import jalview.io.IdentifyFile;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.TFType;
+import jalview.structure.StructureSelectionManager;
import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
private Map<String, AlignFrame> afMap;
- public static void processArgs(ArgParser ap, boolean h)
+ public static boolean processArgs(ArgParser ap, boolean h)
{
argParser = ap;
headless = h;
+ boolean argsWereParsed = false;
+ if (headless)
+ {
+ System.setProperty("java.awt.headless", "true");
+ }
+
if (argParser != null && argParser.linkedIds() != null)
{
for (String id : argParser.linkedIds())
{
+ Console.debug("##### id=" + id);
Commands cmds = new Commands();
if (id == null)
{
cmds.processLinked(id);
}
cmds.processImages(id);
+ argsWereParsed |= cmds.wereParsed();
}
- if (argParser.getBool(Arg.QUIT))
- {
- Jalview.getInstance().quit();
- }
}
+ if (argParser.getBool(Arg.QUIT))
+ {
+ Jalview.getInstance().quit();
+ return true;
+ }
+ // carry on with jalview.bin.Jalview
+ return argsWereParsed;
+ }
+
+ boolean argsWereParsed = false;
+
+ private boolean wereParsed()
+ {
+ return argsWereParsed;
}
public Commands()
protected void processUnlinked(String id)
{
+ Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+
processLinked(id);
}
FileFormatI format = null;
DataSourceType protocol = null;
*/
-
if (ArgParser.getArgValues(m, Arg.OPEN) != null)
{
long progress = -1;
boolean first = true;
AlignFrame af;
- OPEN: for (String openFile : ArgParser.getValues(m, Arg.OPEN))
+ for (String openFile : ArgParser.getValues(m, Arg.OPEN))
{
if (openFile == null)
- continue OPEN;
+ continue;
+ argsWereParsed = true;
if (first)
{
first = false;
if (!(new File(openFile)).exists())
{
Console.warn("Can't find file '" + openFile + "'");
- continue OPEN;
}
}
}
// store the AlignFrame for this id
afMap.put(id, af);
+
+ // is it its own structure file?
+ if (format.isStructureFile())
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ SequenceI seq = af.alignPanel.getAlignment().getSequenceAt(0);
+ ssm.computeMapping(false, new SequenceI[] { seq }, null,
+ openFile, DataSourceType.FILE, null);
+ }
}
else
{
Console.error("Could not open any files in headless mode");
System.exit(1);
}
- }
- else
- {
- Console.warn("No more files to open");
- if (desktop != null)
- desktop.setProgressBar(null, progress);
+ // TOREMOVE COMMENT
+ // @Ben assumed this was the GUI version of above, rather then the
+ // first==false state
+ else
+ {
+ Console.warn("No more files to open");
+ if (desktop != null)
+ desktop.setProgressBar(null, progress);
+ }
}
}
{
SubVal subVal = ArgParser.getSubVal(val);
File paeFile = new File(subVal.content);
- if ("structid".equals(subVal.index))
+ String structId = "structid".equals(subVal.keyName)
+ ? subVal.keyValue
+ : null;
+ if (subVal.notSet())
+ {
+ // take structid from pdbfilename
+ }
+ if ("structfile".equals(subVal.keyName))
{
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
- subVal.index, subVal.keyValue);
+ subVal.index, subVal.keyValue, false);
+ }
+ else if ("structid".equals(subVal.keyName))
+ {
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index, subVal.keyValue, true);
}
else
{
AlignFrame af = afMap.get(id);
if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
{
- STRUCTURE: for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
+ for (String val : ArgParser.getValues(m, Arg.STRUCTURE))
{
SubVal subId = new SubVal(val);
SequenceI seq = getSpecifiedSequence(af, subId);
if (structureFile == null)
{
Console.warn("Not provided structure file with '" + val + "'");
- continue STRUCTURE;
+ continue;
}
if (!structureFile.exists())
{
Console.warn("Structure file '"
+ structureFile.getAbsoluteFile() + "' not found.");
- continue STRUCTURE;
+ continue;
}
Console.debug("Using structure file "
}
}
}
+ // for moment we disable JSON export
+ Cache.setPropsAreReadOnly(true);
+ Cache.setProperty("EXPORT_EMBBED_BIOJSON", "false");
+
switch (type)
{
case "svg":