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Recfactor track color implementation to enforce the following hierarc… #1814

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Merged
jrobinso merged 5 commits into from
Jan 21, 2026
Merged

Recfactor track color implementation to enforce the following hierarc… #1814

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b4994a3
Recfactor track color implementation to enforce the following hierarc…
jrobinso Jan 21, 2026
b1c7c77
Update src/main/java/org/igv/track/AbstractTrack.java
jrobinso Jan 21, 2026
0e97baa
Update src/main/java/org/igv/track/AbstractTrack.java
jrobinso Jan 21, 2026
2dc2c13
Update src/main/java/org/igv/track/AbstractTrack.java
jrobinso Jan 21, 2026
59ddcc9
Update src/main/java/org/igv/track/AbstractTrack.java
jrobinso Jan 21, 2026
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3 changes: 3 additions & 0 deletions src/main/java/org/igv/Globals.java
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Expand Up @@ -4,6 +4,7 @@
import org.igv.logging.Logger;

import javax.swing.*;
import java.awt.*;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
Expand All @@ -15,6 +16,8 @@
* Date: Feb 3, 2010
*/
public class Globals {
public static final Color DULL_BLUE = new Color(0, 0, 200);
public static final Color DULL_RED = new Color(200, 0, 0);
private static Logger log = LogManager.getLogger(Globals.class);

public static final int DESIGN_DPI = 96;
Expand Down
7 changes: 2 additions & 5 deletions src/main/java/org/igv/bedpe/HicInteractionTrack.java
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Expand Up @@ -2,7 +2,6 @@

import org.igv.hic.HicFile;
import org.igv.renderer.ContinuousColorScale;
import org.igv.track.RenderContext;
import org.igv.track.TrackClickEvent;
import org.igv.ui.IGV;
import org.igv.ui.panel.FrameManager;
Expand Down Expand Up @@ -31,9 +30,9 @@ public HicInteractionTrack(ResourceLocator locator, HicSource source) {
// HiC-specific defaults
maxFeatureCount = 5000;
graphType = GraphType.NESTED_ARC;
useScore = true;
isHIC = true;
setColor(Color.red);
setUseScore(false); // Alpha score is set in the renderer based
setDefaultColor(Color.red);
}

@Override
Expand Down Expand Up @@ -147,8 +146,6 @@ void addHICItems(TrackClickEvent te, IGVPopupMenu menu) {
menu.add(mapItem);
}



@Override
public void marshalXML(Document document, Element element) {
super.marshalXML(document, element);
Expand Down
12 changes: 8 additions & 4 deletions src/main/java/org/igv/bedpe/InteractionTrack.java
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Expand Up @@ -71,13 +71,9 @@ enum ArcOption {ALL, ONE_END, BOTH_ENDS}
double maxScore = -1;
int gap = 5;
boolean showBlocks = false;
protected boolean useScore = false;
protected boolean isHIC = false;
private Map<GraphType, BedPERenderer> renderers;

private Color defaultColor = new Color(180, 25, 137);


ContactMapView contactMapView;
float transparency = 1.0f;
protected String normalization = "NONE";
Expand All @@ -99,6 +95,7 @@ public InteractionTrack(ResourceLocator locator, InteractionSource src) {
this.featureSource = src;

setHeight(250, true);
setDefaultColor( new Color(180, 25, 137));

renderers = new HashMap<>();
renderers.put(GraphType.NESTED_ARC, new NestedArcRenderer(this));
Expand Down Expand Up @@ -305,6 +302,13 @@ public IGVPopupMenu getPopupMenu(TrackClickEvent te) {
item.addActionListener(evt -> TrackMenuUtils.changeTrackColor(Collections.singleton(InteractionTrack.this)));
menu.add(item);

item = new JMenuItem("Unset Track Color");
item.addActionListener(evt -> {
this.setColor(null);
repaint();
});
menu.add(item);

if (!isHIC) {
menu.addSeparator();
menu.add(new JLabel("<html><b>Graph Type</b>"));
Expand Down
15 changes: 9 additions & 6 deletions src/main/java/org/igv/bedpe/NestedArcRenderer.java
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Expand Up @@ -42,7 +42,6 @@ public void render(List<BedPE> features,
g = (Graphics2D) context.getGraphics().create();
double origin = context.getOrigin();
double locScale = context.getScale();
Color trackColor = track.getColor() == null ? DEFAULT_TRACK_COLOR : track.getColor();
int gap = track.gap;

if (track.thickness > 1) {
Expand Down Expand Up @@ -100,12 +99,16 @@ public void render(List<BedPE> features,
}


