JAL-1479 refactored SequenceI interface - changed getDBRef() to getDBRefs() since...

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 898e4f7..da5bc2f 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -1284,7 +1284,7 @@ public class AlignmentUtils
       return false;
     }
     String name = seq2.getName();
-    final DBRefEntry[] xrefs = seq1.getDBRef();
+    final DBRefEntry[] xrefs = seq1.getDBRefs();
     if (xrefs != null)
     {
       for (DBRefEntry xref : xrefs)
@@ -1402,7 +1402,7 @@ public class AlignmentUtils
       String cdsAccId = FeatureProperties
               .getCodingFeature(DBRefSource.EMBL);
       DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(seqMapping.getTo()
-              .getDBRef(), DBRefSource.CODINGDBS);
+              .getDBRefs(), DBRefSource.CODINGDBS);
       if (cdsRefs != null)
       {
         for (DBRefEntry cdsRef : cdsRefs)

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 2e6431c..a71e614 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -97,7 +97,7 @@ public class CrossRef
         {
           dss = dss.getDatasetSequence();
         }
-        DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRef());
+        DBRefEntry[] rfs = findXDbRefs(dna, dss.getDBRefs());
         for (int r = 0; rfs != null && r < rfs.length; r++)
         {
           if (!refs.contains(rfs[r].getSource()))
@@ -109,13 +109,13 @@ public class CrossRef
         {
           // search for references to this sequence's direct references.
           DBRefEntry[] lrfs = CrossRef
-                  .findXDbRefs(!dna, seqs[s].getDBRef());
+                  .findXDbRefs(!dna, seqs[s].getDBRefs());
           List<SequenceI> rseqs = new ArrayList<SequenceI>();
           CrossRef.searchDatasetXrefs(seqs[s], !dna, lrfs, dataset, rseqs,
                   null); // don't need to specify codon frame for mapping here
           for (SequenceI rs : rseqs)
           {
-            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRef()); // not used??
+            DBRefEntry[] xrs = findXDbRefs(dna, rs.getDBRefs()); // not used??
             for (int r = 0; rfs != null && r < rfs.length; r++)
             {
               if (!refs.contains(rfs[r].getSource()))
@@ -159,7 +159,7 @@ public class CrossRef
     Vector cseqs = new Vector();
     for (int s = 0; s < seqs.length; s++)
     {
-      DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRef());
+      DBRefEntry[] cdna = findXDbRefs(true, seqs[s].getDBRefs());
       for (int c = 0; c < cdna.length; c++)
       {
         if (cdna[c].getSource().equals(DBRefSource.EMBLCDS))
@@ -219,11 +219,11 @@ public class CrossRef
         dss = dss.getDatasetSequence();
       }
       boolean found = false;
-      DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRef());
+      DBRefEntry[] xrfs = CrossRef.findXDbRefs(dna, dss.getDBRefs());
       if ((xrfs == null || xrfs.length == 0) && dataset != null)
       {
         System.out.println("Attempting to find ds Xrefs refs.");
-        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef());
+        DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRefs());
         // less ambiguous would be a 'find primary dbRefEntry' method.
         // filter for desired source xref here
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
@@ -330,7 +330,7 @@ public class CrossRef
               {
                 // TODO: examine each sequence for 'redundancy'
                 jalview.datamodel.DBRefEntry[] dbr = retrieved[rs]
-                        .getDBRef();
+                        .getDBRefs();
                 if (dbr != null && dbr.length > 0)
                 {
                   for (int di = 0; di < dbr.length; di++)
@@ -500,7 +500,7 @@ public class CrossRef
             }
 
             // look for direct or indirect references in common
-            DBRefEntry[] poss = nxt.getDBRef(), cands = null;
+            DBRefEntry[] poss = nxt.getDBRefs(), cands = null;
             if (direct)
             {
               cands = jalview.util.DBRefUtils.searchRefs(poss, xrf);

