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Update with many changes to improve supplemental alignment display an…
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…d navigation.

Major rework of the previous alignment dialog popup to make it interactive and clearer.
Use it to navigate between reads in a supplemenary alignment group.
   Click to move to the selected read.
   Shift + Click to add it as a split screen.

When jumping to a selected read/mate the selected reads will be now be sorted to the top.

Renamed several classes and moved them to the ui/supdiagram package
Refactoring some methods around Frame creation, this could still be improved.
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@lbergelson
lbergelson committed Oct 19, 2023
1 parent 2d82d8e commit 3156369
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Showing 17 changed files with 877 additions and 422 deletions.
1 change: 1 addition & 0 deletions src/main/java/module-info.java
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Expand Up @@ -6,6 +6,7 @@
exports org.broad.igv.logging;
exports org.broad.igv.util.liftover;
exports org.broad.igv.sam.smrt;
exports org.broad.igv.ui.supdiagram;

requires com.google.common;
requires commons.math3;
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2 changes: 1 addition & 1 deletion src/main/java/org/broad/igv/jbrowse/Chord.java
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Expand Up @@ -65,7 +65,7 @@ public static List<Chord> fromSAString(Alignment a) {
c.refName = shortName(a.getChr());
c.start = a.getStart();
c.end = a.getEnd();
c.mate = new Mate(shortName(sa.chr), sa.start, sa.start + sa.getLenOnRef());
c.mate = new Mate(shortName(sa.chr), sa.start, sa.start + sa.getLengthOnReference());
chords.add(c);
}
}
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19 changes: 7 additions & 12 deletions src/main/java/org/broad/igv/lists/GeneList.java
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,6 @@
package org.broad.igv.lists;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;

Expand All @@ -43,7 +42,11 @@ public class GeneList {
private List<String> loci;

public GeneList(String name, String description, String group, List<String> loci) {
init(name, description, group, loci);
this.group = group;
this.description = description;
this.name = name;
//We do this to guarantee that certain operations will be supported
this.loci = loci;
}

public GeneList(String name, List<String> loci) {
Expand All @@ -54,14 +57,6 @@ public GeneList() {
this.group = GeneListManager.USER_GROUP;
}

private void init(String name, String description, String group, List<String> loci) {
this.group = group;
this.description = description;
this.name = name;
//We do this to guarantee that certain operations will be supported
this.loci = loci;
}

public String getName() {
return name;
}
Expand All @@ -76,13 +71,13 @@ public int size() {

public void add(String gene) {
if (loci == null) {
loci = new ArrayList<String>(1);
loci = new ArrayList<>(1);
}
try {
//Can't guarantee that list will support this operation
loci.add(gene);
} catch (Exception e) {
loci = new ArrayList<String>(loci);
loci = new ArrayList<>(loci);
loci.add(gene);
}
}
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4 changes: 3 additions & 1 deletion src/main/java/org/broad/igv/sam/AlignmentDataManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -265,7 +265,7 @@ public AlignmentInterval getLoadedInterval(ReferenceFrame frame) {
}

public AlignmentInterval getLoadedInterval(ReferenceFrame frame, boolean includeOverlaps) {
// Search for interval completely containining reference frame region
// Search for interval completely containing reference frame region
for (AlignmentInterval interval : intervalCache) {
if (interval.contains(frame.getCurrentRange())) {
return interval;
Expand Down Expand Up @@ -358,8 +358,10 @@ public void load(ReferenceFrame frame,
currentlyLoading = null;
}


IGVEventBus.getInstance().post(new DataLoadedEvent(frame));


}

/**
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25 changes: 16 additions & 9 deletions src/main/java/org/broad/igv/sam/AlignmentTrack.java
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Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.MessageUtils;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.StringUtils;
import org.broad.igv.util.blat.BlatClient;
Expand Down Expand Up @@ -82,6 +83,14 @@ public class AlignmentTrack extends AbstractTrack implements IGVEventObserver {
// Alignment colors
static final Color DEFAULT_ALIGNMENT_COLOR = new Color(185, 185, 185); //200, 200, 200);

public static void sortSelectedReadsToTheTop(final Set<String> selectedReadNames) {
//copy this in case it changes out from under us
Set<String> selectedReadNameCopy = new HashSet<>(selectedReadNames);
//Run this on the event thread to make sure it happens after loading begins
UIUtilities.invokeOnEventThread(() ->
IGV.getInstance().sortAlignmentTracks(SortOption.NONE, null, null, false, selectedReadNameCopy));
}

