X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;fp=src%2Fjalview%2Fbin%2FCommands.java;h=737c9eb94a9903d46e8f65c4713de5d56b166f67;hb=d79e3747b8ce78b1ac7aa83402e31b7e5dccfe1b;hp=9a85f1ef615439f6085c6fa5897642531ed6747d;hpb=650e1941339ab7fad576b2edeb8a41fd96a87049;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 9a85f1e..737c9eb 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -456,35 +456,31 @@ public class Commands
                     + 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;
@@ -500,6 +496,8 @@ public class Commands
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
+          argParser.setStructureFilename(structureFilename);
+
           // open structure view
           AlignmentPanel ap = af.alignPanel;
           if (headless)
@@ -634,8 +632,8 @@ public class Commands
             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;
@@ -682,6 +680,10 @@ public class Commands
                 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,