+ Arg.STRUCTURE.argString() + "=" + val);
continue;
}
+ String structureFilename = null;
File structureFile = null;
if (subVals.getContent() != null
&& subVals.getContent().length() != 0)
{
- structureFile = new File(subVals.getContent());
+ structureFilename = subVals.getContent();
Console.debug("Using structure file (from argument) '"
- + structureFile.getAbsolutePath() + "'");
+ + structureFilename + "'");
+ structureFile = new File(structureFilename);
}
- // TRY THIS
- /*
- * PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- * .associatePdbWithSeq(selectedPdbFileName, DataSourceType.FILE,
- * selectedSequence, true, Desktop.instance);
- *
- * sViewer = launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap, new
- * SequenceI[] { selectedSequence });
- *
- */
/* THIS DOESN'T WORK */
else if (seq.getAllPDBEntries() != null
&& seq.getAllPDBEntries().size() > 0)
{
structureFile = new File(
seq.getAllPDBEntries().elementAt(0).getFile());
- Console.debug("Using structure file (from sequence) '"
- + structureFile.getAbsolutePath() + "'");
+ if (structureFile != null)
+ {
+ Console.debug("Using structure file (from sequence) '"
+ + structureFile.getAbsolutePath() + "'");
+ }
+ structureFilename = structureFile.getAbsolutePath();
}
- if (structureFile == null)
+ if (structureFilename == null || structureFile == null)
{
addWarn("Not provided structure file with '" + val + "'");
continue;
Console.debug("Using structure file "
+ structureFile.getAbsolutePath());
+ argParser.setStructureFilename(structureFilename);
+
// open structure view
AlignmentPanel ap = af.alignPanel;
if (headless)
for (ArgValue structureImageArgValue : avm
.getArgValueList(Arg.STRUCTUREIMAGE))
{
- String structureImageFilename = structureImageArgValue
- .getValue();
+ String structureImageFilename = argParser.makeSubstitutions(
+ structureImageArgValue.getValue(), id, true);
if (structureViewer != null && structureImageFilename != null)
{
SubVals structureImageSubVals = null;
this.colourAlignFrame(af, imageColour);
List<String> extraCommands = new ArrayList<>();
+ // these don't actually do anything to the output image since we
+ // renderScreenImage
+ // extraCommands.add("set antialiasImages on");
+ // extraCommands.add("set antialiasTranslucent on");
String bgcolour = avm.getValueFromSubValOrArg(
structureImageArgValue, Arg.BGCOLOUR,