public enum ColorOption {
INSERT_SIZE,
READ_STRAND,
Expand Down Expand Up @@ -188,7 +197,7 @@ enum OrientationType {
private static final int GROUP_MARGIN = 5;
private static final int TOP_MARGIN = 20;
private static final int DS_MARGIN_0 = 2;
private static final int DOWNAMPLED_ROW_HEIGHT = 3;
private static final int DOWNSAMPLED_ROW_HEIGHT = 3;
private static final int INSERTION_ROW_HEIGHT = 9;

public enum BisulfiteContext {
Expand Down Expand Up @@ -373,8 +382,7 @@ public void receiveEvent(Object event) {
// Trim insertionInterval map to current frames


} else if (event instanceof AlignmentTrackEvent) {
AlignmentTrackEvent e = (AlignmentTrackEvent) event;
} else if (event instanceof AlignmentTrackEvent e) {
AlignmentTrackEvent.Type eventType = e.getType();
switch (eventType) {
case ALLELE_THRESHOLD:
Expand All @@ -388,8 +396,7 @@ public void receiveEvent(Object event) {
break;
}

} else if (event instanceof DataLoadedEvent) {
final DataLoadedEvent dataLoaded = (DataLoadedEvent) event;
} else if (event instanceof DataLoadedEvent dataLoaded) {
actionToPerformOnFrameLoad.computeIfPresent(dataLoaded.getReferenceFrame(), (k, v) -> {
v.accept(k);
return null;
Expand Down Expand Up @@ -475,7 +482,7 @@ public int getHeight() {

int nGroups = dataManager.getMaxGroupCount();
int h = Math.max(minHeight, getNLevels() * getRowHeight() + nGroups * GROUP_MARGIN + TOP_MARGIN
+ DS_MARGIN_0 + DOWNAMPLED_ROW_HEIGHT);
+ DS_MARGIN_0 + DOWNSAMPLED_ROW_HEIGHT);
return Math.max(minimumHeight, h);
}

Expand Down Expand Up @@ -542,7 +549,7 @@ public void render(RenderContext context, Rectangle rect) {
rect.y += DS_MARGIN_0;

downsampleRect = new Rectangle(rect);
downsampleRect.height = DOWNAMPLED_ROW_HEIGHT;
downsampleRect.height = DOWNSAMPLED_ROW_HEIGHT;
renderDownsampledIntervals(context, downsampleRect);

alignmentsRect = new Rectangle(rect);
Expand Down Expand Up @@ -694,7 +701,7 @@ private void renderAlignments(RenderContext context, Rectangle inputRect) {
public void renderExpandedInsertion(InsertionMarker insertionMarker, RenderContext context, Rectangle inputRect) {

boolean leaveMargin = getDisplayMode() != DisplayMode.SQUISHED;
inputRect.y += DS_MARGIN_0 + DOWNAMPLED_ROW_HEIGHT + DS_MARGIN_0;
inputRect.y += DS_MARGIN_0 + DOWNSAMPLED_ROW_HEIGHT + DS_MARGIN_0;

final AlignmentInterval loadedInterval = dataManager.getLoadedInterval(context.getReferenceFrame(), true);
PackedAlignments groups = dataManager.getGroups(loadedInterval, renderOptions);
Expand Down Expand Up @@ -911,7 +918,7 @@ public boolean handleDataClick(TrackClickEvent te) {
return false;
}

void setSelectedAlignment(Alignment alignment) {
public void setSelectedAlignment(Alignment alignment) {
Color c = readNamePalette.get(alignment.getReadName());
selectedReadNames.put(alignment.getReadName(), c);
}
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73 changes: 7 additions & 66 deletions src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java
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Original file line number Diff line number Diff line change
@@ -1,26 +1,24 @@
package org.broad.igv.sam;

