JAL-3035 more das bits removed

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ea6c5f2..5dbb6c4 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -26,18 +26,14 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
-import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.CutAndPasteTransfer;
-import jalview.gui.DasSourceBrowser;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureSettings;
 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;
@@ -62,6 +58,8 @@ public class DBRefFetcher implements Runnable
 {
   private static final String NEWLINE = System.lineSeparator();
 
+  public static final String TRIM_RETRIEVED_SEQUENCES = "TRIM_FETCHED_DATASET_SEQS";
+
   public interface FetchFinishedListenerI
   {
     void finished();
@@ -118,7 +116,7 @@ public class DBRefFetcher implements Runnable
           DbSourceProxy[] sources, FeatureSettings featureSettings,
           boolean isNucleotide)
   {
-    listeners = new ArrayList<FetchFinishedListenerI>();
+    listeners = new ArrayList<>();
     this.progressWindow = progressIndicatorFrame;
     alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
@@ -140,7 +138,7 @@ public class DBRefFetcher implements Runnable
             .getSequenceFetcherSingleton(progressIndicatorFrame);
     // set default behaviour for transferring excess sequence data to the
     // dataset
-    trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
+    trimDsSeqs = Cache.getDefault(TRIM_RETRIEVED_SEQUENCES, true);
     if (sources == null)
     {
       setDatabaseSources(featureSettings, isNucleotide);
@@ -164,23 +162,7 @@ public class DBRefFetcher implements Runnable
   {
     // af.featureSettings_actionPerformed(null);
     String[] defdb = null;
-    List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
-    Vector<jalviewSourceI> dasselsrc = (featureSettings != null)
-            ? featureSettings.getSelectedSources()
-            : new DasSourceBrowser().getSelectedSources();
-
-    for (jalviewSourceI src : dasselsrc)
-    {
-      List<DbSourceProxy> sp = src.getSequenceSourceProxies();
-      if (sp != null)
-      {
-        selsources.addAll(sp);
-        if (sp.size() > 1)
-        {
-          Cache.log.debug("Added many Db Sources for :" + src.getTitle());
-        }
-      }
-    }
+    List<DbSourceProxy> selsources = new ArrayList<>();
     // select appropriate databases based on alignFrame context.
     if (forNucleotide)
     {
@@ -190,7 +172,7 @@ public class DBRefFetcher implements Runnable
     {
       defdb = DBRefSource.PROTEINDBS;
     }
-    List<DbSourceProxy> srces = new ArrayList<DbSourceProxy>();
+    List<DbSourceProxy> srces = new ArrayList<>();
     for (String ddb : defdb)
     {
       List<DbSourceProxy> srcesfordb = sfetcher.getSourceProxy(ddb);
@@ -234,30 +216,6 @@ public class DBRefFetcher implements Runnable
   }
 
   /**
-   * retrieve all the das sequence sources and add them to the list of db
-   * sources to retrieve from
-   */
-  public void appendAllDasSources()
-  {
-    if (dbSources == null)
-    {
-      dbSources = new DbSourceProxy[0];
-    }
-    // append additional sources
-    DbSourceProxy[] otherdb = sfetcher
-            .getDbSourceProxyInstances(DasSequenceSource.class);
-    if (otherdb != null && otherdb.length > 0)
-    {
-      DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length
-              + otherdb.length];
-      System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
-      System.arraycopy(otherdb, 0, newsrc, dbSources.length,
-              otherdb.length);
-      dbSources = newsrc;
-    }
-  }
-
-  /**
    * start the fetcher thread
    * 
    * @param waitTillFinished
@@ -310,14 +268,14 @@ public class DBRefFetcher implements Runnable
       }
       else if (seqs == null)
       {
-        seqs = new Vector<SequenceI>();
+        seqs = new Vector<>();
         seqs.addElement(seq);
       }
 
     }
     else
     {
-      seqs = new Vector<SequenceI>();
+      seqs = new Vector<>();
       seqs.addElement(seq);
     }
 
@@ -356,9 +314,9 @@ public class DBRefFetcher implements Runnable
       e.printStackTrace();
     }
 
-    Vector<SequenceI> sdataset = new Vector<SequenceI>(
+    Vector<SequenceI> sdataset = new Vector<>(
             Arrays.asList(dataset));
-    List<String> warningMessages = new ArrayList<String>();
+    List<String> warningMessages = new ArrayList<>();
 
     int db = 0;
     while (sdataset.size() > 0 && db < dbSources.length)
@@ -370,8 +328,8 @@ public class DBRefFetcher implements Runnable
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];
       sdataset.copyInto(currSeqs);// seqs that are to be validated against
       // dbSources[db]
-      Vector<String> queries = new Vector<String>(); // generated queries curSeq
-      seqRefs = new Hashtable<String, Vector<SequenceI>>();
+      Vector<String> queries = new Vector<>(); // generated queries curSeq
+      seqRefs = new Hashtable<>();
 
       int seqIndex = 0;
 
@@ -573,7 +531,7 @@ public class DBRefFetcher implements Runnable
     {
       // Work out which sequences this sequence matches,
       // taking into account all accessionIds and names in the file
-      Vector<SequenceI> sequenceMatches = new Vector<SequenceI>();
+      Vector<SequenceI> sequenceMatches = new Vector<>();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = DBRefUtils
               .selectRefs(retrievedSeq.getDBRefs(), new String[]
@@ -706,28 +664,13 @@ public class DBRefFetcher implements Runnable
 
           if (updateRefFrame)
           {
-            SequenceFeature[] sfs = sequence.getSequenceFeatures();
-            if (sfs != null)
+            /*
+             * relocate existing sequence features by offset
+             */
+            int startShift = absStart - sequenceStart + 1;
+            if (startShift != 0)
             {
-              /*
-               * relocate existing sequence features by offset
-               */
-              int start = sequenceStart;
-              int end = sequence.getEnd();
-              int startShift = 1 - absStart - start;
-
-              if (startShift != 0)
-              {
-                for (SequenceFeature sf : sfs)
-                {
-                  if (sf.getBegin() >= start && sf.getEnd() <= end)
-                  {
-                    sf.setBegin(sf.getBegin() + startShift);
-                    sf.setEnd(sf.getEnd() + startShift);
-                    modified = true;
-                  }
-                }
-              }
+              modified |= sequence.getFeatures().shiftFeatures(startShift);
             }
           }
         }
@@ -811,8 +754,6 @@ public class DBRefFetcher implements Runnable
         // and remove it from the rest
         // TODO: decide if we should remove annotated sequence from set
         sdataset.remove(sequence);
-        // TODO: should we make a note of sequences that have received new DB
-        // ids, so we can query all enabled DAS servers for them ?
       }
     }
     return modified;
@@ -840,7 +781,7 @@ public class DBRefFetcher implements Runnable
    */
   private SequenceI[] recoverDbSequences(SequenceI[] sequencesArray)
   {
-    Vector<SequenceI> nseq = new Vector<SequenceI>();
+    Vector<SequenceI> nseq = new Vector<>();
     for (int i = 0; sequencesArray != null
             && i < sequencesArray.length; i++)
     {