JAL-4028 experiment - THISISAPLACEHOLDER sequences get additional sequence data ...

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 950ee05..1563dff 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -20,14 +20,6 @@
  */
 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;
@@ -39,6 +31,13 @@ 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;
 
 /**
  * 
@@ -472,18 +471,19 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Answers the sequence name, with '/start-end' appended if jvsuffix is true
    * 
-   * @return DOCUMENT ME!
+   * @return
    */
   @Override
   public String getDisplayId(boolean jvsuffix)
   {
-    StringBuffer result = new StringBuffer(name);
-    if (jvsuffix)
+    if (!jvsuffix)
     {
-      result.append("/" + start + "-" + end);
+      return name;
     }
+    StringBuilder result = new StringBuilder(name);
+    result.append("/").append(start).append("-").append(end);
 
     return result.toString();
   }
@@ -522,6 +522,7 @@ public class Sequence extends ASequence implements SequenceI
   public void setStart(int start)
   {
     this.start = start;
+    sequenceChanged();
   }
 
   /**
@@ -1413,6 +1414,7 @@ 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);
@@ -1423,6 +1425,7 @@ 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++)
     {
@@ -1598,33 +1601,46 @@ public class Sequence extends ASequence implements SequenceI
               getStart(), getEnd());
 
       datasetSequence = dsseq;
+      updateDatasetFrom(dsseq, this);
+    }
+    return datasetSequence;
+  }
 
-      dsseq.setDescription(description);
-      // move features and database references onto dataset sequence
-      dsseq.sequenceFeatureStore = sequenceFeatureStore;
-      sequenceFeatureStore = null;
-      dsseq.dbrefs = dbrefs;
-      dbrefs = null;
-      // TODO: search and replace any references to this sequence with
-      // references to the dataset sequence in Mappings on dbref
-      dsseq.pdbIds = pdbIds;
-      pdbIds = null;
-      datasetSequence.updatePDBIds();
-      if (annotation != null)
+  /**
+   * used by createDatasetSequence - transfers dataset-only properties to dsseq
+   * from sequence2
+   * 
+   * @param dsseq
+   *          - newly created dataset sequenceI for sequence
+   * @param sequence2
+   *          - sequence object that needs a dataset
+   */
+  protected void updateDatasetFrom(Sequence dsseq, Sequence sequence2)
+  {
+    dsseq.setDescription(description);
+    // move features and database references onto dataset sequence
+    dsseq.sequenceFeatureStore = sequenceFeatureStore;
+    sequenceFeatureStore = null;
+    dsseq.dbrefs = dbrefs;
+    dbrefs = null;
+    // TODO: search and replace any references to this sequence with
+    // references to the dataset sequence in Mappings on dbref
+    dsseq.pdbIds = pdbIds;
+    pdbIds = null;
+    datasetSequence.updatePDBIds();
+    if (annotation != null)
+    {
+      // annotation is cloned rather than moved, to preserve what's currently
+      // on the alignment
+      for (AlignmentAnnotation aa : annotation)
       {
-        // annotation is cloned rather than moved, to preserve what's currently
-        // on the alignment
-        for (AlignmentAnnotation aa : annotation)
-        {
-          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
-          _aa.sequenceRef = datasetSequence;
-          _aa.adjustForAlignment(); // uses annotation's own record of
-                                    // sequence-column mapping
-          datasetSequence.addAlignmentAnnotation(_aa);
-        }
+        AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+        _aa.sequenceRef = datasetSequence;
+        _aa.adjustForAlignment(); // uses annotation's own record of
+                                  // sequence-column mapping
+        datasetSequence.addAlignmentAnnotation(_aa);
       }
     }
-    return datasetSequence;
   }
 
   /*
@@ -1797,13 +1813,30 @@ 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);
         }
@@ -1935,15 +1968,6 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
-    if (datasetSequence != null)
-    {
-      result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
-              types);
-    }
-    else
-    {
-      result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
-    }
 
     /*
      * if end column is gapped, endPos may be to the right,