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 9ce00cc..2939e3c 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -208,13 +208,13 @@ public class Dna
     for (int gd = 0; gd < selection.length; gd++)
     {
       SequenceI dna = selection[gd];
-      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+      DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
               jalview.datamodel.DBRefSource.DNACODINGDBS);
       if (dnarefs != null)
       {
         // intersect with pep
         List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
-        DBRefEntry[] refs = dna.getDBRef();
+        DBRefEntry[] refs = dna.getDBRefs();
         for (int d = 0; d < refs.length; d++)
         {
           if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
@@ -773,7 +773,7 @@ public class Dna
   {
     SequenceFeature[] sfs = dna.getSequenceFeatures();
     Boolean fgstate;
-    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
+    DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
             DBRefSource.DNACODINGDBS);
     if (dnarefs != null)
     {

diff --git a/src/jalview/analysis/SequenceIdMatcher.java b/src/jalview/analysis/SequenceIdMatcher.java
index 35a72e3..454bc09 100755 (executable)
--- a/src/jalview/analysis/SequenceIdMatcher.java
+++ b/src/jalview/analysis/SequenceIdMatcher.java
@@ -63,9 +63,9 @@ public class SequenceIdMatcher
         dbseq = dbseq.getDatasetSequence();
       }
       // add in any interesting identifiers
-      if (dbseq.getDBRef() != null)
+      if (dbseq.getDBRefs() != null)
       {
-        DBRefEntry dbr[] = dbseq.getDBRef();
+        DBRefEntry dbr[] = dbseq.getDBRefs();
         SeqIdName sid = null;
         for (int r = 0; r < dbr.length; r++)
         {

diff --git a/src/jalview/api/DBRefEntryI.java b/src/jalview/api/DBRefEntryI.java
index 731c258..3238781 100644 (file)
--- a/src/jalview/api/DBRefEntryI.java
+++ b/src/jalview/api/DBRefEntryI.java
@@ -16,4 +16,12 @@ public interface DBRefEntryI
   public void setSource(String source);
 
   public void setVersion(String version);
+
+  public void setStartRes(int startRes);
+
+  public int getStartRes();
+
+  public void setEndRes(int endRes);
+
+  public int getEndRes();
 }

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 1d2feb2..748954a 100644 (file)
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -274,7 +274,7 @@ public class APopupMenu extends java.awt.PopupMenu implements
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[] { target });
+                  seq.getDBRefs(), new String[] { target });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 0d6f68d..142d996 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -26,6 +26,7 @@ public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
 
+  private int startRes, endRes;
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
@@ -209,4 +210,24 @@ public class DBRefEntry implements DBRefEntryI
   {
     return getSrcAccString();
   }
+
+  public int getStartRes()
+  {
+    return startRes;
+  }
+
+  public void setStartRes(int startRes)
+  {
+    this.startRes = startRes;
+  }
+
+  public int getEndRes()
+  {
+    return endRes;
+  }
+
+  public void setEndRes(int endRes)
+  {
+    this.endRes = endRes;
+  }
 }

