JAL-1807 explicit imports (jalview.ws.*)

[jalview.git] / src / jalview / ws / DBRefFetcher.java

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d71c653..455d98e 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -30,11 +30,14 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.DasSourceBrowser;
 import jalview.gui.Desktop;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
+import jalview.util.DBRefUtils;
 import jalview.util.MessageManager;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
+import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.ArrayList;
@@ -45,6 +48,8 @@ import java.util.StringTokenizer;
 import java.util.Vector;
 
 import uk.ac.ebi.picr.model.UPEntry;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface;
+import uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator;
 
 /**
  * Implements a runnable for validating a sequence against external databases
@@ -68,7 +73,7 @@ public class DBRefFetcher implements Runnable
   /**
    * picr client instance
    */
-  uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperInterface picrClient = null;
+  AccessionMapperInterface picrClient = null;
 
   // /This will be a collection of Vectors of sequenceI refs.
   // The key will be the seq name or accession id of the seq
@@ -125,9 +130,13 @@ public class DBRefFetcher implements Runnable
     {
       alseqs[i] = seqs[i];
       if (seqs[i].getDatasetSequence() != null)
+      {
         ds[i] = seqs[i].getDatasetSequence();
+      }
       else
+      {
         ds[i] = seqs[i];
+      }
     }
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
@@ -139,10 +148,10 @@ public class DBRefFetcher implements Runnable
     {
       // af.featureSettings_actionPerformed(null);
       String[] defdb = null, otherdb = sfetcher
-              .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+              .getDbInstances(DasSequenceSource.class);
       List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
       Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
-              .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+              .getSelectedSources() : new DasSourceBrowser()
               .getSelectedSources();
       Enumeration<jalviewSourceI> en = dasselsrc.elements();
       while (en.hasMoreElements())
@@ -201,7 +210,7 @@ public class DBRefFetcher implements Runnable
     }
     // append additional sources
     DbSourceProxy[] otherdb = sfetcher
-            .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
+            .getDbSourceProxyInstances(DasSequenceSource.class);
     if (otherdb != null && otherdb.length > 0)
     {
       DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
@@ -292,7 +301,7 @@ public class DBRefFetcher implements Runnable
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
       {
-        picrClient = new uk.ac.ebi.www.picr.AccessionMappingService.AccessionMapperServiceLocator()
+        picrClient = new AccessionMapperServiceLocator()
                 .getAccessionMapperPort();
       }
     } catch (Exception e)
@@ -321,7 +330,7 @@ public class DBRefFetcher implements Runnable
 
       int seqIndex = 0;
 
-      jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];
+      DbSourceProxy dbsource = dbSources[db];
       {
         // for moment, we dumbly iterate over all retrieval sources for a
         // particular database
@@ -364,9 +373,9 @@ public class DBRefFetcher implements Runnable
             AlignmentI retrieved = null;
             try
             {
-              if (jalview.bin.Cache.log.isDebugEnabled())
+              if (Cache.log.isDebugEnabled())
               {
-                jalview.bin.Cache.log.debug("Querying "
+                Cache.log.debug("Querying "
                         + dbsource.getDbName() + " with : '"
                         + queryString.toString() + "'");
               }
@@ -392,7 +401,7 @@ public class DBRefFetcher implements Runnable
             for (int i = 0; (seqIndex < dataset.length) && (i < 50); seqIndex++, i++)
             {
               SequenceI sequence = dataset[seqIndex];
-              DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
+              DBRefEntry[] uprefs = DBRefUtils.selectRefs(
                       sequence.getDBRef(), new String[]
                       { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
@@ -516,7 +525,7 @@ public class DBRefFetcher implements Runnable
       // taking into account all accessionIds and names in the file
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
-      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
+      DBRefEntry[] entryRefs = DBRefUtils.selectRefs(
               entry.getDBRef(), new String[]
               { dbSource });
       if (entryRefs == null)
@@ -595,7 +604,7 @@ public class DBRefFetcher implements Runnable
 
         int absStart = entrySeq.indexOf(nonGapped);
         int mapStart = entry.getStart();
-        jalview.datamodel.Mapping mp;
+        Mapping mp;
 
         if (absStart == -1)
         {
@@ -734,7 +743,7 @@ public class DBRefFetcher implements Runnable
     {
       nseq.addElement(sequencesArray[i]);
       DBRefEntry dbr[] = sequencesArray[i].getDBRef();
-      jalview.datamodel.Mapping map = null;
+      Mapping map = null;
       for (int r = 0; (dbr != null) && r < dbr.length; r++)
       {
         if ((map = dbr[r].getMap()) != null)