X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=4f9e0abf855c96100002f9abdbf21ac40f49540c;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=da2dab6c00682d60dcf0f23cb3d2fad443733392;hpb=b7885c2f1d36f515354ede5793f5b3cddbc9db04;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index da2dab6..4f9e0ab 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,19 +1,44 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.ws;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Vector;
 
+import org.biojava.dasobert.das2.Das2Source;
+import org.biojava.dasobert.dasregistry.Das1Source;
+import org.biojava.dasobert.dasregistry.DasCoordinateSystem;
+import org.biojava.dasobert.dasregistry.DasSource;
+
 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;
 
 /**
  * This is the the concrete implementation of the sequence retrieval interface
  * and abstract class in jalview.ws.seqfetcher. This implements the run-time
- * discovery of sequence database clients, and provides a hardwired main for testing all registered handlers. 
+ * discovery of sequence database clients, and provides a hardwired main for
+ * testing all registered handlers.
  * 
  */
 public class SequenceFetcher extends ASequenceFetcher
@@ -31,10 +56,74 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);
-  };
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
+    // alignment is
+    // 'default' for
+    // PFAM
+    registerDasSequenceSources();
+  }
+
+  /**
+   * return an ordered list of database sources 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++)
+    {
+      String nm = getSourceProxy(srcs[i]).getDbName();
+      if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.DasSequenceSource)
+      {
+        if (nm.startsWith("das:"))
+        {
+          nm = nm.substring(4);
+        }
+        dassrc.add(new String[]
+        { srcs[i], nm.toUpperCase() });
+      }
+      else
+      {
+        nondas.add(new String[]
+        { srcs[i], nm.toUpperCase() });
+      }
+    }
+    Object[] sorted = nondas.toArray();
+    String[] tosort = new String[sorted.length];
+    nondas.clear();
+    for (int j = 0; j < sorted.length; j++)
+    {
+      tosort[j] = ((String[]) sorted[j])[1];
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    int i = 0;
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = ((String[]) sorted[j])[0];
+      sorted[j] = null;
+    }
+
+    sorted = dassrc.toArray();
+    tosort = new String[sorted.length];
+    dassrc.clear();
+    for (int j = 0; j < sorted.length; j++)
+    {
+      tosort[j] = ((String[]) sorted[j])[1];
+    }
+    jalview.util.QuickSort.sort(tosort, sorted);
+    for (int j = sorted.length - 1; j >= 0; j--, i++)
+    {
+      srcs[i] = ((String[]) sorted[j])[0];
+      sorted[j] = null;
+    }
+    return srcs;
+  }
+
   /**
    * simple run method to test dbsources.
+   * 
    * @param argv
    */
   public static void main(String[] argv)
@@ -42,12 +131,12 @@ public class SequenceFetcher extends ASequenceFetcher
     AlignmentI ds = null;
     Vector noProds = new Vector();
     String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"
-      +"With no arguments, all DbSources will be queried with their test Accession number.\n"
-      +"If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
+            + "With no arguments, all DbSources will be queried with their test Accession number.\n"
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
     if (argv != null && argv.length > 0)
     {
       DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);
-      if (sp!=null)
+      if (sp != null)
       {
         AlignmentI al = null;
         try
@@ -56,40 +145,46 @@ public class SequenceFetcher extends ASequenceFetcher
         } catch (Exception e)
         {
           e.printStackTrace();
-          System.err.println("Error when retrieving "+argv[1]+" from "+argv[0]+"\nUsage: "+usage);
+          System.err.println("Error when retrieving " + argv[1] + " from "
+                  + argv[0] + "\nUsage: " + usage);
         }
         SequenceI[] prod = al.getSequencesArray();
-        if (al!=null)
+        if (al != null)
         {
           for (int p = 0; p < prod.length; p++)
           {
             System.out.println("Prod " + p + ": "
-                    + prod[p].getDisplayId(true) + " : "+prod[p].getDescription());
+                    + prod[p].getDisplayId(true) + " : "
+                    + prod[p].getDescription());
           }
         }
         return;
-      } else {
-        System.err.println("Can't resolve "+argv[0]+" as a database name. Allowed values are :\n"+new SequenceFetcher().getSupportedDb());
       }
-      System.out
-              .println(usage);
+      else
+      {
+        System.err.println("Can't resolve " + argv[0]
+                + " as a database name. Allowed values are :\n"
+                + new SequenceFetcher().getSupportedDb());
+      }
+      System.out.println(usage);
     }
     ASequenceFetcher sfetcher = new SequenceFetcher();
     String[] dbSources = sfetcher.getSupportedDb();
-    for (int dbsource=0; dbsource<dbSources.length;dbsource++)
+    for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
       String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
         continue;
       DbSourceProxy sp = sfetcher.getSourceProxy(db);
-      System.out
-              .println("" + db + ": retrieving test:" + sp.getTestQuery());
+      System.out.println("Source: " + sp.getDbName() + " (" + db
+              + "): retrieving test:" + sp.getTestQuery());
       AlignmentI al = null;
       try
       {
         al = sp.getSequenceRecords(sp.getTestQuery());
-        if (al != null && al.getHeight() > 0)
+        if (al != null && al.getHeight() > 0
+                && sp.getDbSourceProperties() != null)
         {
           boolean dna = sp.getDbSourceProperties().containsKey(
                   DBRefSource.DNACODINGSEQDB)
@@ -189,7 +284,8 @@ public class SequenceFetcher extends ASequenceFetcher
         Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(
                 seqs, dna, null, ds);
         System.out.println("Found "
-                + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");
+                + ((prodal == null) ? "no" : "" + prodal.getHeight())
+                + " products");
         if (prodal != null)
         {
           SequenceI[] prod = prodal.getSequencesArray(); // note
@@ -203,7 +299,7 @@ public class SequenceFetcher extends ASequenceFetcher
           // mapping
           // (if
           // present)
-            for (int p = 0; p < prod.length; p++)
+          for (int p = 0; p < prod.length; p++)
           {
             System.out.println("Prod " + p + ": "
                     + prod[p].getDisplayId(true));
@@ -213,4 +309,99 @@ public class SequenceFetcher extends ASequenceFetcher
 
     }
   }
+
+  /**
+   * query the currently defined DAS source registry for sequence sources and
+   * add a DasSequenceSource instance for each source to the SequenceFetcher
+   * source list.
+   */
+  public void registerDasSequenceSources()
+  {
+    DasSource[] sources = jalview.ws.DasSequenceFeatureFetcher
+            .getDASSources();
+    if (sources != null)
+    {
+      for (int s = 0; sources != null && s < sources.length; s++)
+      {
+        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) source);
+          } catch (Exception e)
+          {
+            System.err.println("Ignoring DAS2 sequence source "
+                    + source.getNickname()
+                    + " - couldn't map to Das1Source.\n");
+            e.printStackTrace();
+          }
+        }
+      }
+      else
+      {
+        if (source instanceof Das1Source)
+        {
+          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(ds = new DasSequenceSource("das:"
+                  + d1s.getNickname() + " (" + css[c].getName() + ")",
+                  css[c].getName(), d1s, css[c]));
+        } catch (Exception e)
+        {
+          System.err.println("Ignoring sequence coord system " + c + " ("
+                  + css[c].getName() + ") for source " + d1s.getNickname()
+                  + "- threw exception when constructing fetcher.\n");
+          e.printStackTrace();
+        }
+      }
+    }
+    return ds;
+  }
 }