From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Mon, 14 May 2018 13:20:19 +0000 (+0100)
Subject: Update spike branch to latest
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d7d522b7784d6ac65a008fe5f89ed7a4e7d8d2f7;p=jalview.git

Update spike branch to latest
---

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index d52aa97..89066cb 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -94,7 +94,6 @@ import jalview.schemes.ColourSchemes;
 import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
 import jalview.util.MessageManager;
-import jalview.util.StringUtils;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.ViewportRanges;
 import jalview.ws.DBRefFetcher;
@@ -143,7 +142,6 @@ import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Scanner;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
@@ -1140,13 +1138,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     return true;
   }
 
+  /**
+   * Opens a file browser and adds the selected file, if in Fasta, Stockholm or
+   * Pfam format, to the list held under preference key "HMMSEARCH_DBS" (as a
+   * comma-separated list)
+   */
   @Override
   public void addDatabase_actionPerformed() throws IOException
   {
-    if (Cache.getProperty(Preferences.HMMSEARCH_DB_PATHS) == null)
+    if (Cache.getProperty(Preferences.HMMSEARCH_DBS) == null)
     {
       Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
-      Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
     }
 
     String path = openFileChooser(false);
@@ -1157,19 +1159,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (format == FileFormat.Fasta || format == FileFormat.Stockholm
               || format == FileFormat.Pfam)
       {
-        String currentDbs = Cache.getProperty(Preferences.HMMSEARCH_DBS);
         String currentDbPaths = Cache
-                .getProperty(Preferences.HMMSEARCH_DB_PATHS);
-        currentDbPaths += " " + path;
-
-        String fileName = StringUtils.getLastToken(path, File.separator);
-        Scanner scanner = new Scanner(fileName).useDelimiter(".");
-        String name = scanner.next();
-        scanner.close();
-        currentDbs += " " + path; // TODO remove path from file name
-        scanner.close();
-
-        Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, currentDbPaths);
+                .getProperty(Preferences.HMMSEARCH_DBS);
+        currentDbPaths += Preferences.COMMA + path;
         Cache.setProperty(Preferences.HMMSEARCH_DBS, currentDbPaths);
       }
       else
diff --git a/src/jalview/gui/OptsAndParamsPage.java b/src/jalview/gui/OptsAndParamsPage.java
index 1843f49..298057f 100644
--- a/src/jalview/gui/OptsAndParamsPage.java
+++ b/src/jalview/gui/OptsAndParamsPage.java
@@ -144,12 +144,17 @@ public class OptsAndParamsPage
         add(enabled);
       }
 
-      val = new JComboBox<>();
-      for (String str : opt.getPossibleValues())
-      {
-        val.addItem(str);
-      }
+      /*
+       * construct the choice box with possible values, 
+       * or their display names if provided
+       */
+      val = buildComboBox(opt);
       val.setSelectedItem(opt.getValue());
+
+      /*
+       * only show the choicebox if there is more than one option,
+       * or the option is mandatory
+       */
       if (opt.getPossibleValues().size() > 1 || opt.isRequired())
       {
         val.addActionListener(this);
@@ -228,31 +233,21 @@ public class OptsAndParamsPage
       poparent.argSetModified(this, !notmod);
     }
 
-    public OptionI getOptionIfEnabled()
+    /**
+     * Answers null if the option is not selected, else a new Option holding the
+     * selected value
+     * 
+     * @return
+     */
+    public ArgumentI getSelectedOption()
     {
       if (!enabled.isSelected())
       {
         return null;
       }
+      String value = getSelectedValue(option, val.getSelectedIndex());
       OptionI opt = option.copy();
-      if (opt.getPossibleValues() != null
-              && opt.getPossibleValues().size() == 1)
-      {
-        // Hack to make sure the default value for an enabled option with only
-        // one value is actually returned
-        opt.setValue(opt.getPossibleValues().get(0));
-      }
-      if (val.getSelectedItem() != null)
-      {
-        opt.setValue((String) val.getSelectedItem());
-      }
-      else
-      {
-        if (option.getValue() != null)
-        {
-          opt.setValue(option.getValue());
-        }
-      }
+      opt.setValue(value);
       return opt;
     }
 
