Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index e0a9d35..33c8ac5 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,17 +20,10 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.features.SequenceFeatures;
-import jalview.datamodel.features.SequenceFeaturesI;
-import jalview.util.Comparison;
-import jalview.util.DBRefUtils;
-import jalview.util.MapList;
-import jalview.util.StringUtils;
-
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.Iterator;
@@ -39,6 +32,14 @@ import java.util.ListIterator;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.features.SequenceFeatures;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.StringUtils;
+import jalview.ws.datamodel.alphafold.MappableContactMatrix;
 
 /**
  * 
@@ -523,6 +524,7 @@ public class Sequence extends ASequence implements SequenceI
   public void setStart(int start)
   {
     this.start = start;
+    sequenceChanged();
   }
 
   /**
@@ -1414,6 +1416,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO JAL-3980 maintain as sorted list
     if (datasetSequence != null)
     {
       datasetSequence.addDBRef(entry);
@@ -1424,6 +1427,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       dbrefs = new DBModList<>();
     }
+    // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
 
     for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
     {
@@ -1622,6 +1626,13 @@ public class Sequence extends ASequence implements SequenceI
           _aa.adjustForAlignment(); // uses annotation's own record of
                                     // sequence-column mapping
           datasetSequence.addAlignmentAnnotation(_aa);
+
+          // transfer contact matrices
+          ContactMatrixI cm = getContactMatrixFor(aa);
+          if (cm != null)
+          {
+            datasetSequence.addContactListFor(_aa, cm);
+          }
         }
       }
     }
@@ -1798,13 +1809,30 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
+    return getAlignmentAnnotations(calcId, label, null, true);
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description)
+  {
+    return getAlignmentAnnotations(calcId, label, description, false);
+  }
+
+  private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description, boolean ignoreDescription)
+  {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
+        if ((ann.calcId != null && ann.calcId.equals(calcId))
+                && (ann.label != null && ann.label.equals(label))
+                && ((ignoreDescription && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
+
         {
           result.add(ann);
         }
@@ -2087,4 +2115,57 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  ////
+  //// Contact Matrix Holder Boilerplate
+  ////
+  ContactMapHolderI cmholder = new ContactMapHolder();
+
+  @Override
+  public Collection<ContactMatrixI> getContactMaps()
+  {
+    return cmholder.getContactMaps();
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+  {
+    return cmholder.getContactMatrixFor(ann);
+  }
+
+  @Override
+  public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    return cmholder.getContactListFor(_aa, column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    AlignmentAnnotation aa = cmholder.addContactList(cm);
+
+    Annotation _aa[] = new Annotation[getLength()];
+
+    for (int i = 0; i < _aa.length; _aa[i++] = new Annotation(0.0f))
+    {
+      ;
+    }
+    aa.annotations = _aa;
+    aa.setSequenceRef(this);
+    if (cm instanceof MappableContactMatrix
+            && !((MappableContactMatrix) cm).hasReferenceSeq())
+    {
+      ((MappableContactMatrix) cm).setRefSeq(this);
+    }
+    aa.createSequenceMapping(this, getStart(), false);
+    addAlignmentAnnotation(aa);
+    return aa;
+  }
+
+  @Override
+  public void addContactListFor(AlignmentAnnotation annotation,
+          ContactMatrixI cm)
+  {
+    cmholder.addContactListFor(annotation, cm);
+  }
 }