X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2FDocumentUpdaterEngine.java;h=19cae2d56acaa50c0ef0e824ca1ec99621093a3b;hb=1eea4b639911330e7cd65e17c5421cc584f0d22e;hp=370fcc82a37d7022c3c8b6340e8a0224c80eafbc;hpb=22724ef036aa4c1c6496b2d07b99d1f07061b7d2;p=vamsas.git

diff --git a/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java b/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java
index 370fcc8..19cae2d 100644
--- a/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java
+++ b/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java
@@ -1,25 +1,179 @@
+/*
+ * This file is part of the Vamsas Client version 0.2. 
+ * Copyright 2010 by Jim Procter, Iain Milne, Pierre Marguerite, 
+ *  Andrew Waterhouse and Dominik Lindner.
+ * 
+ * Earlier versions have also been incorporated into Jalview version 2.4 
+ * since 2008, and TOPALi version 2 since 2007.
+ * 
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *  
+ * The Vamsas Client 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 Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package uk.ac.vamsas.objects;
 
 import uk.ac.vamsas.client.IClientDocument;
+import uk.ac.vamsas.objects.core.*;
 
+/**
+ * Implements a depth first traversal over the document tree calling update
+ * handlers based on the Vobject.isUpdated() and Vobject.isNewInDocument() state
+ * at each backtrack.
+ * 
+ * @author JimP
+ * 
+ */
 public class DocumentUpdaterEngine {
-  private IDocumentUpdater hander;
+  private static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory
+      .getLog(DocumentUpdaterEngine.class);
+
+  private IDocumentUpdater handler;
+
   /**
-   * initialise the engine with an implementation
-   * of the interface.
+   * initialise the engine with an implementation of the interface.
+   * 
    * @param hander
    */
-  public DocumentUpdaterEngine(IDocumentUpdater hander) {
+  public DocumentUpdaterEngine(IDocumentUpdater handler) {
     super();
-    this.hander = hander;
+    this.handler = handler;
   }
+
   /**
-   * call the necessary update handlers at
-   * each point on the VamsasDocument OM
+   * call the necessary update handlers at each point on the VamsasDocument OM
+   * TODO: later: Make this more elegant (use reflection and factor to single
+   * update(Object) method) ? - we take the plodding, explicit approach rather
+   * than a funky generalised one here
    */
   public void callHandlers(IClientDocument cdoc) {
-    // TODO: walk down the hierarchy until we find an update and call the handler for it.
+    if (cdoc == null) {
+      log.debug("Null IClientDocument instance.");
+      return;
+    }
+    VAMSAS[] roots = cdoc.getVamsasRoots();
+    if (roots != null) {
+      for (int r = 0; r < roots.length; r++) {
+        if (roots[r].isNewInDocument() || roots[r].isUpdated()) {
+          if (!updateRoot(roots[r])) {
+            log.debug("Calling handler(VAMSAS)");
+            handler.update(roots[r]);
+          }
+        }
+      }
+    } else {
+      log.debug("No Document Roots.");
+    }
     // TODO: determine if the User, private or public appData has changed
-  
+    log.debug("Finished.");
+  }
+
+  private boolean updateRoot(VAMSAS vamsas) {
+    boolean called = false;
+    DataSet[] dset = vamsas.getDataSet();
+    if (dset != null) {
+      for (int ds = 0; ds < dset.length; ds++) {
+        if (dset[ds].isNewInDocument() || dset[ds].isUpdated()) {
+          if (!updateDataset(dset[ds])) {
+            log.debug("Calling handler(Dataset)");
+            handler.update(dset[ds]);
+            called = true;
+          }
+        }
+      }
+    }
+    return called;
+  }
+
+  private boolean updateDataset(DataSet set) {
+    boolean called = false;
+    // Sequences
+    Sequence[] dseq = set.getSequence();
+    if (dseq != null) {
+      for (int s = 0; s < dseq.length; s++) {
+        if (dseq[s].isNewInDocument() || dseq[s].isUpdated()) {
+          if (!updateSequence(dseq[s])) {
+            log.debug("Calling update(Sequence)");
+            handler.update(dseq[s]);
+            called = true;
+          }
+        }
+      }
+    }
+    // Annotations
+    DataSetAnnotations[] dann = set.getDataSetAnnotations();
+    if (dann != null) {
+      for (int a = 0; a < dann.length; a++) {
+        if (dann[a].isNewInDocument() || dann[a].isUpdated()) {
+          if (!updateDataSetAnnotation(dann[a])) {
+            log.debug("Calling update(DataSetAnnotation)");
+            handler.update(dann[a]);
+            called = true;
+          }
+        }
+      }
+    }
+    // Alignments
+    Alignment[] al = set.getAlignment();
+    if (al != null) {
+      for (int a = 0; a < al.length; a++) {
+        if (al[a].isNewInDocument() || al[a].isUpdated()) {
+          if (!updateAlignment(al[a])) {
+            log.debug("Calling update(Alignment)");
+            handler.update(al[a]);
+            called = true;
+          }
+        }
+      }
+    }
+    // Trees associated with dataset sequences
+    if (updateTrees(set.getTree())) {
+      called = true;
+    }
+    return called;
+  }
+
+  private boolean updateTrees(Tree[] trees) {
+    boolean called = false;
+    if (trees != null) {
+      for (int t = 0; t < trees.length; t++) {
+        if (trees[t].isNewInDocument() || trees[t].isUpdated()) {
+          if (!updateTree(trees[t])) {
+            log.debug("Calling update(tree)");
+            handler.update(trees[t]);
+            called = true;
+          }
+        }
+      }
+    }
+    return called;
+  }
+
+  private boolean updateDataSetAnnotation(DataSetAnnotations annotations) {
+    boolean called = false;
+    return called;
+  }
+
+  private boolean updateTree(Tree tree) {
+    // TODO: if (
+    return false;
+  }
+
+  private boolean updateAlignment(Alignment alignment) {
+    // TODO Auto-generated method stub
+    return false;
+  }
+
+  private boolean updateSequence(Sequence sequence) {
+    // TODO Auto-generated method stub
+    return false;
   }
 }