JAL-629 More docs. Usage statement. Adjust some logging output to respect --quiet.

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 328c6e1..af4c675 100644 (file)
--- 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);
@@ -515,7 +488,7 @@ 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 +821,9 @@ 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())