Panels

.gitignore

@@ -5,3 +5,4 @@
 
 #JENV local config file
 .java-version
+/test/batch/snapshots/

CLAUDE.md

@@ -0,0 +1,68 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Overview
+
+IGV (Integrative Genomics Viewer) is a desktop Java application for visualizing genomic data. It supports Mac, Windows, and Linux. Requires Java 21.
+
+## Build & Run Commands
+
+```bash
+# Build distribution (output: build/IGV-dist/)
+./gradlew createDist
+
+# Run all tests (headless, 2GB max heap)
+./gradlew test
+
+# Run a single test class or method
+./gradlew test --tests org.igv.ucsc.TrixTest
+./gradlew test --tests org.igv.ucsc.TrixTest.testMethod
+
+# Build jar only
+./gradlew jar
+
+# Platform-specific distributions
+./gradlew createMacDistZip
+./gradlew createLinuxDistZip
+./gradlew createWinDist
+```
+
+After `createDist`, launch with `build/IGV-dist/igv.sh` (Linux), `igv.command` (Mac), or `igv.bat` (Windows).
+
+## Test Notes
+
+- Tests run headless (`java.awt.headless=true`); long-running tests excluded by default
+- Large test data (~1GB) available separately from ftp://ftp.broadinstitute.org/pub/igv/largedata.zip — unzip to `test/largedata/`
+
+## Architecture
+
+**Entry point:** `org.igv.ui.Main` → creates the Swing JFrame and calls `open()` which initializes the singleton `org.igv.ui.IGV`.
+
+**Core singleton:** `org.igv.ui.IGV` manages the main window, genome, data model, and track list. Only one IGV instance is allowed per JVM.
+
+**Key subsystems:**
+
+| Package | Responsibility |
+|---|---|
+| `org.igv.ui` | Swing GUI: main window, panels, dialogs, menus |
+| `org.igv.track` | Track abstraction — all data types extend `Track`; `TrackMenuUtils` builds context menus |
+| `org.igv.renderer` | Rendering engine; each track type has a corresponding renderer |
+| `org.igv.feature.genome` | Reference genome management (`Genome`, `GenomeManager`) |
+| `org.igv.session` | Session save/load (XML and JSON formats) |
+| `org.igv.data` | Data loading and caching layer |
+| `org.igv.sam` | SAM/BAM alignment handling |
+| `org.igv.variant` | VCF/variant track (`VariantTrack`) |
+| `org.igv.seg` | Segmentation data (`SegTrack`) |
+| `org.igv.ucsc` | UCSC formats: BigBed, BigWig, TwoBit, TDF |
+| `org.igv.batch` | Headless batch mode command execution |
+| `org.igv.event` | Pub/sub event bus (`IGVEventBus`, `IGVEventObserver`) |
+| `org.igv.prefs` | User preferences (`PreferencesManager`) |
+| `org.igv.util` | HTTP, file I/O, stream utilities |
+| `org.igv.aws` | AWS S3 / Cognito integration |
+
+**UI panel hierarchy:** `MainPanel` contains a `DataPanel` (the scrollable genome view) composed of `TrackPanel` rows. Each `TrackPanel` has a `TrackNamePanel` (left label area) and a `DataPanelContainer` (right drawing area). Panels communicate via `IGVEventBus`.
+
+**Track rendering:** `Track.render(Graphics2D g, RenderContext context)` is the core drawing method. `RenderContext` carries the current viewport locus, scale, and panel dimensions.
+
+**Session files:** Supported in both XML (legacy `.xml`) and JSON (`.json`) formats. The `session/` package handles serialization; example sessions are in `test/sessions/`.

examples/web/StaticLinkExamples.html

@@ -32,7 +32,7 @@ <h2>IGV desktop links</h2>
         Load with name -- allow dups</a>
 </p>
 <p>
-    <a href="http://localhost:60151/load?file=gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam&locus=myc&dup=true">
+    <a href="http://localhost:60151/load?file=https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12877/alignment/NA12877.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram&locus=myc&dup=true">
         Load BAM -- allow dups</a>
 </p>
 <p>
@@ -52,7 +52,7 @@ <h2>IGV desktop links</h2>
         Load with index</a>
 </p>
 <p>
-    <a href="http://localhost:60151/load?file=https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz,gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam&index=https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz.tbi,gs://genomics-public-data/platinum-genomes/bam/NA12877_S1.bam.bai&locus=chr1&name=SNPs,Alignments&locus=myc">
+    <a href="http://localhost:60151/load?file=https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz,https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12877/alignment/NA12877.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram&index=https://data.broadinstitute.org/igvdata/annotations/hg19/dbSnp/snp137.hg19.bed.gz.tbi,https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/illumina_platinum_pedigree/data/CEU/NA12877/alignment/NA12877.alt_bwamem_GRCh38DH.20150706.CEU.illumina_platinum_ped.cram.bai&locus=chr1&name=SNPs,Alignments&locus=myc">
         Load with index - multiple files</a>
 </p>
 <p>

