X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArgParser.java;h=e5b3a9d13722d75a73c5cad0c6a38af165ad957c;hb=3d64f036a9efc527f8f45ef43ead4c3bb64ae448;hp=7581ddeddb151cd86f23f4be6ddafefb3976e5d6;hpb=3613fa2821de21019a4b45ea3eec562a5a730c71;p=jalview.git

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 7581dde..e5b3a9d 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -31,10 +31,8 @@ import java.util.EnumSet;
 import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.List;
-import java.util.Locale;
 import java.util.Map;
 
-import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.bin.Jalview.ExitCode;
@@ -121,6 +119,46 @@ public class ArgParser
   private static final String LINKEDIDDIRNAME = "{dirname}";
 
   /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * structure filename extension
+   */
+  private static final String STRUCTUREEXTENSION = "{structureextension}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * structure filename base
+   */
+  private static final String STRUCTUREBASENAME = "{structurebasename}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * structure filename dir path
+   */
+  private static final String STRUCTUREDIRNAME = "{structuredirname}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! increment the
+   * on-the-fly counter and substitute the incremented value
+   */
+  private static final String INCREMENTONTHEFLYCOUNTER = "{++m}";
+
+  /**
+   * On-the-fly substitution (not made at argument parsing time)! the current
+   * substitute with the on-the-fly counter
+   */
+  private static final String ONTHEFLYCOUNTER = "{m}";
+
+  /**
+   * the string used for on-the-fly structure filename substitutions
+   */
+  private String currentStructureFilename = null;
+
+  /**
+   * the counter used for on-the-fly {m} substitutions
+   */
+  private int ontheflyCounter = 0;
+
+  /**
    * the current argfile
    */
   private String argFile = null;
@@ -156,6 +194,15 @@ public class ArgParser
    */
   private boolean allStructures = false;
 
+  /**
+   * flag to say whether to ignore or reject non-string values args with a value
+   * e.g., --wrap=hello
+   * 
+   * Default is false (i.e. reject non-string args that have a value. It is set
+   * to true for JalviewJS in Platform.getURLCommandArguments().
+   */
+  private static boolean ignoreNonStringValues = false;
+
   protected static final Map<String, Arg> argMap;
 
   protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
@@ -280,9 +327,13 @@ public class ArgParser
     }
 
     if (bsa != null)
+    {
       this.bootstrapArgs = bsa;
+    }
     else
+    {
       this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
+    }
     parse(args, initsubstitutions, allowPrivate);
   }
 
@@ -427,11 +478,20 @@ public class ArgParser
         }
         if (!a.hasOption(Opt.STRING) && equalPos > -1)
         {
-          // set --argname=value when arg does not accept values
-          Console.error("Argument '" + a.argString()
-                  + "' does not expect a value (given as '" + arg
-                  + "').  Ignoring.");
-          continue;
+          if (!getIgnoreNonStringValues())
+          {
+            // delete equals sign and value
+            val = null;
+            arg = arg.substring(0, equalPos);
+          }
+          else
+          {
+            // set --argname=value when arg does not accept values
+            Console.error("Argument '" + a.argString()
+                    + "' does not expect a value (given as '" + arg
+                    + "').  Ignoring.");
+            continue;
+          }
         }
         if (!a.hasOption(Opt.LINKED) && linkedId != null)
         {
@@ -619,10 +679,9 @@ public class ArgParser
 
         // set allstructures to all non-primary structure options in this linked
         // id if --allstructures has been set
-        if (allStructures
-                && (a.getType() == Type.STRUCTURE
-                        || a.getType() == Type.STRUCTUREIMAGE)
-                && !a.hasOption(Opt.PRIMARY))
+        if (allStructures && (a.getType() == Type.STRUCTURE
+        // || a.getType() == Type.STRUCTUREIMAGE)
+        ) && !a.hasOption(Opt.PRIMARY))
         {
           if (!subvals.has(Arg.ALLSTRUCTURES.getName()))
           // && !subvals.has("structureid"))
@@ -727,6 +786,12 @@ public class ArgParser
 
   public String makeSubstitutions(String val, String linkedId)
   {
+    return makeSubstitutions(val, linkedId, false);
+  }
+
+  public String makeSubstitutions(String val, String linkedId,
+          boolean onthefly)
+  {
     if (!this.substitutions || val == null)
       return val;
 
