X-Git-Url: http://source.jalview.org/gitweb/?p=vamsas.git;a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2FDocumentUpdaterEngine.java;h=715d7e488befc035ecc0dccd1980089d25c4514f;hp=cb2d2c36c8cec1c73f8ba80e21eb102b8e22994f;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f

diff --git a/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java b/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java
index cb2d2c3..715d7e4 100644
--- a/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java
+++ b/src/uk/ac/vamsas/objects/DocumentUpdaterEngine.java
@@ -1,38 +1,67 @@
+/*
+ * This file is part of the Vamsas Client version 0.1. 
+ * Copyright 2009 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.
+ * 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 static org.apache.commons.logging.Log log = org.apache.commons.logging.LogFactory.getLog(DocumentUpdaterEngine.class);
+  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 handler) {
     super();
     this.handler = handler;
   }
+
   /**
-   * 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
+   * 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) {
-    if (cdoc==null) {
+    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 != 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)");
@@ -46,96 +75,103 @@ public class DocumentUpdaterEngine {
     // TODO: determine if the User, private or public appData has changed
     log.debug("Finished.");
   }
+
   private boolean updateRoot(VAMSAS vamsas) {
-    boolean called=false;
+    boolean called = false;
     DataSet[] dset = vamsas.getDataSet();
-    if (dset!=null) {
-      for (int ds=0; ds<dset.length; ds++) {
+    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;
+            called = true;
           }
         }
       }
     }
     return called;
   }
+
   private boolean updateDataset(DataSet set) {
-    boolean called=false;
+    boolean called = false;
     // Sequences
     Sequence[] dseq = set.getSequence();
-    if (dseq!=null) {
-      for (int s=0;s<dseq.length; s++) {
+    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;
+            called = true;
           }
         }
       }
     }
     // Annotations
-    DataSetAnnotations[] dann=set.getDataSetAnnotations();
-    if (dann!=null) {
-      for (int a=0; a<dann.length; a++) {
+    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;
+            called = true;
           }
         }
       }
     }
     // Alignments
-    Alignment[] al=set.getAlignment();
-    if (al!=null) {
-      for (int a=0;a<al.length;a++) {
+    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;
+            called = true;
           }
         }
       }
     }
     // Trees associated with dataset sequences
     if (updateTrees(set.getTree())) {
-      called=true;
+      called = true;
     }
     return called;
   }
+
   private boolean updateTrees(Tree[] trees) {
-    boolean called=false;
-    if (trees!=null) {
-      for (int t=0;t<trees.length; t++) {
+    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;
+            called = true;
           }
         }
       }
     }
     return called;
   }
+
   private boolean updateDataSetAnnotation(DataSetAnnotations annotations) {
-    boolean called=false;
+    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;