synching of all db references and sequence features

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