JAL-4131 Replace usages of requireNonNullElse

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index 5a246f8..adb70e3 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -36,7 +36,6 @@ import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
-import java.util.Objects;
 import java.util.Optional;
 import java.util.Vector;
 import static java.lang.String.format;
@@ -79,8 +78,8 @@ public class SeqsetUtils
       ArrayList<SequenceFeature> feats = new ArrayList<>(
           seq.getFeatures().getAllFeatures());
       sqinfo.features = Optional.of(feats);
-      sqinfo.pdbId = Optional.of(Objects.requireNonNullElse(
-          seq.getAllPDBEntries(), new ArrayList<>()));
+      var pdbEntries = seq.getAllPDBEntries();
+      sqinfo.pdbId = Optional.of(pdbEntries != null ? pdbEntries : new ArrayList<>());
     }
     if (seq.hasHMMProfile())
     {

diff --git a/src/jalview/ws/params/simple/BooleanOption.java b/src/jalview/ws/params/simple/BooleanOption.java
index cd492cf..87e4ad1 100644 (file)
--- a/src/jalview/ws/params/simple/BooleanOption.java
+++ b/src/jalview/ws/params/simple/BooleanOption.java
@@ -24,8 +24,6 @@ import java.net.URL;
 import java.util.Arrays;
 import java.util.List;
 
-import static java.util.Objects.requireNonNullElse;
-
 public class BooleanOption extends Option
 {
   public static class Builder extends Option.Builder
@@ -38,12 +36,12 @@ public class BooleanOption extends Option
 
     public void setDefaultValue(Boolean defaultValue)
     {
-      this.defaultValue = requireNonNullElse(defaultValue, false);
+      this.defaultValue = defaultValue != null ? defaultValue : false;
     }
 
     public void setValue(Boolean value)
     {
-      this.value = requireNonNullElse(value, false);
+      this.value = value != null ? value : false;
     }
 
     public void setReprValue(String reprValue)
@@ -72,7 +70,7 @@ public class BooleanOption extends Option
   protected BooleanOption(Builder builder)
   {
     super(builder);
-    String reprValue = requireNonNullElse(builder.reprValue, name);
+    String reprValue = builder.reprValue != null ? builder.reprValue : name;
     defvalue = builder.defaultValue ? reprValue : null;
     value = builder.value ? reprValue : null;
     possibleVals = List.of(reprValue);

diff --git a/src/jalview/ws/params/simple/DoubleParameter.java b/src/jalview/ws/params/simple/DoubleParameter.java
index 68029a3..97c5fe1 100644 (file)
--- a/src/jalview/ws/params/simple/DoubleParameter.java
+++ b/src/jalview/ws/params/simple/DoubleParameter.java
@@ -2,7 +2,6 @@ package jalview.ws.params.simple;
 
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
-import static java.util.Objects.requireNonNullElse;
 
 /**
  * 
@@ -56,12 +55,12 @@ public class DoubleParameter extends Option implements ParameterI
 
     public void setMin(Double min)
     {
-      this.min = requireNonNullElse(min, Double.POSITIVE_INFINITY);
+      this.min = min != null ? min : Double.POSITIVE_INFINITY;
     }
 
     public void setMax(Double max)
     {
-      this.max = requireNonNullElse(max, Double.NEGATIVE_INFINITY);
+      this.max = max != null ? max : Double.NEGATIVE_INFINITY;
     }
 
     public void setBounds(Double min, Double max)

diff --git a/src/jalview/ws/params/simple/IntegerParameter.java b/src/jalview/ws/params/simple/IntegerParameter.java
index af6c881..e154194 100644 (file)
--- a/src/jalview/ws/params/simple/IntegerParameter.java
+++ b/src/jalview/ws/params/simple/IntegerParameter.java
@@ -22,7 +22,6 @@ package jalview.ws.params.simple;
 
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
-import static java.util.Objects.requireNonNullElse;
 