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9f65f71..c8bd902 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -228,10 +228,10 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     setDatasetSequence(seq.getDatasetSequence());
-    if (datasetSequence == null && seq.getDBRef() != null)
+    if (datasetSequence == null && seq.getDBRefs() != null)
     {
       // only copy DBRefs if we really are a dataset sequence
-      DBRefEntry[] dbr = seq.getDBRef();
+      DBRefEntry[] dbr = seq.getDBRefs();
       for (int i = 0; i < dbr.length; i++)
       {
         addDBRef(new DBRefEntry(dbr[i]));
@@ -917,12 +917,12 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public DBRefEntry[] getDBRef()
+  public DBRefEntry[] getDBRefs()
   {
     if (dbrefs == null && datasetSequence != null
             && this != datasetSequence)
     {
-      return datasetSequence.getDBRef();
+      return datasetSequence.getDBRefs();
     }
     return dbrefs;
   }
@@ -1079,7 +1079,7 @@ public class Sequence extends ASequence implements SequenceI
       datasetSequence.setDescription(getDescription());
       setSequenceFeatures(null);
       // move database references onto dataset sequence
-      datasetSequence.setDBRef(getDBRef());
+      datasetSequence.setDBRef(getDBRefs());
       setDBRef(null);
       datasetSequence.setPDBId(getAllPDBEntries());
       setPDBId(null);
@@ -1255,7 +1255,7 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     // transfer database references
-    DBRefEntry[] entryRefs = entry.getDBRef();
+    DBRefEntry[] entryRefs = entry.getDBRefs();
     if (entryRefs != null)
     {
       for (int r = 0; r < entryRefs.length; r++)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index cc70e25..d79a5f7 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -209,7 +209,7 @@ public class SequenceGroup implements AnnotatedCollectionI
       if (seqs[ipos] != null)
       {
         seqs[ipos].setDescription(seq.getDescription());
-        seqs[ipos].setDBRef(seq.getDBRef());
+        seqs[ipos].setDBRef(seq.getDBRefs());
         seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
         if (seq.getDatasetSequence() != null)
         {

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 49b0e4d..50f88f3 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -300,7 +300,7 @@ public interface SequenceI extends ASequenceI
 
   public void setDBRef(DBRefEntry[] dbs);
 
-  public DBRefEntry[] getDBRef();
+  public DBRefEntry[] getDBRefs();
 
   /**
    * add the given entry to the list of DBRefs for this sequence, or replace a

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 50a8167..fc96edc 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1948,16 +1948,16 @@ public class Jalview2XML
     if (jds.getDatasetSequence() != null)
     {
       vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
-      if (jds.getDatasetSequence().getDBRef() != null)
+      if (jds.getDatasetSequence().getDBRefs() != null)
       {
-        dbrefs = jds.getDatasetSequence().getDBRef();
+        dbrefs = jds.getDatasetSequence().getDBRefs();
       }
     }
     else
     {
       vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
       // dataset sequences only
-      dbrefs = jds.getDBRef();
+      dbrefs = jds.getDBRefs();
     }
     if (dbrefs != null)
     {

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index fee47e5..3491431 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -642,7 +642,7 @@ public class PopupMenu extends JPopupMenu
 
           // collect matching db-refs
           DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
-                  seq.getDBRef(), new String[] { urlLink.getTarget() });
+                  seq.getDBRefs(), new String[] { urlLink.getTarget() });
           // collect id string too
           String id = seq.getName();
           String descr = seq.getDescription();
@@ -896,7 +896,7 @@ public class PopupMenu extends JPopupMenu
       {
         sqi = sqi.getDatasetSequence();
       }
-      DBRefEntry[] dbr = sqi.getDBRef();
+      DBRefEntry[] dbr = sqi.getDBRefs();
       if (dbr != null && dbr.length > 0)
       {
         for (int d = 0; d < dbr.length; d++)

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index a973757..191e8fe 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -661,7 +661,7 @@ public class SequenceFetcher extends JPanel implements Runnable
                 {
                   if (rs[r] != null
                           && (found = DBRefUtils.searchRefs(
-                                  rs[r].getDBRef(), dbr)) != null
+                                  rs[r].getDBRefs(), dbr)) != null
                           && found.length > 0)
                   {
                     rfound = true;

diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java
index 63a8654..2a7da57 100644 (file)
--- a/src/jalview/gui/StructureChooser.java
+++ b/src/jalview/gui/StructureChooser.java
@@ -257,10 +257,10 @@ public class StructureChooser extends GStructureChooser
       }
     }
 
