index].getType()))
+ boolean groupDisplayed = true;
+ if (group != null)
{
- String fgrp = features[index].getFeatureGroup();
- if (fgrp != null)
+ if (featureGroups.containsKey(group))
{
- Boolean groupDisplayed = featureGroups.get(fgrp);
- if (groupDisplayed == null)
- {
- groupDisplayed = Boolean.valueOf(newMadeVisible);
- featureGroups.put(fgrp, groupDisplayed);
- }
- if (!groupDisplayed.booleanValue())
- {
- index++;
- continue;
- }
+ groupDisplayed = featureGroups.get(group);
}
- if (!(features[index].begin == 0 && features[index].end == 0))
+ else
{
- // If beginning and end are 0, the feature is for the whole sequence
- // and we don't want to render the feature in the normal way
-
- if (newMadeVisible
- && !oldfeatures.contains(features[index].getType()))
- {
- // this is a new feature type on the alignment. Mark it for
- // display.
- featuresDisplayed.setVisible(features[index].getType());
- setOrder(features[index].getType(), 0);
- }
+ groupDisplayed = newMadeVisible;
+ featureGroups.put(group, groupDisplayed);
}
}
- if (!allfeatures.contains(features[index].getType()))
- {
- allfeatures.add(features[index].getType());
- }
- if (features[index].score != Float.NaN)
+ if (groupDisplayed)
{
- int nonpos = features[index].getBegin() >= 1 ? 0 : 1;
- float[][] mm = (float[][]) minmax.get(features[index].getType());
- if (mm == null)
+ Set types = asq.getFeatures()
+ .getFeatureTypesForGroups(true, group);
+ for (String type : types)
{
- mm = new float[][]
- { null, null };
- minmax.put(features[index].getType(), mm);
- }
- if (mm[nonpos] == null)
- {
- mm[nonpos] = new float[]
- { features[index].score, features[index].score };
-
- }
- else
- {
- if (mm[nonpos][0] > features[index].score)
- {
- mm[nonpos][0] = features[index].score;
- }
- if (mm[nonpos][1] < features[index].score)
+ if (!allfeatures.contains(type)) // or use HashSet and no test?
{
- mm[nonpos][1] = features[index].score;
+ allfeatures.add(type);
}
+ updateMinMax(asq, type, true); // todo: for all features?
}
}
- index++;
}
}
+
+ // 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;
/**
@@ -427,10 +505,9 @@ public abstract class FeatureRendererModel implements
*/
private void updateRenderOrder(List allFeatures)
{
- List allfeatures = new ArrayList(allFeatures);
+ List allfeatures = new ArrayList<>(allFeatures);
String[] oldRender = renderOrder;
renderOrder = new String[allfeatures.size()];
- Object mmrange, fc = null;
boolean initOrders = (featureOrder == null);
int opos = 0;
if (oldRender != null && oldRender.length > 0)
@@ -441,8 +518,8 @@ public abstract class FeatureRendererModel implements
{
if (initOrders)
{
- setOrder(oldRender[j], (1 - (1 + (float) j)
- / oldRender.length));
+ setOrder(oldRender[j],
+ (1 - (1 + (float) j) / oldRender.length));
}
if (allfeatures.contains(oldRender[j]))
{
@@ -451,16 +528,14 @@ public abstract class FeatureRendererModel implements
allfeatures.remove(oldRender[j]);
if (minmax != null)
{
- mmrange = minmax.get(oldRender[j]);
+ float[][] mmrange = minmax.get(oldRender[j]);
if (mmrange != null)
{
- fc = featureColours.get(oldRender[j]);
- if (fc != null && fc instanceof GraduatedColor
- && ((GraduatedColor) fc).isAutoScale())
+ FeatureColourI fc = featureColours.get(oldRender[j]);
+ if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+ && !fc.isColourByAttribute())
{
- ((GraduatedColor) fc).updateBounds(
- ((float[][]) mmrange)[0][0],
- ((float[][]) mmrange)[0][1]);
+ fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
}
}
@@ -484,15 +559,14 @@ public abstract class FeatureRendererModel implements
if (minmax != null)
{
// update from new features minmax if necessary
- mmrange = minmax.get(newf[i]);
+ float[][] mmrange = minmax.get(newf[i]);
if (mmrange != null)
{
- fc = featureColours.get(newf[i]);
- if (fc != null && fc instanceof GraduatedColor
- && ((GraduatedColor) fc).isAutoScale())
+ FeatureColourI fc = featureColours.get(newf[i]);
+ if (fc != null && !fc.isSimpleColour() && fc.isAutoScaled()
+ && !fc.isColourByAttribute())
{
- ((GraduatedColor) fc).updateBounds(((float[][]) mmrange)[0][0],
- ((float[][]) mmrange)[0][1]);
+ fc.updateBounds(mmrange[0][0], mmrange[0][1]);
}
}
}
@@ -504,7 +578,7 @@ public abstract class FeatureRendererModel implements
setOrder(newf[i], i / (float) denom);
}
// set order from newly found feature from persisted ordering.
