toString on parameters

draeger-lab · Aug 15, 2024 · 294b3bc · 294b3bc
1 parent dfafe97
commit 294b3bc
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Showing 8 changed files with 192 additions and 3 deletions.
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/ADBAnnotationParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/ADBAnnotationParameters.java
@@ -4,6 +4,8 @@
 import de.zbit.util.prefs.SBProperties;
 import edu.ucsd.sbrg.db.adb.AnnotateDBOptions;
 
+import java.util.Objects;
+
 public class ADBAnnotationParameters {
 
     @JsonProperty("annotate-with-adb")
@@ -37,4 +39,25 @@ public boolean annotateWithAdb() {
     public DBParameters dbParameters() {
         return dbParameters;
     }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        ADBAnnotationParameters that = (ADBAnnotationParameters) o;
+        return annotateWithAdb == that.annotateWithAdb && Objects.equals(dbParameters, that.dbParameters);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(annotateWithAdb, dbParameters);
+    }
+
+    @Override
+    public String toString() {
+        return "ADBAnnotationParameters{" +
+                "annotateWithAdb=" + annotateWithAdb +
+                ", dbParameters=" + dbParameters +
+                '}';
+    }
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/AnnotationParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/AnnotationParameters.java
@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import de.zbit.util.prefs.SBProperties;
 
+import java.util.Objects;
+
 public class AnnotationParameters {
 
     @JsonProperty("annotatedb")
@@ -25,4 +27,26 @@ public ADBAnnotationParameters adbAnnotationParameters() {
     public BiGGAnnotationParameters biggAnnotationParameters() {
         return biGGAnnotationParameters;
     }
+
+    @Override
+    public String toString() {
+        return "AnnotationParameters{" +
+                "adbAnnotationParameters=" + adbAnnotationParameters +
+                ", biGGAnnotationParameters=" + biGGAnnotationParameters +
+                '}';
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        AnnotationParameters that = (AnnotationParameters) o;
+        return Objects.equals(adbAnnotationParameters, that.adbAnnotationParameters) && Objects.equals(biGGAnnotationParameters, that.biGGAnnotationParameters);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(adbAnnotationParameters, biGGAnnotationParameters);
+    }
+
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/BiGGAnnotationParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/BiGGAnnotationParameters.java
@@ -4,6 +4,8 @@
 import de.zbit.util.prefs.SBProperties;
 import edu.ucsd.sbrg.db.bigg.BiGGDBOptions;
 
+import java.util.Objects;
+
 public class BiGGAnnotationParameters {
 
     @JsonProperty("annotate-with-bigg")
@@ -64,4 +66,29 @@ public BiGGNotesParameters notesParameters() {
     public DBParameters dbParameters() {
         return dbParameters;
     }
+
+    @Override
+    public String toString() {
+        return "BiGGAnnotationParameters{" +
+                "annotateWithBiGG=" + annotateWithBiGG +
+                ", includeAnyURI=" + includeAnyURI +
+                ", documentTitlePattern='" + documentTitlePattern + '\'' +
+                ", notesParameters=" + notesParameters +
+                ", dbParameters=" + dbParameters +
+                '}';
+    }
+
+    @Override
+    public boolean equals(Object o) {
+
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        BiGGAnnotationParameters that = (BiGGAnnotationParameters) o;
+        return annotateWithBiGG == that.annotateWithBiGG && includeAnyURI == that.includeAnyURI && Objects.equals(documentTitlePattern, that.documentTitlePattern) && Objects.equals(notesParameters, that.notesParameters) && Objects.equals(dbParameters, that.dbParameters);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(annotateWithBiGG, includeAnyURI, documentTitlePattern, notesParameters, dbParameters);
+    }
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/DBParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/DBParameters.java
@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import edu.ucsd.sbrg.db.bigg.BiGGDBOptions;
 
+import java.util.Objects;
+
 
 public class DBParameters {
 
@@ -47,4 +49,29 @@ public Integer port() {
     public String user() {
         return user;
     }
+
+    @Override
+    public String toString() {
+        return "DBParameters{" +
+                "dbName='" + dbName + '\'' +
+                ", host='" + host + '\'' +
+                ", passwd='" + passwd + '\'' +
+                ", port=" + port +
+                ", user='" + user + '\'' +
+                '}';
+    }
+
+    @Override
+    public boolean equals(Object o) {
+
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        DBParameters that = (DBParameters) o;
+        return Objects.equals(dbName, that.dbName) && Objects.equals(host, that.host) && Objects.equals(passwd, that.passwd) && Objects.equals(port, that.port) && Objects.equals(user, that.user);
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(dbName, host, passwd, port, user);
+    }
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/Parameters.java b/src/main/java/edu/ucsd/sbrg/parameters/Parameters.java
@@ -2,6 +2,8 @@
 
 import com.fasterxml.jackson.annotation.JsonProperty;
 