@@ -746,14 +811,20 @@ public class ArgParser
       rest = val;
     }
     if (rest.contains(LINKEDIDAUTOCOUNTER))
+    {
       rest = rest.replace(LINKEDIDAUTOCOUNTER,
               String.valueOf(linkedIdAutoCounter));
+    }
     if (rest.contains(INCREMENTLINKEDIDAUTOCOUNTER))
+    {
       rest = rest.replace(INCREMENTLINKEDIDAUTOCOUNTER,
               String.valueOf(++linkedIdAutoCounter));
+    }
     if (rest.contains(DEFAULTLINKEDIDCOUNTER))
+    {
       rest = rest.replace(DEFAULTLINKEDIDCOUNTER,
               String.valueOf(defaultLinkedIdCounter));
+    }
     ArgValuesMap avm = linkedArgs.get(linkedId);
     if (avm != null)
     {
@@ -783,6 +854,32 @@ public class ArgParser
                 FileUtils.getDirname(new File(argFile)));
       }
     }
+    if (onthefly)
+    {
+      if (rest.contains(ONTHEFLYCOUNTER))
+      {
+        rest = rest.replace(ONTHEFLYCOUNTER,
+                String.valueOf(ontheflyCounter));
+      }
+      if (rest.contains(INCREMENTONTHEFLYCOUNTER))
+      {
+        rest = rest.replace(INCREMENTONTHEFLYCOUNTER,
+                String.valueOf(++ontheflyCounter));
+      }
+      if (currentStructureFilename != null)
+      {
+        if (rest.contains(STRUCTUREBASENAME))
+        {
+          rest = rest.replace(STRUCTUREBASENAME, FileUtils
+                  .getBasename(new File(currentStructureFilename)));
+        }
+        if (rest.contains(STRUCTUREDIRNAME))
+        {
+          rest = rest.replace(STRUCTUREDIRNAME,
+                  FileUtils.getDirname(new File(currentStructureFilename)));
+        }
+      }
+    }
 
     return new StringBuilder(subvals).append(rest).toString();
   }
@@ -971,161 +1068,6 @@ public class ArgParser
     return args;
   }
 
