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Merged
jrobinso merged 3 commits into from
Jan 12, 2026
Merged

Fix minor issues with insertion markers. (1) markers not in sync wit… #1809

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62ca2e0
Fix minor issues with insertion markers. (1) markers not in sync wit…
jrobinso Jan 12, 2026
6c47677
Update src/main/java/org/igv/ui/panel/RulerPanel.java
jrobinso Jan 12, 2026
7844994
Update src/main/java/org/igv/ui/panel/RulerPanel.java
jrobinso Jan 12, 2026
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2 changes: 1 addition & 1 deletion src/main/java/org/igv/sam/AlignmentDataManager.java
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Expand Up @@ -319,7 +319,7 @@ AlignmentInterval loadInterval(String chr, int start, int end, AlignmentTrack.Re
SpliceJunctionHelper spliceJunctionHelper = new SpliceJunctionHelper();

AlignmentTileLoader.AlignmentTile t = getLoader().loadTile(seqName, start, end, spliceJunctionHelper,
downsampleOptions, peStats, bisulfiteContext, renderOptions);
downsampleOptions, peStats, bisulfiteContext, renderOptions, getPreferences());
List<Alignment> alignments = t.getAlignments();
List<DownsampledInterval> downsampledIntervals = t.getDownsampledIntervals();
this.updateBaseModfications(alignments);
Expand Down
34 changes: 17 additions & 17 deletions src/main/java/org/igv/sam/AlignmentTileLoader.java
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Expand Up @@ -2,17 +2,18 @@

import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.util.CloseableIterator;
import org.igv.event.IGVEvent;
import org.igv.logging.*;
import org.igv.Globals;
import org.igv.event.IGVEvent;
import org.igv.event.IGVEventBus;
import org.igv.event.IGVEventObserver;
import org.igv.event.StopEvent;
import org.igv.logging.LogManager;
import org.igv.logging.Logger;
import org.igv.prefs.IGVPreferences;
import org.igv.prefs.PreferencesManager;
import org.igv.sam.reader.AlignmentReader;
import org.igv.sam.reader.ReadGroupFilter;
import org.igv.ui.IGV;
import org.igv.event.IGVEventBus;
import org.igv.event.IGVEventObserver;
import org.igv.event.StopEvent;
import org.igv.ui.util.MessageUtils;
import org.igv.util.ObjectCache;
import org.igv.util.RuntimeUtils;
Expand Down Expand Up @@ -100,21 +101,21 @@ AlignmentTile loadTile(String chr,
AlignmentDataManager.DownsampleOptions downsampleOptions,
Map<String, PEStats> peStats,
AlignmentTrack.BisulfiteContext bisulfiteContext,
AlignmentTrack.RenderOptions renderOptions) {
AlignmentTrack.RenderOptions renderOptions,
IGVPreferences preferences) {

final IGVPreferences prefMgr = PreferencesManager.getPreferences();
boolean filterFailedReads = prefMgr.getAsBoolean(SAM_FILTER_FAILED_READS);
boolean filterSecondaryAlignments = prefMgr.getAsBoolean(SAM_FILTER_SECONDARY_ALIGNMENTS);
boolean filterSupplementaryAlignments = prefMgr.getAsBoolean(SAM_FILTER_SUPPLEMENTARY_ALIGNMENTS);
boolean filterFailedReads = preferences.getAsBoolean(SAM_FILTER_FAILED_READS);
boolean filterSecondaryAlignments = preferences.getAsBoolean(SAM_FILTER_SECONDARY_ALIGNMENTS);
boolean filterSupplementaryAlignments = preferences.getAsBoolean(SAM_FILTER_SUPPLEMENTARY_ALIGNMENTS);
ReadGroupFilter filter = ReadGroupFilter.getFilter();
boolean filterDuplicates = renderOptions != null
? renderOptions.getDuplicatesOption() == AlignmentTrack.DuplicatesOption.FILTER
: prefMgr.getAsBoolean(SAM_FILTER_DUPLICATES);
: preferences.getAsBoolean(SAM_FILTER_DUPLICATES);

int qualityThreshold = prefMgr.getAsInt(SAM_QUALITY_THRESHOLD);
int alignmentScoreTheshold = prefMgr.getAsInt(SAM_ALIGNMENT_SCORE_THRESHOLD);
int qualityThreshold = preferences.getAsInt(SAM_QUALITY_THRESHOLD);
int alignmentScoreTheshold = preferences.getAsInt(SAM_ALIGNMENT_SCORE_THRESHOLD);

boolean reducedMemory = prefMgr.getAsBoolean(SAM_REDUCED_MEMORY_MODE);
boolean reducedMemory = preferences.getAsBoolean(SAM_REDUCED_MEMORY_MODE);

