Update with many changes to improve supplemental alignment display an…

…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.
igvteam · Nov 15, 2023 · b57c9ed · b57c9ed
1 parent 175f234
commit b57c9ed
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diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -7,6 +7,7 @@
     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;

diff --git a/src/main/java/org/broad/igv/jbrowse/Chord.java b/src/main/java/org/broad/igv/jbrowse/Chord.java
@@ -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);
             }
         }

diff --git a/src/main/java/org/broad/igv/lists/GeneList.java b/src/main/java/org/broad/igv/lists/GeneList.java
@@ -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;
 
@@ -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) {
@@ -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;
     }
@@ -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);
         }
     }

diff --git a/src/main/java/org/broad/igv/sam/AlignmentDataManager.java b/src/main/java/org/broad/igv/sam/AlignmentDataManager.java
@@ -266,7 +266,7 @@ 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;
@@ -359,8 +359,10 @@ public void load(ReferenceFrame frame,
             currentlyLoading = null;
         }
 
+
         IGVEventBus.getInstance().post(new DataLoadedEvent(frame));
 
+
     }
 
     /**

diff --git a/src/main/java/org/broad/igv/sam/AlignmentRenderer.java b/src/main/java/org/broad/igv/sam/AlignmentRenderer.java
@@ -944,10 +944,10 @@ private static void drawClippedEnds(final Graphics2D g, final int[] xPoly, final
         try {
             //left side
             if (drawLeftClip) {
-                if (sri != null && sri.previous != null) {
-                    final SupplementaryAlignment previous = sri.previous;
-                    if (previous.contigsMatch(sri.alignment)) {
-                        g.setColor(previous.getStrand() == sri.alignment.getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
+                if (sri != null && sri.previous() != null) {
+                    final SupplementaryAlignment previous = sri.previous();
+                    if (previous.contigsMatch(sri.alignment())) {
+                        g.setColor(previous.getStrand() == sri.alignment().getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
                     } else {
                         if (previous.getContig() != null) {
                             g.setColor(ChromosomeColors.getColor(previous.getContig()));
@@ -969,11 +969,11 @@ private static void drawClippedEnds(final Graphics2D g, final int[] xPoly, final
             }
             //right side
             if (drawRightClip) {
-                if (sri != null && sri.next != null) {
-                    final SupplementaryAlignment next = sri.next;
-                    if (next.contigsMatch(sri.alignment)) {
+                if (sri != null && sri.next() != null) {
+                    final SupplementaryAlignment next = sri.next();
+                    if (next.contigsMatch(sri.alignment())) {
                         //TODO Set to scaled color by contig position
-                        g.setColor(next.getStrand() == sri.alignment.getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
+                        g.setColor(next.getStrand() == sri.alignment().getReadStrand() ? NON_INVERSION_COLOR : INVERSION_COLOR);
                     } else {
                         g.setColor(ChromosomeColors.getColor(next.getContig()));
                         rightContigLabel = next.getContig();

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrack.java b/src/main/java/org/broad/igv/sam/AlignmentTrack.java
@@ -54,6 +54,7 @@
 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;
@@ -83,6 +84,14 @@ 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,
@@ -189,7 +198,7 @@ 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 {
@@ -382,11 +391,13 @@ public void receiveEvent(IGVEvent event) {
                 }
                 case REFRESH -> repaint();
             }
-        } else if (event instanceof final DataLoadedEvent dataLoaded) {
-            actionToPerformOnFrameLoad.computeIfPresent(dataLoaded.referenceFrame(), (k, v) -> {
-                v.accept(k);
-                return null;
-            });
+        } else if (event instanceof DataLoadedEvent dataLoaded) {
+            if (dataManager.isLoaded(dataLoaded.referenceFrame())) {
+                actionToPerformOnFrameLoad.computeIfPresent(dataLoaded.referenceFrame(), (k, v) -> {
+                    v.accept(k);
+                    return null; //remove this action from the map
+                });
+            }
         }
     }
 
@@ -468,7 +479,7 @@ 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);
     }
 
@@ -535,7 +546,7 @@ 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);
@@ -687,7 +698,7 @@ 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);
@@ -904,7 +915,7 @@ 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);
     }

diff --git a/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java b/src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java
@@ -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;
@@ -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);
@@ -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());
@@ -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);
@@ -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.");
@@ -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

diff --git a/src/main/java/org/broad/igv/sam/SAMAlignment.java b/src/main/java/org/broad/igv/sam/SAMAlignment.java
@@ -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;
@@ -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();
     }