Color fcolor = feature.getColor() == null ? trackColor : feature.getColor();
float alpha = track.transparency;
if (track.useScore) {
alpha = track.transparency * Math.min(1.0f, Math.max(0.1f, feature.getScore() / 1000f));
Color fcolor = track.getFeatureColor(feature);

if(track.isHIC) {
float alpha = track.transparency;
if (track.isUseScore()) {
alpha = track.transparency * Math.min(1.0f, Math.max(0.1f, feature.getScore() / 1000f));
}
fcolor = getAlphaColor(fcolor, alpha);
}
fcolor = getAlphaColor(fcolor, alpha);

g.setColor(fcolor);

final int trackBaseLine = trackRectangle.y + trackRectangle.height;
Expand Down
2 changes: 0 additions & 2 deletions src/main/java/org/igv/feature/genome/load/GenomeLoader.java
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Expand Up @@ -83,8 +83,6 @@ public static FeatureTrack createGeneTrack(Genome genome, List<htsjdk.tribble.Fe
geneFeatureTrack = new FeatureTrack(id, name, new FeatureCollectionSource(features, genome));
geneFeatureTrack.setMinimumHeight(5);
geneFeatureTrack.setHeight(35);
//geneFeatureTrack.setRendererClass(GeneRenderer.class);
geneFeatureTrack.setColor(Color.BLUE.darker());

return geneFeatureTrack;
}
Expand Down
74 changes: 3 additions & 71 deletions src/main/java/org/igv/renderer/IGVFeatureRenderer.java
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@@ -1,17 +1,15 @@
package org.igv.renderer;


import org.igv.Globals;
import org.igv.logging.*;
import org.igv.feature.*;
import org.igv.feature.aa.AminoAcidSequence;
import org.igv.feature.aa.CodonAA;
import org.igv.feature.genome.Genome;
import org.igv.feature.genome.GenomeManager;
import org.igv.prefs.PreferencesManager;
import org.igv.track.FeatureTrack;
import org.igv.track.RenderContext;
import org.igv.track.Track;
import org.igv.track.TrackType;
import org.igv.track.*;
import org.igv.ui.FontManager;
import org.igv.ui.color.ColorUtilities;

Expand All @@ -38,8 +36,6 @@ public class IGVFeatureRenderer extends FeatureRenderer {
static final int THIN_BLOCK_HEIGHT = 6;
protected Color AA_COLOR_1 = new Color(92, 92, 164);
protected Color AA_COLOR_2 = new Color(12, 12, 120);
public static final Color DULL_BLUE = new Color(0, 0, 200);
public static final Color DULL_RED = new Color(200, 0, 0);
static final int NON_CODING_HEIGHT = 8;

private static final Color VARIANT_HET_COLOR = Color.blue.brighter();
Expand Down Expand Up @@ -118,8 +114,6 @@ public void render(List<IGVFeature> featureList,


boolean alternateExonColor = (track instanceof FeatureTrack && ((FeatureTrack) track).isAlternateExonColor());
Color trackPosColor = track.getColor();
Color trackNegColor = alternateExonColor ? track.getColor() : track.getAltColor();
String labelField = track.getLabelField();

for (IGVFeature feature : featureList) {
Expand Down Expand Up @@ -176,7 +170,7 @@ public void render(List<IGVFeature> featureList,
continue;
}

Color color = getFeatureColor(feature, track, trackPosColor, trackNegColor);
Color color = ((AbstractTrack) track).getFeatureColor(feature);
Graphics2D g2D = context.getGraphic2DForColor(color);