AlignmentTile t = new AlignmentTile(start, end, spliceJunctionHelper, downsampleOptions, bisulfiteContext, reducedMemory);

Expand Down Expand Up @@ -254,8 +255,8 @@ AlignmentTile loadTile(String chr,
// Compute peStats
if (peStats != null) {
// TODO -- something smarter re the percentiles. For small samples these will revert to min and max
double minPercentile = prefMgr.getAsFloat(SAM_MIN_INSERT_SIZE_PERCENTILE);
double maxPercentile = prefMgr.getAsFloat(SAM_MAX_INSERT_SIZE_PERCENTILE);
double minPercentile = preferences.getAsFloat(SAM_MIN_INSERT_SIZE_PERCENTILE);
double maxPercentile = preferences.getAsFloat(SAM_MAX_INSERT_SIZE_PERCENTILE);
for (PEStats stats : peStats.values()) {
stats.computeInsertSize(minPercentile, maxPercentile);
stats.computeExpectedOrientation();
Expand All @@ -274,7 +275,6 @@ AlignmentTile loadTile(String chr,
}
t.finish();

// TODO -- make this optional (on a preference)
InsertionManager.getInstance().processAlignments(chr, t.alignments);


Expand Down
18 changes: 18 additions & 0 deletions src/main/java/org/igv/sam/AlignmentTrackMenu.java
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Expand Up @@ -140,9 +140,27 @@ class AlignmentTrackMenu extends IGVPopupMenu {
}
renderOptions.setHideSmallIndels(smallIndelsItem.isSelected());
alignmentTrack.repaint();
IGV.getInstance().repaintHeaderPanels();
}));
add(smallIndelsItem);

// Indel size setting
JMenuItem indelSizeItem = new JMenuItem("Set indel size threshold...");
indelSizeItem.setEnabled(renderOptions.isHideSmallIndels());
indelSizeItem.addActionListener(aEvt -> UIUtilities.invokeOnEventThread(() -> {
String sith = MessageUtils.showInputDialog("Small indel threshold: ", String.valueOf(renderOptions.getSmallIndelThreshold()));
if (sith != null) {
try {
renderOptions.setSmallIndelThreshold(Integer.parseInt(sith));
alignmentTrack.repaint();
IGV.getInstance().repaintHeaderPanels();
} catch (NumberFormatException exc) {
log.error("Error setting small indel threshold - not an integer", exc);
}
}
}));
add(indelSizeItem);

// Paired end items
if (dataManager.isPairedEnd()) {
addSeparator();
Expand Down
7 changes: 0 additions & 7 deletions src/main/java/org/igv/sam/InsertionManager.java
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Expand Up @@ -65,17 +65,10 @@ public synchronized void processAlignments(String chr, List<Alignment> alignment
insertionMaps.put(chr, insertionMap);
}

int minLength = 0;
final IGVPreferences preferences = PreferencesManager.getPreferences(Constants.THIRD_GEN);
if(preferences.getAsBoolean(SAM_HIDE_SMALL_INDEL)) {
minLength = preferences.getAsInt(SAM_SMALL_INDEL_BP_THRESHOLD);
}

for (Alignment a : alignments) {
AlignmentBlock[] blocks = a.getInsertions();
if (blocks != null) {
for (AlignmentBlock block : blocks) {
if (block.getBasesLength() < minLength) continue;
Integer key = block.getStart();
InsertionMarker insertionMarker = insertionMap.get(key);
if (insertionMarker == null) {
Expand Down
10 changes: 9 additions & 1 deletion src/main/java/org/igv/ui/IGV.java
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Expand Up @@ -1767,7 +1767,6 @@ private static void startCommandsServer(Main.IGVArgs igvArgs, IGVPreferences pre
}
}


/**
* Swing worker class to startup IGV
*/
Expand Down Expand Up @@ -2157,6 +2156,15 @@ public void repaint(Track track) {
}
}