@@ -613,12 +608,18 @@ public class OptsAndParamsPage
       return Component.BaselineResizeBehavior.CONSTANT_ASCENT;
     }
 
-    public ParameterI getParameter()
+    /**
+     * Answers an argument holding the value entered or selected in the dialog
+     * 
+     * @return
+     */
+    public ArgumentI getParameter()
     {
       ParameterI prm = parameter.copy();
       if (isChoiceParameter)
       {
-        prm.setValue((String) choicebox.getSelectedItem());
+        String value = getSelectedValue(this.parameter, choicebox.getSelectedIndex());
+        prm.setValue(value);
       }
       else
       {
@@ -732,8 +733,7 @@ public class OptsAndParamsPage
       {
         if (isChoiceParameter)
         {
-          choicebox = new JComboBox<>();
-          choicebox.addActionListener(this);
+          choicebox = buildComboBox(parm);
           controlsPanel.add(choicebox, BorderLayout.CENTER);
         }
         else
@@ -765,26 +765,9 @@ public class OptsAndParamsPage
         }
       }
 
-      if (parm != null)
+      if (!isChoiceParameter && parm != null)
       {
-        if (isChoiceParameter)
-        {
-          if (init)
-          {
-            for (String val : parm.getPossibleValues())
-            {
-              choicebox.addItem(val);
-            }
-          }
-          if (parm.getValue() != null)
-          {
-            choicebox.setSelectedItem(parm.getValue());
-          }
-        }
-        else
-        {
-          valueField.setText(parm.getValue());
-        }
+        valueField.setText(parm.getValue());
       }
       lastVal = updateSliderFromValueField();
       adjusting = false;
@@ -810,7 +793,7 @@ public class OptsAndParamsPage
       {
         if (isChoiceParameter)
         {
-          return choicebox.getSelectedItem();
+          return getSelectedValue(this.parameter, choicebox.getSelectedIndex());
         }
         slider.setVisible(false);
         return valueField.getText().trim();
@@ -1048,7 +1031,9 @@ public class OptsAndParamsPage
   }
 
   /**
-   * recover options and parameters from GUI
+   * Answers a list of arguments representing all the options and arguments
+   * selected on the dialog, holding their chosen or input values. Optional
+   * parameters which were not selected are not included.
    * 
    * @return
    */
@@ -1057,7 +1042,7 @@ public class OptsAndParamsPage
     List<ArgumentI> argSet = new ArrayList<>();
     for (OptionBox opts : getOptSet().values())
     {
-      OptionI opt = opts.getOptionIfEnabled();
+      ArgumentI opt = opts.getSelectedOption();
       if (opt != null)
       {
         argSet.add(opt);
@@ -1065,7 +1050,7 @@ public class OptsAndParamsPage
     }
     for (ParamBox parambox : getParamSet().values())
     {
-      ParameterI parm = parambox.getParameter();
+      ArgumentI parm = parambox.getParameter();
       if (parm != null)
       {
         argSet.add(parm);
@@ -1074,4 +1059,64 @@ public class OptsAndParamsPage
 
