refactored ebi soap client and AbstractSequenceFetcher machinery to their own packages.

diff --git a/src/MCview/PDBViewer.java b/src/MCview/PDBViewer.java
index 35e02b8..e586707 100755 (executable)
--- a/src/MCview/PDBViewer.java
+++ b/src/MCview/PDBViewer.java
@@ -27,7 +27,7 @@ import jalview.datamodel.*;
 import jalview.gui.*;
 import jalview.io.*;
 import jalview.schemes.*;
-import jalview.ws.EBIFetchClient;
+import jalview.ws.ebi.EBIFetchClient;
 
 import java.awt.BorderLayout;
 

diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index 5f1a70b..7269e1d 100644 (file)
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -33,7 +33,7 @@ import jalview.structure.*;
 import jalview.datamodel.PDBEntry;
 import jalview.io.*;
 import jalview.schemes.*;
-import jalview.ws.EBIFetchClient;
+import jalview.ws.ebi.EBIFetchClient;
 
 import org.jmol.api.*;
 import org.jmol.adapter.smarter.SmarterJmolAdapter;

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 3b511a0..70dff68 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -31,7 +31,8 @@ import jalview.datamodel.xdb.embl.*;
 import java.io.File;
 import jalview.io.*;
 import jalview.ws.DBRefFetcher;
-import jalview.ws.EBIFetchClient;
+import jalview.ws.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.ASequenceFetcher;
 
 import java.awt.Rectangle;
 import java.awt.BorderLayout;
@@ -40,7 +41,7 @@ import java.awt.Dimension;
 public class SequenceFetcher
 extends JPanel implements Runnable
 {
-  jalview.ws.SequenceFetcher sfetch; 
+  ASequenceFetcher sfetch; 
   JInternalFrame frame;
   AlignFrame alignFrame;
   StringBuffer result;

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index fb7eac9..109f4b4 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -26,6 +26,7 @@ import org.exolab.castor.xml.*;
 import jalview.analysis.*;\r
 import jalview.datamodel.*;\r
 import jalview.gui.*;\r
+import jalview.ws.ebi.EBIFetchClient;\r
 \r
 /**\r
  * DOCUMENT ME!\r

