diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 7240955480c9972b2130230c4cc958ac1fef0dbb..195804790b7d8ad89a89ebadcc31a959663ec57e 100644
--- a/uk/ac/sanger/artemis/components/FeatureDisplay.java
+++ b/uk/ac/sanger/artemis/components/FeatureDisplay.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.16 2004-12-21 13:46:47 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.17 2004-12-22 13:28:31 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import javax.swing.JComponent;
* This component is used for displaying an Entry.
*
* @author Kim Rutherford
- * @version $Id: FeatureDisplay.java,v 1.16 2004-12-21 13:46:47 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.17 2004-12-22 13:28:31 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -1988,7 +1988,7 @@ public class FeatureDisplay extends EntryGroupPanel
final int frame_line = getFrameDisplayLine(FORWARD_FRAME_1 + i);
final AminoAcidSequence this_frame_translation =
- strand.getTranslation(newRange(start_base, end_base), false);
+ strand.getSpacedTranslation(newRange(start_base, end_base), false);
final String this_frame_translation_string =
this_frame_translation.toString();
@@ -2027,7 +2027,7 @@ public class FeatureDisplay extends EntryGroupPanel
final int frame_line = getFrameDisplayLine(REVERSE_FRAME_1 - i);
final AminoAcidSequence this_frame_translation =
- strand.getTranslation(newRange(start_base, end_base), false);
+ strand.getSpacedTranslation(newRange(start_base, end_base), false);
final String this_frame_translation_string =
this_frame_translation.toString();
@@ -2051,11 +2051,9 @@ public class FeatureDisplay extends EntryGroupPanel
* @param direction The direction to draw the letters in(see the
* frame_start parameter).
**/
- private void drawCodonLine(Graphics g,
- int frame_start,
- int line_number,
- String codons,
- int direction)
+ private void drawCodonLine(Graphics g, int frame_start,
+ int line_number, String codons,
+ int direction)
{
final int offset;
@@ -2064,26 +2062,22 @@ public class FeatureDisplay extends EntryGroupPanel
else
offset = 0;
- final String upper_case_codons = codons.toUpperCase();
+ codons = codons.toUpperCase();
final int draw_y_position = line_number * getLineHeight();
-
- // draw each AA letter
- for(int i = 0 ; i < upper_case_codons.length() ; ++i)
+ final int draw_x_position;
+
+ if(direction == REVERSE)
{
- int draw_x_position =
- (int)((offset + frame_start + 3 * i + 1) * getScaleValue());
+ draw_x_position = getLowXPositionOfBase(getLastVisibleForwardBase()) -
+ (int)((offset+frame_start+codons.length()) * getScaleValue());
- if(direction == REVERSE)
- {
- // draw in the opposite direction
- draw_x_position =
- getLowXPositionOfBase(getLastVisibleForwardBase()) -
- draw_x_position;
- }
-
- g.drawString(upper_case_codons.substring(i,i+1),
- draw_x_position, draw_y_position + getFontAscent() + 1);
+ codons = reverse(codons);
}
+ else
+ draw_x_position = (int)((offset + frame_start + 1) * getScaleValue());
+
+ g.drawString(codons, draw_x_position,
+ draw_y_position + getFontAscent() + 1);
}
/**
diff --git a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
index c1c8e56dd1ad72e232c6052f195dfc15365b324e..3ec8812f0ff4f93d3de21a8fb194daa0d7a8c8a9 100644
--- a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
+++ b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java,v 1.4 2004-12-21 10:28:02 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java,v 1.5 2004-12-22 13:28:31 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
@@ -33,7 +33,7 @@ import uk.ac.sanger.artemis.util.*;
* Objects of this class represent a string of amino acids.
*
* @author Kim Rutherford
- * @version $Id: AminoAcidSequence.java,v 1.4 2004-12-21 10:28:02 tjc Exp $
+ * @version $Id: AminoAcidSequence.java,v 1.5 2004-12-22 13:28:31 tjc Exp $
**/
public class AminoAcidSequence
@@ -77,7 +77,36 @@ public class AminoAcidSequence
else
aa_buffer.append (aa);
}
+ return new AminoAcidSequence(aa_buffer.toString());
+ }
+ /**
+ * Translate a sequence of bases into the corresponding single letter amino
+ * acid codes and appending 2 spaces after each amino acid character.
