From f4c035478a53b34b67fabf4729751e546254976e Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 12 Jun 2009 15:57:44 +0000
Subject: [PATCH] synching of all db references and sequence features

---
 src/jalview/io/vamsas/Datasetsequence.java |   94 +++++++++++++++++++++++-----
 1 file changed, 79 insertions(+), 15 deletions(-)

diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index 39ff94d..1412007 100644
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -23,6 +23,7 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.VamsasAppDatastore;
 import uk.ac.vamsas.objects.core.DataSet;
+import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Sequence;
 
 /**
@@ -102,9 +103,47 @@ public class Datasetsequence extends DatastoreItem
         sequence.setName(sq.getName());
         modified = true;
       }
+      modified |= updateJvDbRefs();
+      // updateJvFeatures();
     }    
   }
 
+/*
+  private void updateJvFeatures()
+  {
+    Sequence vsq = (Sequence) vobj;
+    
+    // add or update any new features/references on dataset sequence
+    if (vsq.getgetSequenceFeatures() != null)
+    {
+      int sfSize = sq.getSequenceFeatures().length;
+
+      for (int sf = 0; sf < sfSize; sf++)
+      {
+        new jalview.io.vamsas.Sequencefeature(datastore, (jalview.datamodel.SequenceFeature) sq
+                .getSequenceFeatures()[sf], dataset, (Sequence) vobj);
+      }
+    }    
+  }
+*/
+  private boolean updateSqFeatures()
+  {
+    boolean modified=false;
+    SequenceI sq = (SequenceI) jvobj;
+    
+    // add or update any new features/references on dataset sequence
+    if (sq.getSequenceFeatures() != null)
+    {
+      int sfSize = sq.getSequenceFeatures().length;
+
+      for (int sf = 0; sf < sfSize; sf++)
+      {
+        modified|=new jalview.io.vamsas.Sequencefeature(datastore, (jalview.datamodel.SequenceFeature) sq
+                .getSequenceFeatures()[sf], dataset, (Sequence) vobj).docWasUpdated();
+      }
+    }
+    return modified;
+  }
 
   public void addToDocument()
   {
@@ -120,30 +159,53 @@ public class Datasetsequence extends DatastoreItem
     sequence.setDescription(sq.getDescription());
     dataset.addSequence(sequence);
     vobj = sequence;
-    // add or update any new features/references on dataset sequence
-    if (sq.getSequenceFeatures() != null)
-    {
-      int sfSize = sq.getSequenceFeatures().length;
-
-      for (int sf = 0; sf < sfSize; sf++)
-      {
-        new jalview.io.vamsas.Sequencefeature(datastore, (jalview.datamodel.SequenceFeature) sq
-                .getSequenceFeatures()[sf], dataset, (Sequence) vobj);
-      }
-    }
+    updateSqFeatures();
+    updateDbRefs();//sq,(Sequence) vobj, dataset);
+  }
+  /**
+   * sync database references from jv to document
+   * @return true if document was modified
+   */
+  private boolean updateDbRefs() {
+    boolean modifiedthedoc=false;
+    SequenceI sq = (SequenceI) jvobj;
+    
     if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
     {
       // only sync database references for dataset sequences
       DBRefEntry[] entries = sq.getDBRef();
-      jalview.datamodel.DBRefEntry dbentry;
+      //jalview.datamodel.DBRefEntry dbentry;
       for (int db = 0; db < entries.length; db++)
       {
-        Rangetype dbr = new jalview.io.vamsas.Dbref(datastore,
-                dbentry = entries[db], sq, (Sequence) vobj, dataset);
+        modifiedthedoc|= new jalview.io.vamsas.Dbref(datastore,
+                //dbentry = 
+                  entries[db], sq, (Sequence) vobj, dataset).docWasUpdated();
+        
       }
 
     }
-    
+    return modifiedthedoc;
+  }
+  /**
+   * sync database references from document to jv sequence
+   * @return true if local sequence refs were modified
+   */
+  private boolean updateJvDbRefs() {
+    boolean modifiedtheseq=false;
+    SequenceI sq = (SequenceI) jvobj;
+    Sequence vsq = (Sequence) vobj;
+    if (vsq.getDbRefCount()>0) {
+      // only sync database references for dataset sequences
+      DbRef[] entries = vsq.getDbRef();
+      //DbRef dbentry;
+      for (int db = 0; db < entries.length; db++)
+      {
+        modifiedtheseq|= new jalview.io.vamsas.Dbref(datastore,
+                //dbentry = 
+                  entries[db], vsq, sq).jvWasUpdated();
+      }
+    }
+    return modifiedtheseq;
   }
 
   public void conflict()
@@ -189,6 +251,8 @@ public class Datasetsequence extends DatastoreItem
       sequence.setName(sq.getName());
       modified = true;
     }
+    modified |= updateDbRefs();
+    modified |= updateSqFeatures();
   }
 
   /**
-- 
1.7.10.2