src/main/java/org/igv/Globals.java

@@ -16,6 +16,10 @@
  * Date: Feb 3, 2010
  */
 public class Globals {
+
+    public static final long JS_MAX_SAFE_INTEGER = 9007199254740991L;
+    public static final long JS_MIN_SAFE_INTEGER = -9007199254740991L;
+
     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);
@@ -37,7 +41,7 @@ public class Globals {
     /**
      * Field description
      */
-    final public static String SESSION_FILE_EXTENSION = ".xml";
+    final public static String SESSION_FILE_EXTENSION = ".json";
     /**
      * GENOME ARCHIVE CONSTANTS
      */

src/main/java/org/igv/batch/CommandExecutor.java

@@ -17,7 +17,7 @@
 import org.igv.sam.SortOption;
 import org.igv.session.Session;
 import org.igv.session.SessionReader;
-import org.igv.session.SessionWriter;
+import org.igv.session.JSONSessionWriter;
 import org.igv.track.*;
 import org.igv.ui.IGV;
 import org.igv.ui.action.OverlayTracksMenuAction;
@@ -159,7 +159,7 @@ public String execute(String commandLine) throws IOException {
             String trackName = parseTrackName(param1);
             result = removeTrack(trackName);
         } else if (cmd.equalsIgnoreCase("tweakdivider")) {
-            igv.tweakPanelDivider();
+            //igv.tweakPanelDivider();
         } else if (cmd.equalsIgnoreCase("setDataRange")) {
             result = this.setDataRange(param1, param2);
         } else if (cmd.equalsIgnoreCase("setLogScale")) {
@@ -530,7 +530,7 @@ private String setTrackHeight(String param1, String param2) {
         List<Track> tracks = tracksMatchingName(trackName);
         if (tracks.size() > 0) {
             for (Track track : tracks) {
-                track.setHeight(height, true);
+                track.setHeight(height);
                 igv.repaint(track);
             }
             return "OK";
@@ -628,6 +628,10 @@ private String genome(String param1) {
         String genomeIDorPath = param1;
 
         try {
+            File file = new File(resolveFileReference(genomeIDorPath));
+            if (file.exists()) {
+                genomeIDorPath = file.getAbsolutePath();
+            }
             GenomeManager.getInstance().loadGenomeById(genomeIDorPath);
             result = "OK";
         } catch (IOException e) {
@@ -1126,7 +1130,7 @@ private String createSnapshot(String filename, String region) {
         if (region == null || region.trim().length() == 0) {
             target = this.igv.getContentPane().getMainPanel();
         } else if ("trackpanels".equalsIgnoreCase(region)) {
-            target = this.igv.getMainPanel().getCenterSplitPane();
+            target = this.igv.getMainPanel().getTrackPanelContainer();
         }
 
         if (target == null) {
@@ -1145,14 +1149,14 @@ private String createSnapshot(String filename, String region) {
 
     private String saveSession(String filename) {
         Session currentSession = igv.getSession();
-        if (!filename.endsWith(".xml")) {
-            filename = filename + ".xml";
+        if (!filename.endsWith(".json")) {
+            filename = filename + ".json";
         }
         File targetFile = getFile(filename);
         if (targetFile.getParentFile().exists()) {
             currentSession.setPath(targetFile.getAbsolutePath());
             try {
-                (new SessionWriter()).saveSession(currentSession, targetFile);
+                (new JSONSessionWriter(igv)).saveSession(currentSession, targetFile);
                 return "OK";
             } catch (Exception e) {
                 return "Error writingin sesssion: " + e.getMessage();

src/main/java/org/igv/bedpe/BedPERenderer.java

@@ -2,10 +2,9 @@
 
 import org.igv.track.RenderContext;
 
-import java.awt.*;
 import java.util.List;
 
 public interface BedPERenderer {
-     void render(List<BedPE> features, RenderContext context, Rectangle trackRectangle, InteractionTrack.ArcOption arcOption);
+     void render(List<BedPE> features, RenderContext context, InteractionTrack.ArcOption arcOption);
 
