Merge branch 'features/JAL-4071_visibleFeaturesCounter' into features/JAL-3417_sdppre...

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 6319338..c8a846c 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -28,12 +28,13 @@ import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.IdentityHashMap;
 import java.util.List;
 import java.util.HashMap;
 import java.util.IdentityHashMap;
 import java.util.List;

+import java.util.Locale;

 import java.util.Map;
 import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
 import java.util.Map;
 import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;

-import jalview.bin.Cache;
+import jalview.bin.Console;

 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.OrderCommand;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
 import jalview.commands.OrderCommand;

@@ -320,7 +321,7 @@ public class StructureSelectionManager
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile setMapping(SequenceI[] sequence,

-          String[] targetChains, String pdbFile, DataSourceType protocol, 
+          String[] targetChains, String pdbFile, DataSourceType protocol,

           IProgressIndicator progress)
   {
     return computeMapping(true, sequence, targetChains, pdbFile, protocol,
           IProgressIndicator progress)
   {
     return computeMapping(true, sequence, targetChains, pdbFile, protocol,

@@ -377,9 +378,9 @@ public class StructureSelectionManager
    *          mapping operation
    * @return null or the structure data parsed as a pdb file
    */
    *          mapping operation
    * @return null or the structure data parsed as a pdb file
    */

-  synchronized public StructureFile computeMapping(
-          boolean forStructureView, SequenceI[] sequenceArray,
-          String[] targetChainIds, String pdbFile, DataSourceType sourceType,
+  synchronized public StructureFile computeMapping(boolean forStructureView,
+          SequenceI[] sequenceArray, String[] targetChainIds,
+          String pdbFile, DataSourceType sourceType,

           IProgressIndicator progress)
   {
     long progressSessionId = System.currentTimeMillis() * 3;
           IProgressIndicator progress)
   {
     long progressSessionId = System.currentTimeMillis() * 3;

@@ -410,7 +411,20 @@ public class StructureSelectionManager
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
       // if PDBId is unavailable then skip SIFTS mapping execution path
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
       // if PDBId is unavailable then skip SIFTS mapping execution path

-      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable();
+      // TODO: JAL-3868 need to know if structure is actually from
+      // PDB (has valid PDB ID and has provenance suggesting it
+      // actually came from PDB)
+      boolean isProtein = false;
+      for (SequenceI s : sequenceArray)
+      {
+        if (s.isProtein())
+        {
+          isProtein = true;
+          break;
+        }
+      }
+      isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable()
+              && !pdb.getId().startsWith("AF-") && isProtein;

 
     } catch (Exception ex)
     {
 
     } catch (Exception ex)
     {

@@ -430,7 +444,8 @@ public class StructureSelectionManager
     } catch (SiftsException e)
     {
       isMapUsingSIFTs = false;
     } catch (SiftsException e)
     {
       isMapUsingSIFTs = false;

-      e.printStackTrace();
+      Console.error("SIFTS mapping failed", e);
+      Console.error("Falling back on Needleman & Wunsch alignment");

       siftsClient = null;
     }
 
       siftsClient = null;
     }
 

@@ -521,9 +536,11 @@ public class StructureSelectionManager
       List<StructureMapping> seqToStrucMapping = new ArrayList<>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
       List<StructureMapping> seqToStrucMapping = new ArrayList<>();
       if (isMapUsingSIFTs && seq.isProtein())
       {

-        if (progress!=null) {
-          progress.setProgressBar(MessageManager
-                .getString("status.obtaining_mapping_with_sifts"),
+        if (progress != null)
+        {
+          progress.setProgressBar(
+                  MessageManager
+                          .getString("status.obtaining_mapping_with_sifts"),

                   progressSessionId);
         }
         jalview.datamodel.Mapping sqmpping = maxAlignseq
                   progressSessionId);
         }
         jalview.datamodel.Mapping sqmpping = maxAlignseq

@@ -537,21 +554,23 @@ public class StructureSelectionManager
                     pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(siftsMapping, seq);
                     pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
             seqToStrucMapping.add(siftsMapping);
             maxChain.makeExactMapping(siftsMapping, seq);

-            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");
+            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+                    pdb.getId().toLowerCase(Locale.ROOT));

             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
           } catch (SiftsException e)
           {
             // fall back to NW alignment
             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
 
           } catch (SiftsException e)
           {
             // fall back to NW alignment

-            Cache.log.error(e.getMessage());
+            Console.error(e.getMessage());

             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     targetChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
             maxChain.makeExactMapping(maxAlignseq, seq);

-            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
-                                                                 // this
-                                                        // "IEA:Jalview" ?
+            maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
+                    pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+            // this
+            // "IEA:Jalview" ?

