Merge branch 'master' into hubs

build.gradle

@@ -104,17 +104,17 @@ configurations {
 dependencies {
     implementation(
             fileTree(dir: 'lib', include: '*.jar'), // first search on disk (old behavior), then maven repos
-            [group: 'com.google.code.gson', name: 'gson', version: '2.8.5'],
+            [group: 'com.google.code.gson', name: 'gson', version: '2.8.9'],
             [group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'],
-            [group: 'commons-io', name: 'commons-io', version: '2.6'],
-            [group: 'org.apache.commons', name: 'commons-compress', version: '1.18'],
+            [group: 'commons-io', name: 'commons-io', version: '2.7'],
+            [group: 'org.apache.commons', name: 'commons-compress', version: '1.21'],
             [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.7.3'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
-            [group: 'com.github.samtools', name: 'htsjdk', version: '3.0.5'],
+            [group: 'com.github.samtools', name: 'htsjdk', version: '4.0.2'],
             [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
             [group: 'com.formdev', name: 'jide-oss', version: '3.7.12'],
-            [group: 'com.google.guava', name: 'guava', version: '27.0.1-jre'],
+            [group: 'com.google.guava', name: 'guava', version: '32.1.3-jre'],
             [group: 'org.apache.xmlgraphics', name: 'batik-dom', version: '1.11'],
             [group: 'org.apache.xmlgraphics', name: 'batik-svggen', version: '1.11'],
             [group: 'org.apache.xmlgraphics', name: 'batik-codec', version: '1.11'],
@@ -128,9 +128,9 @@ dependencies {
     )
 
     testImplementation(
-            [group: 'junit', name: 'junit', version: '4.13'],
-            [group: 'com.sparkjava', name: 'spark-core', version: '2.2'],
-            [group: 'org.glassfish.jersey.core', name: 'jersey-common', version: '2.22.4']
+            [group: 'junit', name: 'junit', version: '4.13.1'],
+            [group: 'com.sparkjava', name: 'spark-core', version: '2.7.2'],
+            [group: 'org.glassfish.jersey.core', name: 'jersey-common', version: '2.34']
     )
     testRuntimeOnly(
            [group: 'org.junit.vintage', name:'junit-vintage-engine', version:'5.8.2']

src/main/java/module-info.java

@@ -2,14 +2,16 @@
     exports org.broad.igv;
     exports org.broad.igv.tools;
     exports org.broad.igv.ui;
+    exports org.broad.igv.event;
     exports org.broad.igv.jbrowse;
     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;
-    requires gson;
+    requires com.google.gson;
     requires htsjdk;
     requires java.datatransfer;
     requires java.desktop;

src/main/java/org/broad/igv/batch/CommandListener.java

@@ -181,7 +181,12 @@ private void processClientSession(CommandExecutor cmdExe) throws IOException {
 
                 String cmd = inputLine;
                 if (!cmd.contains("/oauthCallback")) {
-                    log.info(cmd);
+                    if (cmd.startsWith("SetAccessToken")) {
+                        log.info(cmd.substring(0,14) + " *****");
+                    }
+                    else {
+                        log.info(cmd);
+                    }
                 }
 
                 boolean isHTTP = cmd.startsWith("OPTIONS") || cmd.startsWith("HEAD") || cmd.startsWith("GET");

src/main/java/org/broad/igv/event/AlignmentTrackEvent.java

@@ -29,20 +29,6 @@
  * @author Jim Robinson
  * @date 12/2/11
  */
-public class AlignmentTrackEvent {
-
+public record AlignmentTrackEvent(Type type) implements IGVEvent{
     public enum Type {ALLELE_THRESHOLD, RELOAD, REFRESH}
-
-    private Object source;
-    private Type type;
-    private boolean booleanValue;
-
-    public AlignmentTrackEvent(Object source, Type type) {
-        this.source = source;
-        this.type = type;
-    }
-
-    public Type getType() {
-        return type;
-    }
-}
+}

src/main/java/org/broad/igv/event/DataLoadedEvent.java

@@ -31,15 +31,4 @@
  * User: jacob
  * Date: 2013-Feb-06
  */
-public class DataLoadedEvent {
-
-    public final ReferenceFrame referenceFrame;
-
-    public DataLoadedEvent(ReferenceFrame referenceFrame){
-        this.referenceFrame = referenceFrame;
-    }
-
-    public ReferenceFrame getReferenceFrame() {
-        return referenceFrame;
-    }
-}
+public record DataLoadedEvent(ReferenceFrame referenceFrame) implements IGVEvent {}

src/main/java/org/broad/igv/event/GenomeChangeEvent.java

@@ -31,11 +31,4 @@
 /**
  * Created by jrobinso on 1/7/17.
  */
-public class GenomeChangeEvent {
-
-    public Genome genome;
-
-    public GenomeChangeEvent(Genome genome) {
-        this.genome = genome;
-    }
-}
+public record GenomeChangeEvent(Genome genome) implements IGVEvent {}

src/main/java/org/broad/igv/event/GenomeResetEvent.java

@@ -3,5 +3,5 @@
 /**
  * Created by jrobinso on 2/7/17.
  */
-public class GenomeResetEvent {
+public final class GenomeResetEvent implements IGVEvent {
 }

