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

[jalview.git] / src / jalview / ws / seqfetcher / ASequenceFetcher.java

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 8656c25..1e3ae7a 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -20,11 +20,13 @@
  */
 package jalview.ws.seqfetcher;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
+import jalview.util.QuickSort;
 
 import java.util.ArrayList;
 import java.util.Enumeration;
@@ -62,11 +64,11 @@ public class ASequenceFetcher
       return null;
     }
     String[] sf = new String[FETCHABLEDBS.size()];
-    Enumeration e = FETCHABLEDBS.keys();
+    Enumeration<String> e = FETCHABLEDBS.keys();
     int i = 0;
     while (e.hasMoreElements())
     {
-      sf[i++] = (String) e.nextElement();
+      sf[i++] = e.nextElement();
     }
     ;
     return sf;
@@ -74,25 +76,25 @@ public class ASequenceFetcher
 
   public boolean isFetchable(String source)
   {
-    Enumeration e = FETCHABLEDBS.keys();
+    Enumeration<String> e = FETCHABLEDBS.keys();
     while (e.hasMoreElements())
     {
-      String db = (String) e.nextElement();
+      String db = e.nextElement();
       if (source.compareToIgnoreCase(db) == 0)
       {
         return true;
       }
     }
-    jalview.bin.Cache.log.warn("isFetchable doesn't know about '" + source
+    Cache.log.warn("isFetchable doesn't know about '" + source
             + "'");
     return false;
   }
 
-  public SequenceI[] getSequences(jalview.datamodel.DBRefEntry[] refs)
+  public SequenceI[] getSequences(DBRefEntry[] refs)
   {
     SequenceI[] ret = null;
-    Vector<SequenceI> rseqs = new Vector();
-    Hashtable<String, List<String>> queries = new Hashtable();
+    Vector<SequenceI> rseqs = new Vector<SequenceI>();
+    Hashtable<String, List<String>> queries = new Hashtable<String, List<String>>();
     for (int r = 0; r < refs.length; r++)
     {
       if (!queries.containsKey(refs[r].getSource()))
@@ -125,15 +127,12 @@ public class ASequenceFetcher
       while (fetchers.hasNext())
       {
         List<String> queriesMade = new ArrayList<String>();
-        HashSet queriesFound = new HashSet<String>();
+        HashSet<String> queriesFound = new HashSet<String>();
         try
         {
           DbSourceProxy fetcher = fetchers.next();
-          boolean doMultiple = fetcher.getAccessionSeparator() != null; // No
-          // separator
-          // - no
-          // Multiple
-          // Queries
+          boolean doMultiple = fetcher.getAccessionSeparator() != null;
+          // No separator - no Multiple Queries
           while (!queriesLeft.isEmpty())
           {
             StringBuffer qsb = new StringBuffer();
@@ -228,11 +227,11 @@ public class ASequenceFetcher
     if (rseqs.size() > 0)
     {
       ret = new SequenceI[rseqs.size()];
-      Enumeration sqs = rseqs.elements();
+      Enumeration<SequenceI> sqs = rseqs.elements();
       int si = 0;
       while (sqs.hasMoreElements())
       {
-        SequenceI s = (SequenceI) sqs.nextElement();
+        SequenceI s = sqs.nextElement();
         ret[si++] = s;
         s.updatePDBIds();
       }
@@ -288,7 +287,7 @@ public class ASequenceFetcher
       {
         nm[i++] = "" + s.getTier() + s.getDbName().toLowerCase();
       }
-      jalview.util.QuickSort.sort(nm, l);
+      QuickSort.sort(nm, l);
       dbs = new ArrayList<DbSourceProxy>();
       for (i = l.length - 1; i >= 0; i--)
       {
@@ -303,8 +302,7 @@ public class ASequenceFetcher
   }
 
   /**
-   * constructs and instance of the proxy and registers it as a valid
-   * dbrefsource
+   * constructs an instance of the proxy and registers it as a valid dbrefsource
    * 
    * @param dbSourceProxy
    *          reference for class implementing
@@ -312,7 +310,7 @@ public class ASequenceFetcher
    */
   protected void addDBRefSourceImpl(
           Class<? extends DbSourceProxy> dbSourceProxy)
-          throws java.lang.IllegalArgumentException
+          throws IllegalArgumentException
   {
     DbSourceProxy proxy = null;
     try
@@ -359,34 +357,6 @@ public class ASequenceFetcher
   }
 
   /**
-   * test if the database handler for dbName contains the given dbProperty when
-   * a dbName resolves to a set of proxies - this method will return the result
-   * of the test for the first instance. TODO implement additional method to
-   * query all sources for a db to find one with a particular property
-   * 
-   * @param dbName
-   * @param dbProperty
-   * @return true if proxy has the given property
-   */
-  public boolean hasDbSourceProperty(String dbName, String dbProperty)
-  {
-    // TODO: decide if invalidDbName exception is thrown here.
-
-    List<DbSourceProxy> proxies = getSourceProxy(dbName);
-    if (proxies != null)
-    {
-      for (DbSourceProxy proxy : proxies)
-      {
-        if (proxy.getDbSourceProperties() != null)
-        {
-          return proxy.getDbSourceProperties().containsKey(dbProperty);
-        }
-      }
-    }
-    return false;
-  }
-
-  /**
    * select sources which are implemented by instances of the given class
    * 
    * @param class that implements DbSourceProxy
@@ -394,7 +364,7 @@ public class ASequenceFetcher
    */
   public String[] getDbInstances(Class class1)
   {
-    if (!jalview.ws.seqfetcher.DbSourceProxy.class.isAssignableFrom(class1))
+    if (!DbSourceProxy.class.isAssignableFrom(class1))
     {
       throw new Error(
               MessageManager
@@ -407,11 +377,11 @@ public class ASequenceFetcher
       return null;
     }
     String[] sources = null;
-    Vector src = new Vector();
-    Enumeration dbs = FETCHABLEDBS.keys();
+    Vector<String> src = new Vector<String>();
+    Enumeration<String> dbs = FETCHABLEDBS.keys();
     while (dbs.hasMoreElements())
     {
-      String dbn = (String) dbs.nextElement();
+      String dbn = dbs.nextElement();
       for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn).values())
       {
         if (class1.isAssignableFrom(dbp.getClass()))
@@ -429,7 +399,7 @@ public class ASequenceFetcher
 
   public DbSourceProxy[] getDbSourceProxyInstances(Class class1)
   {
-    ArrayList<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> prlist = new ArrayList<DbSourceProxy>();
     for (String fetchable : getSupportedDb())
     {
       for (DbSourceProxy pr : getSourceProxy(fetchable))