Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / ws / rest / InputType.java

diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index df340b0..65d8339 100644 (file)
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,6 +20,8 @@
  */
 package jalview.ws.rest;
 
+import java.util.Locale;
+
 import jalview.ws.params.ArgumentI;
 import jalview.ws.params.InvalidArgumentException;
 import jalview.ws.params.OptionI;
@@ -30,7 +32,6 @@ import jalview.ws.params.simple.Option;
 import java.io.UnsupportedEncodingException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -58,9 +59,9 @@ public abstract class InputType
   {
     NUC, PROT, MIX;
 
-    public static Collection<String> toStringValues()
+    public static List<String> toStringValues()
     {
-      Collection<String> c = new ArrayList<String>();
+      List<String> c = new ArrayList<>();
       for (molType type : values())
       {
         c.add(type.toString());
@@ -75,7 +76,7 @@ public abstract class InputType
 
   public int max = 0; // unbounded
 
-  protected ArrayList<Class> inputData = new ArrayList<Class>();
+  protected List<Class> inputData = new ArrayList<>();
 
   /**
    * initialise the InputType with a list of jalview data classes that the
@@ -104,7 +105,9 @@ public abstract class InputType
   public boolean validFor(RestJob restJob)
   {
     if (!validFor(restJob.rsd))
+    {
       return false;
+    }
     for (Class cl : inputData)
     {
       if (!restJob.hasDataOfType(cl))
@@ -118,7 +121,9 @@ public abstract class InputType
   public boolean validFor(RestServiceDescription restServiceDescription)
   {
     if (!restServiceDescription.inputParams.values().contains(this))
+    {
       return false;
+    }
 
     return true;
   }
@@ -130,13 +135,13 @@ public abstract class InputType
     {
       if (type == null)
       {
-        return new StringBody(utf8.encode(content).asCharBuffer()
-                .toString());
+        return new StringBody(
+                utf8.encode(content).asCharBuffer().toString());
       }
       else
       {
-        return new StringBody(utf8.encode(content).asCharBuffer()
-                .toString(), type, utf8);
+        return new StringBody(
+                utf8.encode(content).asCharBuffer().toString(), type, utf8);
       }
     } catch (Exception ex)
     {
@@ -232,7 +237,7 @@ public abstract class InputType
         {
           valid = false;
           warnings.append("Invalid value for parameter "
-                  + mtch.group(1).toLowerCase() + " '" + mtch.group(2)
+                  + mtch.group(1).toLowerCase(Locale.ROOT) + " '" + mtch.group(2)
                   + "' (expected an integer)\n");
         }
 
@@ -270,7 +275,7 @@ public abstract class InputType
 
   public List<OptionI> getBaseOptions()
   {
-    ArrayList<OptionI> opts = new ArrayList<OptionI>();
+    ArrayList<OptionI> opts = new ArrayList<>();
     opts.add(new IntegerParameter("min",
             "Minimum number of data of this type", true, 1, min, 0, -1));
     opts.add(new IntegerParameter("max",
@@ -295,7 +300,7 @@ public abstract class InputType
   public void configureFromArgumentI(List<ArgumentI> currentSettings)
           throws InvalidArgumentException
   {
-    ArrayList<String> urltoks = new ArrayList<String>();
+    List<String> urltoks = new ArrayList<>();
     String rg;
     for (ArgumentI arg : currentSettings)
     {
@@ -307,9 +312,10 @@ public abstract class InputType
       {
         // TODO: revise architecture - this is counter intuitive - options with
         // different values to their names are actually parameters
-        rg = (arg.getValue().length() > 0) ? (arg.getValue().equals(
-                arg.getName()) ? arg.getName() : arg.getName() + "='"
-                + arg.getValue() + "'") : arg.getName();
+        rg = (arg.getValue().length() > 0)
+                ? (arg.getValue().equals(arg.getName()) ? arg.getName()
+                        : arg.getName() + "='" + arg.getValue() + "'")
+                : arg.getName();
       }
       if (rg.length() > 0)
       {
@@ -317,7 +323,8 @@ public abstract class InputType
       }
     }
     StringBuffer warnings;
-    if (!configureFromURLtokenString(urltoks, warnings = new StringBuffer()))
+    if (!configureFromURLtokenString(urltoks,
+            warnings = new StringBuffer()))
     {
       throw new InvalidArgumentException(warnings.toString());
     }
@@ -326,8 +333,8 @@ public abstract class InputType
   protected OptionI createMolTypeOption(String name, String descr,
           boolean req, molType curType, molType defType)
   {
-    return new Option(name, descr, req, defType == null ? ""
-            : defType.toString(),
+    return new Option(name, descr, req,
+            defType == null ? "" : defType.toString(),
             curType == null ? "" : curType.toString(),
             molType.toStringValues(), null);
   }