igvteam · jrobinso · Jun 26, 2026 · Jun 15, 2026 · Jun 26, 2026
diff --git a/examples/web/StaticLinkExamples.html b/examples/web/StaticLinkExamples.html
@@ -7,6 +7,12 @@
 <body>
 
 <h2>IGV desktop links</h2>
+<p>
+    <a href = "http://localhost:60151/load?file=https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12878/alignment/NA12878.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram">Load Cram (hg38)</a>
+</p>
+<p>
+    <a href = "http://localhost:60151/goto?locus=MYC">Goto MYC</a>
+</p>
 <p>
     <a href="http://localhost:60151/load?genome=hg38&locus=chr8:127733434-127744951&file=https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.bb,https://hgdownload.soe.ucsc.edu/gbdb/hg38/ncbiRefSeq/ncbiRefSeqOther.bb&name=Known genes, Refseq other">
         Load multiple files, new session, specify genome and locaus</a>

diff --git a/src/main/java/org/igv/batch/CommandListener.java b/src/main/java/org/igv/batch/CommandListener.java
@@ -39,6 +39,7 @@ public class CommandListener implements Runnable {
     private static final String NO_CACHE = "Cache-Control: no-cache, no-store";
     private static final String ACCESS_CONTROL_ALLOW_ORIGIN = "Access-Control-Allow-Origin: *";
     private static final String ACCESS_CONTROL_ALLOW_HEADERS = "Access-Control-Allow-Headers: access-control-allow-origin";
+    private static final String ACCESS_CONTROL_PRIVATE_NETWORK = "Access-Control-Allow-Private-Network: true";
 
 
     private int port = -1;
@@ -299,6 +300,8 @@ private void sendHTTPResponse(PrintWriter out, String result, String contentType
         out.print(CRLF);
         out.print(ACCESS_CONTROL_ALLOW_ORIGIN);
         out.print(CRLF);
+        out.print(ACCESS_CONTROL_PRIVATE_NETWORK);
+        out.print(CRLF);
         if (result != null) {
             out.print("Content-Type: " + contentType);
             out.print(CRLF);
@@ -328,7 +331,10 @@ private void sendHTTPOptionsResponse(PrintWriter out) {
         out.print(CRLF);
         out.print(ACCESS_CONTROL_ALLOW_HEADERS);
         out.print(CRLF);
-        out.println("Access-Control-Allow-Methods: HEAD, GET, OPTIONS");
+        out.print(ACCESS_CONTROL_PRIVATE_NETWORK);
+        out.print(CRLF);
+        out.print("Access-Control-Allow-Methods: HEAD, GET, OPTIONS");
+        out.print(CRLF);
         out.print(CRLF);
 
         out.close();

diff --git a/src/main/java/org/igv/bedpe/InteractionTrack.java b/src/main/java/org/igv/bedpe/InteractionTrack.java
@@ -3,7 +3,7 @@
 import org.igv.Globals;
 import org.igv.event.IGVEvent;
 import org.igv.event.IGVEventObserver;
-import org.igv.jbrowse.CircularViewUtilities;
+import org.igv.circview.CircularViewUtilities;
 import org.igv.logging.LogManager;
 import org.igv.logging.Logger;
 import org.igv.prefs.Constants;
@@ -414,21 +414,18 @@ public List<Component> getPopupMenuItems(TrackClickEvent te) {
             items.add(TrackMenuUtils.getChangeFeatureWindow(Collections.singletonList(this)));
 
 
-            // Experimental JBrowse.
-            if (PreferencesManager.getPreferences().getAsBoolean(Constants.CIRC_VIEW_ENABLED) &&
-                    CircularViewUtilities.ping()) {
-                items.add(new JPopupMenu.Separator());
-                JMenuItem circViewItem = new JMenuItem("Add Features to Circular View");
-                circViewItem.addActionListener(e -> {
-                    List<ReferenceFrame> frames = te.getFrame() != null ?
-                            Collections.singletonList(te.getFrame()) :
-                            FrameManager.getFrames();
-                    List<? extends BedPE> visibleFeatures = getVisibleFeatures(frames);
-                    CircularViewUtilities.sendBedpeToJBrowse(visibleFeatures, InteractionTrack.this.getName(), InteractionTrack.this.getColor());
-                });
-                items.add(circViewItem);
-                items.add(new JPopupMenu.Separator());
-            }
+            // Circular view
+            items.add(new JPopupMenu.Separator());
+            JMenuItem circViewItem = new JMenuItem("Add Features to Circular View");
+            circViewItem.addActionListener(e -> {
+                List<ReferenceFrame> frames = te.getFrame() != null ?
+                        Collections.singletonList(te.getFrame()) :
+                        FrameManager.getFrames();
+                List<? extends BedPE> visibleFeatures = getVisibleFeatures(frames);
+                CircularViewUtilities.addBedPE(visibleFeatures, InteractionTrack.this.getName(), InteractionTrack.this.getColor());
+            });
+            items.add(circViewItem);
+            items.add(new JPopupMenu.Separator());
         }
 
