return avs == null ? new ArrayList<>() : avs.getArgValueList();
}
+ public List<ArgValue> getArgValueListFromSubValOrArg(ArgValue av, Arg a,
+ SubVals sv)
+ {
+ return getArgValueListFromSubValArgOrPrefWithSubstitutionsWithinTypes(
+ null, a, Position.AFTER, av, sv, null, null, null, true);
+ }
+
+ public List<ArgValue> getArgValueListFromSubValArgOrPrefWithSubstitutionsWithinTypes(
+ ArgParser ap, Arg a, ArgValuesMap.Position pos, ArgValue av,
+ SubVals sv, String key, String pref, String def,
+ boolean withinTypes)
+ {
+ if (key == null)
+ key = a.getName();
+ List<ArgValue> avList = new ArrayList<>();
+ if (sv != null && sv.has(key) && sv.get(key) != null)
+ {
+ String value = ap == null ? sv.get(key)
+ : sv.getWithSubstitutions(ap, getLinkedId(), key);
+ // protected ArgValue(Arg a, SubVals sv, Type type, String content, int
+ // argIndex)
+
+ avList.add(new ArgValue(a, null, null, value, av.getArgIndex()));
+ }
+ else if (containsArg(a))
+ {
+ if (pos == ArgValuesMap.Position.FIRST && getValue(a) != null)
+ avList.add(getArgValue(a));
+ else if (pos == ArgValuesMap.Position.BEFORE
+ && getClosestPreviousArgValueOfArg(av, a) != null)
+ {
+ for (ArgValue tmpAv : getArgValues(a).getArgValueList())
+ {
+ if (tmpAv.getArgIndex() >= av.getArgIndex())
+ {
+ continue;
+ }
+ avList.add(tmpAv);
+ }
+ }
+ else if (pos == ArgValuesMap.Position.AFTER
+ && getClosestNextArgValueOfArg(av, a, withinTypes) != null)
+ {
+ for (ArgValue tmpAv : getArgValues(a).getArgValueList())
+ {
+ if (tmpAv.getArgIndex() <= av.getArgIndex())
+ {
+ continue;
+ }
+ avList.add(tmpAv);
+ }
+ }
+ }
+
+ // check if withinType the avs don't belong to the next primary arg
+ // of this type. Checking for *any* shared type.
+ if (withinTypes && !avList.isEmpty())
+ {
+ int nextPrimaryArgOfSameTypeIndex = Integer.MAX_VALUE;
+ // run through every Arg used in this ArgValuesMap
+ for (Arg tmpA : this.getArgKeys())
+ {
+ // only interested in Opt.PRIMARY args of the same type
+ if (tmpA.sharesType(a) && tmpA.hasOption(Opt.PRIMARY))
+ {
+ for (ArgValue tmpAv : getArgValueList(tmpA))
+ {
+ int tmpArgIndex = tmpAv.getArgIndex();
+ if (tmpArgIndex > av.getArgIndex()
+ && tmpArgIndex < nextPrimaryArgOfSameTypeIndex)
+ {
+ nextPrimaryArgOfSameTypeIndex = tmpArgIndex;
+ }
+ }
+ }
+ }
+ List<ArgValue> tmpList = List.copyOf(avList);
+ for (ArgValue tmpAv : tmpList)
+ {
+ if (nextPrimaryArgOfSameTypeIndex < tmpAv.getArgIndex())
+ {
+ // looks like this tmpAv actually belongs to a different primary Arg
+ avList.remove(tmpAv);
+ }
+ }
+ }
+
+ return avList;
+ }
+
public ArgValue getArgValue(Arg a)
{
List<ArgValue> vals = getArgValueList(a);
}
public ArgValue getClosestNextArgValueOfArg(ArgValue thisAv, Arg a,
- boolean withinType)
+ boolean withinTypes)
{
// this looks for the *next* arg that *might* be referring back to
// a thisAv. Such an arg would have no subValues (if it does it should
}
// check if withinType this closestAv doesn't belong to the next primary arg
- // of this type
- if (withinType && closestAv != null)
+ // of this type. Checking for *any* shared type.
