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,
-  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
   {
@@ -50,7 +50,10 @@ public enum Arg
               // 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
@@ -89,8 +92,8 @@ public enum Arg
     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);
@@ -103,9 +106,10 @@ public enum Arg
             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);
-    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,
@@ -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);
+    ALLFRAMES.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
   }
 
   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 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;
 
@@ -96,6 +99,10 @@ public class ArgParser
   // 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<>();
@@ -353,6 +360,10 @@ public class ArgParser
         {
           argFile = null;
         }
+        else if (a == Arg.ALLFRAMES)
+        {
+          allLinkedIds = !negated;
+        }
 
         String autoCounterString = null;
         boolean usingAutoCounterLinkedId = false;
@@ -375,11 +386,18 @@ public class ArgParser
             }
             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))
@@ -433,6 +451,10 @@ public class ArgParser
         }
 
         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)
@@ -443,27 +465,26 @@ public class ArgParser
           {
             for (String v : globVals)
             {
-              v = makeSubstitutions(v, linkedId);
               SubVals vsv = new SubVals(globSubVals, v);
-              avs.addValue(vsv, v, argIndex++);
+              addValue(linkedId, avs, vsv, v, argIndex++, true);
               argIndexIncremented = true;
             }
           }
           else
           {
-            avs.addValue(makeSubstitutions(val, linkedId), argIndex);
+            addValue(linkedId, avs, val, argIndex, true);
           }
         }
         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))
         {
-          avs.setBoolean(true, argIndex);
+          setBoolean(linkedId, avs, true, argIndex);
         }
-        avs.incrementCount();
+        incrementCount(linkedId, avs);
         if (!argIndexIncremented)
           argIndex++;
 
@@ -773,4 +794,113 @@ public class ArgParser
     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

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" } };
   }
+
+  @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 },
+        //
+    };
+  }
 }