+import java.util.Objects;
+
 public class Parameters {
 
     @JsonProperty("polishing")
@@ -36,4 +38,28 @@ public boolean sbmlValidation() {
     public ModelPolisherOptions.OutputType outputType() {
         return outputType;
     }
+
+    @Override
+    public String toString() {
+        return "Parameters{" +
+                "polishing=" + polishing +
+                ", annotation=" + annotation +
+                ", sboTerms=" + sboTerms +
+                ", sbmlValidation=" + sbmlValidation +
+                ", outputType=" + outputType +
+            '}';    
+    }
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        Parameters that = (Parameters) o;
+        return sbmlValidation == that.sbmlValidation && Objects.equals(polishing, that.polishing) && Objects.equals(annotation, that.annotation) && Objects.equals(sboTerms, that.sboTerms) && outputType == that.outputType;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hash(polishing, annotation, sboTerms, sbmlValidation, outputType);
+    }
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/PolishingParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/PolishingParameters.java
@@ -3,6 +3,8 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import de.zbit.util.prefs.SBProperties;
 
+import java.util.Objects;
+
 public class PolishingParameters {
 
   @JsonProperty("reactions")
@@ -30,4 +32,25 @@ public ReactionPolishingParameters reactionPolishingParameters() {
   public FluxObjectivesPolishingParameters fluxObjectivesPolishingParameters() {
     return fluxObjectivesPolishingParameters;
   }
+
+  @Override
+  public String toString() {
+    return "PolishingParameters{" +
+            "reactionPolishingParameters=" + reactionPolishingParameters +
+            ", fluxObjectivesPolishingParameters=" + fluxObjectivesPolishingParameters +
+            '}';
+  }
+
+  @Override
+  public boolean equals(Object o) {
+    if (this == o) return true;
+    if (o == null || getClass() != o.getClass()) return false;
+    PolishingParameters that = (PolishingParameters) o;
+    return Objects.equals(reactionPolishingParameters, that.reactionPolishingParameters) && Objects.equals(fluxObjectivesPolishingParameters, that.fluxObjectivesPolishingParameters);
+  }
+
+  @Override
+  public int hashCode() {
+    return Objects.hash(reactionPolishingParameters, fluxObjectivesPolishingParameters);
+  }
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/ReactionPolishingParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/ReactionPolishingParameters.java
@@ -4,6 +4,7 @@
 import de.zbit.util.prefs.SBProperties;
 
 import java.util.Map;
+import java.util.Objects;
 
 public class ReactionPolishingParameters {
 
@@ -28,6 +29,23 @@ public boolean checkMassBalance() {
         return checkMassBalance;
     }
 
+    @Override
+    public String toString() {
+        return "ReactionPolishingParameters{" +
+                "checkMassBalance=" + checkMassBalance +
+                '}';
+    }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        ReactionPolishingParameters that = (ReactionPolishingParameters) o;
+        return checkMassBalance == that.checkMassBalance;
+    }
 
+    @Override
+    public int hashCode() {
+        return Objects.hashCode(checkMassBalance);
+    }
 }
diff --git a/src/main/java/edu/ucsd/sbrg/parameters/SBOParameters.java b/src/main/java/edu/ucsd/sbrg/parameters/SBOParameters.java
@@ -3,20 +3,41 @@
 import com.fasterxml.jackson.annotation.JsonProperty;
 import de.zbit.util.prefs.SBProperties;
 
+import java.util.Objects;
+
 public class SBOParameters {
 
     @JsonProperty("omit-generic-terms")
-    protected boolean omitGenericTerms = ModelPolisherOptions.ADD_GENERIC_TERMS.getDefaultValue();
+    protected boolean addGenericTerms = ModelPolisherOptions.ADD_GENERIC_TERMS.getDefaultValue();
 
     public SBOParameters() {
     }
 
     public SBOParameters(SBProperties args) {
-        omitGenericTerms = args.getBooleanProperty(ModelPolisherOptions.ADD_GENERIC_TERMS);
+        addGenericTerms = args.getBooleanProperty(ModelPolisherOptions.ADD_GENERIC_TERMS);
     }
 
     public boolean addGenericTerms() {
-        return omitGenericTerms;
+        return addGenericTerms;
+    }
+
+    @Override
+    public String toString() {
+        return "SBOParameters{" +
+                "addGenericTerms=" + addGenericTerms +
+                '}';
     }
 
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) return true;
+        if (o == null || getClass() != o.getClass()) return false;
+        SBOParameters that = (SBOParameters) o;
+        return addGenericTerms == that.addGenericTerms;
+    }
+
+    @Override
+    public int hashCode() {
+        return Objects.hashCode(addGenericTerms);
+    }
 }