/**
* Repaint all header panels. Used to force update of insertion markers.
*/
public void repaintHeaderPanels() {
getMainPanel().repaintHeaderPanels();
}




private volatile boolean isLoading = false;
private Set<Track> pendingTracks = null;
Expand Down
4 changes: 4 additions & 0 deletions src/main/java/org/igv/ui/panel/MainPanel.java
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Expand Up @@ -577,5 +577,9 @@ public int getSnapshotHeight(boolean batch) {
}
}

public void repaintHeaderPanels() {
headerPanelContainer.repaint();
}


}
64 changes: 49 additions & 15 deletions src/main/java/org/igv/ui/panel/RulerPanel.java
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Expand Up @@ -8,12 +8,13 @@
*/
package org.igv.ui.panel;

import org.igv.logging.*;
import org.igv.Globals;
import org.igv.feature.Chromosome;
import org.igv.feature.genome.ChromosomeCoordinate;
import org.igv.feature.genome.Genome;
import org.igv.feature.genome.GenomeManager;
import org.igv.logging.LogManager;
import org.igv.logging.Logger;
import org.igv.prefs.PreferencesManager;
import org.igv.sam.AlignmentTrack;
import org.igv.sam.InsertionManager;
Expand All @@ -35,7 +36,7 @@
import java.util.List;
import java.util.function.Consumer;

import static org.igv.prefs.Constants.*;
import static org.igv.prefs.Constants.DEFAULT_GENOME;

/**
* @author jrobinso
Expand All @@ -48,28 +49,31 @@ public class RulerPanel extends JPanel {
private static final DecimalFormat DECIMAL_FORMAT = new DecimalFormat();

private static final int INSERTION_ROW_HEIGHT = 9;

public static final String WHOLE_GENOME_TOOLTIP = "<html>Click on a chromosome number to jump to that chromosome," +
"<br>or click and drag to zoom in.";

public static final String CHROM_TOOLTIP = "Click and drag to zoom in.";

private final boolean darkMode;

// TODO -- get from preferences
boolean drawSpan = true;
private Font tickFont = FontManager.getFont(10);
private Font spanFont = FontManager.getFont(Font.BOLD, 12);

private boolean showInsertions = false;
private List<ClickLink> clickLinks = new ArrayList();

private static Color dragColor = new Color(.5f, .5f, 1f, .3f);
private static Color zoomBoundColor = new Color(0.5f, 0.5f, 0.5f);

private Color expandedInsertionColor = Color.BLUE;
private Color collapsedInsertionColor = Color.BLACK;
private Color zoomedoutInsertionColor = ColorUtilities.modifyAlpha(Color.LIGHT_GRAY, 50);
private Color expandedInsertionColor = Globals.isDarkMode() ? Color.BLUE.brighter() : Color.BLUE;
private Color collapsedInsertionColor = Globals.isDarkMode() ? Color.WHITE : Color.BLACK;
private Color zoomedoutInsertionColor = Globals.isDarkMode() ? Color.darkGray : ColorUtilities.modifyAlpha(collapsedInsertionColor, 20);

boolean dragging = false;
int dragStart;
int dragEnd;
public static final String WHOLE_GENOME_TOOLTIP = "<html>Click on a chromosome number to jump to that chromosome," +
"<br>or click and drag to zoom in.";
public static final String CHROM_TOOLTIP = "Click and drag to zoom in.";

ReferenceFrame frame;

Expand All @@ -88,7 +92,7 @@ protected void paintComponent(Graphics g) {

super.paintComponent(g);

if(darkMode) {
if (darkMode) {
setBackground(UIManager.getColor("Panel.background"));
expandedInsertionColor = Color.CYAN;
collapsedInsertionColor = Color.WHITE;
Expand Down Expand Up @@ -132,7 +136,10 @@ private void render(Graphics g) {
Collection<AlignmentTrack> tracks = IGV.getInstance().getAlignmentTracks();
int maxVizWindow = tracks.size() == 0 ? 0 : tracks.stream().mapToInt(t -> t.getVisibilityWindow()).max().getAsInt();
if (!frame.getChrName().equals(Globals.CHR_ALL) && (frame.getEnd() - frame.getOrigin()) <= maxVizWindow) {
showInsertions = true;
drawInsertionMarkers(g);
} else {
showInsertions = false;
}
}
}
Expand Down Expand Up @@ -300,13 +307,24 @@ private void drawInsertionMarkers(Graphics g) {

if (insertionMarkers == null) return;

int minLength = Integer.MAX_VALUE;
boolean hideSmallIndels = false;
for (AlignmentTrack track : IGV.getInstance().getAlignmentTracks()) {
hideSmallIndels = hideSmallIndels || track.getRenderOptions().isHideSmallIndels();
minLength = Math.min(minLength, track.getRenderOptions().getSmallIndelThreshold());
}

