From 464f89f1ad86859fe19c489817cf1851bde58ef9 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 17 Nov 2004 13:20:55 +0000
Subject: [PATCH] genetic code tables
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2059 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/options | 170 ++++-
uk/ac/sanger/artemis/Feature.java | 16 +-
uk/ac/sanger/artemis/Options.java | 64 +-
.../artemis/components/BasePlotGroup.java | 50 +-
.../artemis/components/FeatureDisplay.java | 34 +-
uk/ac/sanger/artemis/components/Splash.java | 155 +++-
.../artemis/sequence/AminoAcidSequence.java | 691 ++++++++++--------
uk/ac/sanger/artemis/sequence/Bases.java | 13 +-
8 files changed, 801 insertions(+), 392 deletions(-)
diff --git a/etc/options b/etc/options
index ec1fb28e2..7227aa4ce 100644
--- a/etc/options
+++ b/etc/options
@@ -2,7 +2,7 @@
# (Note that comment lines start with a hash (#) symbol)
-# $Header: //tmp/pathsoft/artemis/etc/options,v 1.12 2004-10-05 15:45:06 tjc Exp $
+# $Header: //tmp/pathsoft/artemis/etc/options,v 1.13 2004-11-17 13:20:55 tjc Exp $
# This file should contain option settings that look like this:
#
@@ -100,6 +100,174 @@ prokaryotic_start_codons = atg gtg ttg
# d d e e \
# g g g g
+#
+# Genetic Codes :
+# http://www3.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
+# http://www.ncbi.nlm.nih.gov/collab/FT/#7.5.5
+#
+
+genetic_codes = \
+ Standard \
+ Vertebrate_Mitochondrial \
+ Yeast_Mitochondrial \
+ Mold,_Protozoan,_Coelenterate_Mitochondrial_and_Mycoplasma/Spiroplasma \
+ Invertebrate_Mitochondrial \
+ Ciliate_Dasycladacean_and_Hexamita \
+ - \
+ - \
+ Echinoderm_Flatworm_Mitochondrial \
+ Euplotid \
+ Bacterial_and_Plant_Plastid \
+ Alternative_Yeast_Nuclear \
+ Ascidian_Mitochondrial \
+ Alternative_Flatworm_Mitochondrial \
+ Blepharisma_Nuclear \
+ Chlorophycean_Mitochondrial \
+ - \
+ - \
+ - \
+ - \
+ Trematode_Mitochondrial \
+ Scenedesmus_Obliquus_Mitochondrial \
+ Thraustochytrium_Mitochondrial
+
+
+# 1. standard code (default)
+translation_table_1 = \
+ f f l l \
+ s s s s \
+ y y * * \
+ c c * w \
+ \
+ l l l l \
+ p p p p \
+ h h q q \
+ r r r r \
+ \
+ i i i m \
+ t t t t \
+ n n k k \
+ s s r r \
+ \
+ v v v v \
+ a a a a \
+ d d e e \
+ g g g g
+
+start_codons_1 = atg
+
+#
+# For the following Genetic Code tables the differences
+# from the Standard Code are given.
+#
+#
+# 2. Vertebrate Mitochondrial Code
+#
+translation_table_2 = \
+ aga* agg* atam tgaw
+
+start_codons_2 = atg
+#start_codons_2_bos = ata
+#start_codons_2_homo = ata att
+#start_codons_2_mus = ata att atc
+#start_codons_2_coturnix_gallus = gtg
+
+# 3. Yeast Mitochondrial Code
+translation_table_3 = \
+ atam cttt ctct ctat ctgt tgaw
+
+start_codons_3 = ata atg
+
+# 4. Mold, Protozoan, and Coelenterate Mitochondrial Code and the
+# Mycoplasma/Spiroplasma Code
+translation_table_4 = \
+ tgaw
+
+start_codons_4 = atg
+
+#start_codons_4_Trypanosoma = tta ttg ctg
+#start_codons_4_Leishmania = att ata
+#start_codons_4_Tertrahymena = att ata atg
+#start_codons_4_Paramecium = att ata atg atc gtg gta
+
+# 5. Invertebrate Mitochondrial Code
+translation_table_5 = \
+ agas aggs atam tgaw
+
+start_codons_5 = atg ata att
+#start_codons_5_apis = atg ata atc att
+#start_codons_5_polyplacophora = atg ata gtg
+
+# 6. Ciliate, Dasycladacean and Hexamita Nuclear Code
+translation_table_6 = \
+ taaq tagq
+
+start_codons_6 = atg
+
+# 9. Echinoderm and Flatworm Mitochondrial Code
+translation_table_9 = \
+ aaan agas aggs tgaw
+
+start_codons_9 = atg gtg
+
+# 10. Euplotid Nuclear Code
+translation_table_10 = \
+ tgac
+
+start_codons_10 = atg
+
+# 11. Bacterial and Plant Plastid
+translation_table_11 =
+
+start_codons_11 = atg gtg ttg
+
+# 12. Alternative Yeast Nuclear Code
+translation_table_12 = \
+ ctgs
+
+start_codons_12 = ctg atg
+
+# 13. Ascidian Mitochondrial Code
+translation_table_13 = \
+ agag aggg atam tgaw
+
