if (avm.containsArg(Arg.STRUCTURE))
{
commandArgsProvided = true;
- for (
-
- ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
+ for (ArgValue structureAv : avm.getArgValueList(Arg.STRUCTURE))
{
argParser.setStructureFilename(null);
- String val = av.getValue();
- SubVals subVals = av.getSubVals();
- int argIndex = av.getArgIndex();
- SequenceI seq = getSpecifiedSequence(af, avm, av);
+ String val = structureAv.getValue();
+ SubVals subVals = structureAv.getSubVals();
+ int argIndex = structureAv.getArgIndex();
+ SequenceI seq = getSpecifiedSequence(af, avm, structureAv);
if (seq == null)
{
// Could not find sequence from subId, let's assume the first
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions(
- argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER, av,
- subVals, null, null, null);
+ argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, null);
if (paeFilepath != null)
{
File paeFile = new File(paeFilepath);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
// reference annotations
String tftString = avm.getFromSubValArgOrPrefWithSubstitutions(
- argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER, av,
- subVals, null, null, null);
+ argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, null);
boolean notempfac = avm.getFromSubValArgOrPref(Arg.NOTEMPFAC,
subVals, null, "ADD_TEMPFACT_ANN", false, true);
TFType tft = notempfac ? null : TFType.DEFAULT;
}
String sViewerName = avm.getFromSubValArgOrPref(
- Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER, av,
- subVals, null, null, "jmol");
+ Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER,
+ structureAv, subVals, null, null, "jmol");
ViewerType viewerType = ViewerType.getFromString(sViewerName);
// TODO use ssFromStructure
if (avm.containsArg(Arg.STRUCTUREIMAGE))
{
for (ArgValue structureImageArgValue : avm
- .getArgValueList(Arg.STRUCTUREIMAGE))
+ .getArgValueListFromSubValOrArg(structureAv,
+ Arg.STRUCTUREIMAGE, subVals))
{
String structureImageFilename = argParser.makeSubstitutions(
structureImageArgValue.getValue(), id, true);
import java.util.Collections;
import java.util.Comparator;
import java.util.EnumSet;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
+import java.util.Set;
import java.util.stream.Collectors;
import jalview.bin.argparser.Arg.Opt;
+ "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.MULTIVALUE,
Opt.ALLOWMULTIID, Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
- STRUCTUREIMAGE(Type.IMAGE,
+ STRUCTUREIMAGE(new Type[]
+ { Type.IMAGE, Type.STRUCTUREIMAGE },
"Export an image of a 3D structure opened in JMOL", Opt.STRING,
Opt.LINKED, Opt.MULTIVALUE, Opt.OUTPUTFILE, Opt.ALLOWMULTIID,
Opt.PRIMARY),
BGCOLOUR(Type.IMAGE, "bgcolor", // being a bit soft on the Americans!
"Applies a background colour to the structure image. Valid values are named colours known to Java or RRGGBB 6 digit hex-string.",
Opt.STRING, Opt.LINKED, Opt.MULTIVALUE, Opt.ALLOWMULTIID),
- /*
- STRUCTUREIMAGETYPE(Type.IMAGE,
- "Set the structure image format for the preceding --structureimage. Valid values are:\n"
- + "svg,\n" + "png,\n" + "eps,\n" + "html,\n" + "biojs.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
- STRUCTUREIMAGETEXTRENDERER(Type.IMAGE,
- "Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:\n"
- + "text,\n" + "lineart.",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
- STRUCTUREIMAGESCALE(Type.IMAGE,
- "Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
- STRUCTUREIMAGEWIDTH(Type.IMAGE,
- "Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
- STRUCTUREIMAGEHEIGHT(Type.IMAGE,
- "Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image).",
- Opt.STRING, Opt.LINKED, Opt.ALLOWMULTIID),
- */
-
OUTPUT(Type.OUTPUT,
"Export the open alignment to file filename. The format name is specified by the subval modifier format=name, a following --format name argument or guessed from the file extension. Valid format names (and file extensions) are:\n"
+ "fasta (fa, fasta, mfa, fastq),\n" + "pfam (pfam),\n"
STRUCTURE("arguments used to add and format 3D structure data"),
PROCESS("arguments used to process an alignment once opened"),
OUTPUT("arguments used to save data from a processed alignment"),
- IMAGE("arguments used to export an image of an alignment or structure"),
- // IMAGE("arguments used to export an image of an alignment"),
- // STRUCTUREIMAGE("arguments used to export an image of an structure"),
+ IMAGE("arguments used to export an image of an alignment"),
+ STRUCTUREIMAGE("arguments used to export an image of an structure"),
FLOW("arguments that control processing of the other arguments"), //
ALL("all arguments"), // mostly just a place-holder for --help-all
