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JAL-4371 minimal test and move PDBEntryUtils to correct package
[jalview.git] / src / jalview / structure / StructureSelectionManager.java
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 7456304..0f82650 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,8 +20,23 @@
  */
 package jalview.structure;
 
  */
 package jalview.structure;
 
+import java.io.PrintStream;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.IdentityHashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
+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;
@@ -29,6 +44,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
@@ -39,26 +55,17 @@ import jalview.gui.IProgressIndicator;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
+import jalview.structure.StructureImportSettings.TFType;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;
 import jalview.ws.sifts.SiftsClient;
 import jalview.ws.sifts.SiftsException;
 import jalview.ws.sifts.SiftsSettings;
-
-import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.IdentityHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Vector;
-
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
 
 public class StructureSelectionManager
 {
 
 public class StructureSelectionManager
 {
@@ -151,16 +158,18 @@ public class StructureSelectionManager
   {
     if (mappings.isEmpty())
     {
   {
     if (mappings.isEmpty())
     {
-      System.err.println("reportMapping: No PDB/Sequence mappings.");
+      jalview.bin.Console
+              .errPrintln("reportMapping: No PDB/Sequence mappings.");
     }
     else
     {
     }
     else
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "reportMapping: There are " + mappings.size() + " mappings.");
       int i = 0;
       for (StructureMapping sm : mappings)
       {
               "reportMapping: There are " + mappings.size() + " mappings.");
       int i = 0;
       for (StructureMapping sm : mappings)
       {
-        System.err.println("mapping " + i++ + " : " + sm.pdbfile);
+        jalview.bin.Console
+                .errPrintln("mapping " + i++ + " : " + sm.pdbfile);
       }
     }
   }
       }
     }
   }
@@ -285,7 +294,8 @@ public class StructureSelectionManager
   }
 
   /**
   }
 
   /**
-   * Returns the file name for a mapped PDB id (or null if not mapped).
+   * Returns the filename the PDB id is already mapped to if known, or null if
+   * it is not mapped
    * 
    * @param pdbid
    * @return
    * 
    * @param pdbid
    * @return
@@ -294,7 +304,7 @@ public class StructureSelectionManager
   {
     for (StructureMapping sm : mappings)
     {
   {
     for (StructureMapping sm : mappings)
     {
-      if (sm.getPdbId().equals(pdbid))
+      if (sm.getPdbId().equalsIgnoreCase(pdbid))
       {
         return sm.pdbfile;
       }
       {
         return sm.pdbfile;
       }
@@ -318,11 +328,11 @@ 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,
-            progress);
+            progress, null, null, true);
   }
 
   /**
   }
 
   /**
@@ -345,10 +355,50 @@ public class StructureSelectionManager
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
    */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
-          String pdbFile, DataSourceType sourceType)
+          String pdbFile, DataSourceType sourceType, TFType tft,
+          String paeFilename)
+  {
+    return setMapping(forStructureView, sequenceArray, targetChainIds,
+            pdbFile, sourceType, tft, paeFilename, true);
+  }
+
+  /**
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol). Either constructs a mapping
+   * using NW alignment or derives one from any available SIFTS mapping data.
+   * 
+   * @param forStructureView
+   *          when true, record the mapping for use in mouseOvers
+   * 
+   * @param sequenceArray
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChainIds
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+   *          - this should be List<List<String>>, empty lists indicate no
+   *          predefined mappings
+   * @param pdbFile
+   *          - structure data resource
+   * @param sourceType
+   *          - how to resolve data from resource
+   * @param tft
+   *          - specify how to interpret the temperature factor column in the
+   *          atom data
+   * @param paeFilename
+   *          - when not null, specifies a filename containing a matrix
+   *          formatted in JSON using one of the known PAE formats
+   * @param doXferSettings
+   *          - when true, transfer annotation to mapped sequences in
+   *          sequenceArray
+   * @return null or the structure data parsed as a pdb file
+   */
+  synchronized public StructureFile setMapping(boolean forStructureView,
+          SequenceI[] sequenceArray, String[] targetChainIds,
+          String pdbFile, DataSourceType sourceType, TFType tft,
+          String paeFilename, boolean doXferSettings)
   {
     return computeMapping(forStructureView, sequenceArray, targetChainIds,
   {
     return computeMapping(forStructureView, sequenceArray, targetChainIds,
-            pdbFile, sourceType, null);
+            pdbFile, sourceType, null, tft, paeFilename, doXferSettings);
   }
 