- sortOrder[i] = 2 - ((Float) featureOrder.get(newf[i])).floatValue();
+ sortOrder[i] = 2 - featureOrder.get(newf[i]).floatValue();
if (i < iSize)
{
// only sort if we need to
@@ -522,118 +596,63 @@ public abstract class FeatureRendererModel implements
/**
* get a feature style object for the given type string. Creates a
- * java.awt.Color for a featureType with no existing colourscheme. TODO:
- * replace return type with object implementing standard abstract colour/style
- * interface
+ * java.awt.Color for a featureType with no existing colourscheme.
*
* @param featureType
- * @return java.awt.Color or GraduatedColor
+ * @return
*/
- public Object getFeatureStyle(String featureType)
+ @Override
+ public FeatureColourI getFeatureStyle(String featureType)
{
- Object fc = featureColours.get(featureType);
+ FeatureColourI fc = featureColours.get(featureType);
if (fc == null)
{
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme();
- Color col = ucs.createColourFromName(featureType);
- featureColours.put(featureType, fc = col);
+ Color col = ColorUtils.createColourFromName(featureType);
+ fc = new FeatureColour(col);
+ featureColours.put(featureType, fc);
}
return fc;
}
- /**
- * return a nominal colour for this feature
- *
- * @param featureType
- * @return standard color, or maximum colour for graduated colourscheme
- */
- public Color getColour(String featureType)
+ @Override
+ public Color getColour(SequenceFeature feature)
{
- Object fc = getFeatureStyle(featureType);
-
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).getMaxColor();
- }
- }
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + featureType);
+ FeatureColourI fc = getFeatureStyle(feature.getType());
+ return getColor(feature, fc);
}
/**
- * calculate the render colour for a specific feature using current feature
- * settings.
+ * Answers true if the feature type is currently selected to be displayed,
+ * else false
*
- * @param feature
- * @return render colour for the given feature
+ * @param type
+ * @return
*/
- public Color getColour(SequenceFeature feature)
- {
- Object fc = getFeatureStyle(feature.getType());
- if (fc instanceof Color)
- {
- return (Color) fc;
- }
- else
- {
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).findColor(feature);
- }
- }
- throw new Error("Implementation Error: Unrecognised render object "
- + fc.getClass() + " for features of type " + feature.getType());
- }
-
- protected boolean showFeature(SequenceFeature sequenceFeature)
- {
- Object fc = getFeatureStyle(sequenceFeature.type);
- if (fc instanceof GraduatedColor)
- {
- return ((GraduatedColor) fc).isColored(sequenceFeature);
- }
- else
- {
- return true;
- }
- }
-
- protected boolean showFeatureOfType(String type)
+ public boolean showFeatureOfType(String type)
{
- return av.getFeaturesDisplayed().isVisible(type);
+ return type == null ? false
+ : (av.getFeaturesDisplayed() == null ? true
+ : av.getFeaturesDisplayed().isVisible(type));
}
- public void setColour(String featureType, Object col)
+ @Override
+ public void setColour(String featureType, FeatureColourI col)
{
- // overwrite
- // Color _col = (col instanceof Color) ? ((Color) col) : (col instanceof
- // GraduatedColor) ? ((GraduatedColor) col).getMaxColor() : null;
- // Object c = featureColours.get(featureType);
- // if (c == null || c instanceof Color || (c instanceof GraduatedColor &&
- // !((GraduatedColor)c).getMaxColor().equals(_col)))
- {
- featureColours.put(featureType, col);
- }
+ featureColours.put(featureType, col);
}
+ @Override
public void setTransparency(float value)
{
transparency = value;
}
+ @Override
public float getTransparency()
{
return transparency;
}
- Map featureOrder = null;
-
/**
* analogous to colour - store a normalized ordering for all feature types in
* this rendering context.
