JAL-1238 tier index indicating distance of a source from the primary source for that...

diff --git a/src/jalview/ws/dbsources/EmblCdsSouce.java b/src/jalview/ws/dbsources/EmblCdsSouce.java
index 78f2477..0940f40 100644 (file)
--- a/src/jalview/ws/dbsources/EmblCdsSouce.java
+++ b/src/jalview/ws/dbsources/EmblCdsSouce.java
@@ -83,4 +83,10 @@ public class EmblCdsSouce extends EmblXmlSource implements DbSourceProxy
     return "EMBL (CDS)";
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
+
 }

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 4495be1..c7be59a 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -114,4 +114,10 @@ public class EmblSource extends EmblXmlSource implements DbSourceProxy
   {
     return "EMBL"; // getDbSource();
   }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
index 125a295..81c8ea3 100644 (file)
--- a/src/jalview/ws/dbsources/GeneDbSource.java
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -118,4 +118,9 @@ public class GeneDbSource extends EmblXmlSource implements DbSourceProxy
   {
     return "GeneDB"; // getDbSource();
   }
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index b432dff..b96a65c 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -209,4 +209,9 @@ public class Pdb extends EbiFileRetrievedProxy implements DbSourceProxy
     return "PDB"; // getDbSource();
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/PfamFull.java b/src/jalview/ws/dbsources/PfamFull.java
index 75d4559..077b929 100644 (file)
--- a/src/jalview/ws/dbsources/PfamFull.java
+++ b/src/jalview/ws/dbsources/PfamFull.java
@@ -65,4 +65,9 @@ public class PfamFull extends Pfam implements DbSourceProxy
     return null;
   }
 
+   @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/PfamSeed.java b/src/jalview/ws/dbsources/PfamSeed.java
index cab4999..cb00a1d 100644 (file)
--- a/src/jalview/ws/dbsources/PfamSeed.java
+++ b/src/jalview/ws/dbsources/PfamSeed.java
@@ -62,4 +62,9 @@ public class PfamSeed extends Pfam implements DbSourceProxy
     return "PF03760";
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/RfamFull.java b/src/jalview/ws/dbsources/RfamFull.java
index 3703e41..e20527a 100644 (file)
--- a/src/jalview/ws/dbsources/RfamFull.java
+++ b/src/jalview/ws/dbsources/RfamFull.java
@@ -70,4 +70,9 @@ public class RfamFull extends Rfam implements DbSourceProxy
     return null;
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/RfamSeed.java b/src/jalview/ws/dbsources/RfamSeed.java
index eb3c2c3..75fa62b 100644 (file)
--- a/src/jalview/ws/dbsources/RfamSeed.java
+++ b/src/jalview/ws/dbsources/RfamSeed.java
@@ -69,4 +69,9 @@ public class RfamSeed extends Rfam implements DbSourceProxy
     return null;
   }
 
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 48f8649..1b967c4 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -294,4 +294,10 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return "Uniprot"; // getDbSource();
   }
+
+  @Override
+  public int getTier()
+  {
+    return 0;
+  }
 }

diff --git a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
index 95ff7d0..7bb6436 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/DasSequenceSource.java
@@ -70,6 +70,11 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   protected MultipleConnectionPropertyProviderI connprops = null;
 
   /**
+   * DAS sources are tier 1 - if we have a direct DB connection then we should prefer it
+   */
+  private int tier=1;
+
+  /**
    * create a new DbSource proxy for a DAS 1 source
    * 
    * @param dbnbame
@@ -334,4 +339,10 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   {
     return coordsys;
   }
+
+  @Override
+  public int getTier()
+  {
+    return tier;
+  }
 }

diff --git a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
index eb9d807..f68a005 100644 (file)
--- a/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
+++ b/src/jalview/ws/dbsources/das/datamodel/JalviewSource.java
@@ -366,4 +366,11 @@ public class JalviewSource implements jalviewSourceI
     return isLaterThan(getVersion().getCreated(), other.getVersion()
             .getCreated());
   }
+
+  @Override
+  public boolean isReferenceSource()
+  {
+    // TODO check source object for indication that we are the primary for a DAS coordinate system
+    return false;
+  }
 }

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index cc9997f..e4b76b9 100644 (file)
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -134,4 +134,11 @@ public interface DbSourceProxy
    * @return true if the source has this property
    */
   public boolean isA(Object dbsourceproperty);
+
+  /**
+   * Tier for this data source
+   *  
+   * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
+   */
+  public int getTier();
 }