[Jsbml-svn] SF.net SVN: jsbml:[1423] trunk

[<and...@us...>]

Revision: 1423
          http://jsbml.svn.sourceforge.net/jsbml/?rev=1423&view=rev
Author:   andreas-draeger
Date:     2012-10-04 15:51:38 +0000 (Thu, 04 Oct 2012)
Log Message:
-----------
* New Features:

  - Syntax check for metaids in the setMetaId method.

* Bug Fixes:

  - The method nextMetaId in SBMLDocument sometimes created metaIds containing
    the invalid character '-', but only underscores are allowed there.

Modified Paths:
--------------
    trunk/NEWS.txt
    trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java
    trunk/core/src/org/sbml/jsbml/AbstractSBase.java
    trunk/core/src/org/sbml/jsbml/SBMLDocument.java

Modified: trunk/NEWS.txt
===================================================================
--- trunk/NEWS.txt	2012-10-04 10:06:29 UTC (rev 1422)
+++ trunk/NEWS.txt	2012-10-04 15:51:38 UTC (rev 1423)
@@ -6,6 +6,8 @@
 
 * New Features:
 
+  - Syntax check for metaids in the setMetaId method.
+
   - Some additional methods for more convenient working with tree data
     structures in TreeNodeWithChangeSupport.
 
@@ -63,6 +65,9 @@
 
 * Bug Fixes:
 
+  - The method nextMetaId in SBMLDocument sometimes created metaIds containing
+    the invalid character '-', but only underscores are allowed there.
+
   - Several improvements and corrections in the work with 
     TreeNodeChangeListeners. In many cases listeners were notified too
     early or sometimes even not at all because of inconsistent

Modified: trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java	2012-10-04 10:06:29 UTC (rev 1422)
+++ trunk/core/src/org/sbml/jsbml/AbstractNamedSBase.java	2012-10-04 15:51:38 UTC (rev 1423)
@@ -50,7 +50,7 @@
 	private static final String idChar = "[" + letter + digit + underscore + "]";
 	private static final String SIdL2 = "^[" + letter + underscore + "]" + idChar + '*';
 	private static final Pattern SIdL2Pattern = Pattern.compile(SIdL2);
-		
+
 	/**
 	 * Checks whether the given idCandidate is a valid identifier according to
 	 * the SBML specifications.
@@ -300,8 +300,7 @@
 	 * @see org.sbml.jsbml.NamedSBase#setId(java.lang.String)
 	 */
 	public void setId(String id) {
-		String property = getLevel() == 1 ? TreeNodeChangeEvent.name
-				: TreeNodeChangeEvent.id;
+		String property = getLevel() == 1 ? TreeNodeChangeEvent.name : TreeNodeChangeEvent.id;
 		String oldId = this.id;
 		Model model = getModel();
     if ((oldId != null) && (model != null)) {

Modified: trunk/core/src/org/sbml/jsbml/AbstractSBase.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/AbstractSBase.java	2012-10-04 10:06:29 UTC (rev 1422)
+++ trunk/core/src/org/sbml/jsbml/AbstractSBase.java	2012-10-04 15:51:38 UTC (rev 1423)
@@ -1430,6 +1430,11 @@
 	  if ((metaId != null) && (getLevel() == 1)) {
 	    throw new PropertyNotAvailableException(TreeNodeChangeEvent.metaId, this);
 	  }
+	  // Meta-ids must follow the same restrictions as Ids and are defined since Level 2 (checked above).
+	  if ((metaId == null) || !AbstractNamedSBase.isValidId(metaId, getLevel(), getVersion())) {
+      throw new IllegalArgumentException(MessageFormat.format(
+        "\"{0}\" is not a valid meta-identifier for this {1}.", metaId, getElementName()));
+    }
 	  SBMLDocument doc = getSBMLDocument();
 	  String oldMetaId = this.metaId;
 	  if (doc != null) {

Modified: trunk/core/src/org/sbml/jsbml/SBMLDocument.java
===================================================================
--- trunk/core/src/org/sbml/jsbml/SBMLDocument.java	2012-10-04 10:06:29 UTC (rev 1422)
+++ trunk/core/src/org/sbml/jsbml/SBMLDocument.java	2012-10-04 15:51:38 UTC (rev 1423)
@@ -693,26 +693,34 @@
 	}
 
 	/**
-	 * @return true if the model of this SBMLDocument is not null.
+	 * @return true if the {@link Model} of this {@link SBMLDocument} is not {@code null}.
 	 */
 	public boolean isSetModel() {
 		return model != null;
 	}
 
-	/**
-	 * 
-	 * @return
-	 */
+  /**
+   * Randomly creates a new {@link String} that can be used as a metaid, i.e., a
+   * String that is a valid metaid and that is not yet used by any other element
+   * within this {@link SBMLDocument}.
+   * 
+   * @return
+   */
 	public String nextMetaId() {
 	  String idOne;
 	  do {
-	    idOne = '_' + UUID.randomUUID().toString();
+	    idOne = UUID.randomUUID().toString().replace('-', '_');
+	    if (Character.isDigit(idOne.charAt(0))) {
+	      // Add an underscore at the beginning of the new metaid only if necessary.
+	      idOne = '_' + idOne;
+	    }
 	  } while (containsMetaId(idOne));
 	  return idOne;
 	}
 
 	/**
 	 * 
+	 * @param stream
 	 */
 	public void printErrors(PrintStream stream) {
 		int nbErrors = listOfErrors.getErrorCount();

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