     return argSet;
   }
+
+  /**
+   * A helper method that constructs and returns a CombBox for choice of the
+   * possible option values. If display names are provided, then these are added
+   * as options, otherwise the actual values are added.
+   * 
+   * @param opt
+   * @return
+   */
+  protected JComboBox<String> buildComboBox(OptionI opt)
+  {
+    JComboBox<String> cb = null;
+    List<String> displayNames = opt.getDisplayNames();
+    if (displayNames != null)
+    {
+      cb = JvSwingUtils.buildComboWithTooltips(displayNames,
+              opt.getPossibleValues());
+    }
+    else
+    {
+      cb = new JComboBox<>();
+      for (String v : opt.getPossibleValues())
+      {
+        cb.addItem(v);
+      }
+    }
+    return cb;
+  }
+
+  /*
+   * Answers the value corresponding to the selected item in the choice combo
+   * box. If display names were not provided, this is simply the selected
+   * value. If display names were provided, it is the value corresponding to
+   * the selected item index.
+   * 
+   * @return
+   */
+  protected static String getSelectedValue(OptionI opt, int sel)
+  {
+    List<String> possibleValues = opt.getPossibleValues();
+    String value = null;
+    if (possibleValues != null && possibleValues.size() == 1)
+    {
+      // Hack to make sure the default value for an enabled option with only
+      // one value is actually returned even if this.val is not displayed
+      value = possibleValues.get(0);
+    }
+    else
+    {
+      if (sel >= 0 && sel < possibleValues.size())
+      {
+        value = possibleValues.get(sel);
+      }
+      else
+      {
+        value = opt.getValue();
+      }
+    }
+    return value;
+  }
 }
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 5382f8d..3259909 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -86,6 +86,9 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  */
 public class Preferences extends GPreferences
 {
+  // suggested list delimiter character
+  public static final String COMMA = ",";
+
   public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
 
   public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
@@ -118,8 +121,6 @@ public class Preferences extends GPreferences
 
   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 
-  public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
-
   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
diff --git a/src/jalview/hmmer/HMMERParamStore.java b/src/jalview/hmmer/HMMERParamStore.java
index fbab7a9..00cae85 100644
--- a/src/jalview/hmmer/HMMERParamStore.java
+++ b/src/jalview/hmmer/HMMERParamStore.java
@@ -15,10 +15,10 @@ import jalview.ws.params.simple.LogarithmicParameter;
 import jalview.ws.params.simple.Option;
 import jalview.ws.params.simple.StringParameter;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Collection;
 import java.util.List;
 import java.util.Scanner;
 
@@ -101,39 +101,6 @@ public final class HMMERParamStore implements ParamDatastoreI
     /*
      * 'Options'
      */
-    addChoiceOfHmm(args);
-
-    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
-    if (names != null && !names.isEmpty())
-    {
-      List<String> databases = new ArrayList<>();
-      databases.add(MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY));
-      Scanner nameScanner = new Scanner(names);
-
-      if (nameScanner.hasNext())
-      {
-        while (nameScanner.hasNext())
-        {
-          String next = nameScanner.next();
-          if ("null".equals(next))
-          {
-            Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
-            Cache.setProperty(Preferences.HMMSEARCH_DB_PATHS, "");
-          }
-          else
-          {
-            databases.add(next);
-          }
-        }
-      }
-      nameScanner.close();
-      args.add(new StringParameter(
-              MessageManager.getString(HMMSearch.DATABASE_KEY),
-              MessageManager.getString("label.database_for_hmmsearch"),
-              true, MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY),
-              MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY),
-              databases));
-    }
     args.add(new BooleanOption(
             MessageManager.getString(HMMSearch.AUTO_ALIGN_SEQS_KEY),
             MessageManager.getString("label.auto_align_seqs_desc"), false,
@@ -150,6 +117,10 @@ public final class HMMERParamStore implements ParamDatastoreI
     /*
      * 'Parameters'
      */
+    addChoiceOfHmm(args);
+
+    addChoiceOfDatabase(args);
+
     args.add(new IntegerParameter(
             MessageManager.getString(HMMSearch.NUMBER_OF_RESULTS_KEY),
             MessageManager.getString("label.number_of_results_desc"), true,
@@ -158,7 +129,8 @@ public final class HMMERParamStore implements ParamDatastoreI
             MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
             true, HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_NONE,
             Arrays.asList(HMMSearch.CUTOFF_NONE, HMMSearch.CUTOFF_EVALUE,
-                    HMMSearch.CUTOFF_SCORE)));
+                    HMMSearch.CUTOFF_SCORE),
+            null));
     args.add(new LogarithmicParameter(
             MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
             MessageManager.getString("label.seq_e_value_desc"), false, 1D,
@@ -180,6 +152,56 @@ public final class HMMERParamStore implements ParamDatastoreI
   }
 