-    if (seq.getDBRef() != null && seq.getDBRef().length != 0)
+    if (seq.getDBRefs() != null && seq.getDBRefs().length != 0)
     {
       int count = 0;
-      for (DBRefEntry dbRef : seq.getDBRef())
+      for (DBRefEntry dbRef : seq.getDBRefs())
       {
         if (isValidSeqName(getDBRefId(dbRef)))
         {

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index d2c86c8..9522144 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -840,7 +840,7 @@ public class TreePanel extends GTreePanel
           {
             // search dbrefs, features and annotation
             DBRefEntry[] refs = jalview.util.DBRefUtils.selectRefs(
-                    sq.getDBRef(),
+                    sq.getDBRefs(),
                     new String[] { labelClass.toUpperCase() });
             if (refs != null)
             {

diff --git a/src/jalview/io/ModellerDescription.java b/src/jalview/io/ModellerDescription.java
index 55324ad..1ab9545 100755 (executable)
--- a/src/jalview/io/ModellerDescription.java
+++ b/src/jalview/io/ModellerDescription.java
@@ -268,10 +268,10 @@ public class ModellerDescription
       // sets the local reference field
       int t = 0; // sequence
       if (seq.getDatasetSequence() != null
-              && seq.getDatasetSequence().getDBRef() != null)
+              && seq.getDatasetSequence().getDBRefs() != null)
       {
         jalview.datamodel.DBRefEntry[] dbr = seq.getDatasetSequence()
-                .getDBRef();
+                .getDBRefs();
         int i, j;
         for (i = 0, j = dbr.length; i < j; i++)
         {

diff --git a/src/jalview/io/SequenceAnnotationReport.java b/src/jalview/io/SequenceAnnotationReport.java
index 72f8044..d3a1d09 100644 (file)
--- a/src/jalview/io/SequenceAnnotationReport.java
+++ b/src/jalview/io/SequenceAnnotationReport.java
@@ -230,7 +230,7 @@ public class SequenceAnnotationReport
     {
 
       // collect matching db-refs
-      DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(),
+      DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRefs(),
               new String[] { target });
       // collect id string too
       String id = seq.getName();
@@ -346,7 +346,7 @@ public class SequenceAnnotationReport
     {
       ds = ds.getDatasetSequence();
     }
-    DBRefEntry[] dbrefs = ds.getDBRef();
+    DBRefEntry[] dbrefs = ds.getDBRefs();
     if (showDbRefs && dbrefs != null)
     {
       for (int i = 0; i < dbrefs.length; i++)

diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index 9135b92..23c4d21 100644 (file)
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -900,18 +900,18 @@ public class StockholmFile extends AlignFile
       {
         maxid = tmp.length();
       }
-      if (s[in].getDBRef() != null)
+      if (s[in].getDBRefs() != null)
       {
-        for (int idb = 0; idb < s[in].getDBRef().length; idb++)
+        for (int idb = 0; idb < s[in].getDBRefs().length; idb++)
         {
           if (dataRef == null)
           {
             dataRef = new Hashtable();
           }
 
-          String datAs1 = s[in].getDBRef()[idb].getSource().toString()
+          String datAs1 = s[in].getDBRefs()[idb].getSource().toString()
                   + " ; "
-                  + s[in].getDBRef()[idb].getAccessionId().toString();
+                  + s[in].getDBRefs()[idb].getAccessionId().toString();
           dataRef.put(tmp, datAs1);
         }
       }

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index a6c1111..9d9b940 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -176,7 +176,7 @@ public class WSWUBlastClient
           }
         }
 
-        DBRefEntry[] entries = oldseq.getDBRef();
+        DBRefEntry[] entries = oldseq.getDBRefs();
         if (entries != null)
         {
           oldseq.addDBRef(new jalview.datamodel.DBRefEntry(

diff --git a/src/jalview/io/vamsas/Datasetsequence.java b/src/jalview/io/vamsas/Datasetsequence.java
index f1b9f1a..9db7a8e 100644 (file)
--- a/src/jalview/io/vamsas/Datasetsequence.java
+++ b/src/jalview/io/vamsas/Datasetsequence.java
@@ -175,10 +175,10 @@ public class Datasetsequence extends DatastoreItem
     boolean modifiedthedoc = false;
     SequenceI sq = (SequenceI) jvobj;
 