   /**
   }
 
   /**
@@ -373,12 +423,22 @@ public class StructureSelectionManager
    * @param IProgressIndicator
    *          reference to UI component that maintains a progress bar for the
    *          mapping operation
    * @param IProgressIndicator
    *          reference to UI component that maintains a progress bar for the
    *          mapping operation
+   * @param tft
+   *          - specify how to interpret the temperature factor column in the
+   *          atom data
+   * @param paeFilename
+   *          - when not null, specifies a filename containing a matrix
+   *          formatted in JSON using one of the known PAE formats
+   * @param doXferSettings
+   *          - when true, transfer annotation to mapped sequences in
+   *          sequenceArray
    * @return null or the structure data parsed as a pdb file
    */
    * @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,
-          IProgressIndicator progress)
+  synchronized public StructureFile computeMapping(boolean forStructureView,
+          SequenceI[] sequenceArray, String[] targetChainIds,
+          String pdbFile, DataSourceType sourceType,
+          IProgressIndicator progress, TFType tft, String paeFilename,
+          boolean doXferSettings)
   {
     long progressSessionId = System.currentTimeMillis() * 3;
 
   {
     long progressSessionId = System.currentTimeMillis() * 3;
 
@@ -388,8 +448,7 @@ public class StructureSelectionManager
     // FIXME: possibly should just delete
 
     boolean parseSecStr = processSecondaryStructure
     // FIXME: possibly should just delete
 
     boolean parseSecStr = processSecondaryStructure
-            ? isStructureFileProcessed(pdbFile, sequenceArray)
-            : false;
+            && !isStructureFileProcessed(pdbFile, sequenceArray);
 
     StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
 
     StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
@@ -397,15 +456,40 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      if (paeFilename != null)
+      {
+        pdb.setPAEMatrix(paeFilename);
+      }
+      pdb.setTemperatureFactorType(tft);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
+      // save doXferSettings and reset after doParse()
+      boolean temp = pdb.getDoXferSettings();
+      pdb.setDoXferSettings(doXferSettings);
+      pdb.doParse();
+      pdb.setDoXferSettings(temp);
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {
         registerPDBFile(pdb.getId().trim(), pdbFile);
       }
       // if PDBId is unavailable then skip SIFTS mapping execution path
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {
         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)
     {
@@ -425,7 +509,8 @@ 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;
     }
 
@@ -439,32 +524,15 @@ public class StructureSelectionManager
       {
         ds = ds.getDatasetSequence();
       }
       {
         ds = ds.getDatasetSequence();
       }
-
+      List <PDBEntry> putativePDBe = PDBEntryUtils.selectPutativePDBe(seq,ds, pdb); 
+      
       if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
         targetChainId = targetChainIds[s];
       }
       if (targetChainIds != null && targetChainIds[s] != null)
       {
         infChain = false;
         targetChainId = targetChainIds[s];
       }
-      else if (seq.getName().indexOf("|") > -1)
-      {
-        targetChainId = seq.getName()
-                .substring(seq.getName().lastIndexOf("|") + 1);
-        if (targetChainId.length() > 1)
-        {
-          if (targetChainId.trim().length() == 0)
-          {
-            targetChainId = " ";
-          }
-          else
-          {
-            // not a valid chain identifier
-            targetChainId = "";
-          }
-        }
-      }
-      else
-      {
-        targetChainId = "";
+      else {
+        targetChainId = PDBEntryUtils.inferChainId(seq);
       }
 