@@ -648,9 +667,9 @@ public abstract class FeatureRendererModel implements
{
if (featureOrder == null)
{
- featureOrder = new Hashtable();
+ featureOrder = new Hashtable<>();
}
- featureOrder.put(type, new Float(position));
+ featureOrder.put(type, Float.valueOf(position));
return position;
}
@@ -666,38 +685,51 @@ public abstract class FeatureRendererModel implements
{
if (featureOrder.containsKey(type))
{
- return ((Float) featureOrder.get(type)).floatValue();
+ return featureOrder.get(type).floatValue();
}
}
return -1;
}
@Override
- public Map getFeatureColours()
+ public Map getFeatureColours()
{
- return new ConcurrentHashMap(featureColours);
+ return featureColours;
}
/**
* 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 void setFeaturePriority(Object[][] data)
+ public boolean setFeaturePriority(FeatureSettingsBean[] data)
{
- setFeaturePriority(data, true);
+ 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
- * { 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)
*/
- public void setFeaturePriority(Object[][] data, boolean visibleNew)
+ 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)
{
@@ -707,7 +739,8 @@ public abstract class FeatureRendererModel implements
}
else
{
- av.setFeaturesDisplayed(av_featuresdisplayed = new FeaturesDisplayed());
+ av.setFeaturesDisplayed(
+ av_featuresdisplayed = new FeaturesDisplayed());
}
}
else
@@ -716,10 +749,10 @@ public abstract class FeatureRendererModel implements
}
if (data == null)
{
- return;
+ return false;
}
// The feature table will display high priority
- // features at the top, but theses are the ones
+ // features at the top, but these are the ones
// we need to render last, so invert the data
renderOrder = new String[data.length];
@@ -727,10 +760,9 @@ public abstract class FeatureRendererModel implements
{
for (int i = 0; i < data.length; i++)
{
- String type = data[i][0].toString();
- setColour(type, data[i][1]); // todo : typesafety - feature color
- // interface object
- if (((Boolean) data[i][2]).booleanValue())
+ String type = data[i].featureType;
+ setColour(type, data[i].featureColour);
+ if (data[i].show)
{
av_featuresdisplayed.setVisible(type);
}
@@ -739,6 +771,30 @@ public abstract class FeatureRendererModel implements
}
}
+ /*
+ * 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;
}
/**
@@ -759,7 +815,7 @@ public abstract class FeatureRendererModel implements
changeSupport.removePropertyChangeListener(listener);
}
- public Set getAllFeatureColours()
+ public Set getAllFeatureColours()
{
return featureColours.keySet();
}
@@ -774,12 +830,14 @@ public abstract class FeatureRendererModel implements
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(new String[] {});
}
return Arrays.asList(renderOrder);
}
@@ -794,11 +852,12 @@ public abstract class FeatureRendererModel implements
{
// 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]));
+ return (featureGroups == null) ? Arrays.asList(new String[0])
+ : Arrays.asList(featureGroups.keySet().toArray(new String[0]));
}
- public boolean checkGroupVisibility(String group, boolean newGroupsVisible)
+ public boolean checkGroupVisibility(String group,
+ boolean newGroupsVisible)
{
if (featureGroups == null)
{
@@ -810,7 +869,7 @@ public abstract class FeatureRendererModel implements
