refactored to propery separate addToDocument,addFromDocument, updateToDocument, updat...

[jalview.git] / src / jalview / io / vamsas / Tree.java

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index fd9294b..1866336 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -71,46 +71,14 @@ public class Tree extends DatastoreItem
           uk.ac.vamsas.objects.core.Tree vtree)
   {
     Tree toTree = new Tree(datastore, alignFrame, vtree);
-
   }
 
   public Tree(VamsasAppDatastore datastore,
           jalview.gui.AlignFrame alignFrame,
           uk.ac.vamsas.objects.core.Tree vtree)
   {
-    super(datastore);
-    tree = vtree;
-    TreePanel tp = (TreePanel) getvObj2jv(tree);
-    if (tp != null)
-    {
-      if (tree.isUpdated())
-      {
-        Cache.log
-                .info("Update from vamsas document to alignment associated tree not implemented yet.");
-      }
-    }
-    else
-    {
-      // make a new tree
-      Object[] idata = recoverInputData(tree.getProvenance());
-      try
-      {
-        if (idata != null && idata[0] != null)
-        {
-          inputData = (AlignmentView) idata[0];
-        }
-        ntree = getNtree();
-        title = tree.getNewick(0).getTitle();
-        if (title == null || title.length() == 0)
-        {
-          title = tree.getTitle(); // hack!!!!
-        }
-      } catch (Exception e)
-      {
-        Cache.log.warn("Problems parsing treefile '"
-                + tree.getNewick(0).getContent() + "'", e);
-      }
-    }
+    super(datastore, vtree, TreePanel.class);
+    doJvUpdate();
   }
 
   private NewickFile getNtree() throws IOException
@@ -121,30 +89,111 @@ public class Tree extends DatastoreItem
   public Tree(VamsasAppDatastore datastore, TreePanel tp2, AlignmentI jal2,
           uk.ac.vamsas.objects.core.Alignment alignment2)
   {
-    super(datastore);
+    super(datastore, tp2, uk.ac.vamsas.objects.core.Tree.class);
 
     jal = jal2;
-    tp = tp2;
+    tp = (TreePanel) jvobj;
     alignment = alignment2;
 
-    tree = (uk.ac.vamsas.objects.core.Tree) getjv2vObj(tp);
-    if (tree == null)
+    tree = (uk.ac.vamsas.objects.core.Tree) vobj;
+    doSync();
+  }
+  
+  /* (non-Javadoc)
+   * @see jalview.io.vamsas.DatastoreItem#addFromDocument()
+   */
+  public void addFromDocument()
+  {
+    tree = (uk.ac.vamsas.objects.core.Tree) vobj; // vtree;
+    TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+    // make a new tree
+    Object[] idata = recoverInputData(tree.getProvenance());
+    try
+    {
+      if (idata != null && idata[0] != null)
+      {
+        inputData = (AlignmentView) idata[0];
+      }
+      ntree = getNtree();
+      title = tree.getNewick(0).getTitle();
+      if (title == null || title.length() == 0)
+      {
+        title = tree.getTitle(); // hack!!!!
+      }
+    } catch (Exception e)
     {
-      add();
+      Cache.log.warn("Problems parsing treefile '"
+              + tree.getNewick(0).getContent() + "'", e);
+    }
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.io.vamsas.DatastoreItem#conflict()
+   */
+  public void conflict()
+  {
+    Cache.log
+    .info("Update (with conflict) from vamsas document to alignment associated tree not implemented yet.");
+  }
+
+  /* (non-Javadoc)
+   * @see jalview.io.vamsas.DatastoreItem#update()
+   */
+  public void updateToDoc()
+  {
+    if (isModifiable(tree.getModifiable()))
+    {
+      // synchronize(); // update();
+      // verify any changes.
+      log.info("TODO: Update tree in document from jalview.");
     }
     else
     {
-      if (isModifiable(tree.getModifiable()))
+      // handle conflict
+      log.info("TODO: Add the locally modified tree in Jalview as a new tree in document, leaving locked tree unchanged.");
+    }
+  }
+  /* (non-Javadoc)
+   * @see jalview.io.vamsas.DatastoreItem#updateFromDoc()
+   */
+  public void updateFromDoc()
+  {
+    // should probably just open a new tree panel in the same place as the old one
+    // TODO: Tree.updateFromDoc
+    /*
+    TreePanel tp = (TreePanel) jvobj; // getvObj2jv(tree);
+    
+    // make a new tree
+    Object[] idata = recoverInputData(tree.getProvenance());
+    try
+    {
+      if (idata != null && idata[0] != null)
       {
-        // synchronize(); // update();
-        // verify any changes.
-        System.out.println("Update tree in document.");
+        inputData = (AlignmentView) idata[0];
       }
-      else
+      ntree = getNtree();
+      title = tree.getNewick(0).getTitle();
+      if (title == null || title.length() == 0)
       {
-        // handle conflict
-        System.out.println("Add modified tree as new tree in document.");
+        title = tree.getTitle(); // hack!!!!
       }
+    } catch (Exception e)
+    {
+      Cache.log.warn("Problems parsing treefile '"
+              + tree.getNewick(0).getContent() + "'", e);
+    }*/
+    log.debug("Update the local tree in jalview from the document.");
+
+    if (isModifiable(tree.getModifiable()))
+    {
+      // synchronize(); // update();
+      // verify any changes.
+      log.debug("Update tree in document from jalview.");
+    }
+    else
+    {
+      // handle conflict
+      log.debug("Add modified jalview tree as new tree in document.");
     }
   }
 
@@ -430,7 +479,7 @@ public class Tree extends DatastoreItem
    * add jalview object to vamsas document
    * 
    */
-  public void add()
+  public void addToDocument()
   {
     tree = new uk.ac.vamsas.objects.core.Tree();
     bindjvvobj(tp, tree);