JAL-1926 added supporting model changes to enable saving sourceDBRef data for sequences

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 3ca3d90..527b1ff 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -948,6 +948,7 @@ public class AlignSeq
   public static void displayMatrix(Graphics g, int[][] mat, int n, int m,
           int psize)
   {
+    // TODO method dosen't seem to be referenced anywhere delete??
     int max = -1000;
     int min = 1000;
 

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 0581845..0d6f68d 100755 (executable)
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -20,7 +20,9 @@
  */
 package jalview.datamodel;
 
-public class DBRefEntry
+import jalview.api.DBRefEntryI;
+
+public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
 
@@ -98,7 +100,8 @@ public class DBRefEntry
    * @param entry
    * @return true if source, accession and version are equal with those of entry
    */
-  public boolean equalRef(DBRefEntry entry)
+  @Override
+  public boolean equalRef(DBRefEntryI entry)
   {
     if (entry == null)
     {
@@ -108,28 +111,32 @@ public class DBRefEntry
     {
       return true;
     }
-    if ((source != null && entry.source != null && source
-            .equalsIgnoreCase(entry.source))
-            && (accessionId != null && entry.accessionId != null && accessionId
-                    .equalsIgnoreCase(entry.accessionId))
-            && (version != null && entry.version != null && version
-                    .equalsIgnoreCase(entry.version)))
+    if (entry != null
+            && (source != null && entry.getSource() != null && source
+                    .equalsIgnoreCase(entry.getSource()))
+            && (accessionId != null && entry.getAccessionId() != null && accessionId
+                    .equalsIgnoreCase(entry.getAccessionId()))
+            && (version != null && entry.getVersion() != null && version
+                    .equalsIgnoreCase(entry.getVersion())))
     {
       return true;
     }
     return false;
   }
 
+  @Override
   public String getSource()
   {
     return source;
   }
 
+  @Override
   public String getVersion()
   {
     return version;
   }
 
+  @Override
   public String getAccessionId()
   {
     return accessionId;
@@ -139,6 +146,7 @@ public class DBRefEntry
    * @param accessionId
    *          the accessionId to set
    */
+  @Override
   public void setAccessionId(String accessionId)
   {
     this.accessionId = accessionId;
@@ -148,6 +156,7 @@ public class DBRefEntry
    * @param source
    *          the source to set
    */
+  @Override
   public void setSource(String source)
   {
     this.source = source;
@@ -157,6 +166,7 @@ public class DBRefEntry
    * @param version
    *          the version to set
    */
+  @Override
   public void setVersion(String version)
   {
     this.version = version;
@@ -194,6 +204,7 @@ public class DBRefEntry
             + ((accessionId != null) ? accessionId : "");
   }
 
+  @Override
   public String toString()
   {
     return getSrcAccString();

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index c7581d8..9f65f71 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -21,6 +21,7 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
+import jalview.api.DBRefEntryI;
 import jalview.util.StringUtils;
 
 import java.util.ArrayList;
@@ -55,6 +56,8 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
+  DBRefEntryI sourceDBRef;
+
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -276,11 +279,13 @@ public class Sequence extends ASequence implements SequenceI
    * @param v
    *          DOCUMENT ME!
    */
+  @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
     sequenceFeatures = features;
   }
 
+  @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
     if (sequenceFeatures == null)
@@ -303,6 +308,7 @@ public class Sequence extends ASequence implements SequenceI
     sequenceFeatures = temp;
   }
 
+  @Override
   public void deleteFeature(SequenceFeature sf)
   {
     if (sequenceFeatures == null)
@@ -352,6 +358,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return
    */
+  @Override
   public SequenceFeature[] getSequenceFeatures()
   {
     SequenceFeature[] features = sequenceFeatures;
@@ -367,6 +374,7 @@ public class Sequence extends ASequence implements SequenceI
     return features;
   }
 