         return items;

diff --git a/src/main/java/org/igv/circview/CircularViewUtilities.java b/src/main/java/org/igv/circview/CircularViewUtilities.java
@@ -0,0 +1,246 @@
+package org.igv.circview;
+
+import htsjdk.samtools.SAMTag;
+import htsjdk.tribble.Feature;
+import org.igv.bedpe.BedPE;
+import org.igv.circview.model.Assembly;
+import org.igv.circview.model.Chord;
+import org.igv.circview.model.Chromosome;
+import org.igv.circview.model.Mate;
+import org.igv.circview.ui.CircularView;
+import org.igv.circview.ui.CircularViewConfig;
+import org.igv.circview.ui.CircularViewPanel;
+import org.igv.circview.util.ChrColors;
+import org.igv.circview.util.ColorUtils;
+import org.igv.feature.genome.Genome;
+import org.igv.feature.genome.GenomeManager;
+import org.igv.sam.Alignment;
+import org.igv.ui.IGV;
+import org.igv.util.Downsampler;
+import org.igv.variant.Variant;
+import org.igv.variant.vcf.MateVariant;
+
+import javax.swing.JFrame;
+import javax.swing.SwingUtilities;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+/**
+ * Bridge between IGV and the in-process {@link CircularView} widget.
+ *
+ * <p>This replaces the JBrowse/Electron based {@code org.igv.jbrowse.CircularViewUtilities},
+ * which spoke to an external app over a socket. The view is now a singleton Swing
+ * {@link JFrame} owned by this class; tracks add chords through the static
+ * {@code add*} methods, and the window is created and shown lazily on the first add.
+ *
+ * <p>Chord features are built from IGV model objects via the {@code Chord.from*}
+ * factory methods (the same conversions the old code used), then downsampled to
+ * {@link #MAX_CHORDS} to keep rendering responsive.
+ */
+public class CircularViewUtilities {
+
+    /**
+     * Maximum number of chords to render in a single set.
+     */
+    static int MAX_CHORDS = 10000;
+
+    /**
+     * Flanking bases added on each side when navigating to a clicked chord's regions.
+     */
+    private static final int CLICK_FLANKING = 2000;
+
+    // Singleton view + window, lazily created on the EDT.
+    private static CircularView view;
+    private static CircularViewPanel panel;
+    private static JFrame frame;
+
+    /**
+     * Id of the genome currently set as the assembly, to avoid needless resets.
+     */
+    private static String currentGenomeId;
+
+    private CircularViewUtilities() {
+    }
+
+    // ---- Public API ---------------------------------------------------------
+
+    /**
+     * True if the circular view window currently exists and is showing.
+     */
+    public static boolean isOpen() {
+        return frame != null && frame.isVisible();
+    }
+
+    public static void addBedPE(List<? extends BedPE> features, String trackName, Color color) {
+        List<Chord> chords = new ArrayList<>(features.size());
+        for (BedPE f : features) {
+            chords.add(Chord.fromBedPE(f));
+        }
+        addChords(chords, trackName, color, 0.5f);
+    }
+
+    public static void addAlignments(List<Alignment> alignments, String trackName, Color color) {
+        List<Chord> chords = new ArrayList<>();
+        for (Alignment a : alignments) {
+            if (a.isPaired() && a.getMate().isMapped()) {
+                chords.add(Chord.fromPEAlignment(a));
+            }
+            if (a.getAttribute(SAMTag.SA.name()) != null) {
+                chords.addAll(Chord.fromSAString(a));
+            }
+        }
+        addChords(chords, trackName, color, 0.1f);
+    }
+
+    public static void addVariants(List<Feature> variants, String trackName, Color color) {
+        List<Chord> chords = new ArrayList<>(variants.size());
+        for (Feature f : variants) {
+            if (f instanceof Variant) {
+                Variant v = f instanceof MateVariant ? ((MateVariant) f).mate : (Variant) f;
+                chords.add(Chord.fromVariant(v));
+            }
+        }
+        addChords(chords, trackName, color, 0.5f);
+    }
+
+    /**
+     * Add a set of chords to the view, opening (and creating) the window if needed.
+     *
+     * @param chords    the chord features
+     * @param trackName name for this chord set / track row
+     * @param color     base color; {@code alpha} is applied to it
+     * @param alpha     opacity fraction in [0, 1]
+     */
+    public static void addChords(List<Chord> chords, String trackName, Color color, float alpha) {
+        Chord[] arr = chords.toArray(new Chord[0]);
+        if (arr.length > MAX_CHORDS) {
+            arr = new Downsampler<Chord>().sample(arr, MAX_CHORDS);