// Draw block representing entire feature
Expand Down Expand Up @@ -699,68 +693,6 @@ public String getDisplayName() {
return "Basic Feature";
}

protected Color getFeatureColor(IGVFeature feature, Track track, Color defaultPosColor, Color defaultNegColor) {

// Set color used to draw the feature
Color color = null;

// If an alt color is explicitly set use it for negative strand features;
if (feature.getStrand() == Strand.NEGATIVE) {
color = track.getExplicitAltColor();
}

// If color is explicitly set use it
if (color == null) {
color = track.getExplicitColor();
}

// No explicitly set color, try the feature itself
if (color == null && track.isItemRGB()) {
color = feature.getColor();
}

// If still no color use defaults
if (color == null) {
if (track.getTrackType() == TrackType.CNV) {
color = feature.getName().equals("gain") ? DULL_RED : DULL_BLUE;
} else {
color = feature.getStrand() == Strand.NEGATIVE ? defaultNegColor : defaultPosColor;
}
}

if (track.isUseScore()) {
float min = getViewLimitMin(track);
float max = getViewLimitMax(track);

float score = feature.getScore();
float alpha = Float.isNaN(score) ? 1 : getAlpha(min, max, feature.getScore());
color = ColorUtilities.getCompositeColor(color, alpha);
}

return color;
}

float getViewLimitMin(Track track) {
if (Float.isNaN(viewLimitMin)) {
viewLimitMin = Float.isNaN(track.getViewLimitMin()) ? 0 : track.getViewLimitMin();
}
return viewLimitMin;
}

float getViewLimitMax(Track track) {
if (Float.isNaN(viewLimitMax)) {
viewLimitMax = Float.isNaN(track.getViewLimitMax()) ? 1000 : track.getViewLimitMax();
}
return viewLimitMax;
}

private float getAlpha(float minRange, float maxRange, float value) {
float binWidth = (maxRange - minRange) / 9;
int binNumber = (int) ((value - minRange) / binWidth);
return Math.min(1.0f, 0.2f + (binNumber * 0.8f) / 9);
}


protected int getPixelFromChromosomeLocation(String chr, int chromosomeLocation, double origin,
double locationScale) {
return (int) Math.round((chromosomeLocation - origin) / locationScale);
Expand Down
5 changes: 4 additions & 1 deletion src/main/java/org/igv/renderer/SpliceJunctionRenderer.java
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Expand Up @@ -142,7 +142,10 @@ protected void drawFeature(SpliceJunctionFeature junctionFeature, boolean should
We modify the alpha value of the chosen color to indicate if it is highlighted
*/
final Color color;
final Color trackColor = isPositiveStrand ? track.getExplicitColor() : track.getExplicitAltColor();
Color trackColor = isPositiveStrand ? track.getColor() : track.getAltColor();
if(trackColor == null) {
trackColor = track.getDefaultColor();
}
if (trackColor != null) {
color = adjustAlpha(trackColor, highlight);
} else if (featureColor != null) {
Expand Down
9 changes: 2 additions & 7 deletions src/main/java/org/igv/sam/CoverageTrack.java
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Expand Up @@ -107,14 +107,9 @@ public CoverageTrack(ResourceLocator locator, String name, AlignmentTrack alignm

@Override
public Color getColor() {
return _color == null ?
return color == null ?
ColorUtilities.slightlyDarker(alignmentTrack.getColor()) :
_color;
}

@Override
public void setColor(Color color) {
_color = color;
color;
}

@Override
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/igv/seg/CNFreqTrack.java
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Expand Up @@ -49,7 +49,7 @@ public CNFreqTrack(ResourceLocator rl, String id, String name, FreqData fd) {

float nSamples = data.getNumberOfSamples();
this.setDataRange(new DataRange(-nSamples, 0, nSamples));
this.posColor = Color.red;
this.color = Color.red;
this.altColor = Color.blue;

renderer = new BarChartRenderer();
Expand Down
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