NONE, // mostly a place-holder for --help
private String description;
- private Type type;
+ private Type[] types;
private Arg(Type type, String description, Opt... options)
{
+ this(new Type[] { type }, description, options);
+ }
+
+ private Arg(Type[] type, String description, Opt... options)
+ {
this(type, null, description, false, options);
}
private Arg(Type type, String description, boolean defaultBoolean,
Opt... options)
{
+ this(new Type[] { type }, description, defaultBoolean, options);
+ }
+
+ private Arg(Type[] type, String description, boolean defaultBoolean,
+ Opt... options)
+ {
this(type, null, description, defaultBoolean, options);
}
private Arg(Type type, String alternativeName, String description,
Opt... options)
{
+ this(new Type[] { type }, alternativeName, description, options);
+ }
+
+ private Arg(Type[] type, String alternativeName, String description,
+ Opt... options)
+ {
this(type, alternativeName, description, false, options);
}
private Arg(Type type, String alternativeName, String description,
boolean defaultBoolean, Opt... options)
{
- this.type = type;
+ this(new Type[] { type }, alternativeName, description, defaultBoolean,
+ options);
+ }
+
+ private Arg(Type[] type, String alternativeName, String description,
+ boolean defaultBoolean, Opt... options)
+ {
+ this.types = type;
this.description = description;
this.defaultBoolValue = defaultBoolean;
this.setOptions(options);
if (getNames().length > 0)
sb.append('"');
sb.append(")\n");
- sb.append("\nType: " + type.name());
+ for (Type type : getTypes())
+ {
+ String typeName = type.name();
+ sb.append("\nType: " + typeName);
+ }
sb.append("\nOpt: ");
// map List<Opt> to List<String> for the String.join
List<String> optList = Arrays.asList(argOptions).stream()
return defaultBoolValue;
}
- public Type getType()
+ public Type getFirstType()
+ {
+ return this.getTypes()[0];
+ }
+
+ public Type[] getTypes()
{
- return this.type;
+ return this.types;
+ }
+
+ public boolean hasType(Type t)
+ {
+ for (Type type : getTypes())
+ {
+ if (type == t)
+ {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ public boolean sharesType(Arg a)
+ {
+ List<Type> aTypes = Arrays.asList(a.getTypes());
+ for (Type type : getTypes())
+ {
+ if (aTypes.contains(type))
+ {
+ return true;
+ }
+ }
+ return false;
}
protected String getDescription()
public static final void appendUsageGeneral(StringBuilder sb,
int maxArgLength)
{
+ Set<Type> firstTypes = new HashSet<>();
+ for (Arg a : EnumSet.allOf(Arg.class))
+ {
+ if (!firstTypes.contains(a.getFirstType()))
+ {
+ firstTypes.add(a.getFirstType());
+ }
+ }
for (Type t : EnumSet.allOf(Type.class))
{
- if (t.description() != null)
+ if (t.description() != null && firstTypes.contains(t))
{
StringBuilder argSb = new StringBuilder();
argSb.append(Arg.HELP.argString()).append(ArgParser.SINGLEDASH)
{
List<Arg> args = argsSortedForDisplay(types);
- /*
- * just use a set maxArgLength of DESCRIPTIONINDENT
-
- int maxArgLength = 0;
- for (Arg a : args)
- {
- if (a.hasOption(Opt.PRIVATE) || a.hasOption(Opt.SECRET))
- continue;
-
- String argS = argDisplayString(a);
- if (argS.length() > maxArgLength)
- maxArgLength = argS.length();
- }
- */
int maxArgLength = DESCRIPTIONINDENT;
// always show --help
continue;
}
- if (a.getType() != typeSection)
+ if (a.getFirstType() != typeSection)
{
- typeSection = a.getType();
- String typeDescription = a.getType().description();
+ typeSection = a.getFirstType();
+ String typeDescription = a.getFirstType().description();
if (typeDescription != null && typeDescription.length() > 0)
{
// typeDescription = typeDescription.substring(0,
{
Opt[] opts = options == null ? new Opt[] {} : options;
return EnumSet.allOf(Arg.class).stream().filter(a -> {
- if (a.getType() != type)
+ if (!a.hasType(type))
return false;
for (Opt o : opts)
{
if (b == null)
return -1;
// first compare types (in enum order)
- int i = a.getType().compareTo(b.getType());
+ int i = a.getFirstType().compareTo(b.getFirstType());
if (i != 0)
return i;
// do Opt.LAST next (oddly). Reversed args important!
// set allstructures to all non-primary structure options in this linked
// id if --allstructures has been set
- if (allStructures && (a.getType() == Type.STRUCTURE
+ if (allStructures && (a.hasType(Type.STRUCTURE)
// || a.getType() == Type.STRUCTUREIMAGE)
) && !a.hasOption(Opt.PRIMARY))
{
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))
))
{
argsOptions.add(opt);
}
}
- Type t = a.getType();
- if (!argsTypes.contains(t))
+ for (Type t : a.getTypes())
{
- argsTypes.add(t);
+ if (!argsTypes.contains(t))
+ {
+ argsTypes.add(t);
+ }
}
}
git://source.jalview.org / jalview.git / commitdiff