+start_codons_13 = atg
+
+# 14. Alternative Flatworm Mitochondrial Code
+translation_table_14 = \
+ aaan agas aggs taay tgaw
+
+start_codons_14 = atg
+
+# 15. Blepharisma
+translation_table_15 = \
+ tagq
+
+start_codons_15 = atg
+
+# 16. Chlorophycean Mitochondrial
+translation_table_16 = \
+ tagl
+
+start_codons_16 = atg
+
+# 21. Trematode Mitochondrial
+translation_table_21 = \
+ tgaw atam aaan agas aggs
+
+start_codons_21 = atg gtg
+
+# 22. Scenedesmus obliquus mitochondrial
+translation_table_22 = \
+ tca* tagl
+
+start_codons_22 = atg
+
+# 23. Thraustochytrium Mitochondrial
+translation_table_23 = \
+ tta*
+
+start_codons_23 = att atg gtg
# the sequence of colour numbers must not have any gaps - if for example
# colour_5 is missing then all colours with higher numbers will be ignored
diff --git a/uk/ac/sanger/artemis/Feature.java b/uk/ac/sanger/artemis/Feature.java
index c3eccfc33..4c49dd99b 100644
--- a/uk/ac/sanger/artemis/Feature.java
+++ b/uk/ac/sanger/artemis/Feature.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/Feature.java,v 1.1 2004-06-09 09:44:36 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/Feature.java,v 1.2 2004-11-17 13:20:34 tjc Exp $
*/
package uk.ac.sanger.artemis;
@@ -60,7 +60,7 @@ import java.util.Date;
* embl.Feature and embl.Entry objects.
*
* @author Kim Rutherford
- * @version $Id: Feature.java,v 1.1 2004-06-09 09:44:36 tjc Exp $
+ * @version $Id: Feature.java,v 1.2 2004-11-17 13:20:34 tjc Exp $
**/
public class Feature
@@ -953,11 +953,13 @@ public class Feature
final StringVector start_codons;
- if (Options.getOptions ().isEukaryoticMode ()) {
- start_codons = Options.getOptions ().getEukaryoticStartCodons ();
- } else {
- start_codons = Options.getOptions ().getProkaryoticStartCodons ();
- }
+ start_codons = Options.getOptions().getStartCodons();
+
+// if (Options.getOptions ().isEukaryoticMode ()) {
+// start_codons = Options.getOptions ().getEukaryoticStartCodons ();
+// } else {
+// start_codons = Options.getOptions ().getProkaryoticStartCodons ();
+// }
if (start_codons.contains (first_codon)) {
return true;
diff --git a/uk/ac/sanger/artemis/Options.java b/uk/ac/sanger/artemis/Options.java
index 345bed1c2..341466364 100644
--- a/uk/ac/sanger/artemis/Options.java
+++ b/uk/ac/sanger/artemis/Options.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/Options.java,v 1.3 2004-10-29 09:36:23 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/Options.java,v 1.4 2004-11-17 13:20:46 tjc Exp $
**/
package uk.ac.sanger.artemis;
@@ -44,7 +44,7 @@ import java.util.*;
* read in new options.
*
* @author Kim Rutherford
- * @version $Id: Options.java,v 1.3 2004-10-29 09:36:23 tjc Exp $
+ * @version $Id: Options.java,v 1.4 2004-11-17 13:20:46 tjc Exp $
**/
public class Options extends Properties
@@ -710,36 +710,58 @@ public class Options extends Properties
}
-
/**
* Return a StringVector containing the bases of the possible start codons
* for prokaryotes. This is stored in the prokaryotic_start_codons option
* in the options file.
**/
- public StringVector getProkaryoticStartCodons()
- {
- final StringVector option_values =
- getOptionValues("prokaryotic_start_codons");
+//public StringVector getProkaryoticStartCodons()
+//{
+// final StringVector option_values =
+// getOptionValues("prokaryotic_start_codons");
- for(int i = 0; i<option_values.size() ; ++i)
- {
- final String new_value = option_values.elementAt(i).toLowerCase();
- option_values.setElementAt(new_value, i);
- }
- return option_values;
- }
+// for(int i = 0; i<option_values.size() ; ++i)
+// {
+// final String new_value = option_values.elementAt(i).toLowerCase();
+// option_values.setElementAt(new_value, i);
+// }
+// return option_values;
+//}
/**
* Return a StringVector containing the bases of the possible eukaryotic
* start codons. This is stored in the eukaryotic_start_codons option in
* the options file.
