Platform.timecheck calls removed or commented out.

[jalview.git] / src / jalview / ext / ensembl / EnsemblSeqProxy.java

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;
   }