From 29ea678048298c63f589674ff35f6c026497550c Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 19 Jun 2009 10:10:46 +0000
Subject: [PATCH] debug and cyclefix for dbrefs with embedded sequences

---
 src/jalview/io/vamsas/Dbref.java |   69 +++++++++++++++++++++++++-------------
 1 file changed, 45 insertions(+), 24 deletions(-)

diff --git a/src/jalview/io/vamsas/Dbref.java b/src/jalview/io/vamsas/Dbref.java
index 5698228..d930f14 100644
--- a/src/jalview/io/vamsas/Dbref.java
+++ b/src/jalview/io/vamsas/Dbref.java
@@ -24,6 +24,7 @@ import uk.ac.vamsas.objects.core.DataSet;
 import uk.ac.vamsas.objects.core.DbRef;
 import uk.ac.vamsas.objects.core.Map;
 import uk.ac.vamsas.objects.core.Sequence;
+import uk.ac.vamsas.objects.core.SequenceType;
 import jalview.io.VamsasAppDatastore;
 
 public class Dbref extends Rangetype
@@ -87,43 +88,62 @@ public class Dbref extends Rangetype
         updateMapTo(mp);
       }
     }
-      else
-      {
-        jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
-                + jvobj.getSrcAccString());
-      }
-    
+    else
+    {
+      jalview.bin.Cache.log.debug("Ignoring mapless DbRef.Map "
+              + jvobj.getSrcAccString());
+    }
+
   }
+
   /**
-   * ugly hack to try to get the embedded sequences within a database reference to be stored in the document's dataset.
+   * ugly hack to try to get the embedded sequences within a database reference
+   * to be stored in the document's dataset.
+   * 
    * @param mp
    */
   private void updateMapTo(jalview.datamodel.Mapping mp)
   {
-    log.info("Performing updateMapTo remove this message when we know what we're doing.");
-    // TODO determine how sequences associated with database mappings are stored in the document
-    if (mp!=null && mp.getTo() != null)
+    log
+            .info("Performing updateMapTo remove this message when we know what we're doing.");
+    // TODO determine how sequences associated with database mappings are stored
+    // in the document
+    if (mp != null && mp.getTo() != null)
     {
       if (mp.getTo().getDatasetSequence() == null)
       {
-        if (!dsReg.isInvolvedInDsitem(mp.getTo()))
+        // TODO: fix this hinky sh!t
+        DatastoreItem dssync = dsReg.getDatastoreItemFor(mp.getTo());
+        if (dssync == null)
         {
           // sync the dataset sequence, if it hasn't been done already.
-          Datasetsequence dssync = new Datasetsequence(
-                datastore, mp.getTo(),
-                (mp.getMappedWidth() == mp.getWidth()) ? sequence
-                        .getDictionary()
-                        : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA
-                                : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA),
-                ds);
-          // add a mapping between new dataset sequence and sequence associated with the database reference
+          // TODO: ensure real dataset sequence corresponding to getTo is
+          // recovered
+          dssync = new Datasetsequence(
+                  datastore,
+                  mp.getTo(),
+                  (mp.getMappedWidth() == mp.getWidth()) ? sequence
+                          .getDictionary()
+                          : ((mp.getMappedWidth() == 3) ? uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_NA
+                                  : uk.ac.vamsas.objects.utils.SymbolDictionary.STANDARD_AA),
+                  ds);
         }
+        // 
+        // TODO: NOW add a mapping between new dataset sequence and sequence
+        // associated with the database reference
         
-      } else {
-        log.debug("Ignoring non-dataset sequence mapping.");
+        // dna mappings only...
+        // new jalview.io.vamsas.Sequencemapping(datastore, mp, sequence, ds);
+
       }
+
+    }
+    else
+    {
+      log.debug("Ignoring non-dataset sequence mapping.");
     }
   }
+
   public void updateFromDoc()
   {
     DbRef vobj = (DbRef) this.vobj;
@@ -143,13 +163,13 @@ public class Dbref extends Rangetype
       }
       jalview.datamodel.Mapping mp = new jalview.datamodel.Mapping(
               parsemapType(vobj.getMap(0)));
-      if (jvobj.getMap()==null || !mp.equals(jvobj.getMap()))
+      if (jvobj.getMap() == null || !mp.equals(jvobj.getMap()))
       {
         jvobj.setMap(mp);
       }
     }
   }
-  
+
   public void conflict()
   {
     DbRef vobj = (DbRef) this.vobj;
@@ -196,6 +216,7 @@ public class Dbref extends Rangetype
     dbref.setAccessionId(jvobj.getAccessionId());
     dbref.setSource(jvobj.getSource());
     dbref.setVersion(jvobj.getVersion());
+    sequence.addDbRef(dbref);
     if (jvobj.getMap() != null)
     {
       jalview.datamodel.Mapping mp = jvobj.getMap();
@@ -204,6 +225,7 @@ public class Dbref extends Rangetype
         Map vMap = new Map();
         initMapType(vMap, mp.getMap(), true);
         dbref.addMap(vMap);
+        updateMapTo(mp);
       }
       else
       {
@@ -211,7 +233,6 @@ public class Dbref extends Rangetype
                 + jvobj.getSrcAccString());
       }
     }
-    sequence.addDbRef(dbref);
   }
 
 }
-- 
1.7.10.2