From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 19 Jan 2006 12:12:04 +0000 (+0000)
Subject: set correct get/Set VamsasRoots type, added addVamsasRoot, and some more TODOs
X-Git-Tag: Release_0.2~375
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d04d80167610368f907b02e81be71012b98357ed;p=vamsas.git

set correct get/Set VamsasRoots type, added addVamsasRoot, and some more TODOs


git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@145 be28352e-c001-0410-b1a7-c7978e42abec
---

diff --git a/src/org/vamsas/client/IClientDocument.java b/src/org/vamsas/client/IClientDocument.java
index 89556bb..80eb94a 100644
--- a/src/org/vamsas/client/IClientDocument.java
+++ b/src/org/vamsas/client/IClientDocument.java
@@ -6,6 +6,8 @@
  */
 package org.vamsas.client;
 
+import org.vamsas.objects.core.VAMSAS;
+
 
 /**
  * Defines the API for the Vamsas XML Document 
@@ -28,7 +30,7 @@ package org.vamsas.client;
  * A user may also want to make private notes, not 
  * available to other people using the same application 
  * in the same session.
- * 
+ * TODO: LATER: implement a more sophisticated query interface for quickly identifying new data in a vamsas document and manipulating existing objects
  * @author jimp
  */
 public interface IClientDocument {
@@ -48,9 +50,24 @@ public interface IClientDocument {
   /**
    * Returns all root objects in document. All objects inherit 
    * from org.vamsas.client.object and have valid VorbaIds and provenance entries.
-   * @return array of root Vamsas element objects. (TODO: insert correct class here)
+   * @return array of root Vamsas element objects.
+   */
+  VAMSAS[] getVamsasRoots();
+  /**
+   * set the VAMSAS roots in the document
+   * TODO: decide if objects are verified for provenance and VorbaIds by this call or when document is stored
+   * TODO: decide if this call should throw InvalidVamsasObject exceptions.
+   * TODO: decide how this call deals with applications that 'forget' to include all VAMSAS roots (this is where reference counting/garbage collection happens)
+   * @param roots
+   */
+  void setVamsasRoots(VAMSAS[] roots);
+  /**
+   * Adds a new VAMSAS root entry
+   * TODO: decide on same InvalidVamsasObject exceptions.
+   * TODO: decide if a 'removeVamsasRoot' method is really needed.
+   * @param newroot
    */
-  object[] getVamsasRoots();
+  void addVamsasRoot(VAMSAS newroot);
   /**
    * Returns an object with a valid VorbaId, and provenance element. 
    * The VorbaId is so the application may refer to it in