import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
null, "jmol");
- ViewerType viewerType = null;
- if (!"none".equals(sViewer))
- {
- for (ViewerType v : EnumSet.allOf(ViewerType.class))
- {
- String name = v.name().toLowerCase(Locale.ROOT)
- .replaceAll(" ", "");
- if (sViewer.equals(name))
- {
- viewerType = v;
- break;
- }
- }
- }
+ ViewerType viewerType = ViewerType.getFromString(sViewer);
// TODO use ssFromStructure
StructureViewer sv = StructureChooser
AlignFrame af = afMap.get(id);
if (af != null)
{
- af.setWrapFormat(wrap);
+ af.setWrapFormat(wrap, true);
}
}
case "biojs":
Console.debug(
- "Creating BioJS MSA Viwer HTML file: " + fileName);
+ "Outputting BioJS MSA Viwer HTML file: " + fileName);
try
{
BioJsHTMLOutput.refreshVersionInfo(
break;
case "eps":
- Console.debug("Creating EPS file: " + fileName);
- af.createEPS(file, name);
+ Console.debug("Outputting EPS file: " + fileName);
+ af.createEPS(file, renderer);
break;
case "imagemap":
- Console.debug("Creating ImageMap file: " + fileName);
+ Console.debug("Outputting ImageMap file: " + fileName);
af.createImageMap(file, name);
break;
String val = av.getValue();
SubVals subVals = av.getSubVals();
String fileName = subVals.getContent();
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
!Platform.isHeadless());
// if backups is not true then --overwrite must be specified
- if (file.exists() && !(overwrite || backups))
+ if (file.exists() && !(overwrite || backups || stdout))
{
Console.error("Won't overwrite file '" + fileName + "' without "
+ Arg.OVERWRITE.argString() + " or "
}
if (ff == null)
{
- StringBuilder validSB = new StringBuilder();
- for (String f : validFormats)
- {
- if (validSB.length() > 0)
- validSB.append(", ");
- validSB.append(f);
- FileFormatI tff = ffs.forName(f);
- validSB.append(" (");
- validSB.append(tff.getExtensions());
- validSB.append(")");
+ if (stdout)
+ {
+ ff = FileFormat.Fasta;
}
+ else
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
+ {
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
+ }
- Jalview.exit("No valid format specified for "
- + Arg.OUTPUT.argString() + ". Valid formats are "
- + validSB.toString() + ".", 1);
- // this return really shouldn't happen
- return false;
+ Jalview.exit("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".", 1);
+ // this return really shouldn't happen
+ return false;
+ }
}
String savedBackupsPreference = Cache
Console.info("Writing " + fileName);
- af.saveAlignment(fileName, ff);
+ af.saveAlignment(fileName, ff, stdout);
Console.debug("Returning backups to " + savedBackupsPreference);
if (savedBackupsPreference != null)
Cache.applicationProperties.put(BackupFiles.ENABLED,
seq = al.getSequenceAt(subVals.getIndex());
}
}
- else if (idAv != null)
+ if (seq == null && idAv != null)
{
seq = al.findName(idAv.getValue());
}