       /*
       }
 
       /*
@@ -476,6 +544,7 @@ public class StructureSelectionManager
       String maxChainId = " ";
       PDBChain maxChain = null;
       boolean first = true;
       String maxChainId = " ";
       PDBChain maxChain = null;
       boolean first = true;
+      PDBChain idLengthChain = null;
       for (PDBChain chain : pdb.getChains())
       {
         if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
       for (PDBChain chain : pdb.getChains())
       {
         if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
@@ -483,15 +552,22 @@ public class StructureSelectionManager
         {
           continue; // don't try to map chains don't match.
         }
         {
           continue; // don't try to map chains don't match.
         }
+        PDBEntry putativeChain = null;
+        if (!putativePDBe.isEmpty() && (putativeChain = PDBEntryUtils
+                .selectPutativePDBEntry(putativePDBe, chain)) == null)
+        {
+          continue;
+        }
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
         AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
                 type);
         // TODO: correctly determine sequence type for mixed na/peptide
         // structures
         final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP;
         AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence,
                 type);
-        // equivalent to:
-        // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type);
-        // as.calcScoreMatrix();
-        // as.traceAlignment();
+        // TODO: JAL-4366 determinine of a crummy alignment but exact match should make this chain the one to be mapped to a 3di sequence
+        if (as.s1str.length() == as.s2str.length())
+        {
+          idLengthChain = chain;
+        }
 
         if (first || as.maxscore > max
                 || (as.maxscore == max && chain.id.equals(targetChainId)))
 
         if (first || as.maxscore > max
                 || (as.maxscore == max && chain.id.equals(targetChainId)))
@@ -507,18 +583,20 @@ public class StructureSelectionManager
       {
         continue;
       }
       {
         continue;
       }
-
       if (sourceType == DataSourceType.PASTE)
       {
         pdbFile = "INLINE" + pdb.getId();
       }
       if (sourceType == DataSourceType.PASTE)
       {
         pdbFile = "INLINE" + pdb.getId();
       }
-
       List<StructureMapping> seqToStrucMapping = new ArrayList<>();
       List<StructureMapping> seqToStrucMapping = new ArrayList<>();
+
+      List<StructureMapping> foundSiftsMappings = new ArrayList<>();
       if (isMapUsingSIFTs && seq.isProtein())
       {
       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
@@ -532,87 +610,97 @@ 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");// FIXME: is this
-                                                       // "IEA:SIFTS" ?
+            maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+                    pdb.getId().toLowerCase(Locale.ROOT));
             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
             maxChain.transferResidueAnnotation(siftsMapping, null);
             ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+            foundSiftsMappings.add(siftsMapping);
 
