X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FArgValues.java;h=55e12116726a14371ebc37a5fa829fcc608368cc;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=f25fc9ad0876497c21f86ce411fc64815087b70e;hpb=92c48abf7079358345432e020b72d025fc14f75d;p=jalview.git

diff --git a/src/jalview/bin/argparser/ArgValues.java b/src/jalview/bin/argparser/ArgValues.java
index f25fc9a..55e1211 100644
--- a/src/jalview/bin/argparser/ArgValues.java
+++ b/src/jalview/bin/argparser/ArgValues.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.bin.argparser;
 
 import java.util.ArrayList;
@@ -24,6 +44,8 @@ public class ArgValues
 
   private boolean setByWildcard = false;
 
+  private String givenLinkedId = null;
+
   private int boolIndex = -1;
 
   private List<Integer> argsIndexes;
@@ -32,16 +54,19 @@ public class ArgValues
 
   private Map<String, ArgValue> idMap = new HashMap<>();
 
+  private ArgValuesMap avm;
+
   /*
    * Type type is only really used by --help-type
    */
   private Type type = null;
 
-  protected ArgValues(Arg a)
+  protected ArgValues(Arg a, ArgValuesMap avm)
   {
     this.arg = a;
     this.argValueList = new ArrayList<ArgValue>();
     this.boolValue = arg.getDefaultBoolValue();
+    this.avm = avm;
   }
 
   protected boolean setByWildcard()
@@ -94,7 +119,7 @@ public class ArgValues
   }
 
   protected void setBoolean(Type t, boolean b, int i,
-          boolean beingSetByWildcard)
+          boolean beingSetByWildcard, String givenLinkedId)
   {
     this.setType(t);
     // don't overwrite a wildcard set boolean with a non-wildcard set boolean
@@ -103,6 +128,7 @@ public class ArgValues
     this.boolValue = b;
     this.boolIndex = i;
     this.setSetByWildcard(beingSetByWildcard);
+    this.givenLinkedId = givenLinkedId;
   }
 
   protected boolean getBoolean()
@@ -137,23 +163,25 @@ public class ArgValues
   }
 
   protected void addValue(Type type, String val, int argIndex,
-          boolean wildcard)
+          boolean wildcard, String givenLinkedId)
   {
-    addArgValue(new ArgValue(arg(), type, val, argIndex), wildcard);
+    addArgValue(new ArgValue(arg(), type, val, argIndex, wildcard,
+            givenLinkedId, avm.getLinkedId()), wildcard);
   }
 
   protected void addValue(SubVals sv, Type type, String content,
-          int argIndex, boolean wildcard)
+          int argIndex, boolean wildcard, String givenLinkedId)
   {
-    addArgValue(new ArgValue(arg(), sv, type, content, argIndex), wildcard);
+    addArgValue(new ArgValue(arg(), sv, type, content, argIndex, wildcard,
+            givenLinkedId, avm.getLinkedId()), wildcard);
   }
 
   protected void addArgValue(ArgValue av, boolean beingSetByWildcard)
   {
     // allow a non-wildcard value to overwrite a wildcard set single value
-    boolean overwrite = !arg.hasOption(Opt.MULTI) && setByWildcard
+    boolean overwrite = !arg.hasOption(Opt.MULTIVALUE) && setByWildcard
             && !beingSetByWildcard;
-    if ((!arg.hasOption(Opt.MULTI) && argValueList.size() > 0)
+    if ((!arg.hasOption(Opt.MULTIVALUE) && argValueList.size() > 0)
             && !overwrite)
       return;
     if (arg.hasOption(Opt.NODUPLICATEVALUES)
@@ -182,7 +210,7 @@ public class ArgValues
 
   protected ArgValue getArgValue()
   {
-    if (arg.hasOption(Opt.MULTI))
+    if (arg.hasOption(Opt.MULTIVALUE))
       Console.warn("Requesting single value for multi value argument");
     return argValueList.size() > 0 ? argValueList.get(0) : null;
   }
@@ -218,4 +246,11 @@ public class ArgValues
     }
     return false;
   }
+
+  public boolean setByWildcardLinkedId()
+  {
+    // looking for deliberately user set wildcard
+    return this.setByWildcard && this.givenLinkedId != null;
+  }
+
 }
\ No newline at end of file