more iterators out; some time checks

[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..fb01708 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -171,14 +171,15 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
      * fetch and transfer genomic sequence features,
      * fetch protein product and add as cross-reference
      */
-    for (String accId : allIds)
+    for (int i = 0, n = allIds.size(); i < n; i++) 
     {
-      addFeaturesAndProduct(accId, alignment);
+      addFeaturesAndProduct(allIds.get(i), alignment);
     }
 
-    for (SequenceI seq : alignment.getSequences())
+    List<SequenceI> seqs = alignment.getSequences();
+    for (int i = 0, n = seqs.size(); i < n; i++)
     {
-      getCrossReferences(seq);
+      getCrossReferences(seqs.get(i));
     }
 
     return alignment;
@@ -208,7 +209,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
        */
       SequenceI genomicSequence = null;
       EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
-      EnsemblFeatureType[] features = getFeaturesToFetch();
+      EnsemblFeatureType[] features = getFeaturesToFetch();      
       
       Platform.timeCheck("ESP.getsequencerec1", Platform.TIME_MARK);     
 
@@ -228,9 +229,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
          * 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 +236,7 @@ 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.addprotein", Platform.TIME_MARK);    
+            Platform.timeCheck("ESP.transferFeatures", Platform.TIME_MARK);      
           addProteinProduct(querySeq);
         }
       }
@@ -377,7 +375,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     
     for (int i = 0, n = xrefs.size(); i < n; i++)
     {
-        Platform.timeCheck("ESP. getxref + " + (i) + "/" + n, Platform.TIME_MARK);       
+//        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!
@@ -385,17 +383,17 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       seq.addDBRef(xrefs.get(i));
     }
 
-    System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
+//    System.out.println("primaries are " + seq.getPrimaryDBRefs().toString());
     /*
      * and add a reference to itself
      */
     
-    Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);        
+//    Platform.timeCheck("ESP. getxref self ", Platform.TIME_MARK);      
 
     DBRefEntry self = new DBRefEntry(getDbSource(), getEnsemblDataVersion(),
-            seq.getName());
+    seq.getName());
 
-    Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);    
+//    Platform.timeCheck("ESP. getxref self add ", Platform.TIME_MARK);          
 
     seq.addDBRef(self);
     
@@ -695,7 +693,9 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
    */
   protected abstract List<SequenceFeature> getIdentifyingFeatures(
           SequenceI seq, String accId);
-
+  
+  int bhtest = 0;
+  
   /**
    * Transfers the sequence feature to the target sequence, locating its start
    * and end range based on the mapping. Features which do not overlap the
@@ -717,6 +717,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
     if (mappedRange != null)
     {
+//      Platform.timeCheck(null, Platform.TIME_SET);
       String group = sf.getFeatureGroup();
       if (".".equals(group))
       {
@@ -724,8 +725,11 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
       }
       int newBegin = Math.min(mappedRange[0], mappedRange[1]);
       int newEnd = Math.max(mappedRange[0], mappedRange[1]);
-      SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
-              group, sf.getScore());
+//      Platform.timeCheck(null, Platform.TIME_MARK);
+      bhtest++;
+      // 280 ms/1000 here:
+      SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd, group, sf.getScore());
+      // 0.175 ms here:
       targetSequence.addSequenceFeature(copy);
 
       /*
@@ -830,10 +834,14 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     MapList mapping = getGenomicRangesFromFeatures(sourceSequence,
             accessionId, targetSequence.getStart());
     if (mapping == null)
-    {
+    { 
       return false;
     }
 
+
+    Platform.timeCheck("ESP. xfer " + sfs.size(), Platform.TIME_MARK);   
+
+
     boolean result = transferFeatures(sfs, targetSequence, mapping,
             accessionId);
 //    System.out.println("transferFeatures (" + (sfs.size()) + " --> "
@@ -867,14 +875,23 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     SequenceFeatures.sortFeatures(sfs, forwardStrand);
 
     boolean transferred = false;
-    for (SequenceFeature sf : sfs)
+    
+    for (int i = 0, n = sfs.size(); i < n; i++)
     {
+
+       if ((i%1000) == 0) {
+//         Platform.timeCheck("Feature " + bhtest, Platform.TIME_GET);
+       Platform.timeCheck("ESP. xferFeature + " + (i) + "/" + n, Platform.TIME_MARK);    
+       }
+
+      SequenceFeature sf = sfs.get(i);
       if (retainFeature(sf, parentId))
       {
         transferFeature(sf, targetSequence, mapping, forwardStrand);
         transferred = true;
       }
     }
+
     return transferred;
   }