Add DeNovoGUI compatibility APIs to Utilities

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/software/ToolFactory.java

@@ -44,6 +44,7 @@ public class ToolFactory {
      * The command line argument for mgf files for SearchGUI.
      */
     public static final String SEARCHGUI_SPECTRUM_FILE_OPTION = "-mgf";
+    public static final String searchGuiSpectrumFileOption = SEARCHGUI_SPECTRUM_FILE_OPTION;
     /**
      * The command line argument for FASTA file for SearchGUI.
      */
@@ -56,10 +57,12 @@ public class ToolFactory {
      * The command line argument for a parameters file for SearchGUI.
      */
     public static final String SEARCHGUI_PARAMETERS_FILE_OPTION = "-identification_parameters";
+    public static final String searchGuiParametersFileOption = SEARCHGUI_PARAMETERS_FILE_OPTION;
     /**
      * The command line argument for an output folder.
      */
     public static final String OUTPUT_FOLDER_OPTION = "-output_folder";
+    public static final String outputFolderOption = OUTPUT_FOLDER_OPTION;
     /**
      * The command line argument for the species.
      */

src/main/java/com/compomics/util/Util.java

@@ -1,7 +1,9 @@
 package com.compomics.util;
 
 import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
+import com.compomics.util.gui.file_handling.FileChooserUtil;
 import java.awt.Color;
+import java.awt.Component;
 import java.io.*;
 import java.math.BigDecimal;
 import java.math.RoundingMode;
@@ -695,4 +697,47 @@ public static String keyValueToString(
         return sb.toString();
 
     }
+
+    public static File getUserSelectedFile(
+            Component parent,
+            String fileEnding,
+            String fileFormatDescription,
+            String dialogTitle,
+            String lastSelectedFolder,
+            String suggestedFileName,
+            boolean openDialog
+    ) {
+        return FileChooserUtil.getUserSelectedFile(
+                parent,
+                fileEnding,
+                fileFormatDescription,
+                dialogTitle,
+                lastSelectedFolder,
+                suggestedFileName,
+                openDialog
+        );
+    }
+
+    public static boolean deleteDir(File directory) {
+        if (directory == null || !directory.exists()) {
+            return true;
+        }
+        File[] files = directory.listFiles();
+        if (files != null) {
+            for (File file : files) {
+                if (file.isDirectory()) {
+                    deleteDir(file);
+                } else if (!file.delete()) {
+                    return false;
+                }
+            }
+        }
+        return directory.delete();
+    }
+
+    public static String getFileName(File file) {
+        String name = file.getName();
+        int extensionIndex = name.lastIndexOf('.');
+        return extensionIndex > 0 ? name.substring(0, extensionIndex) : name;
+    }
 }

src/main/java/com/compomics/util/db/object/ObjectsCache.java

@@ -49,6 +49,12 @@ public class ObjectsCache {
      */
     private final int keepObjectsThreshold = 10000;
 
+    /**
+     * Constructor.
+     */
+    public ObjectsCache() {
+    }
+
     /**
      * Constructor.
      *
@@ -466,6 +472,25 @@ public boolean isEmpty() {
         return isEmpty;
     }
 
+    /**
+     * Legacy compatibility method. Automated memory management is handled by
+     * the current cache implementation.
+     *
+     * @param automatedMemoryManagement ignored
+     */
+    public void setAutomatedMemoryManagement(boolean automatedMemoryManagement) {
+    }
+
+    /**
+     * Legacy compatibility method. Delegates to the current memory share.
+     *
+     * @param memoryShare the memory share
+     * @param waitingHandler the waiting handler
+     */
+    public void reduceMemoryConsumption(double memoryShare, WaitingHandler waitingHandler) {
+        setMemoryShare(memoryShare);
+    }
+
     /**
      * Clears the cache.
      */

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/biology/aminoacids/sequence/AminoAcidPattern.java

@@ -1,6 +1,7 @@
 package com.compomics.util.experiment.biology.aminoacids.sequence;
 
 import com.compomics.util.experiment.biology.aminoacids.AminoAcid;
+import com.compomics.util.experiment.identification.matches.ModificationMatch;
 import com.compomics.util.experiment.personalization.ExperimentObject;
 import com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters;
 import com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters.MatchingType;
@@ -146,6 +147,14 @@ public HashMap<Integer, ArrayList<Character>> getAaTargeted() {
         return residueTargeted;
     }
 
+    public ArrayList<Integer> getModificationIndexes() {
+        return new ArrayList<>();
+    }
+
+    public ArrayList<ModificationMatch> getModificationsAt(int site) {
+        return new ArrayList<>();
+    }
+
     /**
      * Convenience constructor giving a list of targeted residues as input. For
      * instance (S, T, Y)

src/main/java/com/compomics/util/experiment/biology/aminoacids/sequence/AminoAcidSequence.java