           } catch (SiftsException e)
           {
 
           } catch (SiftsException e)
           {
-            // fall back to NW alignment
-            System.err.println(e.getMessage());
-            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.transferResidueAnnotation(nwMapping, sqmpping);
-            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+            Console.error(e.getMessage());
           }
         }
         else
         {
           }
         }
         else
         {
-          List<StructureMapping> foundSiftsMappings = new ArrayList<>();
           for (PDBChain chain : pdb.getChains())
           {
             StructureMapping siftsMapping = null;
             try
             {
           for (PDBChain chain : pdb.getChains())
           {
             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)
             {
               // "IEA:SIFTS" ?
               chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
-              System.err.println(e.getMessage());
-            }
-            catch (Exception e)
+              jalview.bin.Console.errPrintln(e.getMessage());
+            } catch (Exception e)
             {
             {
-              System.err
-                      .println(
-                              "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
-              System.err.println(e.getMessage());
+              jalview.bin.Console.errPrintln(
+                      "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+              jalview.bin.Console.errPrintln(e.getMessage());
             }
           }
             }
           }
+          // If sifts was successful, add mappings and return
           if (!foundSiftsMappings.isEmpty())
           {
           if (!foundSiftsMappings.isEmpty())
           {
-            seqToStrucMapping.addAll(foundSiftsMappings);
             ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
           }
             ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
           }
-          else
-          {
-            StructureMapping nwMapping = getNWMappings(seq, pdbFile,
-                    maxChainId, maxChain, pdb, maxAlignseq);
-            seqToStrucMapping.add(nwMapping);
-            maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
-                                                        // "IEA:Jalview" ?
-            maxChain.transferResidueAnnotation(nwMapping, sqmpping);
-            ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
-          }
+        }
+        
+        // If sifts was successful, add mappings and return
+        if (!foundSiftsMappings.isEmpty())
+        {
+          seqToStrucMapping.addAll(foundSiftsMappings);
         }
       }
         }
       }
-      else
+      if (foundSiftsMappings.isEmpty())
       {
       {
-        if (progress != null)
+        // Not doing SIFTS, or SIFTS failed for some reason.
+        
+        // first check if we should use an identity mapping
+        if (idLengthChain != null && maxAlignseq.getS2Coverage() < 0.75)
         {
         {
-          progress.setProgressBar(MessageManager
-                                 .getString("status.obtaining_mapping_with_nw_alignment"),
-                  progressSessionId);
+          Console.info(
+                  "Assuming 3Dsi identity mapping between structure and sequence");
+          StructureMapping matchMapping = getIdMappings(seq, pdbFile,
+                  idLengthChain.id, idLengthChain, pdb);
+          seqToStrucMapping.add(matchMapping);
+          ds.addPDBId(idLengthChain.sequence.getAllPDBEntries().get(0));
+          Console.info("Mapping added.");
+        }
+        else
+        {
+          if (maxAlignseq.getS1Coverage()<0.15 && maxAlignseq.getS2Coverage()<0.15)
+          {
+            // skip this - the NW alignment is spurious
+            continue;
+          }
+          // Construct a needleman wunsch mapping instead.
+          if (progress != null)
+          {
+            progress.setProgressBar(
+                    MessageManager.getString(
+                            "status.obtaining_mapping_with_nw_alignment"),
+                    progressSessionId);
+          }
+          StructureMapping nwMapping = getNWMappings(seq, pdbFile,
+                  maxChainId, maxChain, pdb, maxAlignseq);
+          seqToStrucMapping.add(nwMapping);
+          ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
         }
         }
-        StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
-                maxChain, pdb, maxAlignseq);
-        seqToStrucMapping.add(nwMapping);
-        ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
       }
       if (forStructureView)
       {
       }
       if (forStructureView)
       {
-        mappings.addAll(seqToStrucMapping);
+        for (StructureMapping sm : seqToStrucMapping)
+        {
+          addStructureMapping(sm); // not addAll!
+        }
       }
       if (progress != null)
       {
       }
       if (progress != null)
       {
@@ -633,7 +721,7 @@ public class StructureSelectionManager
   private boolean isStructureFileProcessed(String pdbFile,
           SequenceI[] sequenceArray)
   {
   private boolean isStructureFileProcessed(String pdbFile,
           SequenceI[] sequenceArray)
   {
-    boolean parseSecStr = true;
+    boolean processed = false;
     if (isPDBFileRegistered(pdbFile))
     {
       for (SequenceI sq : sequenceArray)
     if (isPDBFileRegistered(pdbFile))
     {
       for (SequenceI sq : sequenceArray)
@@ -653,18 +741,21 @@ public class StructureSelectionManager
             // passed, not the structure data ID -
             if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
             {
             // passed, not the structure data ID -
             if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
             {
-              parseSecStr = false;
+              processed = true;
             }
           }
         }
       }
     }
             }
           }
         }
       }
     }
-    return parseSecStr;
+    return processed;
   }
 
   public void addStructureMapping(StructureMapping sm)
   {
   }
 
   public void addStructureMapping(StructureMapping sm)
   {
-    mappings.add(sm);
+    if (!mappings.contains(sm))
+    {
+      mappings.add(sm);
+    }
   }
 
   /**
   }
 
   /**
@@ -686,7 +777,8 @@ 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);
@@ -703,6 +795,17 @@ public class StructureSelectionManager
     }
     return curChainMapping;
   }
     }
     return curChainMapping;
   }
+  
+  /**
+   * construct a mapping based on a pairwise alignment of the sequence and chain
+   * @param seq
+   * @param pdbFile
+   * @param maxChainId
+   * @param maxChain
+   * @param pdb
+   * @param maxAlignseq
+   * @return
+   */
 
   private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
           String maxChainId, PDBChain maxChain, StructureFile pdb,
 
