Merge branch 'Jalview-JS/develop' of https://source.jalview.org/git/jalview.git into...

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index bf151bf..771980c 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -20,9 +20,6 @@
  */
 package jalview.ext.ensembl;
 
-import jalview.util.Platform;
-import jalview.util.StringUtils;
-
 import java.io.BufferedReader;
 import java.io.DataOutputStream;
 import java.io.IOException;
@@ -39,6 +36,9 @@ import javax.ws.rs.HttpMethod;
 
 import org.json.simple.parser.ParseException;
 
+import jalview.util.Platform;
+import jalview.util.StringUtils;
+
 /**
  * Base class for Ensembl REST service clients
  * 
@@ -319,10 +319,10 @@ abstract class EnsemblRestClient extends EnsemblSequenceFetcher
 
     InputStream response = connection.getInputStream();
 
-    Platform.timeCheck(null, Platform.TIME_MARK);
+    // Platform.timeCheck(null, Platform.TIME_MARK);
     Object ret = Platform.parseJSON(response);
-    Platform.timeCheck("EnsemblRestClient.getJSON " + url,
-            Platform.TIME_MARK);
+    // Platform.timeCheck("EnsemblRestClient.getJSON " + url,
+    // Platform.TIME_MARK);
 
     return ret;
   }

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index d483c3b..fd8800f 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -20,6 +20,17 @@
  */
 package jalview.ext.ensembl;
 
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+import org.json.simple.parser.ParseException;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.Dna;
 import jalview.bin.Cache;
@@ -40,18 +51,6 @@ import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.IntRangeComparator;
 import jalview.util.MapList;
-import jalview.util.Platform;
-
-import java.io.IOException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Map;
-
-import org.json.simple.parser.ParseException;
 
 /**
  * Base class for Ensembl sequence fetchers
@@ -211,8 +210,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
       EnsemblFeatureType[] features = getFeaturesToFetch();      
       
-      Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);     
-
+      // Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);
       
       AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
               features);
@@ -221,7 +219,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
         genomicSequence = geneFeatures.getSequenceAt(0);
       }
       
-      Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);     
+      // Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);
       
       if (genomicSequence != null)
       {
@@ -236,7 +234,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
            * fetch and map protein product, and add it as a cross-reference
            * of the retrieved sequence
            */
-            Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);      
+          // Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);
           addProteinProduct(querySeq);
         }
       }
@@ -245,7 +243,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       System.err.println(
               "Error transferring Ensembl features: " + e.getMessage());
     }
-    Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);          
+    // Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);
   }
 
   /**
@@ -359,7 +357,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
   protected void getCrossReferences(SequenceI seq)
   {
          
-      Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);        
+    // Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);
 
          
     while (seq.getDatasetSequence() != null)
@@ -367,7 +365,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       seq = seq.getDatasetSequence();
     }
 
-    Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);     
+    // Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);
 
     EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
             getEnsemblDataVersion());
@@ -397,8 +395,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     seq.addDBRef(self);
     
-    Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);        
-
+    // Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);
   }
 
   /**
@@ -419,7 +416,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       inProgress = false;
       throw new JalviewException("ENSEMBL Rest API not available.");
     }
-       Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
+    // Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
 
     List<SequenceI> seqs = parseSequenceJson(ids);
     if (seqs == null)
@@ -486,8 +483,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        * for now, assumes only one sequence returned; refactor if needed
        * in future to handle a JSONArray with more than one
        */
-       
-       Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
+      // Platform.timeCheck("ENS seqproxy", Platform.TIME_MARK);
       Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
       if (val == null)
          return null;
@@ -513,7 +509,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       System.err.println("Error processing JSON response: " + e.toString());
       // ignore
     }
-       Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
+    // Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
     return result;
   }
 
@@ -826,9 +822,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       return false;
     }
 
-
-    Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);   
-
+    // Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);
 
     boolean result = transferFeatures(sfs, targetSequence, mapping,
             accessionId);

diff --git a/src/jalview/fts/service/pdb/PDBFTSRestClient.java b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
index c52da40..22ed591 100644 (file)
--- a/src/jalview/fts/service/pdb/PDBFTSRestClient.java
+++ b/src/jalview/fts/service/pdb/PDBFTSRestClient.java
@@ -20,17 +20,6 @@
  */
 package jalview.fts.service.pdb;
 
-import jalview.datamodel.SequenceI;
-import jalview.fts.api.FTSData;
-import jalview.fts.api.FTSDataColumnI;
-import jalview.fts.api.FTSRestClientI;
-import jalview.fts.core.FTSRestClient;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-import jalview.util.JSONUtils;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-
 import java.net.URI;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -48,6 +37,17 @@ import com.sun.jersey.api.client.ClientResponse;
 import com.sun.jersey.api.client.WebResource;
 import com.sun.jersey.api.client.config.DefaultClientConfig;
 
+import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestClient;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.util.JSONUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * A rest client for querying the Search endpoint of the PDB API
  * 
@@ -165,7 +165,7 @@ public class PDBFTSRestClient extends FTSRestClient
 
       URI uri = webResource.getURI();
 
-      System.out.println(uri);
+      // System.out.println(uri);
 
       // Execute the REST request
       ClientResponse clientResponse = webResource

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 82d38e3..326a378 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -2489,7 +2489,7 @@ public class Desktop extends jalview.jbgui.GDesktop
   @Override
   public void setProgressBar(String message, long id)
   {
-           Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);     
+    // Platform.timeCheck("Desktop " + message, Platform.TIME_MARK);
 
     if (progressBars == null)
     {

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 0609ee5..80ed4c1 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -27,6 +27,21 @@ import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JInternalFrame;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -40,6 +55,7 @@ import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -75,21 +91,6 @@ import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.JInternalFrame;
-
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
@@ -1241,10 +1242,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             DataSourceType.FILE);
     AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
     SequenceI rpep = rap.getAlignment().getSequenceAt(0);
+    DBModList<DBRefEntry> dbrefs = rpep.getDBRefs();
     assertEquals(rpep.getName(), "P30419");
-    DBRefEntry[] dbrefs = (DBRefEntry[]) rpep.getDBRefs().toArray();
-    assertEquals(dbrefs.length, 3);
-    DBRefEntry dbRef = dbrefs[0];
+    assertEquals(dbrefs.size(), 3);
+    DBRefEntry dbRef = dbrefs.get(0);
     assertFalse(dbRef instanceof GeneLocus);
     assertNull(dbRef.getMap());
     assertEquals(dbRef, dbref1);
@@ -1253,7 +1254,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * restored dbrefs with mapping have a different 'map to'
      * sequence but otherwise match the original dbrefs
      */
-    dbRef = dbrefs[1];
+    dbRef = dbrefs.get(1);
     assertFalse(dbRef instanceof GeneLocus);
     assertTrue(dbRef.equalRef(dbref2));
     assertNotNull(dbRef.getMap());
@@ -1265,7 +1266,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     /*
      * GeneLocus map.to is null so can compare Mapping objects
      */
-    dbRef = dbrefs[2];
+    dbRef = dbrefs.get(2);
     assertTrue(dbRef instanceof GeneLocus);
     assertEquals(dbRef, dbref3);
   }