JAL-1705 DbSourceProxy properties converted to methods, tidy/format code

[jalview.git] / src / jalview / ws / dbsources / Uniprot.java

diff --git a/src/jalview/ws/dbsources/Uniprot.java b/src/jalview/ws/dbsources/Uniprot.java
index 1e8eadb..0a252b1 100644 (file)
--- a/src/jalview/ws/dbsources/Uniprot.java
+++ b/src/jalview/ws/dbsources/Uniprot.java
@@ -29,14 +29,15 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.UniprotEntry;
 import jalview.datamodel.UniprotFile;
 import jalview.ws.ebi.EBIFetchClient;
-import jalview.ws.seqfetcher.DbSourceProxy;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 import java.io.File;
 import java.io.FileReader;
 import java.io.Reader;
+import java.net.URL;
 import java.util.Vector;
 
+import org.exolab.castor.mapping.Mapping;
 import org.exolab.castor.xml.Unmarshaller;
 
 import com.stevesoft.pat.Regex;
@@ -45,14 +46,14 @@ import com.stevesoft.pat.Regex;
  * @author JimP
  * 
  */
-public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
+public class Uniprot extends DbSourceProxyImpl
 {
 
   private static final String BAR_DELIMITER = "|";
 
   private static final String NEWLINE = "\n";
 
-  private static org.exolab.castor.mapping.Mapping map;
+  private static Mapping map;
 
   /**
    * Constructor
@@ -60,9 +61,6 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   public Uniprot()
   {
     super();
-    addDbSourceProperty(DBRefSource.SEQDB, DBRefSource.SEQDB);
-    addDbSourceProperty(DBRefSource.PROTSEQDB);
-    // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
   }
 
   /*
@@ -70,6 +68,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
     return null; // ";";
@@ -80,6 +79,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
     return new Regex("([A-Z]+[0-9]+[A-Z0-9]+|[A-Z0-9]+_[A-Z0-9]+)");
@@ -90,6 +90,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbSource()
    */
+  @Override
   public String getDbSource()
   {
     return DBRefSource.UNIPROT;
@@ -100,6 +101,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getDbVersion()
    */
+  @Override
   public String getDbVersion()
   {
     return "0"; // we really don't know what version we're on.
@@ -121,9 +123,8 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
       if (map == null)
       {
         // 1. Load the mapping information from the file
-        map = new org.exolab.castor.mapping.Mapping(uni.getClass()
-                .getClassLoader());
-        java.net.URL url = getClass().getResource("/uniprot_mapping.xml");
+        map = new Mapping(uni.getClass().getClassLoader());
+        URL url = getClass().getResource("/uniprot_mapping.xml");
         map.loadMapping(url);
       }
 
@@ -148,6 +149,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     startQuery();
@@ -302,6 +304,7 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     // TODO: make the following a standard validator
@@ -312,11 +315,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   /**
    * return LDHA_CHICK uniprot entry
    */
+  @Override
   public String getTestQuery()
   {
     return "P00340";
   }
 
+  @Override
   public String getDbName()
   {
     return "Uniprot"; // getDbSource();
@@ -327,4 +332,13 @@ public class Uniprot extends DbSourceProxyImpl implements DbSourceProxy
   {
     return 0;
   }
+
+  @Override
+  public int getMaximumQueryCount()
+  {
+    // relocated this commented out code...
+    // addDbSourceProperty(DBRefSource.MULTIACC, new Integer(50));
+    // return 50;
+    return super.getMaximumQueryCount();
+  }
 }