Platform.timecheck calls removed or commented out.

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 1993516..8520e5c 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -24,7 +24,6 @@ import jalview.api.DBRefEntryI;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 
-import java.util.Arrays;
 import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
@@ -40,7 +39,9 @@ public class DBRefEntry implements DBRefEntryI
 
   String source = "";
 
-  String version = "", ucversion;
+  String version = "";
+  
+  private String ucversion;
 
   String accessionId = "";
   
@@ -386,6 +387,14 @@ public class DBRefEntry implements DBRefEntryI
     return accessionId != null && accessionId.startsWith(CHROMOSOME + ":");
   }
 
+  /**
+   * stores the upper-case canonical name of the source for use in
+   * Sequence.getPrimaryDBRefs().
+   * 
+   * @author Bob Hanson
+   * 
+   * @return
+   */
   public Object getCanonicalSourceName() {
        return canonicalSourceName;
   }

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 6e9e1cd..0acf701 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -80,7 +80,7 @@ SequenceI datasetSequence;
 
   String vamsasId;
 
-  private DBModList<DBRefEntry> dbrefs; // controlled acces
+  private DBModList<DBRefEntry> dbrefs; // controlled access
 
   /**
    * a flag to let us know that elements have changed in dbrefs

diff --git a/src/jalview/ext/ensembl/EnsemblGene.java b/src/jalview/ext/ensembl/EnsemblGene.java
index dd2547b..7904df3 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblGene.java
+++ b/src/jalview/ext/ensembl/EnsemblGene.java
@@ -138,26 +138,16 @@ public class EnsemblGene extends EnsemblSeqProxy
          
          
          
- Platform.timeCheck("EG " + query, Platform.TIME_MARK);          
-         
     /*
      * convert to a non-duplicated list of gene identifiers
      */
     List<String> geneIds = getGeneIds(query);
-
-    
-    Platform.timeCheck("EG genIds " + geneIds.size(), Platform.TIME_MARK);       
-
     AlignmentI al = null;
     for (String geneId : geneIds)
     {
       /*
        * fetch the gene sequence(s) with features and xrefs
        */
-       
-        Platform.timeCheck("EG fetch " + geneId, Platform.TIME_MARK);    
-       
-       
       AlignmentI geneAlignment = super.getSequenceRecords(geneId);
       if (geneAlignment == null)
       {
@@ -168,15 +158,7 @@ public class EnsemblGene extends EnsemblSeqProxy
       {
         // ensure id has 'correct' case for the Ensembl identifier
         geneId = geneAlignment.getSequenceAt(0).getName();
-
-        
-        Platform.timeCheck("EG loci " + geneId, Platform.TIME_MARK);     
-
-        
         findGeneLoci(geneAlignment.getSequenceAt(0), geneId);
-
-        Platform.timeCheck("EG transcript " + geneId, Platform.TIME_MARK);       
-
         getTranscripts(geneAlignment, geneId);
       }
       if (al == null)
@@ -188,9 +170,6 @@ public class EnsemblGene extends EnsemblSeqProxy
         al.append(geneAlignment);
       }
     }
-    
-    Platform.timeCheck("EG done", Platform.TIME_MARK);   
-
     return al;
   }
 

diff --git a/src/jalview/ext/ensembl/EnsemblRestClient.java b/src/jalview/ext/ensembl/EnsemblRestClient.java
index b3113f9..da9d2e5 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblRestClient.java
+++ b/src/jalview/ext/ensembl/EnsemblRestClient.java
@@ -457,8 +457,9 @@ boolean checkEnsembl()
     StringBuilder postBody = new StringBuilder(64);
     postBody.append("{\"ids\":[");
     first = true;
-    for (String id : ids)
+    for (int i = 0, n = ids.size(); i < n; i++)
     {
+      String id = ids.get(i);
       if (!first)
       {
         postBody.append(",");
@@ -500,17 +501,17 @@ boolean checkEnsembl()
        if (url == null)
           url = getUrl(ids);
        
-       Platform.timeCheck("EnsembleRestClient.getJSON0 " + url, Platform.TIME_MARK);
+//     Platform.timeCheck("EnsembleRestClient.getJSON0 " + url, Platform.TIME_MARK);
        
