JAL-391 new Calculate options to Reverse, Reverse Complement nucleotide

diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties
index 54370d8..42dc0f7 100644 (file)
--- a/resources/lang/Messages.properties
+++ b/resources/lang/Messages.properties
@@ -704,6 +704,8 @@ label.load_tree_for_sequence_set = Load a tree for this sequence set
 label.export_image = Export Image
 label.vamsas_store = VAMSAS store
 label.translate_cDNA = Translate as cDNA
 label.export_image = Export Image
 label.vamsas_store = VAMSAS store
 label.translate_cDNA = Translate as cDNA

+label.reverse = Reverse
+label.reverse_complement = Reverse Complement

 label.linked_view_title = Linked cDNA and protein view
 label.align = Align
 label.extract_scores = Extract Scores
 label.linked_view_title = Linked cDNA and protein view
 label.align = Align
 label.extract_scores = Extract Scores

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 9ce00cc..f8bb9f9 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -806,4 +806,154 @@ public class Dna
       }
     }
   }
       }
     }
   }

+
+  /**
+   * Returns an alignment consisting of the reversed (and optionally
+   * complemented) sequences set in this object's constructor
+   * 
+   * @param complement
+   * @return
+   */
+  public AlignmentI reverseCdna(boolean complement)
+  {
+    int sSize = selection.size();
+    List<SequenceI> reversed = new ArrayList<SequenceI>();
+    for (int s = 0; s < sSize; s++)
+    {
+      SequenceI newseq = reverseSequence(selection.get(s).getName(),
+              seqstring[s], complement);
+
+      if (newseq != null)
+      {
+        reversed.add(newseq);
+      }
+    }
+
+    SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]);
+    AlignmentI al = new Alignment(newseqs);
+    ((Alignment) al).createDatasetAlignment();
+    return al;
+  }
+
+  /**
+   * Returns a reversed, and optionally complemented, sequence. The new
+   * sequence's name is the original name with "|rev" or "|revcomp" appended.
+   * aAcCgGtT and DNA ambiguity codes are complemented, any other characters are
+   * left unchanged.
+   * 
+   * @param seq
+   * @param complement
+   * @return
+   */
+  public static SequenceI reverseSequence(String seqName, String sequence,
+          boolean complement)
+  {
+    String newName = seqName + "|rev" + (complement ? "comp" : "");
+    char[] originalSequence = sequence.toCharArray();
+    int length = originalSequence.length;
+    char[] reversedSequence = new char[length];
+
+    for (int i = 0; i < length; i++)
+    {
+      reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+              : originalSequence[i];
+    }
+    SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+    return reversed;
+  }
+
+  /**
+   * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
+   * are treated as on http://reverse-complement.com/. Anything else is left
+   * unchanged.
+   * 
+   * @param c
+   * @return
+   */
+  public static char getComplement(char c)
+  {
+    char result = c;
+    switch (c) {
+    case 'a':
+      result = 't';
+      break;
+    case 'A':
+      result = 'T';
+      break;
+    case 'c':
+      result = 'g';
+      break;
+    case 'C':
+      result = 'G';
+      break;
+    case 'g':
+      result = 'c';
+      break;
+    case 'G':
+      result = 'C';
+      break;
+    case 't':
+      result = 'a';
+      break;
+    case 'T':
+      result = 'A';
+      break;
+    case 'u':
+      result = 'a';
+      break;
+    case 'U':
+      result = 'A';
+      break;
+    case 'r':
+      result = 'y';
+      break;
+    case 'R':
+      result = 'Y';
+      break;
+    case 'y':
+      result = 'r';
+      break;
+    case 'Y':
+      result = 'R';
+      break;
+    case 'k':
+      result = 'm';
+      break;
+    case 'K':
+      result = 'M';
+      break;
+    case 'm':
+      result = 'k';
+      break;
+    case 'M':
+      result = 'K';
+      break;
+    case 'b':
+      result = 'v';
+      break;
+    case 'B':
+      result = 'V';
+      break;
+    case 'v':
+      result = 'b';
+      break;
+    case 'V':
+      result = 'B';
+      break;
+    case 'd':
+      result = 'h';
+      break;
+    case 'D':
+      result = 'H';
+      break;
+    case 'h':
+      result = 'd';
+      break;
+    case 'H':
+      result = 'D';
+      break;
+    }
+
+    return result;
+  }