   /**
+   * Constructs a choice parameter for database to search; always includes 'this
+   * alignment', and also includes any databases held under user preferences key
+   * "HMMSEARCH_DBS" as a comma-delimited list
+   * 
+   * @param args
+   */
+  protected void addChoiceOfDatabase(List<ArgumentI> args)
+  {
+    String names = Cache.getProperty(Preferences.HMMSEARCH_DBS);
+    if (names == null || names.isEmpty())
+    {
+      return;
+    }
+
+    List<String> filePaths = new ArrayList<>();
+    List<String> fileNames = new ArrayList<>();
+
+    String thisAlignment = MessageManager.getString(HMMSearch.THIS_ALIGNMENT_KEY);
+    filePaths.add(thisAlignment);
+    fileNames.add(thisAlignment);
+
+    Scanner nameScanner = new Scanner(names);
+    nameScanner.useDelimiter(Preferences.COMMA);
+
+    while (nameScanner.hasNext())
+    {
+      String next = nameScanner.next();
+      if ("null".equals(next))
+      {
+        Cache.setProperty(Preferences.HMMSEARCH_DBS, "");
+      }
+      else
+      {
+        filePaths.add(next);
+        int pos = next.lastIndexOf(File.separator);
+        String fileName = next.substring(pos + 1);
+        fileNames.add(fileName);
+      }
+    }
+    nameScanner.close();
+    ArgumentI databasesOption = new StringParameter(
+            MessageManager.getString(HMMSearch.DATABASE_KEY),
+            MessageManager.getString("label.database_for_hmmsearch"), true,
+            thisAlignment,
+            thisAlignment,
+            filePaths, fileNames);
+    args.add(databasesOption);
+  }
+
+  /**
    * Answers default parameters for hmmalign, taking into account any configured
    * as user preferences
    * 
@@ -216,7 +238,7 @@ public final class HMMERParamStore implements ParamDatastoreI
       String defseq = options.get(0);
       ArgumentI arg = new StringParameter(
               MessageManager.getString("label.use_hmm"), null, true, defseq,
-              defseq, options);
+              defseq, options, null);
       args.add(arg);
     }
   }
@@ -256,7 +278,7 @@ public final class HMMERParamStore implements ParamDatastoreI
      */
     if (!viewport.getAlignment().getGroups().isEmpty())
     {
-      Collection<String> options = new ArrayList<>();
+      List<String> options = new ArrayList<>();
       options.add(MessageManager.getString("label.alignment"));
       options.add(MessageManager.getString("label.groups_and_alignment"));
       options.add(MessageManager.getString("label.groups"));
diff --git a/src/jalview/util/StringUtils.java b/src/jalview/util/StringUtils.java
index 2e8ace8..3c5ba92 100644
--- a/src/jalview/util/StringUtils.java
+++ b/src/jalview/util/StringUtils.java
@@ -107,29 +107,6 @@ public class StringUtils
   }
 