   private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
           String maxChainId, PDBChain maxChain, StructureFile pdb,
@@ -752,7 +855,8 @@ 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;
@@ -783,6 +887,82 @@ public class StructureSelectionManager
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
     return nwMapping;
   }
     maxChain.transferResidueAnnotation(nwMapping, sqmpping);
     return nwMapping;
   }
+  
+  /**
+   * construct a 1:1 mapping using given residue and sequence numbering 
+   * @param seq
+   * @param pdbFile
+   * @param identityChainId
+   * @param identityChain
+   * @param pdb
+   * @return
+   */
+
+  private StructureMapping getIdMappings(SequenceI seq, String pdbFile,
+          String identityChainId, PDBChain identityChain, StructureFile pdb)
+  {
+    final StringBuilder mappingDetails = new StringBuilder(128);
+    mappingDetails.append(NEWLINE)
+            .append("Sequence \u27f7 Structure mapping details");
+    mappingDetails.append(NEWLINE);
+    mappingDetails.append("Method: Matching length 1:1");
+    mappingDetails.append(NEWLINE).append("PDB Sequence is :")
+            .append(NEWLINE).append("Sequence = ")
+            .append(identityChain.sequence.getSequenceAsString());
+    mappingDetails.append(NEWLINE).append("No of residues = ")
+            .append(identityChain.residues.size()).append(NEWLINE)
+            .append(NEWLINE);
+
+    mappingDetails.append(NEWLINE)
+            .append("Aligned Sequence is: " + seq.getDisplayId(true));
+    mappingDetails.append(NEWLINE)
+            .append("Sequence = " + seq.getSequenceAsString());
+
+    int from = Math.max(seq.getStart(),identityChain.sequence.getStart());
+    int to = Math.min(seq.getEnd(), identityChain.sequence.getEnd());
+    jalview.datamodel.Mapping sqmpping = new jalview.datamodel.Mapping(seq,
+            new MapList(new int[]
+            { from,to },
+                    new int[]
+                    { from,to },
+                    1, 1));
+    identityChain.mapChainWith(sqmpping, seq);
+
+    identityChain.transferRESNUMFeatures(seq, null,
+            pdb.getId().toLowerCase(Locale.ROOT));
+
+    // Construct mapping
+    // TODO REFACTOR TO PDBChain as a builder
+    HashMap<Integer, int[]> mapping = new HashMap<>();
+    int resNum = -10000;
+    int index = 0;
+    char insCode = ' ';
+
+    do
+    {
+      Atom tmp = identityChain.atoms.elementAt(index);
+      if ((resNum != tmp.resNumber || insCode != tmp.insCode)
+              && tmp.alignmentMapping != -1)
+      {
+        resNum = tmp.resNumber;
+        insCode = tmp.insCode;
+        if (tmp.alignmentMapping >= -1)
+        {
+          mapping.put(tmp.alignmentMapping + 1,
+                  new int[]
+                  { tmp.resNumber, tmp.atomIndex });
+        }
+      }
+
+      index++;
+    } while (index < identityChain.atoms.size());
+
+    StructureMapping idMapping = new StructureMapping(seq, pdbFile,
+            pdb.getId(), identityChainId, mapping,
+            mappingDetails.toString());
+    identityChain.transferResidueAnnotation(idMapping, sqmpping);
+    return idMapping;
+  }
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
 
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
@@ -843,18 +1023,65 @@ public class StructureSelectionManager
   }
 
