From: Ben Soares <b.soares@dundee.ac.uk>
Date: Fri, 24 Feb 2023 11:52:19 +0000 (+0000)
Subject: JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code... 
X-Git-Tag: Release_2_11_4_0~477
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7057bdc72cbd324a4316f445118b509db4880499;p=jalview.git

JAL-629 Made ArgValuesMap helper class, simplifies readability/writing of the code and will allow arg position lookups
---

diff --git a/src/jalview/bin/ArgParser.java b/src/jalview/bin/ArgParser.java
index d150db2..2290182 100644
--- a/src/jalview/bin/ArgParser.java
+++ b/src/jalview/bin/ArgParser.java
@@ -696,43 +696,6 @@ public class ArgParser
     return sb.toString();
   }
 
-  // Helper methods with safety checks
-  protected static ArgValues getArgValues(Map<Arg, ArgValues> m, Arg a)
-  {
-    return m == null ? null : m.get(a);
-  }
-
-  public static List<ArgValue> getArgValueList(Map<Arg, ArgValues> m, Arg a)
-  {
-    ArgValues av = getArgValues(m, a);
-    return av == null ? null : av.getArgValueList();
-  }
-
-  public static ArgValue getArgValue(Map<Arg, ArgValues> m, Arg a)
-  {
-    List<ArgValue> vals = getArgValueList(m, a);
-    return (vals == null || vals.size() == 0) ? null : vals.get(0);
-  }
-
-  public static String getValue(Map<Arg, ArgValues> m, Arg a)
-  {
-    ArgValue av = getArgValue(m, a);
-    return av == null ? null : av.getValue();
-  }
-
-  public static boolean hasValue(Map<Arg, ArgValues> m, Arg a)
-  {
-    if (!m.containsKey(a))
-      return false;
-    return getArgValue(m, a) != null;
-  }
-
-  public static boolean getBoolean(Map<Arg, ArgValues> m, Arg a)
-  {
-    ArgValues av = getArgValues(m, a);
-    return av == null ? false : av.getBoolean();
-  }
-
   public static SubVals getSubVals(String item)
   {
     return new SubVals(item);
@@ -858,6 +821,56 @@ public class ArgParser
     }
   }
 
+  /**
+   * Helper class to allow easy extraction of information about specific
+   * argument values (without having to check for null etc all the time)
+   */
+  protected static class ArgValuesMap
+  {
+    protected Map<Arg, ArgValues> m;
+
+    protected ArgValuesMap(Map<Arg, ArgValues> map)
+    {
+      this.m = map;
+    }
+
+    protected ArgValues getArgValues(Arg a)
+    {
+      return m == null ? null : m.get(a);
+    }
+
+    protected List<ArgValue> getArgValueList(Arg a)
+    {
+      ArgValues av = getArgValues(a);
+      return av == null ? null : av.getArgValueList();
+    }
+
+    protected ArgValue getArgValue(Arg a)
+    {
+      List<ArgValue> vals = getArgValueList(a);
+      return (vals == null || vals.size() == 0) ? null : vals.get(0);
+    }
+
+    protected String getValue(Arg a)
+    {
+      ArgValue av = getArgValue(a);
+      return av == null ? null : av.getValue();
+    }
+
+    protected boolean hasValue(Arg a)
+    {
+      if (!m.containsKey(a))
+        return false;
+      return getArgValue(a) != null;
+    }
+
+    protected boolean getBoolean(Arg a)
+    {
+      ArgValues av = getArgValues(a);
+      return av == null ? false : av.getBoolean();
+    }
+  }
+
   private static final Collection<String> bootstrapArgs = new ArrayList(
           Arrays.asList("props", "debug"));
 
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);