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 5243111..a1c391b 100644 (file)
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,7 +1,6 @@
 package jalview.ws;\r
 \r
 import java.util.Enumeration;\r
-import java.util.Hashtable;\r
 import java.util.Vector;\r
 \r
 import jalview.datamodel.Alignment;\r
@@ -12,7 +11,8 @@ import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 \r
 /**\r
- * prototype of abstract sequence retrieval interface\r
+ * This is the the concrete implementation of the sequence retrieval interface\r
+ * and abstract class in jalview.ws.seqfetcher. This implements the discovery \r
  * \r
  */\r
 public class SequenceFetcher extends ASequenceFetcher\r
@@ -25,19 +25,14 @@ public class SequenceFetcher extends ASequenceFetcher
    */\r
   public SequenceFetcher()\r
   {\r
-    FETCHABLEDBS = new Hashtable();\r
-    FETCHABLEDBS.put(DBRefSource.EMBL,\r
-            new jalview.ws.dbsources.EmblSource());\r
-    FETCHABLEDBS.put(DBRefSource.EMBLCDS,\r
-            new jalview.ws.dbsources.EmblCdsSouce());\r
-    FETCHABLEDBS.put(DBRefSource.UNIPROT,\r
-            new jalview.ws.dbsources.Uniprot());\r
-    FETCHABLEDBS.put(DBRefSource.UP_NAME,\r
-            new jalview.ws.dbsources.Uniprot());\r
-    FETCHABLEDBS.put(DBRefSource.PDB, new jalview.ws.dbsources.Pdb());\r
-    FETCHABLEDBS.put(DBRefSource.PFAM, new jalview.ws.dbsources.Pfam());\r
+    addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);\r
+    addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);\r
+    addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);\r
+    addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);\r
+    addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);\r
+    addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);\r
   };\r
-  \r
+\r
   public static void main(String[] argv)\r
   {\r
     AlignmentI ds = null;\r
@@ -47,11 +42,11 @@ public class SequenceFetcher extends ASequenceFetcher
       System.out\r
               .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");\r
     }\r
-    SequenceFetcher sfetcher = new SequenceFetcher();\r
-    Enumeration e = sfetcher.FETCHABLEDBS.keys();\r
-    while (e.hasMoreElements())\r
+    ASequenceFetcher sfetcher = new SequenceFetcher();\r
+    String[] dbSources = sfetcher.getSupportedDb();\r
+    for (int dbsource=0; dbsource<dbSources.length;dbsource++)\r
     {\r
-      String db = (String) e.nextElement();\r
+      String db = dbSources[dbsource];\r
       // skip me\r
       if (db.equals(DBRefSource.PDB))\r
         continue;\r
@@ -75,25 +70,31 @@ public class SequenceFetcher extends ASequenceFetcher
                   dna, al.getSequencesArray());\r
           if (types != null)\r
           {\r
-            System.out.println("Xref Types for: "+(dna ? "dna" : "prot"));\r
+            System.out.println("Xref Types for: " + (dna ? "dna" : "prot"));\r
             for (int t = 0; t < types.length; t++)\r
             {\r
               System.out.println("Type: " + types[t]);\r
-              SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
-                      .getSequencesArray(), dna, types[t]).getSequencesArray();\r
+              SequenceI[] prod = jalview.analysis.CrossRef\r
+                      .findXrefSequences(al.getSequencesArray(), dna,\r
+                              types[t]).getSequencesArray();\r
               System.out.println("Found "\r
                       + ((prod == null) ? "no" : "" + prod.length)\r
                       + " products");\r
-              if (prod!=null)\r
+              if (prod != null)\r
               {\r
-                for (int p=0; p<prod.length; p++)\r
+                for (int p = 0; p < prod.length; p++)\r
                 {\r
-                  System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
+                  System.out.println("Prod " + p + ": "\r
+                          + prod[p].getDisplayId(true));\r
                 }\r
               }\r
             }\r
-          } else {\r
-            noProds.addElement((dna ? new Object[] { al, al } : new Object[] { al }) ); \r
+          }\r
+          else\r
+          {\r
+            noProds.addElement((dna ? new Object[]\r
+            { al, al } : new Object[]\r
+            { al }));\r
           }\r
 \r
         }\r
@@ -138,28 +139,42 @@ public class SequenceFetcher extends ASequenceFetcher
       System.err.flush();\r
 \r
     }\r
-    if (noProds.size()>0)\r
+    if (noProds.size() > 0)\r
     {\r
       Enumeration ts = noProds.elements();\r
       while (ts.hasMoreElements())\r
-        \r
+\r
       {\r
         Object[] typeSq = (Object[]) ts.nextElement();\r
-        boolean dna = (typeSq.length>1);\r
+        boolean dna = (typeSq.length > 1);\r
         AlignmentI al = (AlignmentI) typeSq[0];\r
-        System.out.println("Trying getProducts for "+al.getSequenceAt(0).getDisplayId(true));\r
-        System.out.println("Search DS Xref for: "+(dna ? "dna" : "prot"));\r
-        // have a bash at finding the products amongst all the retrieved sequences.\r
-        SequenceI[] prod = jalview.analysis.CrossRef.findXrefSequences(al\r
-              .getSequencesArray(), dna, null, ds).getSequencesArray(); // note should test rather than throw away codon mapping (if present)\r
+        System.out.println("Trying getProducts for "\r
+                + al.getSequenceAt(0).getDisplayId(true));\r
+        System.out.println("Search DS Xref for: " + (dna ? "dna" : "prot"));\r
+        // have a bash at finding the products amongst all the retrieved\r
+        // sequences.\r
+        SequenceI[] seqs = al.getSequencesArray();\r
+        Alignment prodal = jalview.analysis.CrossRef.findXrefSequences(\r
+                seqs, dna, null, ds);\r
         System.out.println("Found "\r
-                + ((prod == null) ? "no" : "" + prod.length)\r
-                + " products");\r
-        if (prod!=null)\r
+                + ((prodal == null) ? "no" : "" + prodal.getHeight()) + " products");\r
+        if (prodal != null)\r
         {\r
-          for (int p=0; p<prod.length; p++)\r
+          SequenceI[] prod = prodal.getSequencesArray(); // note\r
+          // should\r
+          // test\r
+          // rather\r
+          // than\r
+          // throw\r
+          // away\r
+          // codon\r
+          // mapping\r
+          // (if\r
+          // present)\r
+            for (int p = 0; p < prod.length; p++)\r
           {\r
-            System.out.println("Prod "+p+": "+prod[p].getDisplayId(true));\r
+            System.out.println("Prod " + p + ": "\r
+                    + prod[p].getDisplayId(true));\r
           }\r
         }\r
       }\r

