JAL-629 Added --all arg, [*] linkedId and functionality to apply some args to all...

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 8bb1dcb..91cfe4d 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -12,11 +12,11 @@ public enum Arg
   HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
   COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
   SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,
   HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
   COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
   SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,

-  VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE,
-  PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, QUIT,
-  CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, NEWFRAME, NPP("n++"),
-  SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE,
-  WEBSERVICEDISCOVERY;
+  VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE, PAEMATRIX,
+  WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, QUIT, CLOSE,
+  DEBUG("d"), QUIET("q"), ARGFILE, NEWFRAME, NPP("n++"), SUBSTITUTIONS,
+  INITSUBSTITUTIONS, NIL, SPLASH, SETARGFILE, UNSETARGFILE,
+  WEBSERVICEDISCOVERY, ALLFRAMES;

 
   protected static enum Opt
   {
 
   protected static enum Opt
   {

@@ -50,7 +50,10 @@ public enum Arg
               // flow in ArgParser.parse(args).
     ALLOWSUBSTITUTIONS, // This Arg allows substitutions in its linkedId,
                         // SubVals and values.
               // flow in ArgParser.parse(args).
     ALLOWSUBSTITUTIONS, // This Arg allows substitutions in its linkedId,
                         // SubVals and values.

-    PRIVATE // This Arg is used internally, and cannot be specified by the user.
+    PRIVATE, // This Arg is used internally, and cannot be specified by the
+             // user.
+    ALLOWALL, // This Arg can use the '*' linkedId to apply to all known
+              // linkedIds

   }
 
   static
   }
 
   static

@@ -89,8 +92,8 @@ public enum Arg
     VDOC.setOptions(Opt.UNARY);
     VSESS.setOptions(Opt.UNARY);
 
     VDOC.setOptions(Opt.UNARY);
     VSESS.setOptions(Opt.UNARY);
 

-    OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
-    OUTPUTTYPE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
+    OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
+            Opt.ALLOWALL);

 
     SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
 
     SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);

@@ -103,9 +106,10 @@ public enum Arg
             Opt.ALLOWSUBSTITUTIONS);
     STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
     WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
             Opt.ALLOWSUBSTITUTIONS);
     STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
     WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);

-    IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS);
+    IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
+            Opt.ALLOWALL);

     QUIT.setOptions(Opt.UNARY);
     QUIT.setOptions(Opt.UNARY);

-    CLOSE.setOptions(Opt.UNARY, Opt.LINKED);
+    CLOSE.setOptions(Opt.UNARY, Opt.LINKED, Opt.ALLOWALL);

     DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
     ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,
     DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     QUIET.setOptions(Opt.UNARY, Opt.MULTI, Opt.BOOTSTRAP);
     ARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP, Opt.GLOB,

@@ -118,6 +122,7 @@ public enum Arg
     SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);

+    ALLFRAMES.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);

   }
 
   private final String[] argNames;
   }
 
   private final String[] argNames;

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index e08ae03..19e8bea 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -50,6 +50,9 @@ public class ArgParser
   // the default linked id prefix used for no id (not even square braces)
   protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";
 
   // the default linked id prefix used for no id (not even square braces)
   protected static final String DEFAULTLINKEDIDPREFIX = "JALVIEW:";
 

+  // the linkedId string used to match all linkedIds seen so far
+  protected static final String MATCHALLLINKEDIDS = "*";
+

   // the counter added to the default linked id prefix
   private int defaultLinkedIdCounter = 0;
 
   // the counter added to the default linked id prefix
   private int defaultLinkedIdCounter = 0;
 

@@ -96,6 +99,10 @@ public class ArgParser
   // Turn on and off with --subs and --nosubs
   private boolean substitutions = false;
 
   // Turn on and off with --subs and --nosubs
   private boolean substitutions = false;
 

+  // flag to say whether the default linkedId is the current default linked id
+  // or ALL linkedIds
+  private boolean allLinkedIds = false;
+

   protected static final Map<String, Arg> argMap;
 
   protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
   protected static final Map<String, Arg> argMap;
 
   protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();

