Merge branch 'develop' into bug/JAL-4238_PAEs_not_being_shown_in_JalviewJS

diff --cc src/jalview/bin/Commands.java
Simple merge

diff --cc src/jalview/bin/argparser/ArgParser.java
index 48cbf9c,12e1b1d..f619687
--- 1/src/jalview/bin/argparser/ArgParser.java
--- 2/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@@ -751,7 -719,9 +761,8 @@@ public class ArgParse
          }
          else if (a.hasOption(Opt.BOOLEAN))
          {
-           setBoolean(linkedId, type, avs, !negated, argIndex);
+           setBoolean(linkedId, givenLinkedId, type, avs, !negated,
+                   argIndex);
 -          setNegated(linkedId, avs, negated);
          }
          else if (a.hasOption(Opt.UNARY))
          {
@@@ -1096,38 -1066,44 +1107,38 @@@
    /**
     * This version inserts the subvals sv into all created values
     */
-   private void addValue(String linkedId, Type type, ArgValues avs,
-           SubVals sv, String v, int argIndex, boolean doSubs)
+   private void addValue(String linkedId, String givenLinkedId, Type type,
+           ArgValues avs, SubVals sv, String v, int argIndex, boolean doSubs)
    {
-     this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, sv, v, false,
-             argIndex, doSubs);
+     this.argValueOperation(Op.ADDVALUE, linkedId, givenLinkedId, type, avs,
+             sv, v, false, argIndex, doSubs);
    }
  
-   private void setBoolean(String linkedId, Type type, ArgValues avs,
-           boolean b, int argIndex)
+   private void setBoolean(String linkedId, String givenLinkedId, Type type,
+           ArgValues avs, boolean b, int argIndex)
    {
-     this.argValueOperation(Op.SETBOOLEAN, linkedId, type, avs, null, null,
-             b, argIndex, false);
+     this.argValueOperation(Op.SETBOOLEAN, linkedId, givenLinkedId, type,
+             avs, null, null, b, argIndex, false);
    }
  
 -  private void setNegated(String linkedId, ArgValues avs, boolean b)
 -  {
 -    this.argValueOperation(Op.SETNEGATED, linkedId, null, null, avs, null,
 -            null, b, 0, false);
 -  }
 -
    private void incrementCount(String linkedId, ArgValues avs)
    {
-     this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, avs, null,
-             null, false, 0, false);
+     this.argValueOperation(Op.INCREMENTCOUNT, linkedId, null, null, avs,
+             null, null, false, 0, false);
    }
  
    private enum Op
    {
 -    ADDVALUE, SETBOOLEAN, SETNEGATED, INCREMENTCOUNT
 +    ADDVALUE, SETBOOLEAN, INCREMENTCOUNT
    }
  
-   private void argValueOperation(Op op, String linkedId, Type type,
-           ArgValues avs, SubVals sv, String v, boolean b, int argIndex,
-           boolean doSubs)
+   private void argValueOperation(Op op, String linkedId,
+           String givenLinkedId, Type type, ArgValues avs, SubVals sv,
+           String v, boolean b, int argIndex, boolean doSubs)
    {
      // default to merge subvals if subvals are provided
-     argValueOperation(op, linkedId, type, avs, sv, true, v, b, argIndex,
-             doSubs);
+     argValueOperation(op, linkedId, givenLinkedId, type, avs, sv, true, v,
+             b, argIndex, doSubs);
    }
  
    /**
@@@ -1231,22 -1208,21 +1243,22 @@@
            break;
  
          case SETBOOLEAN:
 -          tavs.setBoolean(type, b, argIndex, true, givenLinkedId);
 -          finaliseStoringArgValue(matchedLinkedId, tavs);
 -          break;
 -
 -        case SETNEGATED:
 -          tavs.setNegated(b, true);
 -          break;
 -
 -        case INCREMENTCOUNT:
 -          tavs.incrementCount();
 -          break;
 -
 -        default:
 +          if (getPrioritisePositiveBooleanValue() && tavs.getCount() > 0
 +                  && tavs.getBoolean())
 +          {
 +            Console.debug("Not setting due to prioritisePositiveValue and '"
 +                    + a.argString() + "' has already been set to true");
 +          }
 +          else
 +          {
-             tavs.setBoolean(type, b, argIndex, true);
++            tavs.setBoolean(type, b, argIndex, true, givenLinkedId);
 +            if (a.hasOption(Opt.BOOLEAN))
 +            {
 +              tavs.setNegated(!b, true);
 +            }
-             finaliseStoringArgValue(id, tavs);
++            finaliseStoringArgValue(matchedLinkedId, tavs);
 +          }
            break;
 -
          }
  
        }
@@@ -1278,21 -1254,12 +1290,21 @@@
          break;
  
        case SETBOOLEAN:
 -        avs.setBoolean(type, b, argIndex, false, givenLinkedId);
 -        finaliseStoringArgValue(linkedId, avs);
 -        break;
 -
 -      case SETNEGATED:
 -        avs.setNegated(b, false);
 +        if (getPrioritisePositiveBooleanValue() && avs.getCount() > 0
 +                && avs.getBoolean())
 +        {
 +          Console.debug("Not setting due to prioritisePositiveValue and '"
 +                  + a.argString() + "' has already been set to true");
 +        }
 +        else
 +        {
-           avs.setBoolean(type, b, argIndex, false);
++          avs.setBoolean(type, b, argIndex, false, givenLinkedId);
 +          if (a.hasOption(Opt.BOOLEAN))
 +          {
 +            avs.setNegated(!b, true);
 +          }
 +          finaliseStoringArgValue(linkedId, avs);
 +        }
          break;
  
        case INCREMENTCOUNT:

diff --cc src/jalview/bin/argparser/ArgValuesMap.java
Simple merge

diff --cc src/jalview/gui/AppJmol.java
Simple merge