X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDasSequenceFeatureFetcher.java;h=4d3dd2f5a03f3eead2a26eac912ee42f75796b78;hb=4decc3e365ce990f54773d24bb9583df48d2797a;hp=e553b09d5ace577d4016a85790f5bdae06b31a5d;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index e553b09..4d3dd2f 100644
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -1,29 +1,36 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws;
 
 import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.FeatureSettings;
+import jalview.gui.JvOptionPane;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
 import jalview.util.UrlLink;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
@@ -40,8 +47,6 @@ import java.util.Set;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import javax.swing.JOptionPane;
-
 import org.biodas.jdas.client.FeaturesClient;
 import org.biodas.jdas.client.adapters.features.DasGFFAdapter;
 import org.biodas.jdas.client.adapters.features.DasGFFAdapter.GFFAdapter;
@@ -177,13 +182,12 @@ public class DasSequenceFeatureFetcher
     int refCount = 0;
     for (int i = 0; i < sequences.length; i++)
     {
-      DBRefEntry[] dbref = sequences[i].getDBRef();
+      DBRefEntry[] dbref = sequences[i].getDBRefs();
       if (dbref != null)
       {
         for (int j = 0; j < dbref.length; j++)
         {
-          if (dbref[j].getSource().equals(
-                  jalview.datamodel.DBRefSource.UNIPROT))
+          if (dbref[j].getSource().equals(DBRefSource.UNIPROT))
           {
             refCount++;
             break;
@@ -195,20 +199,21 @@ public class DasSequenceFeatureFetcher
     if (checkDbrefs && refCount < sequences.length && uniprotCount > 0)
     {
 
-      int reply = JOptionPane.YES_OPTION;
+      int reply = JvOptionPane.YES_OPTION;
       if (promptFetchDbrefs)
       {
-        reply = JOptionPane
+        reply = JvOptionPane
                 .showInternalConfirmDialog(
                         Desktop.desktop,
-                        "Do you want Jalview to find\n"
-                                + "Uniprot Accession ids for given sequence names?",
-                        "Find Uniprot Accession Ids",
-                        JOptionPane.YES_NO_OPTION,
-                        JOptionPane.QUESTION_MESSAGE);
+                        MessageManager
+                                .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+                        MessageManager
+                                .getString("label.find_uniprot_accession_ids"),
+                        JvOptionPane.YES_NO_OPTION,
+                        JvOptionPane.QUESTION_MESSAGE);
       }
 
-      if (reply == JOptionPane.YES_OPTION)
+      if (reply == JvOptionPane.YES_OPTION)
       {
         Thread thread = new Thread(new FetchDBRefs());
         thread.start();
@@ -233,6 +238,7 @@ public class DasSequenceFeatureFetcher
 
   class FetchSeqFeatures implements Runnable
   {
+    @Override
     public void run()
     {
       startFetching();
@@ -242,10 +248,14 @@ public class DasSequenceFeatureFetcher
 
   class FetchDBRefs implements Runnable
   {
+    @Override
     public void run()
     {
       running = true;
-      new DBRefFetcher(sequences, af).fetchDBRefs(true);
+      boolean isNucleotide = af.getViewport().getAlignment().isNucleotide();
+      new DBRefFetcher(sequences, af, null, af.featureSettings,
+              isNucleotide).fetchDBRefs(true);
+
       startFetching();
       setGuiFetchComplete();
     }
@@ -261,7 +271,9 @@ public class DasSequenceFeatureFetcher
     startTime = System.currentTimeMillis();
     if (af != null)
     {
-      af.setProgressBar("Fetching DAS Sequence Features", startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.fetching_das_sequence_features"),
+              startTime);
     }
     if (sourceRegistry == null)
     {
@@ -273,8 +285,7 @@ public class DasSequenceFeatureFetcher
       {
         jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
                 new jalviewSourceI[0]);
-        String active = jalview.bin.Cache.getDefault("DAS_ACTIVE_SOURCE",
-                "uniprot");
+        String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
         StringTokenizer st = new StringTokenizer(active, "\t");
         selectedSources = new Vector();
         String token;
@@ -375,8 +386,7 @@ public class DasSequenceFeatureFetcher
                         source));
         for (String id : idl)
         {
-          List<String> qid = Arrays.asList(new String[]
-          { id });
+          List<String> qid = Arrays.asList(new String[] { id });
           try
           {
             DasGFFAdapter dga = featuresc.fetchData(source, qid);
@@ -493,13 +503,13 @@ public class DasSequenceFeatureFetcher
                 } catch (Exception ex)
                 {
                   Cache.log
-                          .info("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
-                  Cache.log.info("Mapping feature from " + f.getBegin()
+                          .warn("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+                  Cache.log.warn("Mapping feature from " + f.getBegin()
                           + " to " + f.getEnd() + " in dbref "
                           + dbref.getAccessionId() + " in "
                           + dbref.getSource());
-                  Cache.log.info("using das Source " + source);
-                  Cache.log.info("Exception", ex);
+                  Cache.log.warn("using das Source " + source);
+                  Cache.log.warn("Exception", ex);
                 }
 