             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }

@@ -564,23 +583,21 @@ public class StructureSelectionManager
             StructureMapping siftsMapping = null;
             try
             {
             StructureMapping siftsMapping = null;
             try
             {

-              siftsMapping = getStructureMapping(seq,
-                      pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
-                      siftsClient);
+              siftsMapping = getStructureMapping(seq, pdbFile, chain.id,
+                      pdb, chain, sqmpping, maxAlignseq, siftsClient);

               foundSiftsMappings.add(siftsMapping);
               chain.makeExactMapping(siftsMapping, seq);
               foundSiftsMappings.add(siftsMapping);
               chain.makeExactMapping(siftsMapping, seq);

-              chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+              chain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+                      pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this

               // "IEA:SIFTS" ?
               chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
               System.err.println(e.getMessage());
               // "IEA:SIFTS" ?
               chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
               System.err.println(e.getMessage());

-            }
-            catch (Exception e)
+            } catch (Exception e)

             {
             {

-              System.err
-                      .println(
-                              "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+              System.err.println(
+                      "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");

               System.err.println(e.getMessage());
             }
           }
               System.err.println(e.getMessage());
             }
           }

@@ -594,8 +611,9 @@ public class StructureSelectionManager
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     maxChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);
             StructureMapping nwMapping = getNWMappings(seq, pdbFile,
                     maxChainId, maxChain, pdb, maxAlignseq);
             seqToStrucMapping.add(nwMapping);

-            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
-                                                        // "IEA:Jalview" ?
+            maxChain.transferRESNUMFeatures(seq, null,
+                    pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
+            // "IEA:Jalview" ?

             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }
             maxChain.transferResidueAnnotation(nwMapping, sqmpping);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
           }

@@ -605,8 +623,9 @@ public class StructureSelectionManager
       {
         if (progress != null)
         {
       {
         if (progress != null)
         {

-          progress.setProgressBar(MessageManager
-                                 .getString("status.obtaining_mapping_with_nw_alignment"),
+          progress.setProgressBar(
+                  MessageManager.getString(
+                          "status.obtaining_mapping_with_nw_alignment"),

                   progressSessionId);
         }
         StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
                   progressSessionId);
         }
         StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,

@@ -696,7 +715,8 @@ public class StructureSelectionManager
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
   private StructureMapping getStructureMapping(SequenceI seq,
           String pdbFile, String targetChainId, StructureFile pdb,
           PDBChain maxChain, jalview.datamodel.Mapping sqmpping,

-          AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
+          AlignSeq maxAlignseq, SiftsClient siftsClient)
+          throws SiftsException

   {
     StructureMapping curChainMapping = siftsClient
             .getSiftsStructureMapping(seq, pdbFile, targetChainId);
   {
     StructureMapping curChainMapping = siftsClient
             .getSiftsStructureMapping(seq, pdbFile, targetChainId);

@@ -762,7 +782,8 @@ public class StructureSelectionManager
     maxChain.makeExactMapping(maxAlignseq, seq);
     jalview.datamodel.Mapping sqmpping = maxAlignseq
             .getMappingFromS1(false);
     maxChain.makeExactMapping(maxAlignseq, seq);
     jalview.datamodel.Mapping sqmpping = maxAlignseq
             .getMappingFromS1(false);

-    maxChain.transferRESNUMFeatures(seq, null);
+    maxChain.transferRESNUMFeatures(seq, null,
+            pdb.getId().toLowerCase(Locale.ROOT));

 
     HashMap<Integer, int[]> mapping = new HashMap<>();
     int resNum = -10000;
 
     HashMap<Integer, int[]> mapping = new HashMap<>();
     int resNum = -10000;