X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=3608295eded0c99135ac9584447aecb182d31631;hb=79456f40b33e73e2fb5420a3287ae80854281ef6;hp=328c6e18c86ecc6a4620e3d217cf8cbec1e66432;hpb=b4643d75fb09207306e83fa1fee277cc2fd089c5;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 328c6e1..3608295 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -309,7 +309,7 @@ public class Commands
 
           // Show secondary structure annotations?
           boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
-                  Arg.SSANNOTATIONS, av.getSubVals(), null,
+                  Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
           af.setAnnotationsVisibility(showSSAnnotations, true, false);
 
@@ -330,33 +330,6 @@ public class Commands
                     af.getCurrentView().getAlignment(), hideThese, null,
                     false, false);
           }
-          else
-          /*
-           * comment out hacky approach up to here and add this line: if
-           * (showTemperatureFactor)
-           */
-          {
-            /*
-            if (avm.containsArg(Arg.TEMPFAC_LABEL))
-            {
-              AlignmentAnnotation aa = AlignmentUtils
-                      .getFirstSequenceAnnotationOfType(
-                              af.getCurrentView().getAlignment(),
-                              AlignmentAnnotation.LINE_GRAPH);
-              String label = avm.getValue(Arg.TEMPFAC_LABEL);
-              if (aa != null)
-              {
-                aa.label = label;
-              }
-              else
-              {
-                Console.info(
-                        "Could not find annotation to apply tempfac_label '"
-                                + label);
-              }
-            }
-            */
-          }
 
           // store the AlignFrame for this id
           afMap.put(id, af);
@@ -493,14 +466,13 @@ public class Commands
           String structureFilepath = structureFile.getAbsolutePath();
 
           // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
-          String paeFilepath = subVals.getWithSubstitutions(argParser, id,
-                  "paematrix");
-          ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
-                  af, structureFilepath);
-          if (paeFilepath == null && paeAv != null)
+          String paeFilepath = ArgParser
+                  .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+                          Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+                          null, null);
+          if (paeFilepath != null)
           {
-            SubVals sv = paeAv.getSubVals();
-            File paeFile = new File(sv.getContent());
+            File paeFile = new File(paeFilepath);
 
             try
             {
@@ -515,7 +487,7 @@ public class Commands
 
           // showing annotations from structure file or not
           boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
-                  Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+                  Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
                   true);
 
           // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
@@ -848,9 +820,9 @@ public class Commands
       return null;
     if (subVals != null)
     {
-      if (subVals.has("seqid"))
+      if (subVals.has(Arg.SEQID.getName()))
       {
-        seq = al.findName(subVals.get("seqid"));
+        seq = al.findName(subVals.get(Arg.SEQID.getName()));
       }
       else if (-1 < subVals.getIndex()
               && subVals.getIndex() < al.getSequences().size())