**/
- public StringVector getEukaryoticStartCodons()
+//public StringVector getEukaryoticStartCodons()
+//{
+// final StringVector option_values =
+// getOptionValues("eukaryotic_start_codons");
+
+// for(int i = 0; i<option_values.size() ; ++i)
+// {
+// final String new_value = option_values.elementAt(i).toLowerCase();
+// option_values.setElementAt(new_value, i);
+// }
+
+// return option_values;
+//}
+
+ public StringVector getStartCodons()
{
- final StringVector option_values =
- getOptionValues("eukaryotic_start_codons");
+ final StringVector option_values;
- for(int i = 0; i<option_values.size() ; ++i)
+ if(getProperty("start_codons") == null)
+ {
+ if(isEukaryoticMode())
+ option_values = getOptionValues("eukaryotic_start_codons");
+ else
+ option_values = getOptionValues("prokaryotic_start_codons");
+ }
+ else
+ option_values = getOptionValues("start_codons");
+
+ for(int i = 0; i<option_values.size() ; ++i)
{
final String new_value = option_values.elementAt(i).toLowerCase();
option_values.setElementAt(new_value, i);
@@ -977,6 +999,12 @@ public class Options extends Properties
return false;
}
+ public void setGeneticCode(String table)
+ {
+ put("translation_table",table);
+ fireChangeEvent("translation_table");
+ }
+
/**
* Set the organism type to eukaryotic if and only if the argument is
* true. The other alternative is prokaryotic.
diff --git a/uk/ac/sanger/artemis/components/BasePlotGroup.java b/uk/ac/sanger/artemis/components/BasePlotGroup.java
index 2c8011064..8e5a45f49 100644
--- a/uk/ac/sanger/artemis/components/BasePlotGroup.java
+++ b/uk/ac/sanger/artemis/components/BasePlotGroup.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/BasePlotGroup.java,v 1.3 2004-11-09 16:21:16 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/BasePlotGroup.java,v 1.4 2004-11-17 13:19:43 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -42,7 +42,7 @@ import javax.swing.*;
* which can toggled off and on.
*
* @author Kim Rutherford
- * @version $Id: BasePlotGroup.java,v 1.3 2004-11-09 16:21:16 tjc Exp $
+ * @version $Id: BasePlotGroup.java,v 1.4 2004-11-17 13:19:43 tjc Exp $
**/
public class BasePlotGroup extends JPanel
@@ -80,21 +80,24 @@ public class BasePlotGroup extends JPanel
{21,91,4,0,38} // t
};
- final float [] [] test_weights2 = {
+ final float[][] test_weights2 =
+ {
{11,11,10, 8,11,10,11,11, 7, 8,25, 3,100, 0,27},
{29,33,30,30,32,34,37,38,39,36,26,75, 0, 0,14},
{14,12,10,10, 9,11,10, 9, 7, 6,26, 1, 0,100,49},
{46,44,50,52,48,45,42,43,47,51,23,21, 0, 0,10}
};
- final float [] [] test_weights3 = {
+ final float[][] test_weights3 =
+ {
{0,0,1,0,0,0},
{0,0,0,1,0,0},
{1,0,0,0,1,0},
{0,1,0,0,0,1},
};
- final float [] cai_test = {
+ final float[] cai_test =
+ {
0.113F, 1.0F, 0.117F, 1.0F,
1.0F, 0.693F, 0.036F, 0.005F,
0.071F, 1.0F, 0.0F, 0.0F,
@@ -142,6 +145,43 @@ public class BasePlotGroup extends JPanel
addAlgorithm(new GCDeviationAlgorithm(forward_strand));
addAlgorithm(new ATDeviationAlgorithm(forward_strand));
addAlgorithm(new KarlinSigAlgorithm(forward_strand));
+
+
+ //CumulativeATSkewAlgorithm
+ addAlgorithm(new CumulativeATSkewAlgorithm(forward_strand));
+ addAlgorithm(new CumulativeGCSkewAlgorithm(forward_strand));
+
+ //Positional Asymmetry
+ addAlgorithm(new PositionalAsymmetryAlgorithm(forward_strand));
+
+ //Informational Entropy
+ addAlgorithm(new EntropyAlgorithm(forward_strand));
+
+ //Scaled Chi
+ addAlgorithm(new ScaledChiAlgorithm(forward_strand));
+ addAlgorithm(new ScaledChiAlgorithm(reverse_strand));
+// addAlgorithm(new ScaledChiRevAlgorithm(reverse_strand));
+
+ //Corrected Scaled Chi Square
+ addAlgorithm(new CSCSAlgorithm(forward_strand));
+ addAlgorithm(new CSCSAlgorithm(reverse_strand));
+// addAlgorithm(new CSCSRevAlgorithm(reverse_strand));
+
+ //Mutational Response Index
+ addAlgorithm(new MRIAlgorithm(forward_strand));
+ addAlgorithm(new MRIAlgorithm(reverse_strand));
+// addAlgorithm(new MRIRevAlgorithm(reverse_strand));
+
+ //Effective Codon Number
+ addAlgorithm(new NcAlgorithm(forward_strand));
+ addAlgorithm(new NcAlgorithm(reverse_strand));
+// addAlgorithm(new NcRevAlgorithm(reverse_strand));
+
+ //Intrinsic Codon Deviation Index
+ addAlgorithm(new ICDIAlgorithm(forward_strand));
+ addAlgorithm(new ICDIAlgorithm(reverse_strand));
+// addAlgorithm(new ICDIRevAlgorithm(reverse_strand));
+
}
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 8a36c42d2..70e78d442 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 1.8 2004-11-09 14:24:41 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.9 2004-11-17 13:19:43 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -44,7 +44,7 @@ import javax.swing.JComponent;
* This component is used for displaying an Entry.