   /**
-   * Returns the last part of 'input' after the last occurrence of 'token'. For
-   * example to extract only the filename from a full path or URL.
-   * 
-   * @param input
-   * @param token
-   *          a delimiter which must be in regular expression format
-   * @return
-   */
-  public static String getLastToken(String input, String token)
-  {
-    if (input == null)
-    {
-      return null;
-    }
-    if (token == null)
-    {
-      return input;
-    }
-    String[] st = input.split(token);
-    return st[st.length - 1];
-  }
-
-  /**
    * Parses the input string into components separated by the delimiter. Unlike
    * String.split(), this method will ignore occurrences of the delimiter which
    * are nested within single quotes in name-value pair values, e.g. a='b,c'.
@@ -146,7 +123,7 @@ public class StringUtils
     {
       return null;
     }
-    List<String> jv = new ArrayList<String>();
+    List<String> jv = new ArrayList<>();
     int cp = 0, pos, escape;
     boolean wasescaped = false, wasquoted = false;
     String lstitem = null;
diff --git a/src/jalview/workers/InformationThread.java b/src/jalview/workers/InformationThread.java
index d719189..d35025b 100644
--- a/src/jalview/workers/InformationThread.java
+++ b/src/jalview/workers/InformationThread.java
@@ -212,10 +212,13 @@ public class InformationThread extends AlignCalcWorker
     for (SequenceGroup group : alignment.getGroups())
     {
       hmmSeqs = group.getHmmSequences();
-      ProfilesI profiles = group.getHmmProfiles();
-      float m = updateInformationAnnotation(hmmSeqs.get(0), profiles, group,
-              infos);
-      maxInformation = Math.max(maxInformation, m);
+      if (!hmmSeqs.isEmpty())
+      {
+        ProfilesI profiles = group.getHmmProfiles();
+        float m = updateInformationAnnotation(hmmSeqs.get(0), profiles,
+                group, infos);
+        maxInformation = Math.max(maxInformation, m);
+      }
     }
 
     /*
diff --git a/src/jalview/ws/jws2/dm/JabaOption.java b/src/jalview/ws/jws2/dm/JabaOption.java
index cbfbd3b..f1f5014 100644
--- a/src/jalview/ws/jws2/dm/JabaOption.java
+++ b/src/jalview/ws/jws2/dm/JabaOption.java
@@ -117,4 +117,10 @@ public class JabaOption implements jalview.ws.params.OptionI
     return opt;
   }
 
+  @Override
+  public List<String> getDisplayNames()
+  {
+    return null; // not supported for Jaba options
+  }
+
 }
diff --git a/src/jalview/ws/params/OptionI.java b/src/jalview/ws/params/OptionI.java
index 2c5386d..af8ae27 100644
--- a/src/jalview/ws/params/OptionI.java
+++ b/src/jalview/ws/params/OptionI.java
@@ -25,15 +25,49 @@ import java.util.List;
 
 public interface OptionI extends ArgumentI
 {
-
+  /**
+   * Answers a URL with further details for this option, or null if none is
+   * known
+   * 
+   * @return
+   */
   URL getFurtherDetails();
 
+  /**
+   * Answers true if the option is mandatory (a value must be chosen), false if
+   * it is optional
+   * 
+   * @return
+   */
   boolean isRequired();
 
+  /**
+   * Answers the description of the option
+   * 
+   * @return
+   */
   String getDescription();
 
+  /**
+   * Answers a list of possible values that may be chosen for the option (or
+   * null if not applicable)
+   * 
+   * @return
+   */
   List<String> getPossibleValues();
 
-  OptionI copy();
+  /**
+   * Answers a list of display names corresponding to the possible values that
+   * may be chosen for the option (or null if not applicable)
+   * 
+   * @return
+   */
+  List<String> getDisplayNames();
 
+  /**
+   * Answers a new Option with a copy of the settings of this one
+   * 
+   * @return
+   */
+  OptionI copy();
 }
diff --git a/src/jalview/ws/params/simple/Option.java b/src/jalview/ws/params/simple/Option.java
index f0126df..ce5d669 100644
--- a/src/jalview/ws/params/simple/Option.java
+++ b/src/jalview/ws/params/simple/Option.java
@@ -24,7 +24,6 @@ import jalview.ws.params.OptionI;
 
 import java.net.URL;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.List;
 
 public class Option implements OptionI
@@ -43,12 +42,107 @@ public class Option implements OptionI
 
   String description;
 