import htsjdk.samtools.SAMTag;
import htsjdk.samtools.util.Locatable;
import org.broad.igv.Globals;
import org.broad.igv.feature.Locus;
import org.broad.igv.feature.Range;
import org.broad.igv.feature.Strand;
import org.broad.igv.jbrowse.CircularViewUtilities;
import org.broad.igv.lists.GeneList;
import org.broad.igv.logging.LogManager;
import org.broad.igv.logging.Logger;
import org.broad.igv.prefs.Constants;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.sam.mods.BaseModficationFilter;
import org.broad.igv.sam.mods.BaseModificationKey;
import org.broad.igv.sam.mods.BaseModificationUtils;
import org.broad.igv.sashimi.SashimiPlot;
import org.broad.igv.tools.PFMExporter;
import org.broad.igv.track.SequenceTrack;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackClickEvent;
import org.broad.igv.track.TrackMenuUtils;
import org.broad.igv.ui.AlignmentDiagramFrame;
import org.broad.igv.ui.supdiagram.SupplementaryAlignmentDiagramDialog;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.InsertSizeSettingsDialog;
import org.broad.igv.ui.panel.FrameManager;
Expand Down Expand Up @@ -203,7 +201,7 @@ private void addShowChimericRegions(final AlignmentTrack alignmentTrack, final T
try {
List<SupplementaryAlignment> supplementaryAlignments = SupplementaryAlignment.parseFromSATag(saTag);
alignmentTrack.setSelectedAlignment(clickedAlignment);
addNewLociToFrames(e.getFrame(), supplementaryAlignments, alignmentTrack.getSelectedReadNames().keySet());
FrameManager.addNewLociToFrames(e.getFrame(), supplementaryAlignments, alignmentTrack.getSelectedReadNames().keySet());
} catch (final Exception ex) {
MessageUtils.showMessage("Failed to handle SA tag: " + saTag + " due to " + ex.getMessage());
item.setEnabled(false);
Expand All @@ -221,7 +219,7 @@ private void addShowDiagram(final TrackClickEvent e, final Alignment clickedAlig
item.setEnabled(true);
item.addActionListener(aEvt -> {
try {
final AlignmentDiagramFrame frame = new AlignmentDiagramFrame(clickedAlignment, new Dimension(500, 100));
final SupplementaryAlignmentDiagramDialog frame = new SupplementaryAlignmentDiagramDialog(IGV.getInstance().getMainFrame(), clickedAlignment, new Dimension(500, 250));
frame.setVisible(true);
} catch (final Exception ex) {
MessageUtils.showMessage("Failed to handle SA tag: " + clickedAlignment.getAttribute(SAMTag.SA.name()) + " due to " + ex.getMessage());
Expand Down Expand Up @@ -683,7 +681,7 @@ void addColorByMenuItem() {
// Base modifications
JRadioButtonMenuItem bmMenuItem;

Set<String> allModifications = dataManager.getAllBaseModificationKeys().stream().map(bmKey -> bmKey.getModification()).collect(Collectors.toSet());
Set<String> allModifications = dataManager.getAllBaseModificationKeys().stream().map(BaseModificationKey::getModification).collect(Collectors.toSet());
if (allModifications.size() > 0) {
BaseModficationFilter filter = renderOptions.getBasemodFilter();
boolean groupByStrand = alignmentTrack.getPreferences().getAsBoolean(BASEMOD_GROUP_BY_STRAND);
Expand Down Expand Up @@ -1228,7 +1226,7 @@ private void gotoMate(final ReferenceFrame frame, Alignment alignment) {
int newStart = (int) Math.max(0, (start + (alignment.getEnd() - alignment.getStart()) / 2 - range / 2));
int newEnd = newStart + (int) range;
frame.jumpTo(chr, newStart, newEnd);
sortSelectedReadsToTheTop(alignmentTrack.getSelectedReadNames().keySet());
AlignmentTrack.sortSelectedReadsToTheTop(alignmentTrack.getSelectedReadNames().keySet());
frame.recordHistory();
} else {
MessageUtils.showMessage("Alignment does not have mate, or it is not mapped.");
Expand All @@ -1246,70 +1244,13 @@ private void splitScreenMate(ReferenceFrame frame, Alignment alignment) {
ReadMate mate = alignment.getMate();
if (mate != null && mate.isMapped()) {
alignmentTrack.setSelectedAlignment(alignment);
addNewLociToFrames(frame, List.of(mate), alignmentTrack.getSelectedReadNames().keySet());
FrameManager.addNewLociToFrames(frame, List.of(mate), alignmentTrack.getSelectedReadNames().keySet());
} else {
MessageUtils.showMessage("Alignment does not have mate, or it is not mapped.");
}
}
}