 }

src/main/java/org/igv/bedpe/HicInteractionTrack.java

@@ -8,6 +8,7 @@
 import org.igv.ui.panel.IGVPopupMenu;
 import org.igv.ui.panel.ReferenceFrame;
 import org.igv.util.ResourceLocator;
+import org.json.JSONObject;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
@@ -31,6 +32,7 @@ public HicInteractionTrack(ResourceLocator locator, HicSource source) {
         maxFeatureCount = 5000;
         graphType = GraphType.NESTED_ARC;
         isHIC = true;
+        transparency = 0.1f;
         setUseScore(false);   // Alpha score is set in the renderer based
         setDefaultColor(Color.red);
     }
@@ -55,7 +57,7 @@ protected List<BedPE> filterFeaturesForZoom(List<BedPE> features, LoadedInterval
         return features;
     }
 
-    void addHICItems(TrackClickEvent te, IGVPopupMenu menu) {
+    void addHICItems(TrackClickEvent te, List<Component> items) {
 
         final JMenuItem transparencyItem = new JMenuItem("Set Transparency...");
         transparencyItem.addActionListener(e -> {
@@ -81,7 +83,7 @@ void addHICItems(TrackClickEvent te, IGVPopupMenu menu) {
             final Frame parent = IGV.hasInstance() ? IGV.getInstance().getMainFrame() : null;
             JOptionPane.showMessageDialog(parent, panel, "Set Transparency for " + this.getDisplayName(), JOptionPane.PLAIN_MESSAGE);
         });
-        menu.add(transparencyItem);
+        items.add(transparencyItem);
 
 
         final JMenuItem maxFeatureCountItem = new JMenuItem("Set Maximum Feature Count...");
@@ -108,13 +110,13 @@ void addHICItems(TrackClickEvent te, IGVPopupMenu menu) {
             final Frame parent = IGV.hasInstance() ? IGV.getInstance().getMainFrame() : null;
             JOptionPane.showMessageDialog(parent, panel, "Set Max Feature Count for " + this.getDisplayName(), JOptionPane.PLAIN_MESSAGE);
         });
-        menu.add(maxFeatureCountItem);
+        items.add(maxFeatureCountItem);
 
         // Add normalization options for HiC tracks
         List<String> normalizationTypes = featureSource.getNormalizationTypes();
         if (normalizationTypes != null && normalizationTypes.size() > 1) {
-            menu.addSeparator();
-            menu.add(new JLabel("<html><b>Normalization</b>"));
+            items.add(new JPopupMenu.Separator());
+            items.add(new JLabel("<html><b>Normalization</b>"));
             ButtonGroup normGroup = new ButtonGroup();
             for (String type : normalizationTypes) {
                 String label = normalizationLabels.getOrDefault(type, type);
@@ -128,11 +130,11 @@ void addHICItems(TrackClickEvent te, IGVPopupMenu menu) {
                     this.repaint();
                 });
                 normGroup.add(normItem);
-                menu.add(normItem);
+                items.add(normItem);
             }
         }
 
-        menu.addSeparator();
+        items.add(new JPopupMenu.Separator());
         JMenuItem mapItem = new JMenuItem("Contact Map View...");
         mapItem.setEnabled(contactMapView == null && !FrameManager.isGeneListMode());
         mapItem.addActionListener(e -> {
@@ -143,18 +145,9 @@ void addHICItems(TrackClickEvent te, IGVPopupMenu menu) {
                 ContactMapView.showPopup(this, hicFile, normalization, frame, colorScale.getMaxColor());
             }
         });
-        menu.add(mapItem);
+        items.add(mapItem);
     }
 
-    @Override
-    public void marshalXML(Document document, Element element) {
-        super.marshalXML(document, element);
-
-        String nviString = ((HicSource) featureSource).getNVIString();
-        if (nviString != null) {
-            element.setAttribute("nvi", nviString);
-        }
-    }
 
     @Override
     public void unmarshalXML(Element element, Integer version) {
@@ -165,5 +158,28 @@ public void unmarshalXML(Element element, Integer version) {
             ((HicSource) featureSource).setNVIString(nviString);
         }
     }
+
+    @Override
+    public void marshalJSON(JSONObject json) {
+        super.marshalJSON(json);
+        String nviString = ((HicSource) featureSource).getNVIString();
+        if (nviString != null) {
+            json.put("nvi", nviString);
+        }
+        if(!"NONE".equals(normalization)) {
+            json.put("normalization", normalization);
+        }
+    }
+
+    public void unmarshalJSON(JSONObject jsonObject) {
+        super.unmarshalJSON(jsonObject);
+        if (jsonObject.has("nvi")) {
+            String nviString = jsonObject.getString("nvi");
+            ((HicSource) featureSource).setNVIString(nviString);
+        }
+        if(jsonObject.has("normalization")) {
+            this.normalization = jsonObject.getString("normalization");
+        }
+    }
 }