JAL-1628 new method to get a list of insertions in a SequenceI

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 9cc7d54..96e469a 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,7 +22,9 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 
+import java.util.ArrayList;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.Vector;
 
 import fr.orsay.lri.varna.models.rna.RNA;
@@ -491,7 +493,9 @@ public class Sequence implements SequenceI
   public char[] getSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
+    }
     // JBPNote - left to user to pad the result here (TODO:Decide on this
     // policy)
     if (start >= sequence.length)
@@ -510,16 +514,7 @@ public class Sequence implements SequenceI
     return reply;
   }
 
-  /**
-   * make a new Sequence object from start to end (including gaps) over this
-   * seqeunce
-   * 
-   * @param start
-   *          int
-   * @param end
-   *          int
-   * @return SequenceI
-   */
+  @Override
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
@@ -619,14 +614,7 @@ public class Sequence implements SequenceI
     }
   }
 
-  /**
-   * Returns the sequence position for an alignment position
-   * 
-   * @param i
-   *          column index in alignment (from 1)
-   * 
-   * @return residue number for residue (left of and) nearest ith column
-   */
+  @Override
   public int findPosition(int i)
   {
     int j = 0;
@@ -673,11 +661,7 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#findPositionMap()
-   */
+  @Override
   public int[] findPositionMap()
   {
     int map[] = new int[sequence.length];
@@ -697,11 +681,43 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
-   */
+  @Override
+  public List<int[]> getInsertions()
+  {
+    ArrayList<int[]> map = new ArrayList<int[]>();
+    int lastj = -1, j = 0;
+    int pos = start;
+    int seqlen = sequence.length;
+    while ((j < seqlen))
+    {
+      if (jalview.util.Comparison.isGap(sequence[j]))
+      {
+        if (lastj == -1)
+        {
+          lastj = j;
+        }
+      }
+      else
+      {
+        if (lastj != -1)
+        {
+          map.add(new int[]
+          { lastj, j - 1 });
+          lastj = -1;
+        }
+      }
+      j++;
+    }
+    if (lastj != -1)
+    {
+      map.add(new int[]
+      { lastj, j - 1 });
+      lastj = -1;
+    }
+    return map;
+  }
+
+  @Override
   public void deleteChars(int i, int j)
   {
     int newstart = start, newend = end;
@@ -780,16 +796,7 @@ public class Sequence implements SequenceI
     sequence = tmp;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param i
-   *          DOCUMENT ME!
-   * @param c
-   *          DOCUMENT ME!
-   * @param chop
-   *          DOCUMENT ME!
-   */
+  @Override
   public void insertCharAt(int i, int length, char c)
   {
     char[] tmp = new char[sequence.length + length];
@@ -819,26 +826,31 @@ public class Sequence implements SequenceI
     sequence = tmp;
   }
 
+  @Override
   public void insertCharAt(int i, char c)
   {
     insertCharAt(i, 1, c);
   }
 
+  @Override
   public String getVamsasId()
   {
     return vamsasId;
   }
 
+  @Override
   public void setVamsasId(String id)
   {
     vamsasId = id;
   }
 
+  @Override
   public void setDBRef(DBRefEntry[] dbref)
   {
     dbrefs = dbref;
   }
 
+  @Override
   public DBRefEntry[] getDBRef()
   {
     if (dbrefs == null && datasetSequence != null
@@ -849,6 +861,7 @@ public class Sequence implements SequenceI
     return dbrefs;
   }
 
+  @Override
   public void addDBRef(DBRefEntry entry)
   {
     if (dbrefs == null)
@@ -881,32 +894,33 @@ public class Sequence implements SequenceI
     dbrefs = temp;
   }
 
+  @Override
   public void setDatasetSequence(SequenceI seq)
   {
     datasetSequence = seq;
   }
 
+  @Override
   public SequenceI getDatasetSequence()
   {
     return datasetSequence;
   }
 
+  @Override
   public AlignmentAnnotation[] getAnnotation()
   {
-    if (annotation == null)
-    {
-      return null;
-    }
+    return annotation == null ? null : annotation
+            .toArray(new AlignmentAnnotation[annotation.size()]);
+  }
 
-    AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()];
-    for (int r = 0; r < ret.length; r++)
-    {
-      ret[r] = (AlignmentAnnotation) annotation.elementAt(r);
-    }
 
-    return ret;
+  @Override
+  public boolean hasAnnotation(AlignmentAnnotation ann)
+  {
+    return annotation == null ? false : annotation.contains(ann);
   }
 
+  @Override
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
@@ -926,7 +940,9 @@ public class Sequence implements SequenceI
     {
       this.annotation.removeElement(annotation);
       if (this.annotation.size() == 0)
+      {
         this.annotation = null;
+      }
     }
   }
 
@@ -950,11 +966,7 @@ public class Sequence implements SequenceI
     return true;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#deriveSequence()
-   */
+  @Override
   public SequenceI deriveSequence()
   {
     SequenceI seq = new Sequence(this);
@@ -1007,14 +1019,13 @@ public class Sequence implements SequenceI
       datasetSequence.updatePDBIds();
       if (annotation != null)
       {
-        Vector<AlignmentAnnotation> _annot = annotation;
-        annotation = null;
-        for (AlignmentAnnotation aa : _annot)
+        for (AlignmentAnnotation aa : annotation)
         {
-          aa.sequenceRef = datasetSequence;
-          aa.adjustForAlignment(); // uses annotation's own record of
+          AlignmentAnnotation _aa = new AlignmentAnnotation(aa);
+          _aa.sequenceRef = datasetSequence;
+          _aa.adjustForAlignment(); // uses annotation's own record of
                                    // sequence-column mapping
-          datasetSequence.addAlignmentAnnotation(aa);
+          datasetSequence.addAlignmentAnnotation(_aa);
         }
       }
     }
@@ -1039,16 +1050,14 @@ public class Sequence implements SequenceI
       for (int i = 0; i < annotations.length; i++)
       {
         if (annotations[i] != null)
+        {
           addAlignmentAnnotation(annotations[i]);
+        }
       }
     }
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
-   */
+  @Override
   public AlignmentAnnotation[] getAnnotation(String label)
   {
     if (annotation == null || annotation.size() == 0)
@@ -1081,6 +1090,7 @@ public class Sequence implements SequenceI
     return anns;
   }
 
+  @Override
   public boolean updatePDBIds()
   {
     if (datasetSequence != null)
@@ -1134,13 +1144,7 @@ public class Sequence implements SequenceI
     return false;
   }
 
-  /*
-   * (non-Javadoc)
-   * 
-   * @see
-   * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI,
-   * jalview.datamodel.Mapping)
-   */
+  @Override
   public void transferAnnotation(SequenceI entry, Mapping mp)
   {
     if (datasetSequence != null)
@@ -1236,4 +1240,21 @@ public class Sequence implements SequenceI
     return rna;
   }
 
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label)
+  {
+    List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+    if (this.annotation != null) {
+      for (AlignmentAnnotation ann : annotation) {
+        if (ann.calcId != null && ann.calcId.equals(calcId)
+                && ann.label != null && ann.label.equals(label))
+        {
+          result.add(ann);
+        }
+      }
+    }
+    return result;
+  }
+
 }