@@ -353,6 +360,10 @@ public class ArgParser
         {
           argFile = null;
         }
         {
           argFile = null;
         }

+        else if (a == Arg.ALLFRAMES)
+        {
+          allLinkedIds = !negated;
+        }

 
         String autoCounterString = null;
         boolean usingAutoCounterLinkedId = false;
 
         String autoCounterString = null;
         boolean usingAutoCounterLinkedId = false;

@@ -375,11 +386,18 @@ public class ArgParser
             }
             else
             {
             }
             else
             {

-              // use default linkedId for linked arguments
-              linkedId = defaultLinkedId;
-              usingDefaultLinkedId = true;
-              Console.debug("Changing linkedId to '" + linkedId + "' from "
-                      + arg);
+              if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+              {
+                linkedId = this.MATCHALLLINKEDIDS;
+              }
+              else
+              {
+                // use default linkedId for linked arguments
+                linkedId = defaultLinkedId;
+                usingDefaultLinkedId = true;
+                Console.debug("Changing linkedId to '" + linkedId
+                        + "' from " + arg);
+              }

             }
           }
           else if (linkedId.contains(LINKEDIDAUTOCOUNTER))
             }
           }
           else if (linkedId.contains(LINKEDIDAUTOCOUNTER))

@@ -433,6 +451,10 @@ public class ArgParser
         }
 
         boolean argIndexIncremented = false;
         }
 
         boolean argIndexIncremented = false;

+        /* TODO
+         * Change all avs.addValue() avs.setBoolean avs.setNegated() avs.incrementCount calls to checkfor linkedId == "*"
+         * DONE, need to check
+         */

         ArgValues avs = avm.getOrCreateArgValues(a);
 
         // store appropriate String value(s)
         ArgValues avs = avm.getOrCreateArgValues(a);
 
         // store appropriate String value(s)

@@ -443,27 +465,26 @@ public class ArgParser
           {
             for (String v : globVals)
             {
           {
             for (String v : globVals)
             {

-              v = makeSubstitutions(v, linkedId);

               SubVals vsv = new SubVals(globSubVals, v);
               SubVals vsv = new SubVals(globSubVals, v);

-              avs.addValue(vsv, v, argIndex++);
+              addValue(linkedId, avs, vsv, v, argIndex++, true);

               argIndexIncremented = true;
             }
           }
           else
           {
               argIndexIncremented = true;
             }
           }
           else
           {

-            avs.addValue(makeSubstitutions(val, linkedId), argIndex);
+            addValue(linkedId, avs, val, argIndex, true);

           }
         }
         else if (a.hasOption(Opt.BOOLEAN))
         {
           }
         }
         else if (a.hasOption(Opt.BOOLEAN))
         {

-          avs.setBoolean(!negated, argIndex);
-          avs.setNegated(negated);
+          setBoolean(linkedId, avs, !negated, argIndex);
+          setNegated(linkedId, avs, negated);

         }
         else if (a.hasOption(Opt.UNARY))
         {
         }
         else if (a.hasOption(Opt.UNARY))
         {

-          avs.setBoolean(true, argIndex);
+          setBoolean(linkedId, avs, true, argIndex);

         }
         }

-        avs.incrementCount();
+        incrementCount(linkedId, avs);

         if (!argIndexIncremented)
           argIndex++;
 
         if (!argIndexIncremented)
           argIndex++;
 