   /**
   }
 
   /**
+   * hack to highlight a range of positions at once on any structure views
+   * 
+   * @param sequenceRef
+   * @param is
+   *          - series of int start-end ranges as positions on sequenceRef
+   * @param i
+   * @param object
+   */
+  public void highlightPositionsOn(SequenceI sequenceRef, int[][] is,
+          Object source)
+  {
+    boolean hasSequenceListeners = handlingVamsasMo
+            || !seqmappings.isEmpty();
+    SearchResultsI results = null;
+    ArrayList<Integer> listOfPositions = new ArrayList<Integer>();
+    for (int[] s_e : is)
+    {
+      for (int p = s_e[0]; p <= s_e[1]; listOfPositions.add(p++))
+        ;
+    }
+    int seqpos[] = new int[listOfPositions.size()];
+    int i = 0;
+    for (Integer p : listOfPositions)
+    {
+      seqpos[i++] = p;
+    }
+
+    for (i = 0; i < listeners.size(); i++)
+    {
+      Object listener = listeners.elementAt(i);
+      if (listener == source)
+      {
+        // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+        // Temporary fudge with SequenceListener.getVamsasSource()
+        continue;
+      }
+      if (listener instanceof StructureListener)
+      {
+        highlightStructure((StructureListener) listener, sequenceRef,
+                seqpos);
+      }
+
+    }
+  }
+
+  /**
    * Propagate mouseover of a single position in a structure
    * 
    * @param pdbResNum
    * @param chain
    * @param pdbfile
    * Propagate mouseover of a single position in a structure
    * 
    * @param pdbResNum
    * @param chain
    * @param pdbfile
+   * @return
    */
    */
-  public void mouseOverStructure(int pdbResNum, String chain,
+  public String mouseOverStructure(int pdbResNum, String chain,
           String pdbfile)
   {
     AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
     List<AtomSpec> atoms = Collections.singletonList(atomSpec);
           String pdbfile)
   {
     AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
     List<AtomSpec> atoms = Collections.singletonList(atomSpec);
-    mouseOverStructure(atoms);
+    return mouseOverStructure(atoms);
   }
 
   /**
   }
 
   /**
@@ -862,12 +1089,12 @@ public class StructureSelectionManager
    * 
    * @param atoms
    */
    * 
    * @param atoms
    */
-  public void mouseOverStructure(List<AtomSpec> atoms)
+  public String mouseOverStructure(List<AtomSpec> atoms)
   {
     if (listeners == null)
     {
       // old or prematurely sent event
   {
     if (listeners == null)
     {
       // old or prematurely sent event
-      return;
+      return null;
     }
     boolean hasSequenceListener = false;
     for (int i = 0; i < listeners.size(); i++)
     }
     boolean hasSequenceListener = false;
     for (int i = 0; i < listeners.size(); i++)
@@ -879,18 +1106,24 @@ public class StructureSelectionManager
     }
     if (!hasSequenceListener)
     {
     }
     if (!hasSequenceListener)
     {
-      return;
+      return null;
     }
 
     SearchResultsI results = findAlignmentPositionsForStructurePositions(
             atoms);
     }
 
     SearchResultsI results = findAlignmentPositionsForStructurePositions(
             atoms);
+    String result = null;
     for (Object li : listeners)
     {
       if (li instanceof SequenceListener)
       {
     for (Object li : listeners)
     {
       if (li instanceof SequenceListener)
       {
-        ((SequenceListener) li).highlightSequence(results);
+        String s = ((SequenceListener) li).highlightSequence(results);
+        if (s != null)
+        {
+          result = s;
+        }
       }
     }
       }
     }
+    return result;
   }
 
   /**
   }
 
   /**
@@ -917,7 +1150,7 @@ public class StructureSelectionManager
           int indexpos = sm.getSeqPos(atom.getPdbResNum());
           if (lastipos != indexpos || lastseq != sm.sequence)
           {
           int indexpos = sm.getSeqPos(atom.getPdbResNum());
           if (lastipos != indexpos || lastseq != sm.sequence)
           {
-            results.addResult(sm.sequence, indexpos, indexpos);
+            results.appendResult(sm.sequence, indexpos, indexpos);
             lastipos = indexpos;
             lastseq = sm.sequence;
             // construct highlighted sequence list
             lastipos = indexpos;
             lastseq = sm.sequence;
             // construct highlighted sequence list
@@ -1045,6 +1278,62 @@ public class StructureSelectionManager
     sl.highlightAtoms(atoms);
   }
 
