JAL-629 fixing test EBIAlphaFoldTest.checkImportPAEToStructure(). not fixed yet

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 3437bfd..30fdc30 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -452,14 +452,6 @@ public class Commands
           Console.debug("Using structure file "
                   + structureFile.getAbsolutePath());
 
-          // ##### Does this need to happen? Follow
-          // openStructureFileForSequence() below
-          /*
-          PDBEntry fileEntry = new AssociatePdbFileWithSeq()
-                  .associatePdbWithSeq(structureFile.getAbsolutePath(),
-                          DataSourceType.FILE, seq, true, Desktop.instance);
-                          */
-
           // open structure view
           AlignmentPanel ap = af.alignPanel;
           if (headless)
@@ -505,15 +497,6 @@ public class Commands
                   Arg.NOTEMPFAC, subVals, null, "ADD_TEMPFACT_ANN", false,
                   true);
           TFType tft = notempfac ? null : TFType.DEFAULT;
-          /*
-          String tftString = subVals.get("tempfac");
-          ArgValue tftAv = getArgAssociatedWithStructure(Arg.TEMPFAC, avm,
-                  af, structureFilepath);
-          if (tftString == null && tftAv != null)
-          {
-            tftString = tftAv.getSubVals().getContent();
-          }
-          */
           if (tftString != null && !notempfac)
           {
             // get kind of temperature factor annotation
@@ -574,17 +557,24 @@ 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);