}
if (newGroupsVisible)
{
- featureGroups.put(group, new Boolean(true));
+ featureGroups.put(group, Boolean.valueOf(true));
return true;
}
return false;
@@ -824,13 +883,13 @@ public abstract class FeatureRendererModel implements
* @return list of groups
*/
@Override
- public List getGroups(boolean visible)
+ public List getGroups(boolean visible)
{
if (featureGroups != null)
{
- ArrayList gp = new ArrayList();
+ List gp = new ArrayList<>();
- for (Object grp : featureGroups.keySet())
+ for (String grp : featureGroups.keySet())
{
Boolean state = featureGroups.get(grp);
if (state.booleanValue() == visible)
@@ -846,7 +905,7 @@ public abstract class FeatureRendererModel implements
@Override
public void setGroupVisibility(String group, boolean visible)
{
- featureGroups.put(group, new Boolean(visible));
+ featureGroups.put(group, Boolean.valueOf(visible));
}
@Override
@@ -858,7 +917,7 @@ public abstract class FeatureRendererModel implements
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());
@@ -872,19 +931,18 @@ public abstract class FeatureRendererModel implements
}
@Override
- public Hashtable getDisplayedFeatureCols()
+ public Map getDisplayedFeatureCols()
{
- Hashtable fcols = new Hashtable();
+ Map fcols = new Hashtable<>();
if (getViewport().getFeaturesDisplayed() == null)
{
return fcols;
}
- Iterator en = getViewport().getFeaturesDisplayed()
+ Set features = getViewport().getFeaturesDisplayed()
.getVisibleFeatures();
- while (en.hasNext())
+ for (String feature : features)
{
- String col = en.next();
- fcols.put(col, getColour(col));
+ fcols.put(feature, getFeatureStyle(feature));
}
return fcols;
}
@@ -895,55 +953,381 @@ public abstract class FeatureRendererModel implements
return av.getFeaturesDisplayed();
}
+ /**
+ * Returns a (possibly empty) list of visible feature types, in render order
+ * (last is on top)
+ */
@Override
- public String[] getDisplayedFeatureTypes()
+ public List getDisplayedFeatureTypes()
{
- String[] typ = null;
- typ = getRenderOrder().toArray(new String[0]);
+ List typ = getRenderOrder();
+ List displayed = new ArrayList<>();
FeaturesDisplayedI feature_disp = av.getFeaturesDisplayed();
if (feature_disp != null)
{
synchronized (feature_disp)
{
- for (int i = 0; i < typ.length; i++)
+ for (String type : typ)
{
- if (feature_disp.isVisible(typ[i]))
+ if (feature_disp.isVisible(type))
{
- typ[i] = null;
+ displayed.add(type);
}
}
}
}
- return typ;
+ return displayed;
}
@Override
- public String[] getDisplayedFeatureGroups()
+ public List getDisplayedFeatureGroups()
{
- String[] gps = null;
- ArrayList _gps = new ArrayList();
- Iterator en = getFeatureGroups().iterator();
- int g = 0;
- boolean valid = false;
- while (en.hasNext())
+ List _gps = new ArrayList<>();
+ for (String gp : getFeatureGroups())
{
- String gp = (String) en.next();
if (checkGroupVisibility(gp, false))
{
- valid = true;
_gps.add(gp);
}
- if (!valid)
+ }
+ 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)
{
- return null;
+ result.add(sf);
}
- else
+ }
+ 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()))
{
- gps = new String[_gps.size()];
- _gps.toArray(gps);
+ 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);
}
- return gps;
}
+ /**
+ * 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;
+ }
}