 }
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 4e5083d..9113b66 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -131,7 +131,6 @@ import java.util.Deque;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;
 import java.util.Enumeration;
 import java.util.Hashtable;
 import java.util.List;

-import java.util.Set;

 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;
 import java.util.Vector;
 
 import javax.swing.JCheckBoxMenuItem;

@@ -828,6 +827,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible(nucleotide);
   public void setGUINucleotide(boolean nucleotide)
   {
     showTranslation.setVisible(nucleotide);

+    showReverse.setVisible(nucleotide);
+    showReverseComplement.setVisible(nucleotide);

     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);
     conservationMenuItem.setEnabled(!nucleotide);
     modifyConservation.setEnabled(!nucleotide);
     showGroupConservation.setEnabled(!nucleotide);

@@ -4783,7 +4784,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
             // TODO 1: no mappings are set up for EMBL product
             // TODO 2: if they were, should add them to protein alignment, not
             // dna
             // TODO 1: no mappings are set up for EMBL product
             // TODO 2: if they were, should add them to protein alignment, not
             // dna

-            Set<AlignedCodonFrame> cf = prods.getCodonFrames();
+            List<AlignedCodonFrame> cf = prods.getCodonFrames();

             for (AlignedCodonFrame acf : cf)
             {
               al.addCodonFrame(acf);
             for (AlignedCodonFrame acf : cf)
             {
               al.addCodonFrame(acf);

@@ -5960,7 +5961,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     // TODO no longer a menu action - refactor as required
     final AlignmentI alignment = getViewport().getAlignment();
   {
     // TODO no longer a menu action - refactor as required
     final AlignmentI alignment = getViewport().getAlignment();

-    Set<AlignedCodonFrame> mappings = alignment.getCodonFrames();
+    List<AlignedCodonFrame> mappings = alignment.getCodonFrames();

     if (mappings == null)
     {
       return;
     if (mappings == null)
     {
       return;

@@ -6015,6 +6016,27 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sf.setComplementVisible(this, show);
     }
   }
       sf.setComplementVisible(this, show);
     }
   }

+
+  /**
+   * Generate the reverse (optionally complemented) of the selected sequences,
+   * and add them to the alignment
+   */
+  @Override
+  protected void showReverse_actionPerformed(boolean complement)
+  {
+    AlignmentI al = null;
+    try
+    {
+      Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
+
+      al = dna.reverseCdna(complement);
+      viewport.addAlignment(al, "");
+    } catch (Exception ex)
+    {
+      System.err.println(ex.getMessage());
+      return;
+    }
+  }

 }
 
 class PrintThread extends Thread
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 73d34c2..205b9c6 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -173,6 +173,10 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem showTranslation = new JMenuItem();
 
 
   protected JMenuItem showTranslation = new JMenuItem();
 

+  protected JMenuItem showReverse = new JMenuItem();
+
+  protected JMenuItem showReverseComplement = new JMenuItem();
+

   protected JMenu showProducts = new JMenu();
 
   protected JMenuItem rnahelicesColour = new JMenuItem();
   protected JMenu showProducts = new JMenu();
 
   protected JMenuItem rnahelicesColour = new JMenuItem();

@@ -1686,6 +1690,25 @@ public class GAlignFrame extends JInternalFrame
         showTranslation_actionPerformed(e);
       }
     });
         showTranslation_actionPerformed(e);
       }
     });

+    showReverse.setText(MessageManager.getString("label.reverse"));
+    showReverse.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showReverse_actionPerformed(false);
+      }
+    });
+    showReverseComplement.setText(MessageManager
+            .getString("label.reverse_complement"));
+    showReverseComplement.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        showReverse_actionPerformed(true);
+      }
+    });

 
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));
 
     JMenuItem extractScores = new JMenuItem(
             MessageManager.getString("label.extract_scores"));

@@ -2252,6 +2275,8 @@ public class GAlignFrame extends JInternalFrame
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);
     calculateMenu.add(PCAMenuItem);
     calculateMenu.addSeparator();
     calculateMenu.add(showTranslation);

+    calculateMenu.add(showReverse);
+    calculateMenu.add(showReverseComplement);