src/main/java/org/broad/igv/event/IGVEvent.java

@@ -0,0 +1,23 @@
+package org.broad.igv.event;
+
+import org.broad.igv.oauth.OAuthProvider;
+import org.broad.igv.prefs.PreferencesChangeEvent;
+import org.broad.igv.sam.InsertionSelectionEvent;
+import org.broad.igv.ui.panel.FrameManager;
+
+public sealed interface IGVEvent
+        permits
+        AlignmentTrackEvent,
+        DataLoadedEvent,
+        GenomeChangeEvent,
+        GenomeResetEvent,
+        RefreshEvent,
+        StopEvent,
+        TrackGroupEvent,
+        ViewChange,
+        OAuthProvider.AuthStateEvent,
+        PreferencesChangeEvent,
+        InsertionSelectionEvent,
+        FrameManager.ChangeEvent {
+
+}

src/main/java/org/broad/igv/event/IGVEventBus.java

@@ -36,9 +36,7 @@
  */
 public class IGVEventBus {
 
-    static final Logger log = LogManager.getLogger(IGVEventBus.class);
-
-    Map<Class, Set<IGVEventObserver>> observerMap;
+    final Map<Class<?>, Set<IGVEventObserver>> observerMap;
 
     private static IGVEventBus instance;
 
@@ -54,13 +52,8 @@ public IGVEventBus() {
         this.observerMap = new HashMap<>();
     }
 
-    public synchronized void subscribe(Class eventClass, IGVEventObserver observer) {
-
-        Set<IGVEventObserver> observerSet = observerMap.get(eventClass);
-        if (observerSet == null) {
-            observerSet = Collections.newSetFromMap(new WeakHashMap<IGVEventObserver, Boolean>());
-            observerMap.put(eventClass, observerSet);
-        }
+    public synchronized void subscribe(Class<?> eventClass, IGVEventObserver observer) {
+        Set<IGVEventObserver> observerSet = observerMap.computeIfAbsent(eventClass, k -> Collections.newSetFromMap(new WeakHashMap<>()));
         observerSet.add(observer);
     }
 
@@ -74,7 +67,7 @@ public synchronized void unsubscribe(IGVEventObserver observer) {
         }
     }
 
-    public void post(Object event) {
+    public void post(IGVEvent event) {
         Set<IGVEventObserver> observerSet = observerMap.get(event.getClass());
         if (observerSet != null) {
             // Make a copy in case original is modified during loop

src/main/java/org/broad/igv/event/IGVEventObserver.java

@@ -31,6 +31,6 @@
  */
 public interface IGVEventObserver {
 
-    void receiveEvent(Object event);
+    void receiveEvent(IGVEvent event);
 
 }

src/main/java/org/broad/igv/event/RefreshEvent.java

@@ -3,5 +3,5 @@
 /**
  * Created by jrobinso on 6/24/17.
  */
-public class RefreshEvent {
+public final class RefreshEvent implements IGVEvent {
 }

src/main/java/org/broad/igv/event/StopEvent.java

@@ -3,5 +3,5 @@
 /**
  * Created by jrobinso on 6/24/17.
  */
-public class StopEvent {
+public final class StopEvent implements IGVEvent{
 }

src/main/java/org/broad/igv/event/TrackGroupEvent.java

@@ -29,13 +29,5 @@
  * @author Jim Robinson
  * @date 10/28/11
  */
-public class TrackGroupEvent  {
-
-    Object source;
-
-    public TrackGroupEvent(Object source) {
-        this.source = source;
-    }
-
-
+public final class TrackGroupEvent implements IGVEvent {
 }

src/main/java/org/broad/igv/event/ViewChange.java

@@ -37,46 +37,34 @@
  * User: jacob
  * Date: 2013-Jan-30
  */
-public class ViewChange {
+public final class ViewChange implements IGVEvent{
 
     public enum Type {ChromosomeChange, LocusChange}
 
-    boolean recordHistory = false;
-    public Type type;
-    public String chrName;
-    public double start;
-    public double end;
+    final boolean recordHistory;
+    final public Type type;
+    final public String chrName;
+    final public double start;
+    final public double end;
 
-    private ViewChange(Type type) {
-        this.type = type;
-    }
-
-    private ViewChange(Type type, String chrName) {
-        this.type = type;
-        this.chrName = chrName;
-    }
-
-    private ViewChange(Type type, String chrName, double start, double end) {
+    private ViewChange(Type type, String chrName, double start, double end, boolean recordHistory) {
         this.type = type;
         this.chrName = chrName;
         this.start = start;
         this.end = end;
+        this.recordHistory = recordHistory;
     }
 
     public boolean recordHistory() {
         return this.recordHistory;
     }
 
-    public void setRecordHistory(boolean recordHistory) {
-        this.recordHistory = recordHistory;
-    }
-
-    public static ViewChange ChromosomeChangeResult(String chrName) {
-        return new ViewChange(Type.ChromosomeChange, chrName);
+    public static ViewChange ChromosomeChangeResult(String chrName, boolean recordHistory) {
+        return new ViewChange(Type.ChromosomeChange, chrName, 0.0, 0.0, recordHistory);
     }
 
-    public static ViewChange LocusChangeResult(String chrName, double start, double end) {
-        return new ViewChange(Type.LocusChange, chrName, start, end);
+    public static ViewChange LocusChangeResult(String chrName, double start, double end, boolean recordHistory) {
+        return new ViewChange(Type.LocusChange, chrName, start, end, recordHistory);
     }
 
 }

src/main/java/org/broad/igv/feature/Cytoband.java

@@ -26,7 +26,7 @@
 package org.broad.igv.feature;
 
 
-public class Cytoband implements NamedFeature {
+public class Cytoband implements IGVNamedFeature {
     String chromosome;
     String name;
     int end;