-    if (sq.getDatasetSequence() == null && sq.getDBRef() != null)
+    if (sq.getDatasetSequence() == null && sq.getDBRefs() != null)
     {
       // only sync database references for dataset sequences
-      DBRefEntry[] entries = sq.getDBRef();
+      DBRefEntry[] entries = sq.getDBRefs();
       // jalview.datamodel.DBRefEntry dbentry;
       for (int db = 0; db < entries.length; db++)
       {

diff --git a/src/jalview/io/vamsas/Sequencemapping.java b/src/jalview/io/vamsas/Sequencemapping.java
index 31ccc48..160f5e2 100644 (file)
--- a/src/jalview/io/vamsas/Sequencemapping.java
+++ b/src/jalview/io/vamsas/Sequencemapping.java
@@ -386,7 +386,7 @@ public class Sequencemapping extends Rangetype
   private void matchConjugateDBRefs(SequenceI from, SequenceI to,
           jalview.util.MapList smap)
   {
-    if (from.getDBRef() == null && to.getDBRef() == null)
+    if (from.getDBRefs() == null && to.getDBRefs() == null)
     {
       if (jalview.bin.Cache.log.isDebugEnabled())
       {
@@ -400,11 +400,11 @@ public class Sequencemapping extends Rangetype
       jalview.bin.Cache.log.debug("Matching conjugate refs for "
               + from.getName() + " and " + to.getName());
     }
-    jalview.datamodel.DBRefEntry[] fdb = from.getDBRef();
+    jalview.datamodel.DBRefEntry[] fdb = from.getDBRefs();
     jalview.datamodel.DBRefEntry[] tdb = new jalview.datamodel.DBRefEntry[to
-            .getDBRef().length];
-    int tdblen = to.getDBRef().length;
-    System.arraycopy(to.getDBRef(), 0, tdb, 0, tdblen);
+            .getDBRefs().length];
+    int tdblen = to.getDBRefs().length;
+    System.arraycopy(to.getDBRefs(), 0, tdb, 0, tdblen);
     Vector matched = new Vector();
     jalview.util.MapList smapI = smap.getInverse();
     for (int f = 0; f < fdb.length; f++)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 59d8631..e9d736f 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -33,6 +33,7 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
 import jalview.io.AppletFormatAdapter;
+import jalview.io.SiftsClient;
 import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 
@@ -479,6 +480,8 @@ public class StructureSelectionManager
         }
       };
 
+      // mapWithNWAlignment();
+      // mapWithSIFTS();
       maxAlignseq.printAlignment(ps);
 