     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
     calculateMenu.add(sortByTree);
     calculateMenu.add(showProducts);
     calculateMenu.add(autoCalculate);
     calculateMenu.add(sortByTree);

@@ -2320,6 +2345,16 @@ public class GAlignFrame extends JInternalFrame
   }
 
   /**
   }
 
   /**

+   * Generate the reverse sequence (or reverse complement if the flag is true)
+   * and add it to the alignment
+   * 
+   * @param complement
+   */
+  protected void showReverse_actionPerformed(boolean complement)
+  {
+  }
+
+  /**

    * Adds the given action listener and key accelerator to the given menu item.
    * Also saves in a lookup table to support lookup of action by key stroke.
    * 
    * Adds the given action listener and key accelerator to the given menu item.
    * Also saves in a lookup table to support lookup of action by key stroke.
    * 

@@ -3107,7 +3142,7 @@ public class GAlignFrame extends JInternalFrame
     return this.splitFrame;
   }
 
     return this.splitFrame;
   }
 

-  protected void showComplement_actionPerformed(boolean state)
+  protected void showComplement_actionPerformed(boolean complement)

   {
   }
 }
   {
   }
 }

diff --git a/test/jalview/analysis/DnaTest.java b/test/jalview/analysis/DnaTest.java
index 8f878f0..9a4c357 100644 (file)
--- a/test/jalview/analysis/DnaTest.java
+++ b/test/jalview/analysis/DnaTest.java
@@ -457,4 +457,58 @@ public class DnaTest
     assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
     assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
   }
     assertEquals("[0, 2, 5]", convertCodon("A-A--A").toString());
     assertEquals("[1, 3, 4]", convertCodon("-A-AA-").toString());
   }

+
+  /**
+   * Test dna complementing
+   */
+  @Test(groups = "Functional")
+  public void testGetComplement()
+  {
+    assertEquals('t', Dna.getComplement('a'));
+    assertEquals('T', Dna.getComplement('A'));
+    assertEquals('a', Dna.getComplement('t'));
+    assertEquals('A', Dna.getComplement('T'));
+    assertEquals('c', Dna.getComplement('g'));
+    assertEquals('C', Dna.getComplement('G'));
+    assertEquals('g', Dna.getComplement('c'));
+    assertEquals('G', Dna.getComplement('C'));
+    // note uU --> aA but not vice versa
+    assertEquals('a', Dna.getComplement('u'));
+    assertEquals('A', Dna.getComplement('U'));
+    // ambiguity codes, see http://www.bioinformatics.org/sms/iupac.html
+    assertEquals('r', Dna.getComplement('y'));
+    assertEquals('R', Dna.getComplement('Y'));
+    assertEquals('y', Dna.getComplement('r'));
+    assertEquals('Y', Dna.getComplement('R'));
+    assertEquals('k', Dna.getComplement('m'));
+    assertEquals('K', Dna.getComplement('M'));
+    assertEquals('m', Dna.getComplement('k'));
+    assertEquals('M', Dna.getComplement('K'));
+    assertEquals('b', Dna.getComplement('v'));
+    assertEquals('B', Dna.getComplement('V'));
+    assertEquals('v', Dna.getComplement('b'));
+    assertEquals('V', Dna.getComplement('B'));
+    assertEquals('d', Dna.getComplement('h'));
+    assertEquals('D', Dna.getComplement('H'));
+    assertEquals('h', Dna.getComplement('d'));
+    assertEquals('H', Dna.getComplement('D'));
+    assertEquals('Q', Dna.getComplement('Q'));
+  }
+
+  @Test(groups = "Functional")
+  public void testReverseSequence()
+  {
+    String seq = "AcGtUrYkMbVdHNX";
+
+    // reverse:
+    SequenceI reversed = Dna.reverseSequence("Seq1", seq, false);
+    assertEquals(new StringBuilder(seq).reverse()
+            .toString(), reversed.getSequenceAsString());
+    assertEquals("Seq1|rev", reversed.getName());
+
+    // reverse complement:
+    SequenceI revcomp = Dna.reverseSequence("Seq1", seq, true);
+    assertEquals("XNDhBvKmRyAaCgT", revcomp.getSequenceAsString());
+    assertEquals("Seq1|revcomp", revcomp.getName());
+  }

 }
 }