From 5d55702b40b8a0b198a0a22b4fbb8458fa2bc7f4 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 4 Dec 2008 10:27:03 +0000
Subject: [PATCH] sequence fetchers generated for local das sequence sources

---
 src/jalview/ws/SequenceFetcher.java |   57 ++++++++++++++++++++++++++---------
 1 file changed, 43 insertions(+), 14 deletions(-)

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index b20ebbb..2be142a 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -31,6 +31,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
+import jalview.ws.dbsources.DasSequenceSource;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -319,23 +320,45 @@ public class SequenceFetcher extends ASequenceFetcher
   {
     DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher
             .getDASSources();
-    for (int s = 0; s < sources.length; s++)
+    if (sources!=null)
     {
-      Das1Source d1s = null;
-      if (sources[s].hasCapability("sequence"))
+      for (int s=0; sources!=null && s<sources.length; s++)
       {
-        if (sources[s] instanceof Das2Source)
-        {
-          if (((Das2Source) sources[s]).hasDas1Capabilities())
+        addDasSequenceSource(sources[s]);
+      }
+    }
+    
+    Vector localsources = jalview.bin.Cache.getLocalDasSources();
+    if (localsources!=null)
+    {   
+      for (Enumeration ls = localsources.elements(); ls.hasMoreElements(); )
+      {
+        addDasSequenceSource((DasSource) ls.nextElement());
+      }
+    } 
+  }
+  /**
+   * Try to create and add a DasSequenceSource to the list of sources.
+   * @param source
+   * @return null if no source was added, or the new DasSequenceSource created
+   */
+  DasSequenceSource addDasSequenceSource(DasSource source) {
+    DasSequenceSource ds=null;
+    Das1Source d1s = null;
+    if (source.hasCapability("sequence"))
+    {
+      if (source instanceof Das2Source)
+      {
+          if (((Das2Source) source).hasDas1Capabilities())
           {
             try
             {
               d1s = org.biojava.dasobert.das2.DasSourceConverter
-                      .toDas1Source((Das2Source) sources[s]);
+                      .toDas1Source((Das2Source) source);
             } catch (Exception e)
             {
               System.err.println("Ignoring DAS2 sequence source "
-                      + sources[s].getNickname()
+                      + source.getNickname()
                       + " - couldn't map to Das1Source.\n");
               e.printStackTrace();
             }
@@ -343,20 +366,28 @@ public class SequenceFetcher extends ASequenceFetcher
         }
         else
         {
-          if (sources[s] instanceof Das1Source)
+          if (source instanceof Das1Source)
           {
-            d1s = (Das1Source) sources[s];
+            d1s = (Das1Source) source;
           }
         }
       }
       if (d1s != null)
       {
         DasCoordinateSystem[] css = d1s.getCoordinateSystem();
+        if (css==null || css.length==0)
+        {
+          // TODO: query das source directly to identify coordinate system... or
+          // have to make up a coordinate system
+          css = new DasCoordinateSystem[] { new DasCoordinateSystem()};
+          css[0].setName(d1s.getNickname());
+          css[0].setUniqueId(d1s.getNickname());
+        }
         for (int c = 0; c < css.length; c++)
         {
           try
           {
-            addDbRefSourceImpl(new jalview.ws.dbsources.DasSequenceSource(
+            addDbRefSourceImpl(ds=new DasSequenceSource(
                     "das:" + d1s.getNickname() + " (" + css[c].getName()
                             + ")", css[c].getName(), d1s, css[c]));
           } catch (Exception e)
@@ -369,8 +400,6 @@ public class SequenceFetcher extends ASequenceFetcher
           }
         }
       }
-
-    }
+      return ds;
   }
-
 }
-- 
1.7.10.2