@@ -773,4 +794,113 @@ public class ArgParser
     return pref != null ? Cache.getDefault(pref, def) : def;
   }
 
     return pref != null ? Cache.getDefault(pref, def) : def;
   }
 

+  // the following methods look for the "*" linkedId and add the argvalue to all
+  // linkedId ArgValues if it does
+  private void addValue(String linkedId, ArgValues avs, SubVals sv,
+          String v, int argIndex, boolean doSubs)
+  {
+    Arg a = avs.arg();
+    if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+    {
+      for (String id : linkedOrder)
+      {
+        ArgValuesMap avm = linkedArgs.get(id);
+        ArgValues tavs = avm.getArgValues(a);
+        String val = v;
+        if (doSubs)
+        {
+          val = makeSubstitutions(v, linkedId);
+          sv = new SubVals(sv, val);
+        }
+        tavs.addValue(sv, val, argIndex);
+      }
+    }
+    else
+    {
+      String val = v;
+      if (doSubs)
+      {
+        val = makeSubstitutions(v, linkedId);
+        sv = new SubVals(sv, val);
+      }
+      avs.addValue(sv, val, argIndex);
+    }
+  }
+
+  private void addValue(String linkedId, ArgValues avs, String v,
+          int argIndex, boolean doSubs)
+  {
+    Arg a = avs.arg();
+    if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+    {
+      for (String id : linkedOrder)
+      {
+        ArgValuesMap avm = linkedArgs.get(id);
+        ArgValues tavs = avm.getArgValues(a);
+        String val = doSubs ? makeSubstitutions(v, linkedId) : v;
+        tavs.addValue(val, argIndex);
+      }
+    }
+    else
+    {
+      String val = doSubs ? makeSubstitutions(v, linkedId) : v;
+      avs.addValue(val, argIndex);
+    }
+  }
+
+  private void setBoolean(String linkedId, ArgValues avs, boolean b,
+          int argIndex)
+  {
+    Arg a = avs.arg();
+    if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+    {
+      for (String id : linkedOrder)
+      {
+        ArgValuesMap avm = linkedArgs.get(id);
+        ArgValues tavs = avm.getArgValues(a);
+        tavs.setBoolean(b, argIndex);
+      }
+    }
+    else
+    {
+      avs.setBoolean(b, argIndex);
+    }
+  }
+
+  private void setNegated(String linkedId, ArgValues avs, boolean b)
+  {
+    Arg a = avs.arg();
+    if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+    {
+      for (String id : linkedOrder)
+      {
+        ArgValuesMap avm = linkedArgs.get(id);
+        ArgValues tavs = avm.getArgValues(a);
+        tavs.setNegated(b);
+      }
+    }
+    else
+    {
+      avs.setNegated(b);
+    }
+  }
+
+  private void incrementCount(String linkedId, ArgValues avs)
+  {
+    Arg a = avs.arg();
+    if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
+    {
+      for (String id : linkedOrder)
+      {
+        ArgValuesMap avm = linkedArgs.get(id);
+        ArgValues tavs = avm.getArgValues(a);
+        tavs.incrementCount();
+      }
+    }
+    else
+    {
+      avs.incrementCount();
+    }
+  }
+

 }
\ No newline at end of file
 }
\ No newline at end of file

diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java
index b724af0..8d4540a 100644 (file)
--- a/test/jalview/bin/argparser/ArgParserTest.java
+++ b/test/jalview/bin/argparser/ArgParserTest.java
@@ -259,4 +259,25 @@ public class ArgParserTest
         "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
         Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
   }
         "--argfile=test/jalview/bin/argparser/testfiles/argfile0.txt --open=shouldntbeabootstrap",
         Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
   }

+
+  @DataProvider(name = "allLinkedIdData")
+  public Object[][] allLinkedIdData()
+  {
+    return new Object[][] {
+        //
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+            Arg.OUTPUT, new String[]
+            { "test/jalview/bin/argfiles/testfiles/test1.stk",
+                "test/jalview/bin/argfiles/testfiles/test2.stk",
+                "test/jalview/bin/argfiles/testfiles/test3.stk", } },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+            Arg.IMAGE, new String[]
+            { "test/jalview/bin/argfiles/testfiles/test1.png",
+                "test/jalview/bin/argfiles/testfiles/test2.png",
+                "test/jalview/bin/argfiles/testfiles/test3.png", } },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+            Arg.CLOSE, null },
+        //
+    };
+  }

 }
 }