     sl.highlightAtoms(atoms);
   }
 
+  public void highlightStructureRegionsFor(StructureListener sl,
+          SequenceI[] seqs, int... columns)
+  {
+    List<SequenceI> to_highlight = new ArrayList<SequenceI>();
+    for (SequenceI seq : seqs)
+    {
+      if (sl.isListeningFor(seq))
+      {
+        to_highlight.add(seq);
+      }
+    }
+    if (to_highlight.size() == 0)
+    {
+      return;
+    }
+    List<AtomSpec> atoms = new ArrayList<>();
+    for (SequenceI seq : to_highlight)
+    {
+      int atomNo;
+      for (StructureMapping sm : mappings)
+      {
+        if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
+                || (sm.sequence.getDatasetSequence() != null && sm.sequence
+                        .getDatasetSequence() == seq.getDatasetSequence()))
+        {
+
+          for (int i = 0; i < columns.length; i += 2)
+          {
+            ContiguousI positions = seq.findPositions(columns[i] + 1,
+                    columns[i + 1] + 1);
+            if (positions == null)
+            {
+              continue;
+            }
+            for (int index = positions.getBegin(); index <= positions
+                    .getEnd(); index++)
+            {
+
+              atomNo = sm.getAtomNum(index);
+
+              if (atomNo > 0)
+              {
+                atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+                        sm.getPDBResNum(index), atomNo));
+              }
+            }
+          }
+        }
+      }
+      if (atoms.size() > 0)
+      {
+        sl.highlightAtoms(atoms);
+      }
+    }
+  }
+
   /**
    * true if a mouse over event from an external (ie Vamsas) source is being
    * handled
   /**
    * true if a mouse over event from an external (ie Vamsas) source is being
    * handled
@@ -1090,7 +1379,7 @@ public class StructureSelectionManager
      * 
      * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
      * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
      * 
      * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
      * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
-     * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+     * jalview.bin.Console.outPrintln(pdbid+" "+mappings[j].getPdbId() +"
      * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
      * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
@@ -1160,7 +1449,8 @@ public class StructureSelectionManager
     StringBuilder sb = new StringBuilder(64);
     for (StructureMapping sm : mappings)
     {
     StringBuilder sb = new StringBuilder(64);
     for (StructureMapping sm : mappings)
     {
-      if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+      if (Platform.pathEquals(sm.pdbfile, pdbfile)
+              && seqs.contains(sm.sequence))
       {
         sb.append(sm.mappingDetails);
         sb.append(NEWLINE);
       {
         sb.append(sm.mappingDetails);
         sb.append(NEWLINE);
@@ -1186,7 +1476,7 @@ public class StructureSelectionManager
       boolean removed = seqmappings.remove(acf);
       if (removed && seqmappings.isEmpty())
       { // debug
       boolean removed = seqmappings.remove(acf);
       if (removed && seqmappings.isEmpty())
       { // debug
-        System.out.println("All mappings removed");
+        jalview.bin.Console.outPrintln("All mappings removed");
       }
     }
   }
       }
     }
   }
@@ -1333,7 +1623,10 @@ public class StructureSelectionManager
         instances.remove(jalviewLite);
         try
         {
         instances.remove(jalviewLite);
         try
         {
-          mnger.finalize();
+          /* bsoares 2019-03-20 finalize deprecated, no apparent external
+           * resources to close
+           */
+          // mnger.finalize();
         } catch (Throwable x)
         {
         }
         } catch (Throwable x)
         {
         }
@@ -1419,4 +1712,44 @@ public class StructureSelectionManager
     return seqmappings;
   }
 
     return seqmappings;
   }
 
+  /**
+   * quick and dirty route to just highlight all structure positions for a range
+   * of columns
+   * 
+   * @param sequencesArray
+   * @param is
+   *          start-end columns on sequencesArray
+   * @param source
+   *          origin parent AlignmentPanel
+   */
+  public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is,
+          Object source)
+  {
+    for (int i = 0; i < listeners.size(); i++)
+    {
+      Object listener = listeners.elementAt(i);
+      if (listener == source)
+      {
+        // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+        // Temporary fudge with SequenceListener.getVamsasSource()
+        continue;
+      }
+      if (listener instanceof StructureListener)
+      {
+        highlightStructureRegionsFor((StructureListener) listener,
+                sequencesArray, is);
+      }
+    }
+  }
+
+  public Map<String, String> getPdbFileNameIdMap()
+  {
+    return pdbFileNameId;
+  }
+
+  public Map<String, String> getPdbIdFileNameMap()
+  {
+    return pdbIdFileName;
+  }
+
 }
 }