@@ -443,6 +443,48 @@ public ModificationMatch[] getVariableModifications() {
 
     }
 
+    public ArrayList<Integer> getModificationIndexes() {
+        ArrayList<Integer> result = new ArrayList<>();
+        for (ModificationMatch modificationMatch : getVariableModifications()) {
+            if (!result.contains(modificationMatch.getSite())) {
+                result.add(modificationMatch.getSite());
+            }
+        }
+        return result;
+    }
+
+    public ArrayList<ModificationMatch> getModificationsAt(int site) {
+        ArrayList<ModificationMatch> result = new ArrayList<>();
+        for (ModificationMatch modificationMatch : getVariableModifications()) {
+            if (modificationMatch.getSite() == site) {
+                result.add(modificationMatch);
+            }
+        }
+        return result;
+    }
+
+    public static String getTaggedResidue(
+            char aminoAcid,
+            String modificationName,
+            ModificationParameters modificationParameters,
+            int modificationType,
+            boolean useHtmlColorCoding,
+            boolean useShortName
+    ) {
+        String[] variableModifications = new String[3];
+        variableModifications[1] = modificationName;
+        return ModificationUtils.getTaggedModifiedSequence(
+                modificationParameters,
+                Character.toString(aminoAcid),
+                variableModifications,
+                null,
+                null,
+                new String[3],
+                useHtmlColorCoding,
+                useShortName
+        );
+    }
+
     /**
      * Returns the variable modifications indexed by site. Modifications are
      * indexed by site as follows: N-term modifications are at index 0, C-term

src/main/java/com/compomics/util/experiment/biology/ions/Charge.java

@@ -8,12 +8,26 @@
  */
 public class Charge {
 
+    /**
+     * Legacy charge value field.
+     */
+    public int value;
+
     /**
      * Empty default constructor.
      */
     public Charge() {
     }
 
+    /**
+     * Constructor with a charge value.
+     *
+     * @param value the charge value
+     */
+    public Charge(int value) {
+        this.value = value;
+    }
+
     /**
      * Returns a string representing the charge. For example 2+.
      *

src/main/java/com/compomics/util/experiment/biology/modifications/Modification.java

@@ -18,6 +18,16 @@
  */
 public class Modification extends ExperimentObject {
 
+    public static final int MODAA = ModificationType.modaa.index;
+    public static final int MODN = ModificationType.modn_protein.index;
+    public static final int MODNAA = ModificationType.modnaa_protein.index;
+    public static final int MODC = ModificationType.modc_protein.index;
+    public static final int MODCAA = ModificationType.modcaa_protein.index;
+    public static final int MODNP = ModificationType.modn_peptide.index;
+    public static final int MODNPAA = ModificationType.modnaa_peptide.index;
+    public static final int MODCP = ModificationType.modc_peptide.index;
+    public static final int MODCPAA = ModificationType.modcaa_peptide.index;
+
     /**
      * The version UID for backward compatibility.
      */
@@ -171,6 +181,18 @@ public ModificationType getModificationType() {
         return modificationType;
     }
 
+    public int getType() {
+        return modificationType.index;
+    }
+
+    public boolean isNTerm() {
+        return modificationType.isNTerm();
+    }
+
+    public boolean isCTerm() {
+        return modificationType.isCTerm();
+    }
+
     /**
      * Getter for the modification name.
      *

src/main/java/com/compomics/util/experiment/biology/modifications/ModificationFactory.java

@@ -281,6 +281,10 @@ public boolean containsModification(String name) {
         return modificationMap.containsKey(name);
     }
 
+    public boolean containsPTM(String name) {
+        return containsModification(name);
+    }
+
     /**
      * Returns the names of the default modifications.
      *
@@ -337,6 +341,10 @@ public ArrayList<String> getModifications() {
         return new ArrayList<>(modificationMap.keySet());
     }
 
+    public ArrayList<String> getPTMs() {
+        return getModifications();
+    }
+
     /**
      * Convenience method returning a boolean indicating whether a Modification
      * is user defined or default.
@@ -407,6 +415,18 @@ public void setColor(String expectedModification, int color) {
         userColors.put(expectedModification, color);
     }
 
+    public void setColor(String expectedModification, Color color) {
+        setColor(expectedModification, color.getRGB());
+    }
+
+    public void addFixedModifications(
+            ModificationParameters modificationParameters,
+            com.compomics.util.experiment.identification.amino_acid_tags.Tag tag,
+            com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters
+    ) {
+        // Fixed modifications are resolved on demand in Utilities 5.
+    }
+
     /**
      * Returns a default color based on the modification name.
      *