 /**
  * @author jimp
@@ -67,12 +66,12 @@ public class IntegerParameter extends Option implements ParameterI
 
     public void setMin(Integer min)
     {
-      this.min = requireNonNullElse(min, Integer.MAX_VALUE);
+      this.min = min != null ? min : Integer.MAX_VALUE;
     }
 
     public void setMax(Integer max)
-    {
-      this.max = requireNonNullElse(max, Integer.MIN_VALUE);
+    { 
+      this.max = max != null ? max : Integer.MIN_VALUE;
     }
 
     public void setBounds(Integer min, Integer max)

diff --git a/src/jalview/ws/params/simple/LogarithmicParameter.java b/src/jalview/ws/params/simple/LogarithmicParameter.java
index 12a7be1..b4e2e50 100644 (file)
--- a/src/jalview/ws/params/simple/LogarithmicParameter.java
+++ b/src/jalview/ws/params/simple/LogarithmicParameter.java
@@ -1,7 +1,5 @@
 package jalview.ws.params.simple;
 
-import static java.util.Objects.requireNonNullElse;
-
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
 
@@ -58,12 +56,12 @@ public class LogarithmicParameter extends Option implements ParameterI
 
     public void setMin(Double min)
     {
-      this.min = requireNonNullElse(min, Double.POSITIVE_INFINITY);
+      this.min = min != null ? min : Double.POSITIVE_INFINITY;
     }
 
     public void setMax(Double max)
     {
-      this.max = requireNonNullElse(max, Double.NEGATIVE_INFINITY);
+      this.max = max != null ? max : Double.NEGATIVE_INFINITY;
     }
 
     public void setBounds(Double min, Double max)

diff --git a/src/jalview/ws/params/simple/Option.java b/src/jalview/ws/params/simple/Option.java
index 44f9f5d..d6f3e7c 100644 (file)
--- a/src/jalview/ws/params/simple/Option.java
+++ b/src/jalview/ws/params/simple/Option.java
@@ -26,7 +26,6 @@ import java.net.URL;
 import java.util.ArrayList;
 import java.util.List;
 import static java.util.Objects.requireNonNull;
-import static java.util.Objects.requireNonNullElse;
 
 public class Option implements OptionI
 {
@@ -143,7 +142,7 @@ public class Option implements OptionI
   {
     requireNonNull(builder.name);
     name = builder.name;
-    label = requireNonNullElse(builder.label, name);
+    label = builder.label != null ? builder.label : name;
     description = builder.description;
     required = builder.required;
     defvalue = builder.defaultValue;

diff --git a/src/jalview/ws2/actions/annotation/AnnotationTask.java b/src/jalview/ws2/actions/annotation/AnnotationTask.java
index 165e132..271d9ed 100644 (file)
--- a/src/jalview/ws2/actions/annotation/AnnotationTask.java
+++ b/src/jalview/ws2/actions/annotation/AnnotationTask.java
@@ -43,8 +43,6 @@ import jalview.ws2.client.api.AnnotationWebServiceClientI;
 import jalview.ws2.helpers.DelegateJobEventListener;
 import jalview.ws2.helpers.TaskEventSupport;
 
-import static java.util.Objects.requireNonNullElse;
-
 public class AnnotationTask implements TaskI<AnnotationResult>
 {
   private final long uid = MathUtils.getUID();
@@ -185,7 +183,7 @@ public class AnnotationTask implements TaskI<AnnotationResult>
 
     private void updateOurAnnots(List<AlignmentAnnotation> newAnnots)
     {
-      List<AlignmentAnnotation> oldAnnots = requireNonNullElse(ourAnnots, Collections.emptyList());
+      List<AlignmentAnnotation> oldAnnots = ourAnnots != null ? ourAnnots : Collections.emptyList();
       ourAnnots = newAnnots;
       AlignmentI alignment = viewport.getAlignment();
       for (AlignmentAnnotation an : oldAnnots)

diff --git a/src/jalview/ws2/client/slivka/SlivkaParamStoreFactory.java b/src/jalview/ws2/client/slivka/SlivkaParamStoreFactory.java
index a848798..fba6d2b 100644 (file)
--- a/src/jalview/ws2/client/slivka/SlivkaParamStoreFactory.java
+++ b/src/jalview/ws2/client/slivka/SlivkaParamStoreFactory.java
@@ -1,7 +1,5 @@
 package jalview.ws2.client.slivka;
 
