JAL-2629 add sort by evalue and bit score

[jalview.git] / src / jalview / analysis / AlignmentSorter.java

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 8473904..2d05865 100755 (executable)
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -86,6 +86,10 @@ public class AlignmentSorter
 
   private static boolean sortLengthAscending;
 
+  private static boolean sortEValueAscending;
+
+  private static boolean sortBitScoreAscending;
+
   /**
    * Sorts sequences in the alignment by Percentage Identity with the given
    * reference sequence, sorting the highest identity to the top
@@ -182,7 +186,7 @@ public class AlignmentSorter
     List<SequenceI> algn;
     synchronized (algn = align.getSequences())
     {
-      List<SequenceI> tmp = new ArrayList<SequenceI>();
+      List<SequenceI> tmp = new ArrayList<>();
 
       for (int i = 0; i < seqs.length; i++)
       {
@@ -268,6 +272,90 @@ public class AlignmentSorter
   }
 
   /**
+   * Sorts by sequence evalue. Currently moves all sequences without an evalue to
+   * the top of the alignment.
+   * 
+   * @param align
+   *                The alignment object to sort
+   */
+  public static void sortByEValue(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
+
+    double[] evalue = new double[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+
+    for (int i = 0; i < nSeq; i++)
+    {
+      seqs[i] = align.getSequenceAt(i);
+      AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
+      if (ann != null)
+      {
+        evalue[i] = ann[0].getEValue();
+      }
+      else
+      {
+        evalue[i] = -1;
+      }
+    }
+
+    QuickSort.sort(evalue, seqs);
+
+    if (sortEValueAscending)
+    {
+      setReverseOrder(align, seqs);
+    }
+    else
+    {
+      setOrder(align, seqs);
+    }
+
+    sortEValueAscending = !sortEValueAscending;
+  }
+
+  /**
+   * Sorts by sequence bit score. Currently moves all sequences without a bit
+   * score to the top of the alignment
+   * 
+   * @param align
+   *                The alignment object to sort
+   */
+  public static void sortByBitScore(AlignmentI align)
+  {
+    int nSeq = align.getHeight();
+
+    double[] score = new double[nSeq];
+    SequenceI[] seqs = new SequenceI[nSeq];
+
+    for (int i = 0; i < nSeq; i++)
+    {
+      seqs[i] = align.getSequenceAt(i);
+      AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores");
+      if (ann != null)
+      {
+        score[i] = ann[0].getEValue();
+      }
+      else
+      {
+        score[i] = -1;
+      }
+    }
+
+    QuickSort.sort(score, seqs);
+
+    if (sortBitScoreAscending)
+    {
+      setReverseOrder(align, seqs);
+    }
+    else
+    {
+      setOrder(align, seqs);
+    }
+
+    sortBitScoreAscending = !sortBitScoreAscending;
+  }
+
+  /**
    * Sorts the alignment by size of group. <br>
    * Maintains the order of sequences in each group by order in given alignment
    * object.
@@ -279,7 +367,7 @@ public class AlignmentSorter
   {
     // MAINTAINS ORIGNAL SEQUENCE ORDER,
     // ORDERS BY GROUP SIZE
-    List<SequenceGroup> groups = new ArrayList<SequenceGroup>();
+    List<SequenceGroup> groups = new ArrayList<>();
 
     if (groups.hashCode() != lastGroupHash)
     {
@@ -315,7 +403,7 @@ public class AlignmentSorter
 
     // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER
     // /////////////////////////////////////////////
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
 
     for (int i = 0; i < groups.size(); i++)
     {
@@ -357,7 +445,7 @@ public class AlignmentSorter
     // tmp2 = tmp.retainAll(mask);
     // return tmp2.addAll(mask.removeAll(tmp2))
 
-    ArrayList<SequenceI> seqs = new ArrayList<SequenceI>();
+    ArrayList<SequenceI> seqs = new ArrayList<>();
     int i, idx;
     boolean[] tmask = new boolean[mask.size()];
 
@@ -436,7 +524,7 @@ public class AlignmentSorter
   {
     int nSeq = align.getHeight();
 
-    List<SequenceI> tmp = new ArrayList<SequenceI>();
+    List<SequenceI> tmp = new ArrayList<>();
 
     tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences());