X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=b1d3f3c01d4b8793588efadda07a65cffa8f1bf3;hb=13e2ec04aa9db3447f2888c604d1479d0b901d56;hp=077ce14396ed2f095d1afc0b071e2f1add557b8d;hpb=994985c6ff0ea1ebadb8e184e8090dbb780e3c10;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 077ce14..b1d3f3c 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -22,6 +22,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -63,12 +64,86 @@ public class SequenceFetcher extends ASequenceFetcher
   }
 
   /**
-   * return an ordered list of database sources suitable for using in a GUI
-   * element
+   * return an ordered list of database sources where non-das database classes
+   * appear before das database classes
    */
   public String[] getOrderedSupportedSources()
   {
     String[] srcs = this.getSupportedDb();
+    ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
+    for (int i = 0; i < srcs.length; i++)
+    {
+      boolean das = false,skip=false;
+      String nm;
+      for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
+      {
+        // Skip the alignment databases for the moment - they're not useful for verifying a single sequence against its reference source
+        if (dbs.isA(DBRefSource.ALIGNMENTDB))
+        {
+          skip=true;
+        } else {
+          nm = dbs.getDbName();
+          if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
+          {
+            if (nm.startsWith("das:"))
+            {
+              nm = nm.substring(4);
+              das = true;
+            }
+            break;
+          }
+        }
+      }
+      if (skip)
+      {
+        continue;
+      }
+      if (das)
+      {
+        dassrc.add(srcs[i]);
+      }
+      else
+      {
+        nondas.add(srcs[i]);
+      }
+    }
+    String[] tosort = nondas.toArray(new String[0]), sorted = nondas
+            .toArray(new String[0]);
+    for (int j = 0, jSize = sorted.length; j < jSize; j++)
+    {
+      tosort[j] = tosort[j].toLowerCase();
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    // construct array with all sources listed
+
+    srcs = new String[sorted.length + dassrc.size()];
+    int i = 0;
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = sorted[j];
+      sorted[j] = null;
+    }
+
+    sorted = dassrc.toArray(new String[0]);
+    tosort = dassrc.toArray(new String[0]);
+    for (int j = 0, jSize = sorted.length; j < jSize; j++)
+    {
+      tosort[j] = tosort[j].toLowerCase();
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = sorted[j];
+    }
+    return srcs;
+  }
+
+  /**
+   * return plaintext databse list suitable for using in a GUI element
+   */
+  public String[] _getOrderedSupportedSources()
+  {
+    String[] srcs = this.getSupportedDb();
     ArrayList dassrc = new ArrayList(), nondas = new ArrayList();
     for (int i = 0; i < srcs.length; i++)
     {
@@ -347,4 +422,5 @@ public class SequenceFetcher extends ASequenceFetcher
       }
     }
   }
+
 }