+        }
+        final List<Chord> sampled = new ArrayList<>(Arrays.asList(arr));
+        final Color c = ColorUtils.setAlpha(color, alpha);
+        runOnEdt(() -> {
+            CircularView v = getInstance();
+            ensureAssembly(v);
+            v.addChords(sampled, trackName, c);
+            open();
+        });
+    }
+
+    /**
+     * Update the assembly to the given genome. No-op unless the view already
+     * exists; on a genome switch the previously added chords no longer apply, so
+     * this resets the view (matching {@link CircularView#setAssembly}).
+     */
+    public static void changeGenome(Genome genome) {
+        if (view == null || genome == null) {
+            return;
+        }
+        runOnEdt(() -> {
+            view.setAssembly(toAssembly(genome));
+            currentGenomeId = genome.getId();
+        });
+    }
+
+    public static void clearChords() {
+        if (view != null) {
+            runOnEdt(view::clearChords);
+        }
+    }
+
+    // ---- Internals ----------------------------------------------------------
+
+    /**
+     * Lazily create the singleton view and its window. Must run on the EDT.
+     */
+    private static CircularView getInstance() {
+        if (view == null) {
+            CircularViewConfig config = new CircularViewConfig();
+            config.onChordClick = CircularViewUtilities::onChordClick;
+
+            view = new CircularView(config);
+            panel = new CircularViewPanel(view);
+
+            frame = new JFrame("Circular View");
+            frame.setDefaultCloseOperation(JFrame.HIDE_ON_CLOSE);
+            frame.setContentPane(panel);
+            frame.pack();
+            frame.setLocationRelativeTo(IGV.hasInstance() ? IGV.getInstance().getMainFrame() : null);
+        }
+        return view;
+    }
+
+    /**
+     * Must run on the event thread
+     */
+    public static void open() {
+        if (frame == null) {
+            getInstance();
+        }
+        if (!frame.isVisible()) {
+            frame.setVisible(true);
+        }
+        frame.toFront();
+
+    }
+
+    /**
+     * Set the assembly from the current genome if it differs from what's shown.
+     */
+    private static void ensureAssembly(CircularView v) {
+        Genome genome = GenomeManager.getInstance().getCurrentGenome();
+        if (genome != null && !genome.getId().equals(currentGenomeId)) {
+            v.setAssembly(toAssembly(genome));
+            currentGenomeId = genome.getId();
+        }
+    }
+
+    /**
+     * Convert an IGV genome to a circular-view {@link Assembly}. Only the "long"
+     * (whole-genome) chromosomes are drawn; names are shortened so they match the
+     * shortened {@code refName}s on the chords.
+     */
+    private static Assembly toAssembly(Genome genome) {
+        List<Chromosome> chromosomes = new ArrayList<>();
+        for (String chr : genome.getLongChromosomeNames()) {
+            org.igv.feature.Chromosome c = genome.getChromosome(chr);
+            String shortName = Chromosome.shortChrName(chr);
+            chromosomes.add(new Chromosome(shortName, c.getLength(), ChrColors.getChrColor(shortName)));
+        }
+        return new Assembly(genome.getDisplayName(), genome.getId(), chromosomes);
+    }
+
+    /**
+     * Navigate IGV to a clicked chord's two regions (with flanking), shown
+     * side-by-side. Port of the onChordClick callback in circularView.js.
+     */
+    private static void onChordClick(Chord feature) {
+        if (!IGV.hasInstance()) {
+            return;
+        }
+        Mate mate = feature.getMate();
+        if (mate == null) {
+            return;
+        }
+        Genome genome = GenomeManager.getInstance().getCurrentGenome();
+        String locus1 = locusString(genome, feature.getRefName(), feature.getStart(), feature.getEnd());
+        String locus2 = locusString(genome, mate.getRefName(), mate.getStart(), mate.getEnd());
+        IGV.getInstance().goToLocus(locus1 + " " + locus2);
+    }
+
+    private static String locusString(Genome genome, String refName, long start, long end) {
+        String chr = (genome != null) ? genome.getCanonicalChrName(refName) : refName;
+        long s = Math.max(0, start - CLICK_FLANKING);
+        long e = end + CLICK_FLANKING;
+        return chr + ":" + s + "-" + e;
+    }
+
+    private static void runOnEdt(Runnable r) {
+        if (SwingUtilities.isEventDispatchThread()) {
+            r.run();
+        } else {
+            SwingUtilities.invokeLater(r);
+        }
+    }
+}