X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=98868ce64edbae6634dd50e80337b580a6ed6613;hb=d716c9b072f989bef39c6eba038f779ce98396a8;hp=738c4dc831caf71090ddf09bd57ff458f468be44;hpb=ea36a0b44f1661422284e55ad5e137a0c81821f1;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 738c4dc..98868ce 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -22,11 +22,26 @@ package jalview.datamodel;
 
 import jalview.api.DBRefEntryI;
 
+import java.util.Arrays;
+import java.util.List;
+
 public class DBRefEntry implements DBRefEntryI
 {
-  String source = "", version = "", accessionId = "";
+  /*
+   * the mapping to chromosome (genome) is held as an instance with
+   * source = speciesId
+   * version = assemblyId
+   * accessionId = "chromosome:" + chromosomeId
+   * map = mapping from sequence to reference assembly
+   */
+  public static final String CHROMOSOME = "chromosome";
+
+  String source = "";
+
+  String version = "";
+
+  String accessionId = "";
 
-  private int startRes, endRes;
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
@@ -37,7 +52,6 @@ public class DBRefEntry implements DBRefEntryI
 
   }
 
-
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -67,10 +81,10 @@ public class DBRefEntry implements DBRefEntryI
   public DBRefEntry(DBRefEntryI entry)
   {
     this((entry.getSource() == null ? "" : new String(entry.getSource())),
-            (entry.getVersion() == null ? "" : new String(
-                    entry.getVersion())),
-            (entry.getAccessionId() == null ? "" : new String(
-                    entry.getAccessionId())),
+            (entry.getVersion() == null ? ""
+                    : new String(entry.getVersion())),
+            (entry.getAccessionId() == null ? ""
+                    : new String(entry.getAccessionId())),
             (entry.getMap() == null ? null : new Mapping(entry.getMap())));
   }
 
@@ -88,9 +102,8 @@ public class DBRefEntry implements DBRefEntryI
     {
       return true;
     }
-    if (equalRef(entry)
-            && ((map == null && entry.map == null) || (map != null
-                    && entry.map != null && map.equals(entry.map))))
+    if (equalRef(entry) && ((map == null && entry.map == null)
+            || (map != null && entry.map != null && map.equals(entry.map))))
     {
       return true;
     }
@@ -103,7 +116,8 @@ public class DBRefEntry implements DBRefEntryI
    * <ul>
    * <li>source and accession are identical (ignoring case)</li>
    * <li>version is identical (ignoring case), or this version is of the format
-   * "someSource:0", in which case the version for the other entry replaces it</li>
+   * "someSource:0", in which case the version for the other entry replaces
+   * it</li>
    * <li>mappings are not compared but if this entry has no mapping, replace
    * with that for the other entry</li>
    * </ul>
@@ -112,7 +126,7 @@ public class DBRefEntry implements DBRefEntryI
    * @return
    */
   @Override
-  public boolean updateFrom(DBRefEntry other)
+  public boolean updateFrom(DBRefEntryI other)
   {
     if (other == null)
     {
@@ -140,7 +154,8 @@ public class DBRefEntry implements DBRefEntryI
     String otherAccession = other.getAccessionId();
     if ((accessionId == null && otherAccession != null)
             || (accessionId != null && otherAccession == null)
-            || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+            || (accessionId != null
+                    && !accessionId.equalsIgnoreCase(otherAccession)))
     {
       return false;
     }
@@ -150,6 +165,7 @@ public class DBRefEntry implements DBRefEntryI
      * otherwise the versions have to match
      */
     String otherVersion = other.getVersion();
+
     if ((version == null || version.equals("0") || version.endsWith(":0"))
             && otherVersion != null)
     {
@@ -157,7 +173,8 @@ public class DBRefEntry implements DBRefEntryI
     }
     else
     {
-      if (!version.equalsIgnoreCase(otherVersion))
+      if (version != null && (otherVersion == null
+              || !version.equalsIgnoreCase(otherVersion)))
       {
         return false;
       }
@@ -192,12 +209,12 @@ public class DBRefEntry implements DBRefEntryI
       return true;
     }
     if (entry != null
-            && (source != null && entry.getSource() != null && source
-                    .equalsIgnoreCase(entry.getSource()))
-            && (accessionId != null && entry.getAccessionId() != null && accessionId
-                    .equalsIgnoreCase(entry.getAccessionId()))
-            && (version != null && entry.getVersion() != null && version
-                    .equalsIgnoreCase(entry.getVersion())))
+            && (source != null && entry.getSource() != null
+                    && source.equalsIgnoreCase(entry.getSource()))
+            && (accessionId != null && entry.getAccessionId() != null
+                    && accessionId.equalsIgnoreCase(entry.getAccessionId()))
+            && (version != null && entry.getVersion() != null
+                    && version.equalsIgnoreCase(entry.getVersion())))
     {
       return true;
     }
@@ -222,28 +239,24 @@ public class DBRefEntry implements DBRefEntryI
     return accessionId;
   }
 
-
   @Override
   public void setAccessionId(String accessionId)
   {
     this.accessionId = accessionId;
   }
 
-
   @Override
   public void setSource(String source)
   {
     this.source = source;
   }
 
-
   @Override
   public void setVersion(String version)
   {
     this.version = version;
   }
 
-
   @Override
   public Mapping getMap()
   {
@@ -281,26 +294,64 @@ public class DBRefEntry implements DBRefEntryI
   }
 
   @Override
-  public int getStartRes()
+  public boolean isPrimaryCandidate()
   {
-    return startRes;
-  }
-
-  @Override
-  public void setStartRes(int startRes)
-  {
-    this.startRes = startRes;
-  }
-
-  @Override
-  public int getEndRes()
-  {
-    return endRes;
+    /*
+     * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.  
+     */
+    if (map != null)
+    {
+      if (map.getTo() != null)
+      {
+        return false;
+      }
+      if (map.getMap().getFromRatio() != map.getMap().getToRatio()
+              || map.getMap().getFromRatio() != 1)
+      {
+        return false;
+      }
+      // check map is between identical single contiguous ranges
+      List<int[]> fromRanges = map.getMap().getFromRanges();
+      List<int[]> toRanges = map.getMap().getToRanges();
+      if (fromRanges.size() != 1 || toRanges.size() != 1)
+      {
+        return false;
+      }
+      if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+              || fromRanges.get(0)[1] != toRanges.get(0)[1])
+      {
+        return false;
+      }
+    }
+    if (version == null)
+    {
+      // no version string implies the reference has not been verified at all.
+      return false;
+    }
+    // tricky - this test really needs to search the sequence's set of dbrefs to
+    // see if there is a primary reference that derived this reference.
+    String ucv = version.toUpperCase();
+    for (String primsrc : Arrays.asList(DBRefSource.allSources()))
+    {
+      if (ucv.startsWith(primsrc.toUpperCase()))
+      {
+        // by convention, many secondary references inherit the primary
+        // reference's
+        // source string as a prefix for any version information from the
+        // secondary reference.
+        return false;
+      }
+    }
+    return true;
   }
 
-  @Override
-  public void setEndRes(int endRes)
+  /**
+   * Mappings to chromosome are held with accessionId as "chromosome:id"
+   * 
+   * @return
+   */
+  public boolean isChromosome()
   {
-    this.endRes = endRes;
+    return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
   }
 }