+  @Override
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
@@ -419,6 +427,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String getDisplayId(boolean jvsuffix)
   {
     StringBuffer result = new StringBuffer(name);
@@ -436,6 +445,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param name
    *          DOCUMENT ME!
    */
+  @Override
   public void setName(String name)
   {
     this.name = name;
@@ -447,6 +457,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String getName()
   {
     return this.name;
@@ -458,6 +469,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param start
    *          DOCUMENT ME!
    */
+  @Override
   public void setStart(int start)
   {
     this.start = start;
@@ -468,6 +480,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getStart()
   {
     return this.start;
@@ -479,6 +492,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param end
    *          DOCUMENT ME!
    */
+  @Override
   public void setEnd(int end)
   {
     this.end = end;
@@ -489,6 +503,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getEnd()
   {
     return this.end;
@@ -499,6 +514,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public int getLength()
   {
     return this.sequence.length;
@@ -510,22 +526,26 @@ public class Sequence extends ASequence implements SequenceI
    * @param seq
    *          DOCUMENT ME!
    */
+  @Override
   public void setSequence(String seq)
   {
     this.sequence = seq.toCharArray();
     checkValidRange();
   }
 
+  @Override
   public String getSequenceAsString()
   {
     return new String(sequence);
   }
 
+  @Override
   public String getSequenceAsString(int start, int end)
   {
     return new String(getSequence(start, end));
   }
 
+  @Override
   public char[] getSequence()
   {
     return sequence;
@@ -536,6 +556,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#getSequence(int, int)
    */
+  @Override
   public char[] getSequence(int start, int end)
   {
     if (start < 0)
@@ -596,6 +617,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public char getCharAt(int i)
   {
     if (i < sequence.length)
@@ -614,6 +636,7 @@ public class Sequence extends ASequence implements SequenceI
    * @param desc
    *          DOCUMENT ME!
    */
+  @Override
   public void setDescription(String desc)
   {
     this.description = desc;
@@ -624,6 +647,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @return DOCUMENT ME!
    */
+  @Override
   public String getDescription()
   {
     return this.description;
@@ -634,6 +658,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#findIndex(int)
    */
+  @Override
   public int findIndex(int pos)
   {
     // returns the alignment position for a residue
@@ -686,6 +711,7 @@ public class Sequence extends ASequence implements SequenceI
    * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
    *         residues in SequenceI object
    */
+  @Override
   public int[] gapMap()
   {
     String seq = jalview.analysis.AlignSeq.extractGaps(
@@ -973,6 +999,7 @@ public class Sequence extends ASequence implements SequenceI
     annotation.setSequenceRef(this);
   }
 
+  @Override
   public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation != null)
@@ -1040,6 +1067,7 @@ public class Sequence extends ASequence implements SequenceI
    * 
    * @see jalview.datamodel.SequenceI#createDatasetSequence()
    */
+  @Override
   public SequenceI createDatasetSequence()
   {
     if (datasetSequence == null)
@@ -1078,6 +1106,7 @@ public class Sequence extends ASequence implements SequenceI
    * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[]
    * annotations)
    */
+  @Override
   public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
   {
     if (annotation != null)
@@ -1250,6 +1279,7 @@ public class Sequence extends ASequence implements SequenceI
    * @return The index (zero-based) on this sequence in the MSA. It returns
    *         {@code -1} if this information is not available.
    */
+  @Override
   public int getIndex()
   {
     return index;
@@ -1263,16 +1293,19 @@ public class Sequence extends ASequence implements SequenceI
    *          position for this sequence. This value is zero-based (zero for
    *          this first sequence)
    */
+  @Override
   public void setIndex(int value)
   {
     index = value;
   }
 
+  @Override
   public void setRNA(RNA r)
   {
     rna = r;
   }
 
+  @Override
   public RNA getRNA()
   {
     return rna;
@@ -1297,6 +1330,7 @@ public class Sequence extends ASequence implements SequenceI
     return result;
   }
 
+  @Override
   public String toString()
   {
     return getDisplayId(false);
@@ -1321,4 +1355,16 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
+  @Override
+  public void setSourceDBRef(DBRefEntryI dbRef)
+  {
+    this.sourceDBRef = dbRef;
+  }
+
+  @Override
+  public DBRefEntryI getSourceDBRef()
+  {
+    return this.sourceDBRef;
+  }
+
 }

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 0e649c0..49b0e4d 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import jalview.api.DBRefEntryI;
+
 import java.util.List;
 import java.util.Vector;
 
@@ -429,4 +431,8 @@ public interface SequenceI extends ASequenceI
    * @return
    */
   public PDBEntry getPDBEntry(String pdbId);
+
+  public void setSourceDBRef(DBRefEntryI dbRef);
+
+  public DBRefEntryI getSourceDBRef();
 }

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 26b7d48..59d8631 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -485,8 +485,8 @@ public class StructureSelectionManager
       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(" ");