InsertionMarker expanded = frame.getExpandedInsertion();

int w = (int) ((1.41 * INSERTION_ROW_HEIGHT) / 2);
int y = getHeight() - INSERTION_ROW_HEIGHT - 1;

for (InsertionMarker insertionMarker : insertionMarkers) {

if (hideSmallIndels && insertionMarker.size < minLength) {
continue;
}

int x0;
int x1;
Polygon p;
Expand All @@ -332,9 +350,10 @@ private void drawInsertionMarkers(Graphics g) {
p = new Polygon(new int[]{x0 - w, x1 + w, x0},
new int[]{y, y, y + INSERTION_ROW_HEIGHT}, 3);


double expandedInsertionWidth = insertionMarker.size / frame.getScale();

if (expandedInsertionWidth > 5) {
if (expandedInsertionWidth > 1) {
c = collapsedInsertionColor;
String tooltipText = "Click to expand insertion (" + (insertionMarker.size + "bases)");
Rectangle clickArea = p.getBounds();
Expand All @@ -349,7 +368,7 @@ private void drawInsertionMarkers(Graphics g) {
}
}

if (x1 + w >= 0 && x0 - w <= getWidth()) {
if (x1 + w >= 0 && x0 - w <= getWidth() && c != null) {
g.setColor(c);
g.fillPolygon(p);
}
Expand Down Expand Up @@ -419,9 +438,12 @@ public void mouseMoved(MouseEvent e) {
return;
}
}
if(inInsertionArea(e)) {
// In insertion area
return;
}
setCursor(Cursor.getDefaultCursor());
setToolTipText(isWholeGenomeView() ? WHOLE_GENOME_TOOLTIP : CHROM_TOOLTIP);

}

@Override
Expand All @@ -437,6 +459,9 @@ public void mouseEntered(MouseEvent e) {

@Override
public void mouseDragged(MouseEvent e) {
if(inInsertionArea(e)) {
return;
}
if (Math.abs(e.getPoint().getX() - dragStart) > 1) {
dragEnd = e.getX();
dragging = true;
Expand All @@ -449,12 +474,13 @@ public void mousePressed(final MouseEvent e) {
if (e.isPopupTrigger()) {
// ignore
} else {
dragStart = e.getX();
if(!inInsertionArea(e)){
dragStart = e.getX();
}
mouseDown = e;
}
}


@Override
public void mouseReleased(MouseEvent e) {
if (e.isPopupTrigger()) {
Expand All @@ -472,6 +498,10 @@ public void mouseReleased(MouseEvent e) {
}
}

private boolean inInsertionArea(MouseEvent e) {
return showInsertions && e.getY() >= getHeight() - INSERTION_ROW_HEIGHT - 1;
}

private double distance(MouseEvent e1, MouseEvent e2) {
double dx = e1.getX() - e2.getX();
double dy = e1.getY() - e2.getY();
Expand All @@ -497,6 +527,10 @@ public void doMouseClick(MouseEvent evt) {
clickHandled = true;
}
}
if(showInsertions && e.getY() >= getHeight() - INSERTION_ROW_HEIGHT) {
// In insertion area
return;
}
if (!clickHandled && !isWholeGenomeView()) {
double newLocation = frame.getChromosomePosition(e);
frame.centerOnLocation(newLocation);
Expand Down
5 changes: 4 additions & 1 deletion src/test/java/org/igv/sam/AlignmentTileLoaderTest.java
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Expand Up @@ -2,6 +2,7 @@

import org.igv.AbstractHeadlessTest;
import org.igv.prefs.Constants;
import org.igv.prefs.IGVPreferences;
import org.igv.prefs.PreferencesManager;
import org.igv.sam.reader.AlignmentReader;
import org.igv.sam.reader.AlignmentReaderFactory;
Expand Down Expand Up @@ -79,7 +80,9 @@ private AlignmentTileLoader.AlignmentTile tstKeepPairsDownsample(String path, St

AlignmentDataManager.DownsampleOptions downsampleOptions = new AlignmentDataManager.DownsampleOptions(true, 50, actMaxDepth);

AlignmentTileLoader.AlignmentTile tile = loader.loadTile(sequence, start, end, null, downsampleOptions, null, null, null);
IGVPreferences preferences = new IGVPreferences();
AlignmentTileLoader.AlignmentTile tile = loader.loadTile(sequence, start, end, null,
downsampleOptions, null, null, null, preferences);
List<Alignment> alignments = tile.getAlignments();
int count = 0;
Map<String, Integer> pairedReads = new HashMap<String, Integer>();
Expand Down
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