Add InstaNovo and InstaNovo+ import support

pom.xml

@@ -444,7 +444,7 @@
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-api</artifactId>
-            <version>2.23.1</version>
+            <version>2.25.4</version>
         </dependency>
 
         <dependency>

src/main/java/com/compomics/util/exceptions/ExceptionHandler.java

@@ -32,14 +32,53 @@ public ExceptionHandler() {
     public synchronized void catchException(Exception e) {
 
         if (!ignoreExceptions && !exceptionCaught.contains(getExceptionType(e))) {
-            
+
             e.printStackTrace();
             exceptionCaught.add(getExceptionType(e));
+
+            // @TODO: remove once the underlying Nimbus look and feel bug is fixed.
+            // On recent JDKs the Nimbus look and feel can throw a benign
+            // ClassCastException ("ColorUIResource cannot be cast to Boolean" in
+            // NimbusStyle.isOpaque) while building chart popup menus. It does not
+            // affect functionality, so it is logged above but not shown to the user.
+            if (isBenignLookAndFeelException(e)) {
+                return;
+            }
+
             notifyUser(e);
-            
+
         }
     }
 
+    /**
+     * Indicates whether the given exception is the known benign look and feel
+     * ClassCastException thrown while rendering (e.g. "ColorUIResource cannot be
+     * cast to Boolean" in NimbusStyle). Such exceptions do not affect
+     * functionality and should not be reported to the user.
+     *
+     * @param e the exception to inspect
+     *
+     * @return true if the exception is a benign look and feel rendering exception
+     */
+    private static boolean isBenignLookAndFeelException(Exception e) {
+
+        if (!(e instanceof ClassCastException)) {
+            return false;
+        }
+
+        for (StackTraceElement element : e.getStackTrace()) {
+
+            String className = element.getClassName();
+
+            if (className.startsWith("javax.swing.plaf.nimbus.")
+                    || className.startsWith("javax.swing.plaf.synth.")) {
+                return true;
+            }
+        }
+
+        return false;
+    }
+
     /**
      * Notifies the user that an exception was caught.
      *

src/main/java/com/compomics/util/experiment/identification/Advocate.java

@@ -182,6 +182,18 @@ public enum AdvocateType {
      * The MSFragger search engine.
      */
     public static final Advocate msFragger = new Advocate(37, "MSFragger", AdvocateType.search_engine, new java.awt.Color(128, 128, 0));
+    /**
+     * The InstaNovo de novo sequencing algorithm.
+     */
+    public static final Advocate instanovo = new Advocate(38, "InstaNovo", AdvocateType.sequencing_algorithm, new Color(95, 158, 160));
+    /**
+     * The InstaNovo+ de novo sequencing algorithm.
+     */
+    public static final Advocate instanovoPlus = new Advocate(39, "InstaNovo+", AdvocateType.sequencing_algorithm, new Color(123, 104, 238));
+    /**
+     * The InstaNovo predictions refined with InstaNovo+ de novo sequencing algorithm.
+     */
+    public static final Advocate instanovoRefined = new Advocate(40, "InstaNovo with refinement", AdvocateType.sequencing_algorithm, new Color(72, 209, 204));
     /**
      * Advocate type for mzId files where no software is annotated.
      */
@@ -311,7 +323,7 @@ public String toString() {
      * @return the implemented advocates in an array
      */
     public static Advocate[] values() {
-        Advocate[] result = new Advocate[40 + userAdvocates.size()];
+        Advocate[] result = new Advocate[43 + userAdvocates.size()];
         int i = 0;
         result[i] = peptideShaker;
         result[++i] = onyaseEngine;
@@ -353,6 +365,9 @@ public static Advocate[] values() {
         result[++i] = coss;
         result[++i] = sage;
         result[++i] = msFragger;
+        result[++i] = instanovo;
+        result[++i] = instanovoPlus;
+        result[++i] = instanovoRefined;
 
         for (Advocate advocate : userAdvocates.values()) {
             result[++i] = advocate;
@@ -489,6 +504,8 @@ public String getPmid() {
             return "37819886";
         } else if (this == msFragger) {
             return "28394336";
+        } else if (this == instanovo || this == instanovoPlus || this == instanovoRefined) {
+            return null;
         } else {
             return null;
         }