X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;h=7a6e3ac9b2cea03c1fe157bfb64143b0620a9c04;hb=7057bdc72cbd324a4316f445118b509db4880499;hp=a0a3e590a55f892d98b7243df805177413d6ff6d;hpb=3de8bf931e7b9e2a71a8959a7dd1260d33dc9034;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index a0a3e59..7a6e3ac 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -15,7 +15,7 @@ import jalview.analysis.AlignmentUtils;
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.ArgParser.Arg;
 import jalview.bin.ArgParser.ArgValue;
-import jalview.bin.ArgParser.ArgValues;
+import jalview.bin.ArgParser.ArgValuesMap;
 import jalview.bin.ArgParser.SubVals;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -109,14 +109,14 @@ public class Commands
 
   protected void processUnlinked(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
 
     processLinked(id);
   }
 
   protected void processLinked(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
 
     /*
     // script to execute after all loading is completed one way or another
@@ -128,13 +128,13 @@ public class Commands
     FileFormatI format = null;
     DataSourceType protocol = null;
     */
-    if (ArgParser.getArgValues(m, Arg.OPEN) != null)
+    if (avm.hasValue(Arg.OPEN))
     {
       long progress = -1;
 
       boolean first = true;
       AlignFrame af;
-      for (ArgValue av : ArgParser.getArgValueList(m, Arg.OPEN))
+      for (ArgValue av : avm.getArgValueList(Arg.OPEN))
       {
         String openFile = av.getValue();
         if (openFile == null)
@@ -216,14 +216,13 @@ public class Commands
 
           // get kind of temperature factor annotation
           StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
-          if ((!ArgParser.getBoolean(m, Arg.NOTEMPFAC))
-                  && ArgParser.getArgValues(m, Arg.TEMPFAC) != null)
+          if ((!avm.getBoolean(Arg.NOTEMPFAC)) && avm.hasValue(Arg.TEMPFAC))
           {
             try
             {
               tempfacType = StructureImportSettings.TFType
-                      .valueOf(ArgParser.getArgValue(m, Arg.TEMPFAC)
-                              .getValue().toUpperCase(Locale.ROOT));
+                      .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+                              .toUpperCase(Locale.ROOT));
               Console.debug("Obtained Temperature Factor type of '"
                       + tempfacType + "'");
             } catch (IllegalArgumentException e)
@@ -256,25 +255,24 @@ public class Commands
                   format);
 
           // wrap alignment?
-          if (ArgParser.getBoolean(m, Arg.WRAP))
+          if (avm.getBoolean(Arg.WRAP))
           {
             af.getCurrentView().setWrapAlignment(true);
           }
 
           // colour aligment?
-          if (ArgParser.hasValue(m, Arg.COLOUR))
+          if (avm.hasValue(Arg.COLOUR))
           {
-            af.changeColour_actionPerformed(
-                    ArgParser.getValue(m, Arg.COLOUR));
+            af.changeColour_actionPerformed(avm.getValue(Arg.COLOUR));
           }
 
           // change alignment frame title
-          if (ArgParser.getValue(m, Arg.TITLE) != null)
-            af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+          if (avm.hasValue(Arg.TITLE))
+            af.setTitle(avm.getValue(Arg.TITLE));
 
           /* hacky approach to hiding the annotations */
           // show secondary structure annotations?
-          if (ArgParser.getBoolean(m, Arg.SSANNOTATION))
+          if (avm.getBoolean(Arg.SSANNOTATION))
           {
             // do this better (annotation types?)
             AlignmentUtils.showOrHideSequenceAnnotations(
@@ -284,7 +282,7 @@ public class Commands
           }
 
           // show temperature factor annotations?
-          if (ArgParser.getBoolean(m, Arg.NOTEMPFAC))
+          if (avm.getBoolean(Arg.NOTEMPFAC))
           {
             // do this better (annotation types?)
             List<String> hideThese = new ArrayList<>();
@@ -299,13 +297,13 @@ public class Commands
            if (showTemperatureFactor)
              */
           {
-            if (ArgParser.getValue(m, Arg.TEMPFAC_LABEL) != null)
+            if (avm.hasValue(Arg.TEMPFAC_LABEL))
             {
               AlignmentAnnotation aa = AlignmentUtils
                       .getFirstSequenceAnnotationOfType(
                               af.getCurrentView().getAlignment(),
                               AlignmentAnnotation.LINE_GRAPH);
-              String label = ArgParser.getValue(m, Arg.TEMPFAC_LABEL);
+              String label = avm.getValue(Arg.TEMPFAC_LABEL);
               if (aa != null)
               {
                 aa.label = label;
@@ -360,12 +358,12 @@ public class Commands
     }
 
     // open the structure (from same PDB file or given PDBfile)
-    if (!ArgParser.getBoolean(m, Arg.NOSTRUCTURE))
+    if (!avm.getBoolean(Arg.NOSTRUCTURE))
     {
       AlignFrame af = afMap.get(id);
-      if (ArgParser.getArgValues(m, Arg.STRUCTURE) != null)
+      if (avm.hasValue(Arg.STRUCTURE))
       {
-        for (ArgValue av : ArgParser.getArgValueList(m, Arg.STRUCTURE))
+        for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
           String val = av.getValue();
           SubVals subId = new SubVals(val);
@@ -421,12 +419,12 @@ public class Commands
     }
 
     // load a pAE file if given
-    if (ArgParser.getArgValueList(m, Arg.PAEMATRIX) != null)
+    if (avm.hasValue(Arg.PAEMATRIX))
     {
       AlignFrame af = afMap.get(id);
       if (af != null)
       {
-        for (ArgValue av : ArgParser.getArgValueList(m, Arg.PAEMATRIX))
+        for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
         {
           String val = av.getValue();
           SubVals subVals = ArgParser.getSubVals(val);
@@ -480,7 +478,7 @@ public class Commands
       }
     }
 
-    boolean doShading = ArgParser.getBoolean(m, Arg.TEMPFAC_SHADING);
+    boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)
     {
       AlignFrame af = afMap.get(id);
@@ -498,7 +496,7 @@ public class Commands
 
   protected void processImages(String id)
   {
-    Map<Arg, ArgValues> m = argParser.linkedArgs(id);
+    ArgValuesMap avm = new ArgValuesMap(argParser.linkedArgs(id));
     AlignFrame af = afMap.get(id);
 
     if (af == null)
@@ -507,9 +505,9 @@ public class Commands
       return;
     }
 
-    if (ArgParser.getArgValueList(m, Arg.IMAGE) != null)
+    if (avm.hasValue(Arg.IMAGE))
     {
-      for (ArgValue av : ArgParser.getArgValueList(m, Arg.IMAGE))
+      for (ArgValue av : avm.getArgValueList(Arg.IMAGE))
       {
         String val = av.getValue();
         SubVals subVal = new SubVals(val);