diff --git a/src/jalview/ws/dbsources/EmblSource.java b/src/jalview/ws/dbsources/EmblSource.java
index 6b7756e..5ae7a72 100644 (file)
--- a/src/jalview/ws/dbsources/EmblSource.java
+++ b/src/jalview/ws/dbsources/EmblSource.java
@@ -15,7 +15,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.datamodel.xdb.embl.EmblEntry;\r
-import jalview.ws.EBIFetchClient;\r
+import jalview.ws.ebi.EBIFetchClient;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r

diff --git a/src/jalview/ws/dbsources/EmblXmlSource.java b/src/jalview/ws/dbsources/EmblXmlSource.java
index 3179110..68fa87c 100644 (file)
--- a/src/jalview/ws/dbsources/EmblXmlSource.java
+++ b/src/jalview/ws/dbsources/EmblXmlSource.java
@@ -4,7 +4,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;\r
 import jalview.datamodel.SequenceI;\r
 import jalview.datamodel.xdb.embl.EmblEntry;\r
-import jalview.ws.EBIFetchClient;\r
+import jalview.ws.ebi.EBIFetchClient;\r
 \r
 import java.io.File;\r
 import java.util.Iterator;\r

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 8da1525..0548583 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -21,7 +21,7 @@ import com.stevesoft.pat.Regex;
 \r
 import jalview.datamodel.AlignmentI;\r
 import jalview.io.FileParse;\r
-import jalview.ws.EBIFetchClient;\r
+import jalview.ws.ebi.EBIFetchClient;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4d9c93d..4077c51 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -44,7 +44,7 @@ public class Pfam extends DbSourceProxyImpl implements DbSourceProxy
   public String getDbSource()\r
   {\r
     // TODO Auto-generated method stub\r
-    return null;\r
+    return jalview.datamodel.DBRefSource.PFAM;\r
   }\r
 \r
   /* (non-Javadoc)\r

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 8dc000e..23bfbca 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -22,7 +22,7 @@ import jalview.datamodel.UniprotEntry;
 import jalview.io.FormatAdapter;\r
 import jalview.io.IdentifyFile;\r
 import jalview.ws.DBRefFetcher;\r
-import jalview.ws.EBIFetchClient;\r
+import jalview.ws.ebi.EBIFetchClient;\r
 import jalview.ws.seqfetcher.DbSourceProxy;\r
 import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
 \r

diff --git a/src/jalview/ws/dbsources/UnprotName.java b/src/jalview/ws/dbsources/UnprotName.java
new file mode 100644 (file)
index 0000000..4fbbe97
--- /dev/null
+++ b/src/jalview/ws/dbsources/UnprotName.java
@@ -0,0 +1,19 @@
+package jalview.ws.dbsources;\r
+\r
+/**\r
+ * Canonical Uniprot fetcher instance specifically retrieving UP_NAME references.\r
+ * @author JimP\r
+ *\r
+ */\r
+public class UnprotName extends Uniprot implements jalview.ws.seqfetcher.DbSourceProxy\r
+{\r
+\r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.dbsources.Uniprot#getDbSource()\r
+   */\r
+  public String getDbSource()\r
+  {\r
+    return jalview.datamodel.DBRefSource.UP_NAME;\r
+  }\r
+  \r
+}\r

diff --git a/src/jalview/ws/EBIFetchClient.java b/src/jalview/ws/ebi/EBIFetchClient.java
similarity index 99%
rename from src/jalview/ws/EBIFetchClient.java
rename to src/jalview/ws/ebi/EBIFetchClient.java
index f691d5c..e9aff35 100644 (file)
--- a/src/jalview/ws/EBIFetchClient.java
+++ b/src/jalview/ws/ebi/EBIFetchClient.java
@@ -16,7 +16,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-package jalview.ws;
+package jalview.ws.ebi;
 
 import java.io.*;
 import java.util.*;