-import static java.util.Objects.requireNonNullElse;
-
 import java.io.File;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -31,6 +29,7 @@ import uk.ac.dundee.compbio.slivkaclient.SlivkaService;
 class SlivkaParamStoreFactory
 {
   private final SlivkaService service;
+
   private final ParamManager manager;
 
   SlivkaParamStoreFactory(SlivkaService service, ParamManager manager)
@@ -38,7 +37,7 @@ class SlivkaParamStoreFactory
     this.service = service;
     this.manager = manager;
   }
-  
+
   ParamDatastoreI createParamDatastore()
   {
     URL url = null;
@@ -57,7 +56,7 @@ class SlivkaParamStoreFactory
     List<ArgumentI> arguments = createPresetArguments(Collections.emptyMap());
     return new SimpleParamDatastore(url, arguments, presets, manager);
   }
-  
+
   WsParamSetI createPreset(SlivkaService.Preset preset)
   {
     var builder = SimpleParamSet.newBuilder();
@@ -156,7 +155,7 @@ class SlivkaParamStoreFactory
 
   private List<Option> createChoiceOptions(Parameter.ChoiceParameter param, List<String> value)
   {
-    value = requireNonNullElse(value, Collections.emptyList());
+    value = value != null ? value : Collections.emptyList();
     if (param.isArray())
     {
       /*
@@ -164,8 +163,9 @@ class SlivkaParamStoreFactory
        * Use multiple boolean checkboxes to represent the value.
        */
       List<Option> options = new ArrayList<>();
-      List<?> selected = requireNonNullElse(
-          (List<?>) param.getDefault(), Collections.emptyList());
+      List<?> selected = param.getDefault() != null
+              ? (List<?>) param.getDefault()
+              : Collections.emptyList();
       int i = 0;
       var builder = BooleanOption.newBuilder();
       setCommonProperties(param, builder);

diff --git a/src/jalview/ws2/gui/AlignmentServiceGuiHandler.java b/src/jalview/ws2/gui/AlignmentServiceGuiHandler.java
index 59683a7..fd1d0ad 100644 (file)
--- a/src/jalview/ws2/gui/AlignmentServiceGuiHandler.java
+++ b/src/jalview/ws2/gui/AlignmentServiceGuiHandler.java
@@ -1,7 +1,5 @@
 package jalview.ws2.gui;
 
-import static java.util.Objects.requireNonNullElse;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
@@ -62,7 +60,7 @@ class AlignmentServiceGuiHandler
     String panelInfo = String.format("%s using service hosted at %s%n%s",
         service.getName(), service.getUrl(), service.getDescription());
     infoPanel = new WebserviceInfo(service.getName(), panelInfo, false);
-    String actionName = requireNonNullElse(action.getName(), "Alignment");
+    String actionName = action.getName() != null ? action.getName() : "Alignment";
     alnTitle = String.format("%s %s of %s", service.getName(), actionName,
         frame.getTitle());
   }

diff --git a/src/jalview/ws2/gui/WebServicesMenuManager.java b/src/jalview/ws2/gui/WebServicesMenuManager.java
index 8a799c5..c9b53a9 100644 (file)
--- a/src/jalview/ws2/gui/WebServicesMenuManager.java
+++ b/src/jalview/ws2/gui/WebServicesMenuManager.java
@@ -42,7 +42,6 @@ import jalview.ws2.api.WebService;
 import jalview.ws2.client.api.WebServiceProviderI;
 
 import static java.lang.String.format;
-import static java.util.Objects.requireNonNullElse;
 
 public class WebServicesMenuManager
 {
@@ -146,7 +145,7 @@ public class WebServicesMenuManager
       {
         actionsByCategory
             .computeIfAbsent(
-                Objects.requireNonNullElse(action.getSubcategory(), ""),
+                action.getSubcategory() != null ? action.getSubcategory() : "",
                 k -> new ArrayList<>())
             .add(action);
       }
@@ -316,7 +315,7 @@ public class WebServicesMenuManager
         {
           actionsByCategory
               .computeIfAbsent(
-                  requireNonNullElse(action.getSubcategory(), ""),
+                  action.getSubcategory() != null ? action.getSubcategory() : "",
                   k -> new ArrayList<>())
               .add(action);
         }