JAL-629 Updated help docs and fixed structure image subvalues

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 3437bfd..753ded2 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -574,17 +574,24 @@ public class Commands
                   avm, av, Arg.STRUCTUREIMAGE, subVals);
           if (sv != null && structureImageFilename != null)
           {
+            ArgValue siAv = avm.getClosestNextArgValueOfArg(av,
+                    Arg.STRUCTUREIMAGE);
+            SubVals sisv = null;
+            if (structureImageFilename.equals(siAv.getValue()))
+            {
+              sisv = siAv.getSubVals();
+            }
             File structureImageFile = new File(structureImageFilename);
             String width = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGEWIDTH, subVals);
+                    Arg.STRUCTUREIMAGEWIDTH, sisv);
             String height = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGEHEIGHT, subVals);
+                    Arg.STRUCTUREIMAGEHEIGHT, sisv);
             String scale = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGESCALE, subVals);
+                    Arg.STRUCTUREIMAGESCALE, sisv);
             String renderer = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGETEXTRENDERER, subVals);
+                    Arg.STRUCTUREIMAGETEXTRENDERER, sisv);
             String typeS = ArgParser.getValueFromSubValOrArg(avm, av,
-                    Arg.STRUCTUREIMAGETYPE, subVals);
+                    Arg.STRUCTUREIMAGETYPE, sisv);
             if (typeS == null || typeS.length() == 0)
             {
               typeS = FileUtils.getExtension(structureImageFile);