Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 3bd7b4b..cc21f35 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 +32,16 @@ import java.util.ListIterator;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.analysis.AlignSeq;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.SeqsetUtils;
+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;
 
 /**
  * 
@@ -171,7 +174,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (name == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
       name = "";
     }
@@ -349,6 +352,11 @@ public class Sequence extends ASequence implements SequenceI
         {
           // only copy the given annotation
           AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+          ContactMatrixI cm = seq.getContactMatrixFor(sqann[i]);
+          if (cm != null)
+          {
+            addContactListFor(newann, cm);
+          }
           addAlignmentAnnotation(newann);
         }
       }
@@ -379,7 +387,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sf.getType() == null)
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "SequenceFeature type may not be null: " + sf.toString());
       return false;
     }
@@ -1415,6 +1423,7 @@ 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);
@@ -1425,6 +1434,7 @@ 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++)
     {
@@ -1623,8 +1633,20 @@ public class Sequence extends ASequence implements SequenceI
           _aa.adjustForAlignment(); // uses annotation's own record of
                                     // sequence-column mapping
           datasetSequence.addAlignmentAnnotation(_aa);
+
+          if (_cmholder != null)
+          { // transfer contact matrices
+            ContactMatrixI cm = _cmholder.getContactMatrixFor(aa);
+            if (cm != null)
+            {
+              datasetSequence.addContactListFor(_aa, cm);
+              datasetSequence.addContactListFor(aa, cm);
+            }
+          }
         }
       }
+      // all matrices should have been transferred. so we clear the local holder
+      _cmholder = null;
     }
     return datasetSequence;
   }
@@ -1732,6 +1754,14 @@ public class Sequence extends ASequence implements SequenceI
       transferAnnotation(entry.getDatasetSequence(), mp);
       return;
     }
+    // transfer from entry to sequence
+    // if entry has a description and sequence doesn't, then transfer
+    if (entry.getDescription() != null
+            && (description == null || description.trim().length() == 0))
+    {
+      description = entry.getDescription();
+    }
+
     // transfer any new features from entry onto sequence
     if (entry.getSequenceFeatures() != null)
     {
@@ -1810,18 +1840,16 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
-          String label, String description, boolean nullWildcard)
+          String label, String description, boolean ignoreDescription)
   {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (((nullWildcard && calcId == null)
-                || (ann.calcId != null && ann.calcId.equals(calcId)))
-                && ((nullWildcard && label == null)
-                        || (ann.label != null && ann.label.equals(label)))
-                && ((nullWildcard && description == null)
+        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))))
 
@@ -2107,4 +2135,85 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  ////
+  //// Contact Matrix Holder Boilerplate
+  ////
+  ContactMapHolderI _cmholder = null;
+
+  private ContactMapHolderI getContactMapHolder()
+  {
+    if (datasetSequence != null)
+    {
+      return ((Sequence) datasetSequence).getContactMapHolder();
+    }
+    if (_cmholder == null)
+    {
+      _cmholder = new ContactMapHolder();
+    }
+    return _cmholder;
+  }
+
+  @Override
+  public Collection<ContactMatrixI> getContactMaps()
+  {
+    return getContactMapHolder().getContactMaps();
+  }
+
+  @Override
+  public ContactMatrixI getContactMatrixFor(AlignmentAnnotation ann)
+  {
+    return getContactMapHolder().getContactMatrixFor(ann);
+  }
+
+  @Override
+  public ContactListI getContactListFor(AlignmentAnnotation _aa, int column)
+  {
+    return getContactMapHolder().getContactListFor(_aa, column);
+  }
+
+  @Override
+  public AlignmentAnnotation addContactList(ContactMatrixI cm)
+  {
+    AlignmentAnnotation aa;
+
+    if (datasetSequence != null)
+    {
+      aa = datasetSequence.addContactList(cm);
+      // clone the annotation for the local sequence
+      aa = new AlignmentAnnotation(aa);
+      aa.restrict(start, end);
+      aa.adjustForAlignment();
+      getContactMapHolder().addContactListFor(aa, cm);
+      addAlignmentAnnotation(aa);
+      return aa;
+    }
+
+    // construct new annotation for matrix on dataset sequence
+    aa = getContactMapHolder().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)
+  {
+    getContactMapHolder().addContactListFor(annotation, cm);
+  }
 }