-  ArrayList<String> possibleVals = new ArrayList<>();
+  List<String> possibleVals;
+
+  /*
+   * optional display names corresponding to possibleVals
+   */
+  List<String> displayVals;
 
   boolean required;
 
   URL fdetails;
 
+  /**
+   * Copy constructor
+   * 
+   * @param opt
+   */
+  public Option(Option opt)
+  {
+    name = opt.name;
+    value = opt.value;
+    defvalue = opt.defvalue;
+    description = opt.description;
+    if (opt.possibleVals != null)
+    {
+      possibleVals = new ArrayList<>(opt.possibleVals);
+    }
+    required = opt.required;
+    // URLs are singletons - so we copy by reference. nasty but true.
+    fdetails = opt.fdetails;
+  }
+
+  public Option()
+  {
+  }
+
+  /**
+   * Constructor including display names for possible values
+   * 
+   * @param name2
+   * @param description2
+   * @param isrequired
+   * @param defValue
+   * @param val
+   * @param possibleVals
+   * @param fdetails
+   */
+  public Option(String name2, String description2, boolean isrequired,
+          String defValue, String val, List<String> possibleVals,
+          List<String> displayNames, URL fdetails)
+  {
+    name = name2;
+    description = description2;
+    this.value = val;
+    this.required = isrequired;
+    this.defvalue = defValue;
+    if (possibleVals != null)
+    {
+      this.possibleVals = new ArrayList<>(possibleVals);
+    }
+    if (displayNames != null)
+    {
+      this.displayVals = new ArrayList<>(displayNames);
+    }
+    this.fdetails = fdetails;
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param name2
+   * @param description2
+   * @param isrequired
+   * @param defValue
+   * @param val
+   * @param possibleVals
+   * @param fdetails
+   */
+  public Option(String name2, String description2, boolean isrequired,
+          String defValue, String val, List<String> possibleVals,
+          URL fdetails)
+  {
+    this(name2, description2, isrequired, defValue, val, possibleVals, null,
+            fdetails);
+  }
+
+  @Override
+  public OptionI copy()
+  {
+    Option opt = new Option(this);
+    return opt;
+  }
+
+  /**
+   * toString method to help identify options in the debugger only
+   */
+  @Override
+  public String toString()
+  {
+    return this.getClass().getName() + ":" + name;
+  }
+
   @Override
   public String getName()
   {
@@ -91,64 +185,9 @@ public class Option implements OptionI
     return possibleVals;
   }
 
-  public Option(Option opt)
-  {
-    name = new String(opt.name);
-    if (opt.value != null)
-    {
-      value = new String(opt.value);
-    }
-    if (opt.defvalue != null)
-    {
-      defvalue = new String(opt.defvalue);
-    }
-    if (opt.description != null)
-    {
-      description = new String(opt.description);
-    }
-    if (opt.possibleVals != null)
-    {
-      possibleVals = (ArrayList<String>) opt.possibleVals.clone();
-    }
-    required = opt.required;
-    // URLs are singletons - so we copy by reference. nasty but true.
-    fdetails = opt.fdetails;
-  }
-
-  public Option()
-  {
-  }
-
-  public Option(String name2, String description2, boolean isrequired,
-          String defValue, String value, Collection<String> possibleVals,
-          URL fdetails)
-  {
-    name = name2;
-    description = description2;
-    this.value = value;
-    this.required = isrequired;
-    this.defvalue = defValue;
-    if (possibleVals != null)
-    {
-      this.possibleVals = new ArrayList<>();
-      this.possibleVals.addAll(possibleVals);
-    }
-    this.fdetails = fdetails;
-  }
-
   @Override
-  public OptionI copy()
-  {
-    Option opt = new Option(this);
-    return opt;
-  }
-
-  /**
-   * toString method to help identify options in the debugger only
-   */
-  @Override
-  public String toString()
+  public List<String> getDisplayNames()
   {
-    return this.getClass().getName() + ":" + name;
+    return displayVals;
   }
 }
diff --git a/src/jalview/ws/params/simple/StringParameter.java b/src/jalview/ws/params/simple/StringParameter.java
index b61836a..d3d899c 100644
--- a/src/jalview/ws/params/simple/StringParameter.java
+++ b/src/jalview/ws/params/simple/StringParameter.java
@@ -3,7 +3,7 @@ package jalview.ws.params.simple;
 import jalview.ws.params.ParameterI;
 import jalview.ws.params.ValueConstrainI;
 