        Reader br = null;
        try {
       br = (url == null ? null : getHttpResponse(url, ids, msDelay));
 
-      Platform.timeCheck("EnsembleRestClient.getJSON1 parsing... ", Platform.TIME_MARK);
+//      Platform.timeCheck("EnsembleRestClient.getJSON1 parsing... ", Platform.TIME_MARK);
        
       Object ret = (br == null ? null : JSONUtils.parse(br));
 
-      Platform.timeCheck("EnsembleRestClient.getJSON2 ...done ", Platform.TIME_MARK);
+//      Platform.timeCheck("EnsembleRestClient.getJSON2 ...done ", Platform.TIME_MARK);
 
       if (ret != null && mapKey != null)
            ret = ((Map<String, Object>) ret).get(mapKey);

diff --git a/src/jalview/ext/ensembl/EnsemblSeqProxy.java b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index 1d6b354..a558ad2 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -208,29 +208,19 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        */
       SequenceI genomicSequence = null;
       EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
-      EnsemblFeatureType[] features = getFeaturesToFetch();
-      
-      Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);     
-
-      
+      EnsemblFeatureType[] features = getFeaturesToFetch();      
       AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
               features);
       if (geneFeatures != null && geneFeatures.getHeight() > 0)
       {
         genomicSequence = geneFeatures.getSequenceAt(0);
       }
-      
-      Platform.timeCheck("ESP.getsequencerec2", Platform.TIME_MARK);     
-      
       if (genomicSequence != null)
       {
         /*
          * transfer features to the query sequence
          */
         SequenceI querySeq = alignment.findName(accId, true);
-        
-        Platform.timeCheck("ESP.transferfeat", Platform.TIME_MARK);      
-
         if (transferFeatures(accId, genomicSequence, querySeq))
         {
 
@@ -238,7 +228,6 @@ 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.addprotein", Platform.TIME_MARK);    
           addProteinProduct(querySeq);
         }
       }
@@ -247,7 +236,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       System.err.println(
               "Error transferring Ensembl features: " + e.getMessage());
     }
-    Platform.timeCheck("ESP.addfeat done", Platform.TIME_MARK);          
   }
 
   /**
@@ -360,47 +348,28 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    */
   protected void getCrossReferences(SequenceI seq)
   {
-         
-      Platform.timeCheck("ESP. getdataseq ", Platform.TIME_MARK);        
-
-         
     while (seq.getDatasetSequence() != null)
     {
       seq = seq.getDatasetSequence();
     }
-
-    Platform.timeCheck("ESP. getxref ", Platform.TIME_MARK);     
-
     EnsemblXref xrefFetcher = new EnsemblXref(getDomain(), getDbSource(),
             getEnsemblDataVersion());
     List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName());
     
     for (int i = 0, n = xrefs.size(); i < n; i++)
     {
-        Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK);       
         // BH 2019.01.25 this next method was taking 174 ms PER addition for a 266-reference example.
         //    DBRefUtils.ensurePrimaries(seq) 
         //        was at the end of seq.addDBRef, so executed after ever addition!
         //        This method was moved to     seq.getPrimaryDBRefs()
       seq.addDBRef(xrefs.get(i));
     }
-
-    System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
     /*
      * and add a reference to itself
      */
-    
-    Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);        
-
     DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
-            seq.getName());
-
-    Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);    
-
+    seq.getName());
     seq.addDBRef(self);
-    
-    Platform.timeCheck("ESP. seqprox done ", Platform.TIME_MARK);        
-
   }
 
   /**
@@ -421,8 +390,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       inProgress = false;
       throw new JalviewException("ENSEMBL Rest API not available.");
     }
-       Platform.timeCheck("EnsemblSeqProx.fetchSeq ", Platform.TIME_MARK);
-
     List<SequenceI> seqs = parseSequenceJson(ids);
     if (seqs == null)
        return alignment;
@@ -488,8 +455,6 @@ 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);
       Map<String, Object> val = (Map<String, Object>) getJSON(null, ids, -1, MODE_MAP, null);
       if (val == null)
          return null;
@@ -515,7 +480,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       System.err.println("Error processing JSON response: " + e.toString());
       // ignore
     }
-       Platform.timeCheck("ENS seqproxy2", Platform.TIME_MARK);
     return result;
   }