private static void addNewLociToFrames(final ReferenceFrame frame, final List<? extends Locatable> toIncludeInSplit, final Set<String> selectedReadNames) {
final List<String> newLoci = toIncludeInSplit.stream()
.map(locatable -> getLocusStringForAlignment(frame, locatable))
.collect(Collectors.toList());
List<String> loci = createLociList(frame, newLoci);
String listName = String.join(" ", loci); // TODO check the trailing " " was unnecessary
//Need to sort the frames by position
GeneList geneList = new GeneList(listName, loci);
geneList.sort(Comparator.comparing(Locus::fromString, SortOption.POSITION_COMPARATOR));
IGV.getInstance().getSession().setCurrentGeneList(geneList);
IGV.getInstance().resetFrames();

/*
We want the sort to happen after the frame refresh / track loading begins.
This puts the sort onto the event thread so that it happens after loading has already started.
Since loading reads happens asynchronously on a different thread from the event thread, it is likely
that the loading won't be done by the time the sort fires. In that case the sort will be set as the
action to perform when the load is finished
See {@link AlignmentTrack#sortRows(SortOption, Double, String, boolean, Set)}
*/
sortSelectedReadsToTheTop(selectedReadNames);
}

private static void sortSelectedReadsToTheTop(final Set<String> selectedReadNames) {
//copy this in case it changes out from under us
Set<String> selectedReadNameCopy = new HashSet<>(selectedReadNames);
UIUtilities.invokeOnEventThread(() ->
IGV.getInstance().sortAlignmentTracks(SortOption.NONE, null, null, false, selectedReadNameCopy));
}

private static List<String> createLociList(final ReferenceFrame frame, final List<String> lociToAdd) {
final List<String> loci = new ArrayList<>(FrameManager.getFrames().size() + lociToAdd.size());
if (FrameManager.isGeneListMode()) {
for (ReferenceFrame ref : FrameManager.getFrames()) {
//If the frame-name is a locus, we use it unaltered
//Don't want to reprocess, easy to get off-by-one
String name = ref.getName();
loci.add(Locus.fromString(name) != null ? name : ref.getFormattedLocusString());
}
} else {
loci.add(frame.getFormattedLocusString());
}
loci.addAll(lociToAdd);
return loci;
}

private static String getLocusStringForAlignment(final ReferenceFrame frame, final Locatable alignment) {
int adjustedMateStart = alignment.getStart() - 1;

// Generate a locus string for the alignment. Keep the window width (in base pairs) == to the current range
Range range = frame.getCurrentRange();
int length = range.getLength();
int start = Math.max(0, adjustedMateStart - length / 2);
int end = start + length;
return Locus.getFormattedLocusString(alignment.getContig(), start, end);
}


/**
* Get the most "specific" alignment at the specified location. Specificity refers to the smallest alignment
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11 changes: 5 additions & 6 deletions src/main/java/org/broad/igv/sam/SAMAlignment.java
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Original file line number Diff line number Diff line change
Expand Up @@ -974,7 +974,7 @@ private String getMlTagString(SAMRecord.SAMTagAndValue tag) {

private String getSupplAlignmentString() {
StringBuilder sb = new StringBuilder();
sb.append("SupplementaryAlignments");
sb.append("Supplementary Alignments");
final List<SupplementaryAlignment> supplementaryAlignments = getSupplementaryAlignments();
final int insertionIndex = SupplementaryAlignment.getInsertionIndex(this, supplementaryAlignments);
int i = 0;
Expand All @@ -996,14 +996,13 @@ private String getSupplAlignmentString() {
}

private String getThisReadDescriptionForSAList() {
return "<br>" +
"<b>"
return "<br>"
+ "<b>"
+ chr + ":" + Globals.DECIMAL_FORMAT.format(getAlignmentStart() + 1) + "-" + Globals.DECIMAL_FORMAT.format(getAlignmentEnd())
+ " (" + getReadStrand().toShortString() + ")" +
"</b>";
+ " (" + this.getReadStrand().toShortString() + ") = " + Globals.DECIMAL_FORMAT.format(getLengthOnReference()) + "bp @MAPQ " + this.getMappingQuality() + " NM" + getAttribute(SAMTag.NM)
+ "</b>";
}


public float getScore() {
return getMappingQuality();
}
Expand Down
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