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.type;
+ return this.getTypes()[0];
+ }
+
+ public Type[] getTypes()
+ {
+ return this.types;
+ }
+
+ public boolean sharesType(Arg a)
+ {
+ return this.hasType(a.getTypes());
+ }
+
+ public boolean hasType(Type... types)
+ {
+ Set<Type> typesSet = new HashSet<>(Arrays.asList(types));
+ return this.hasType(typesSet);
+ }
+
+ public boolean hasType(Set<Type> typesSet)
+ {
+ for (Type type : getTypes())
+ {
+ if (typesSet.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!
git://source.jalview.org / jalview.git / blobdiff