+ if (withinTypes && closestAv != null)
{
int nextPrimaryArgOfSameTypeIndex = Integer.MAX_VALUE;
for (Arg tmpA : this.getArgKeys())
{
// interested in Opt.PRIMARY args of the same type
- if (tmpA.getType() == a.getType() && tmpA.hasOption(Opt.PRIMARY))
+ if (tmpA.sharesType(a) && tmpA.hasOption(Opt.PRIMARY))
{
for (ArgValue tmpAv : getArgValueList(tmpA))
{
}
if (nextPrimaryArgOfSameTypeIndex < closestAv.getArgIndex())
{
- // looks licke closestAv actually belongs to a different primary Arg
+ // looks like closestAv actually belongs to a different primary Arg
return null;
}
}
public String getFromSubValArgOrPref(ArgValue av, Arg a, SubVals sv,
String key, String pref, String def)
{
- return getFromSubValArgOrPref(a, ArgValuesMap.Position.AFTER, av, sv,
- key, pref, def);
+ return getFromSubValArgOrPref(a, Position.AFTER, av, sv, key, pref,
+ def);
}
/**
* get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
* Arg of type a or subval key or preference pref or default def
*/
- public String getFromSubValArgOrPref(Arg a, ArgValuesMap.Position pos,
- ArgValue av, SubVals sv, String key, String pref, String def)
+ public String getFromSubValArgOrPref(Arg a, Position pos, ArgValue av,
+ SubVals sv, String key, String pref, String def)
{
return getFromSubValArgOrPrefWithSubstitutions(null, a, pos, av, sv,
key, pref, def);
}
public String getFromSubValArgOrPrefWithSubstitutions(ArgParser ap, Arg a,
- ArgValuesMap.Position pos, ArgValue av, SubVals sv, String key,
- String pref, String def)
+ Position pos, ArgValue av, SubVals sv, String key, String pref,
+ String def)
{
- return getFromSubValArgOrPrefWithSubstitutionsWithinType(ap, a, pos, av,
- sv, key, pref, def, true);
+ return getFromSubValArgOrPrefWithSubstitutionsWithinTypes(ap, a, pos,
+ av, sv, key, pref, def, true);
}
- public String getFromSubValArgOrPrefWithSubstitutionsWithinType(
- ArgParser ap, Arg a, ArgValuesMap.Position pos, ArgValue av,
- SubVals sv, String key, String pref, String def,
- boolean withinType)
+ public String getFromSubValArgOrPrefWithSubstitutionsWithinTypes(
+ ArgParser ap, Arg a, Position pos, ArgValue av, SubVals sv,
+ String key, String pref, String def, boolean withinTypes)
{
if (key == null)
key = a.getName();
&& getClosestPreviousArgValueOfArg(av, a) != null)
value = getClosestPreviousArgValueOfArg(av, a).getValue();
else if (pos == ArgValuesMap.Position.AFTER
- && getClosestNextArgValueOfArg(av, a, withinType) != null)
- value = getClosestNextArgValueOfArg(av, a, withinType).getValue();
+ && getClosestNextArgValueOfArg(av, a, withinTypes) != null)
+ value = getClosestNextArgValueOfArg(av, a, withinTypes).getValue();
// look for allstructures subval for Type.STRUCTURE
Arg arg = av.getArg();
if (value == null && arg.hasOption(Opt.PRIMARY)
- && arg.getType() == Type.STRUCTURE
- && !a.hasOption(Opt.PRIMARY) && (a.getType() == Type.STRUCTURE
+ && arg.hasType(Type.STRUCTURE) && !a.hasOption(Opt.PRIMARY)
+ && (a.getFirstType() == Type.STRUCTURE
// || a.getType() == Type.STRUCTUREIMAGE))
))
{
git://source.jalview.org / jalview.git / blobdiff