Merge branch 'develop' into JAL-1705_trialMerge

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

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index 9d91e31..dff1b98 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -28,9 +28,9 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
 import jalview.gui.CutAndPasteTransfer;
 import jalview.gui.Desktop;
+import jalview.gui.FeatureSettings;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
 import jalview.util.MessageManager;
@@ -57,7 +57,7 @@ public class DBRefFetcher implements Runnable
 {
   SequenceI[] dataset;
 
-  IProgressIndicator af;
+  IProgressIndicator progressWindow;
 
   CutAndPasteTransfer output = new CutAndPasteTransfer();
 
@@ -91,34 +91,25 @@ public class DBRefFetcher implements Runnable
   }
 
   /**
-   * Creates a new SequenceFeatureFetcher object and fetches from the currently
-   * selected set of databases.
+   * Creates a new DBRefFetcher object and fetches from the currently selected
+   * set of databases, if this is null then it fetches based on feature settings
    * 
    * @param seqs
-   *          fetch references for these sequences
-   * @param af
-   *          the parent alignframe for progress bar monitoring.
-   */
-  public DBRefFetcher(SequenceI[] seqs, AlignFrame af)
-  {
-    this(seqs, af, null);
-  }
-
-  /**
-   * Creates a new SequenceFeatureFetcher object and fetches from the currently
-   * selected set of databases.
-   * 
-   * @param seqs
-   *          fetch references for these sequences
-   * @param af
-   *          the parent alignframe for progress bar monitoring.
+   *          fetch references for these SequenceI array
+   * @param progressIndicatorFrame
+   *          the frame for progress bar monitoring
    * @param sources
-   *          array of database source strings to query references from
+   *          array of DbSourceProxy to query references form
+   * @param featureSettings
+   *          FeatureSettings to get alternative DbSourceProxy from
+   * @param isNucleotide
+   *          indicates if the array of SequenceI are Nucleotides or not
    */
-  public DBRefFetcher(SequenceI[] seqs, AlignFrame af,
-          DbSourceProxy[] sources)
+  public DBRefFetcher(SequenceI[] seqs,
+          IProgressIndicator progressIndicatorFrame,
+          DbSourceProxy[] sources, FeatureSettings featureSettings, boolean isNucleotide)
   {
-    this.af = af;
+    this.progressWindow = progressIndicatorFrame;
     alseqs = new SequenceI[seqs.length];
     SequenceI[] ds = new SequenceI[seqs.length];
     for (int i = 0; i < seqs.length; i++)
@@ -135,7 +126,8 @@ public class DBRefFetcher implements Runnable
     }
     this.dataset = ds;
     // TODO Jalview 2.5 lots of this code should be in the gui package!
-    sfetcher = jalview.gui.SequenceFetcher.getSequenceFetcherSingleton(af);
+    sfetcher = jalview.gui.SequenceFetcher
+            .getSequenceFetcherSingleton(progressIndicatorFrame);
     // set default behaviour for transferring excess sequence data to the
     // dataset
     trimDsSeqs = Cache.getDefault("TRIM_FETCHED_DATASET_SEQS", true);
@@ -145,7 +137,7 @@ public class DBRefFetcher implements Runnable
       String[] defdb = null, otherdb = sfetcher
               .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
       List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();
-      Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings
+      Vector dasselsrc = (featureSettings != null) ? featureSettings
               .getSelectedSources() : new jalview.gui.DasSourceBrowser()
               .getSelectedSources();
       Enumeration<jalviewSourceI> en = dasselsrc.elements();
@@ -163,7 +155,7 @@ public class DBRefFetcher implements Runnable
         }
       }
       // select appropriate databases based on alignFrame context.
-      if (af.getViewport().getAlignment().isNucleotide())
+      if (isNucleotide)
       {
         defdb = DBRefSource.DNACODINGDBS;
       }
@@ -294,8 +286,12 @@ public class DBRefFetcher implements Runnable
     }
     running = true;
     long startTime = System.currentTimeMillis();
-    af.setProgressBar(MessageManager.getString("status.fetching_db_refs"),
+    if (progressWindow != null)
+    {
+      progressWindow.setProgressBar(
+              MessageManager.getString("status.fetching_db_refs"),
             startTime);
+    }
     try
     {
       if (Cache.getDefault("DBREFFETCH_USEPICR", false))
@@ -393,7 +389,7 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(),
+                      sequence.getDBRefs(),
                       new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
@@ -472,11 +468,14 @@ public class DBRefFetcher implements Runnable
       // of the viewed sequence
 
     }
+    if (progressWindow != null)
+    {
+      progressWindow.setProgressBar(
+              MessageManager.getString("label.dbref_search_completed"),
+              startTime);
+      // promptBeforeBlast();
 
-    af.setProgressBar(
-            MessageManager.getString("label.dbref_search_completed"),
-            startTime);
-    // promptBeforeBlast();
+    }
 
     running = false;
 
@@ -517,7 +516,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[] { dbSource });
+              entry.getDBRefs(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -584,8 +583,8 @@ public class DBRefFetcher implements Runnable
         // no existing references
         // TODO: test for legacy where uniprot or EMBL refs exist but no
         // mappings are made (but content matches retrieved set)
-        boolean updateRefFrame = sequence.getDBRef() == null
-                || sequence.getDBRef().length == 0;
+        boolean updateRefFrame = sequence.getDBRefs() == null
+                || sequence.getDBRefs().length == 0;
         // TODO:
         // verify sequence against the entry sequence
 
@@ -730,7 +729,7 @@ public class DBRefFetcher implements Runnable
     for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
     {
       nseq.addElement(sequencesArray[i]);
-      DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+      DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
       jalview.datamodel.Mapping map = null;
       for (int r = 0; (dbr != null) && r < dbr.length; r++)
       {