                 if (vf != null)
@@ -534,7 +544,9 @@ public class DasSequenceFeatureFetcher
 
     if (af != null)
     {
-      af.setProgressBar("No DAS Sources Active", startTime);
+      af.setProgressBar(
+              MessageManager.getString("status.no_das_sources_active"),
+              startTime);
     }
     if (getFeatSettings() != null)
     {
@@ -564,7 +576,9 @@ public class DasSequenceFeatureFetcher
   {
     if (af != null)
     {
-      af.setProgressBar("DAS Feature Fetching Cancelled", startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_cancelled"),
+              startTime);
     }
     cancelled = true;
   }
@@ -579,12 +593,13 @@ public class DasSequenceFeatureFetcher
     if (!cancelled && af != null)
     {
       // only update the progress bar if we've completed the fetch normally
-      af.setProgressBar("DAS Feature Fetching Complete", startTime);
+      af.setProgressBar(MessageManager
+              .getString("status.das_feature_fetching_complete"), startTime);
     }
 
     if (af != null && af.featureSettings != null)
     {
-      af.featureSettings.setTableData();
+      af.featureSettings.discoverAllFeatureData();
     }
 
     if (getFeatSettings() != null)
@@ -602,8 +617,8 @@ public class DasSequenceFeatureFetcher
     }
     af.getFeatureRenderer().featuresAdded();
 
-    int start = af.getViewport().getStartSeq();
-    int end = af.getViewport().getEndSeq();
+    int start = af.getViewport().getRanges().getStartSeq();
+    int end = af.getViewport().getRanges().getEndSeq();
     int index;
     for (index = start; index < end; index++)
     {
@@ -623,12 +638,13 @@ public class DasSequenceFeatureFetcher
   Object[] nextSequence(jalviewSourceI dasSource, SequenceI seq)
   {
     if (cancelled)
+    {
       return null;
-    DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-            seq.getDBRef(), new String[]
-            {
+    }
+    DBRefEntry[] uprefs = DBRefUtils.selectRefs(seq.getDBRefs(),
+            new String[] {
             // jalview.datamodel.DBRefSource.PDB,
-            jalview.datamodel.DBRefSource.UNIPROT,
+            DBRefSource.UNIPROT,
             // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
             // sys sources
             });
@@ -647,8 +663,8 @@ public class DasSequenceFeatureFetcher
 
         for (COORDINATES csys : dasSource.getVersion().getCOORDINATES())
         {
-          if (jalview.util.DBRefUtils.isDasCoordinateSystem(
-                  csys.getAuthority(), uprefs[j]))
+          if (DBRefUtils.isDasCoordinateSystem(csys.getAuthority(),
+                  uprefs[j]))
           {
             debug("Launched fetcher for coordinate system "
                     + csys.getAuthority());
@@ -665,7 +681,9 @@ public class DasSequenceFeatureFetcher
             qstring.add(uprefs[j].getAccessionId());
           }
           else
+          {
             System.out.println("IGNORE " + csys.getAuthority());
+          }
         }
       }
     }
@@ -703,8 +721,7 @@ public class DasSequenceFeatureFetcher
       }
     }
 
-    return new Object[]
-    { ids, qstring };
+    return new Object[] { ids, qstring };
   }
 
   /**
@@ -836,7 +853,7 @@ public class DasSequenceFeatureFetcher
       {
         for (String note : feat.getNOTE())
         {
-          desc += (String) note;
+          desc += note;
         }
       }