-  public static enum Position
-  {
-    FIRST, BEFORE, AFTER
-  }
-
-  /**
-   * get from following Arg of type a or subval of same name (lowercase)
-   */
-  public static String getValueFromSubValOrArg(ArgValuesMap avm,
-          ArgValue av, Arg a, SubVals sv)
-  {
-    return getFromSubValArgOrPref(avm, av, a, sv, null, null, null);
-  }
-
-  /**
-   * get from following Arg of type a or subval key or preference pref or
-   * default def
-   */
-  public static String getFromSubValArgOrPref(ArgValuesMap avm, ArgValue av,
-          Arg a, SubVals sv, String key, String pref, String def)
-  {
-    return getFromSubValArgOrPref(avm, a, Position.AFTER, av, sv, key, pref,
-            def);
-  }
-
-  /**
-   * get from following(AFTER), first occurence of (FIRST) or previous (BEFORE)
-   * Arg of type a or subval key or preference pref or default def
-   */
-  public static String getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
-          Position pos, ArgValue av, SubVals sv, String key, String pref,
-          String def)
-  {
-    return getFromSubValArgOrPrefWithSubstitutions(null, avm, a, pos, av,
-            sv, key, pref, def);
-  }
-
-  public static String getFromSubValArgOrPrefWithSubstitutions(ArgParser ap,
-          ArgValuesMap avm, Arg a, Position pos, ArgValue av, SubVals sv,
-          String key, String pref, String def)
-  {
-    if (key == null)
-      key = a.getName();
-    String value = null;
-    if (sv != null && sv.has(key) && sv.get(key) != null)
-    {
-      value = ap == null ? sv.get(key)
-              : sv.getWithSubstitutions(ap, avm.getLinkedId(), key);
-    }
-    else if (avm != null && avm.containsArg(a))
-    {
-      if (pos == Position.FIRST && avm.getValue(a) != null)
-        value = avm.getValue(a);
-      else if (pos == Position.BEFORE
-              && avm.getClosestPreviousArgValueOfArg(av, a) != null)
-        value = avm.getClosestPreviousArgValueOfArg(av, a).getValue();
-      else if (pos == Position.AFTER
-              && avm.getClosestNextArgValueOfArg(av, a) != null)
-        value = avm.getClosestNextArgValueOfArg(av, a).getValue();
-
-      // look for allstructures subval for Type.STRUCTURE*
-      Arg arg = av.getArg();
-      if (value == null && arg.hasOption(Opt.PRIMARY)
-              && arg.getType() == Type.STRUCTURE
-              && !a.hasOption(Opt.PRIMARY) && (a.getType() == Type.STRUCTURE
-                      || a.getType() == Type.STRUCTUREIMAGE))
-      {
-        ArgValue av2 = avm.getArgValueOfArgWithSubValKey(a,
-                Arg.ALLSTRUCTURES.getName());
-        if (av2 != null)
-        {
-          value = av2.getValue();
-        }
-      }
-    }
-    if (value == null)
-    {
-      value = pref != null ? Cache.getDefault(pref, def) : def;
-    }
-    return value;
-  }
-
-  public static boolean getBoolFromSubValOrArg(ArgValuesMap avm, Arg a,
-          SubVals sv)
-  {
-    return getFromSubValArgOrPref(avm, a, sv, null, null, false);
-  }
-
-  public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
-          SubVals sv, String key, String pref, boolean def)
-  {
-    return getFromSubValArgOrPref(avm, a, sv, key, pref, def, false);
-  }
-
-  public static boolean getFromSubValArgOrPref(ArgValuesMap avm, Arg a,
-          SubVals sv, String key, String pref, boolean def,
-          boolean invertPref)
-  {
-    if ((key == null && a == null) || (sv == null && a == null))
-      return false;
-
-    boolean usingArgKey = false;
-    if (key == null)
-    {
-      key = a.getName();
-      usingArgKey = true;
-    }
-
-    String nokey = ArgParser.NEGATESTRING + key;
-
-    // look for key or nokey in subvals first (if using Arg check options)
-    if (sv != null)
-    {
-      // check for true boolean
-      if (sv.has(key) && sv.get(key) != null)
-      {
-        if (usingArgKey)
-        {
-          if (!(a.hasOption(Opt.BOOLEAN) || a.hasOption(Opt.UNARY)))
-          {
-            Console.debug(
-                    "Looking for boolean in subval from non-boolean/non-unary Arg "
-                            + a.getName());
-            return false;
-          }
-        }
-        return sv.get(key).toLowerCase(Locale.ROOT).equals("true");
-      }
-
-      // check for negative boolean (subval "no..." will be "true")
-      if (sv.has(nokey) && sv.get(nokey) != null)
-      {
-        if (usingArgKey)
-        {
-          if (!(a.hasOption(Opt.BOOLEAN)))
-          {
-            Console.debug(
-                    "Looking for negative boolean in subval from non-boolean Arg "
-                            + a.getName());
-            return false;
-          }
-        }
-        return !sv.get(nokey).toLowerCase(Locale.ROOT).equals("true");
-      }
-    }
-
-    // check argvalues
-    if (avm != null && avm.containsArg(a))
-      return avm.getBoolean(a);
-
-    // return preference or default
-    boolean prefVal = pref != null ? Cache.getDefault(pref, def) : false;
-    return pref != null ? (invertPref ? !prefVal : prefVal) : def;
-  }
-
   // the following methods look for the "*" linkedId and add the argvalue to all
   // linkedId ArgValues if it does.
   /**
@@ -1138,13 +1080,6 @@ public class ArgParser
             argIndex, doSubs);
   }
 
-  private void addValue(String linkedId, Type type, ArgValues avs, String v,
-          int argIndex, boolean doSubs)
-  {
-    this.argValueOperation(Op.ADDVALUE, linkedId, type, avs, null, v, false,
-            argIndex, doSubs);
-  }
-
   private void setBoolean(String linkedId, Type type, ArgValues avs,
           boolean b, int argIndex)
   {
@@ -1367,4 +1302,19 @@ public class ArgParser
   {
     return mixedExamples;
   }
+
+  public void setStructureFilename(String s)
+  {
+    this.currentStructureFilename = s;
+  }
+
+  public static boolean getIgnoreNonStringValues()
+  {
+    return ignoreNonStringValues;
+  }
+
+  public static void setIgnoreNonStringValues(boolean b)
+  {
+    ignoreNonStringValues = b;
+  }
 }
\ No newline at end of file