Merge branch 'bug/JAL-4353_cannot_output_multiple_different_structure_images_for_one_...

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 475eba2..e01d40a 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -501,15 +501,13 @@ public class Commands
       if (avm.containsArg(Arg.STRUCTURE))
       {
         commandArgsProvided = true;
-        for (
-
-        ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
+        for (ArgValue structureAv : avm.getArgValueList(Arg.STRUCTURE))
         {
           argParser.setStructureFilename(null);
-          String val = av.getValue();
-          SubVals subVals = av.getSubVals();
-          int argIndex = av.getArgIndex();
-          SequenceI seq = getSpecifiedSequence(af, avm, av);
+          String val = structureAv.getValue();
+          SubVals subVals = structureAv.getSubVals();
+          int argIndex = structureAv.getArgIndex();
+          SequenceI seq = getSpecifiedSequence(af, avm, structureAv);
           if (seq == null)
           {
             // Could not find sequence from subId, let's assume the first
@@ -578,8 +576,8 @@ public class Commands
 
           // get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
           String paeFilepath = avm.getFromSubValArgOrPrefWithSubstitutions(
-                  argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER, av,
-                  subVals, null, null, null);
+                  argParser, Arg.PAEMATRIX, ArgValuesMap.Position.AFTER,
+                  structureAv, subVals, null, null, null);
           if (paeFilepath != null)
           {
             File paeFile = new File(paeFilepath);
@@ -603,8 +601,8 @@ public class Commands
           // get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
           // reference annotations
           String tftString = avm.getFromSubValArgOrPrefWithSubstitutions(
-                  argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER, av,
-                  subVals, null, null, null);
+                  argParser, Arg.TEMPFAC, ArgValuesMap.Position.AFTER,
+                  structureAv, subVals, null, null, null);
           boolean notempfac = avm.getFromSubValArgOrPref(Arg.NOTEMPFAC,
                   subVals, null, "ADD_TEMPFACT_ANN", false, true);
           TFType tft = notempfac ? null : TFType.DEFAULT;
@@ -636,8 +634,8 @@ public class Commands
           }
 
           String sViewerName = avm.getFromSubValArgOrPref(
-                  Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER, av,
-                  subVals, null, null, "jmol");
+                  Arg.STRUCTUREVIEWER, ArgValuesMap.Position.AFTER,
+                  structureAv, subVals, null, null, "jmol");
           ViewerType viewerType = ViewerType.getFromString(sViewerName);
 
           // TODO use ssFromStructure
@@ -698,7 +696,8 @@ public class Commands
           if (avm.containsArg(Arg.STRUCTUREIMAGE))
           {
             for (ArgValue structureImageArgValue : avm
-                    .getArgValueList(Arg.STRUCTUREIMAGE))
+                    .getArgValueListFromSubValOrArg(structureAv,
+                            Arg.STRUCTUREIMAGE, subVals))
             {
               String structureImageFilename = argParser.makeSubstitutions(
                       structureImageArgValue.getValue(), id, true);