       mappingDetails.append(NEWLINE).append("PDB start/end ");
@@ -528,8 +531,10 @@ public class StructureSelectionManager
       {
         pdbFile = "INLINE" + pdb.id;
       }
-      StructureMapping newMapping = new StructureMapping(seq, pdbFile,
-              pdb.id, maxChainId, mapping, mappingDetails.toString());
+      // StructureMapping newMapping = new StructureMapping(seq, pdbFile,
+      // pdb.id, maxChainId, mapping, mappingDetails.toString());
+      StructureMapping newMapping = new SiftsClient(pdb.id)
+              .getSiftsMappingsFor(seq, pdbFile, maxChainId);
       if (forStructureView)
       {
         mappings.add(newMapping);
@@ -541,6 +546,58 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  private StructureMapping mapWithNWAlignment(StringBuilder mappingDetails,
+          PDBChain maxChain, AlignSeq maxAlignseq, SequenceI seq,
+          PrintStream ps)
+  {
+    maxAlignseq.printAlignment(ps);
+
+    mappingDetails.append(NEWLINE).append("PDB start/end ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq2start))
+            .append(" ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
+    mappingDetails.append(NEWLINE).append("SEQ start/end ");
+    // TODO JAL-1887 should be fixed from here
+    mappingDetails.append(
+            String.valueOf(maxAlignseq.seq1start + seq.getStart() - 1))
+            .append(" ");
+    mappingDetails.append(String.valueOf(maxAlignseq.seq1end + seq.getEnd()
+            - 1));
+
+    maxChain.makeExactMapping(maxAlignseq, seq);
+    jalview.datamodel.Mapping sqmpping = maxAlignseq
+            .getMappingFromS1(false);
+    jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(sqmpping
+            .getMap().getInverse());
+    maxChain.transferRESNUMFeatures(seq, null);
+
+    // allocate enough slots to store the mapping from positions in
+    // sequence[s] to the associated chain
+    int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2];
+    int resNum = -10000;
+    int index = 0;
+
+    do
+    {
+      Atom tmp = maxChain.atoms.elementAt(index);
+      if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
+      {
+        resNum = tmp.resNumber;
+        if (tmp.alignmentMapping >= -1)
+        {
+          // TODO (JAL-1836) address root cause: negative residue no in PDB
+          // file
+          mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+          mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+        }
+      }
+
+      index++;
+    } while (index < maxChain.atoms.size());
+
+    return null;
+  }
+
   public void removeStructureViewerListener(Object svl, String[] pdbfiles)
   {
     listeners.removeElement(svl);

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index d531fea..b708ec1 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -400,7 +400,7 @@ public class DBRefFetcher implements Runnable
             {
               SequenceI sequence = dataset[seqIndex];
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-                      sequence.getDBRef(),
+                      sequence.getDBRefs(),
                       new String[] { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT
               // });
               // check for existing dbrefs to use
@@ -524,7 +524,7 @@ public class DBRefFetcher implements Runnable
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
       DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
-              entry.getDBRef(), new String[] { dbSource });
+              entry.getDBRefs(), new String[] { dbSource });
       if (entryRefs == null)
       {
         System.err
@@ -591,8 +591,8 @@ public class DBRefFetcher implements Runnable
         // no existing references
         // TODO: test for legacy where uniprot or EMBL refs exist but no
         // mappings are made (but content matches retrieved set)
-        boolean updateRefFrame = sequence.getDBRef() == null
-                || sequence.getDBRef().length == 0;
+        boolean updateRefFrame = sequence.getDBRefs() == null
+                || sequence.getDBRefs().length == 0;
         // TODO:
         // verify sequence against the entry sequence
 
@@ -737,7 +737,7 @@ public class DBRefFetcher implements Runnable
     for (int i = 0; sequencesArray != null && i < sequencesArray.length; i++)
     {
       nseq.addElement(sequencesArray[i]);
-      DBRefEntry dbr[] = sequencesArray[i].getDBRef();
+      DBRefEntry dbr[] = sequencesArray[i].getDBRefs();
       jalview.datamodel.Mapping map = null;
       for (int r = 0; (dbr != null) && r < dbr.length; r++)
       {

diff --git a/src/jalview/ws/DasSequenceFeatureFetcher.java b/src/jalview/ws/DasSequenceFeatureFetcher.java
index 808d9a0..8faba60 100644 (file)
--- a/src/jalview/ws/DasSequenceFeatureFetcher.java
+++ b/src/jalview/ws/DasSequenceFeatureFetcher.java
@@ -181,7 +181,7 @@ public class DasSequenceFeatureFetcher
     int refCount = 0;
     for (int i = 0; i < sequences.length; i++)
     {
-      DBRefEntry[] dbref = sequences[i].getDBRef();
+      DBRefEntry[] dbref = sequences[i].getDBRefs();
       if (dbref != null)
       {
         for (int j = 0; j < dbref.length; j++)
@@ -638,7 +638,7 @@ public class DasSequenceFeatureFetcher
       return null;
     }
     DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
-            seq.getDBRef(), new String[] {
+            seq.getDBRefs(), new String[] {
             // jalview.datamodel.DBRefSource.PDB,
             jalview.datamodel.DBRefSource.UNIPROT,
             // jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index 8656c25..0fe7275 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -171,7 +171,7 @@ public class ASequenceFetcher
                 {
                   rseqs.addElement(seqs[is]);
                   DBRefEntry[] frefs = DBRefUtils.searchRefs(seqs[is]
-                          .getDBRef(), new DBRefEntry(db, null, null));
+                          .getDBRefs(), new DBRefEntry(db, null, null));
                   if (frefs != null)
                   {
                     for (DBRefEntry dbr : frefs)

diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 84b9817..9756849 100644 (file)
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -1124,8 +1124,8 @@ public class AlignmentUtilsTests
 
     assertEquals("GGGTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12345", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    DBRefEntry cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    DBRefEntry cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("2", cdsRef.getVersion());
     assertEquals("A12345", cdsRef.getAccessionId());
@@ -1195,8 +1195,8 @@ public class AlignmentUtilsTests
     SequenceI exon = exons.get(0);
     assertEquals("GGGTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12345", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    DBRefEntry cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    DBRefEntry cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("2", cdsRef.getVersion());
     assertEquals("A12345", cdsRef.getAccessionId());
@@ -1204,8 +1204,8 @@ public class AlignmentUtilsTests
     exon = exons.get(1);
     assertEquals("aaaccc", exon.getSequenceAsString());
     assertEquals("dna1|A12346", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("3", cdsRef.getVersion());
     assertEquals("A12346", cdsRef.getAccessionId());
@@ -1213,8 +1213,8 @@ public class AlignmentUtilsTests
     exon = exons.get(2);
     assertEquals("aaaTTT", exon.getSequenceAsString());
     assertEquals("dna1|A12347", exon.getName());
-    assertEquals(1, exon.getDBRef().length);
-    cdsRef = exon.getDBRef()[0];
+    assertEquals(1, exon.getDBRefs().length);
+    cdsRef = exon.getDBRefs()[0];
     assertEquals("EMBLCDS", cdsRef.getSource());
     assertEquals("4", cdsRef.getVersion());
     assertEquals("A12347", cdsRef.getAccessionId());

diff --git a/test/jalview/util/DBRefUtilsTest.java b/test/jalview/util/DBRefUtilsTest.java
index 4a55a0d..7a6dc35 100644 (file)
--- a/test/jalview/util/DBRefUtilsTest.java
+++ b/test/jalview/util/DBRefUtilsTest.java
@@ -137,7 +137,7 @@ public class DBRefUtilsTest
   {
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "EMBL", "1.2", "a7890");
-    DBRefEntry[] refs = seq.getDBRef();
+    DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
     assertEquals("EMBL", ref.getSource());
@@ -155,7 +155,7 @@ public class DBRefUtilsTest
     SequenceI seq = new Sequence("Seq1", "ABCD");
     DBRefEntry ref = DBRefUtils.parseToDbRef(seq, "pdb", "1.2",
             "1WRI A; 7-80;");
-    DBRefEntry[] refs = seq.getDBRef();
+    DBRefEntry[] refs = seq.getDBRefs();
     assertEquals(1, refs.length);
     assertSame(ref, refs[0]);
     assertEquals("PDB", ref.getSource());

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index ddd8b33..902498b 100644 (file)
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -166,7 +166,7 @@ public class DbRefFetcherTest
             FeatureProperties.isCodingFeature(embl.getDbSource(),
                     sfs[0].getType()));
     assertEquals(embl.getDbSource(), sfs[0].getFeatureGroup());
-    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRef(),
+    DBRefEntry[] dr = DBRefUtils.selectRefs(seq.getDBRefs(),
             DBRefSource.PROTEINSEQ);
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.length);