+ * @param bases The bases to translated. If the string length is not a
+ * multiple of three the last codon is incomplete and will not be
+ * translated.
+ * @param unknown_is_x If this parameter is true codons that contain
+ * ambiguous bases will be translated as 'x', if false they will be
+ * translated as '.'
+ * @return The translated sequence in one letter abbreviated form.
+ **/
+ public static AminoAcidSequence getSpacedTranslation(final String bases,
+ final boolean unknown_is_x)
+ {
+ final StringBuffer aa_buffer = new StringBuffer();
+ final int number_of_codons = bases.length() / 3;
+ for(int i = 0 ; i < number_of_codons * 3 ; i += 3)
+ {
+ final char aa = getCodonTranslation(bases.charAt(i),
+ bases.charAt(i+1),
+ bases.charAt(i+2));
+ if(aa == '.' && unknown_is_x)
+ aa_buffer.append('x');
+ else
+ aa_buffer.append(aa);
+ aa_buffer.append(" ");
+ }
return new AminoAcidSequence(aa_buffer.toString());
}
diff --git a/uk/ac/sanger/artemis/sequence/Bases.java b/uk/ac/sanger/artemis/sequence/Bases.java
index 4a78d30ae76a178c7435d17bc6cff1fa3714baca..d16d56aca939321fd6a504425b7e6f023eae1feb 100644
--- a/uk/ac/sanger/artemis/sequence/Bases.java
+++ b/uk/ac/sanger/artemis/sequence/Bases.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.2 2004-11-17 13:20:10 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.3 2004-12-22 13:28:31 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
@@ -45,7 +45,7 @@ import java.util.Iterator;
* non-base letter returns '@'.
*
* @author Kim Rutherford
- * @version $Id: Bases.java,v 1.2 2004-11-17 13:20:10 tjc Exp $ */
+ * @version $Id: Bases.java,v 1.3 2004-12-22 13:28:31 tjc Exp $ */
public class Bases {
/**
@@ -249,6 +249,17 @@ public class Bases {
return AminoAcidSequence.getTranslation (sub_sequence, unknown_is_x);
}
+
+ public AminoAcidSequence getSpacedTranslation (final Range range,
+ final int direction,
+ final boolean unknown_is_x) {
+ // getSubSequence () will return a sequence going in the right direction
+ // so we don't have to worry.
+ final String sub_sequence = getSubSequence (range, direction);
+
+ return AminoAcidSequence.getSpacedTranslation (sub_sequence, unknown_is_x);
+ }
+
/**
* Return an array containing the positions of the codons that match the
* strings given by the query_codons argument. Only those codons that are
diff --git a/uk/ac/sanger/artemis/sequence/Strand.java b/uk/ac/sanger/artemis/sequence/Strand.java
index 51984032bd1e2c4b0c6d2552ff5bbb0f98936270..ff96b9b3f31394a78ed005780895751d9f974dfd 100644
--- a/uk/ac/sanger/artemis/sequence/Strand.java
+++ b/uk/ac/sanger/artemis/sequence/Strand.java
@@ -20,7 +20,7 @@
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Strand.java,v 1.1 2004-06-09 09:52:27 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Strand.java,v 1.2 2004-12-22 13:28:31 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
@@ -39,7 +39,7 @@ import org.biojava.bio.symbol.IllegalSymbolException;
* what direction the Strand represents.
*
* @author Kim Rutherford
- * @version $Id: Strand.java,v 1.1 2004-06-09 09:52:27 tjc Exp $
+ * @version $Id: Strand.java,v 1.2 2004-12-22 13:28:31 tjc Exp $
**/
public class Strand {
@@ -583,11 +583,17 @@ public class Strand {
* translated as '.'
* @return The translated sequence in one letter abbreviated form.
**/
- public AminoAcidSequence getTranslation (final Range range,
- final boolean unknown_is_x) {
+ public AminoAcidSequence getTranslation(final Range range,
+ final boolean unknown_is_x) {
return getBases ().getTranslation (range, getDirection (), unknown_is_x);
}
+ public AminoAcidSequence getSpacedTranslation(final Range range,
+ final boolean unknown_is_x) {
+ return getBases ().getSpacedTranslation (range, getDirection (), unknown_is_x);
+ }
+
+
/**
* Return a sub-sequence of bases from this strand.
* @param range The inclusive range of bases to return.