JAL-3949 - refactor logging from jalview.bin.Cache to jalview.bin.Console

[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 fb01708..e4fa53d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@ -20,9 +20,20 @@
  */
 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;
+import jalview.bin.Console;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -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);
   }
 
   /**
@@ -314,7 +312,7 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
 
               if (upx.size() > 1)
               {
-                Cache.log.warn(
+                Console.warn(
                         "Implementation issue - multiple uniprot acc on product sequence.");
               }
             }
@@ -340,8 +338,8 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
          * copy exon features to protein, compute peptide variants from dna 
          * variants and add as features on the protein sequence ta-da
          */
-        AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq,
-                mapList);
+        // JAL-3187 render on the fly instead
+        // AlignmentUtils.computeProteinFeatures(querySeq, proteinSeq, mapList);
       }
     } catch (Exception e)
     {
@@ -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;
   }
 
@@ -765,18 +761,6 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     String comp = complement.toString();
     sf.setValue(Gff3Helper.ALLELES, comp);
     sf.setDescription(comp);
-
-    /*
-     * replace value of "alleles=" in sf.ATTRIBUTES as well
-     * so 'output as GFF' shows reverse complement alleles
-     */
-    String atts = sf.getAttributes();
-    if (atts != null)
-    {
-      atts = atts.replace(Gff3Helper.ALLELES + "=" + alleles,
-              Gff3Helper.ALLELES + "=" + comp);
-      sf.setAttributes(atts);
-    }
   }
 
   /**
@@ -838,9 +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);
@@ -879,10 +861,10 @@ public abstract class EnsemblSeqProxy extends EnsemblRestClient
     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);    
-       }
+//     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))