-import java.util.Collection;
+import java.util.List;
 
 public class StringParameter extends Option implements ParameterI
 {
@@ -46,6 +46,8 @@ public class StringParameter extends Option implements ParameterI
   {
     this.name = parm.name;
     this.defvalue = parm.defvalue;
+    this.possibleVals = parm.possibleVals;
+    this.displayVals = parm.displayVals;
   }
 
   public StringParameter(String name, String description, boolean required,
@@ -65,7 +67,8 @@ public class StringParameter extends Option implements ParameterI
   }
 
   /**
-   * Constructor for a parameter with a list of possible values
+   * Constructor for a parameter with a list of possible values and (optionally)
+   * corresponding display names
    * 
    * @param name2
    * @param description2
@@ -73,12 +76,13 @@ public class StringParameter extends Option implements ParameterI
    * @param defValue
    * @param value
    * @param possibleVals
+   * @param displayNames
    */
   public StringParameter(String name2, String description2,
           boolean isrequired, String defValue, String value,
-          Collection<String> possibleVals)
+          List<String> possibleVals, List<String> displayNames)
   {
     super(name2, description2, isrequired, defValue, value, possibleVals,
-            null);
+            displayNames, null);
   }
 }
diff --git a/src/jalview/ws/rest/InputType.java b/src/jalview/ws/rest/InputType.java
index 88431a6..c83879a 100644
--- a/src/jalview/ws/rest/InputType.java
+++ b/src/jalview/ws/rest/InputType.java
@@ -30,7 +30,6 @@ 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 +57,9 @@ 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 +74,7 @@ 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 +103,9 @@ 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 +119,9 @@ public abstract class InputType
   public boolean validFor(RestServiceDescription restServiceDescription)
   {
     if (!restServiceDescription.inputParams.values().contains(this))
+    {
       return false;
+    }
 
     return true;
   }
@@ -270,7 +273,7 @@ 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 +298,7 @@ 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)
     {
diff --git a/test/jalview/util/StringUtilsTest.java b/test/jalview/util/StringUtilsTest.java
index 084219a..9d805cc 100644
--- a/test/jalview/util/StringUtilsTest.java
+++ b/test/jalview/util/StringUtilsTest.java
@@ -87,19 +87,6 @@ public class StringUtilsTest
   }
 
   @Test(groups = { "Functional" })
-  public void testGetLastToken()
-  {
-    assertNull(StringUtils.getLastToken(null, null));
-    assertNull(StringUtils.getLastToken(null, "/"));
-    assertEquals("a", StringUtils.getLastToken("a", null));
-
-    assertEquals("abc", StringUtils.getLastToken("abc", "/"));
-    assertEquals("c", StringUtils.getLastToken("abc", "b"));
-    assertEquals("file1.dat", StringUtils.getLastToken(
-            "file://localhost:8080/data/examples/file1.dat", "/"));
-  }
-
-  @Test(groups = { "Functional" })
   public void testSeparatorListToArray()
   {
     String[] result = StringUtils.separatorListToArray(
@@ -145,7 +132,7 @@ public class StringUtilsTest
   public void testListToDelimitedString()
   {
     assertEquals("", StringUtils.listToDelimitedString(null, ";"));
-    List<String> list = new ArrayList<String>();
+    List<String> list = new ArrayList<>();
     assertEquals("", StringUtils.listToDelimitedString(list, ";"));
     list.add("now");
     assertEquals("now", StringUtils.listToDelimitedString(list, ";"));