*
* @author Kim Rutherford
- * @version $Id: FeatureDisplay.java,v 1.8 2004-11-09 14:24:41 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.9 2004-11-17 13:19:43 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -1010,6 +1010,7 @@ public class FeatureDisplay extends EntryGroupPanel
**/
public void optionChanged(OptionChangeEvent event)
{
+ getBases().clearStopCodonCache();
repaint();
}
@@ -1832,7 +1833,8 @@ public class FeatureDisplay extends EntryGroupPanel
if(show_stop_codons)
{
- forward_stop_codons = new int [][] {
+ forward_stop_codons = new int [][]
+ {
strand.getStopCodons(newRange(start_base, end_base)),
strand.getStopCodons(newRange(start_base + 1, end_base)),
strand.getStopCodons(newRange(start_base + 2, end_base))
@@ -1844,14 +1846,15 @@ public class FeatureDisplay extends EntryGroupPanel
if(show_start_codons)
{
- final StringVector start_codons;
-
- if(Options.getOptions().isEukaryoticMode())
- start_codons = Options.getOptions().getEukaryoticStartCodons();
- else
- start_codons = Options.getOptions().getProkaryoticStartCodons();
+ final StringVector start_codons = Options.getOptions().getStartCodons();
+
+// if(Options.getOptions().isEukaryoticMode())
+// start_codons = Options.getOptions().getEukaryoticStartCodons();
+// else
+// start_codons = Options.getOptions().getProkaryoticStartCodons();
- forward_start_codons = new int [][] {
+ forward_start_codons = new int [][]
+ {
strand.getMatchingCodons(newRange(start_base, end_base),
start_codons),
strand.getMatchingCodons(newRange(start_base + 1, end_base),
@@ -1864,7 +1867,6 @@ public class FeatureDisplay extends EntryGroupPanel
for(int i = 0 ; i < 3 ; ++i)
{
final int frame_line = getFrameDisplayLine(FORWARD_FRAME_1 + i);
-
final int frame_x_start = i;
if(show_start_codons)
@@ -1933,12 +1935,12 @@ public class FeatureDisplay extends EntryGroupPanel
if(show_start_codons)
{
- final StringVector start_codons;
+ final StringVector start_codons = Options.getOptions().getStartCodons();;
- if(Options.getOptions().isEukaryoticMode())
- start_codons = Options.getOptions().getEukaryoticStartCodons();
- else
- start_codons = Options.getOptions().getProkaryoticStartCodons();
+// if(Options.getOptions().isEukaryoticMode())
+// start_codons = Options.getOptions().getEukaryoticStartCodons();
+// else
+// start_codons = Options.getOptions().getProkaryoticStartCodons();
reverse_start_codons = new int [][] {
strand.getMatchingCodons(newRange(start_base, end_base),
diff --git a/uk/ac/sanger/artemis/components/Splash.java b/uk/ac/sanger/artemis/components/Splash.java
index 7e67f4194..240662b0a 100644
--- a/uk/ac/sanger/artemis/components/Splash.java
+++ b/uk/ac/sanger/artemis/components/Splash.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/Splash.java,v 1.1 2004-06-09 09:47:48 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/Splash.java,v 1.2 2004-11-17 13:19:43 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -30,6 +30,8 @@ import uk.ac.sanger.artemis.EntrySourceVector;
import uk.ac.sanger.artemis.Logger;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
+import uk.ac.sanger.artemis.util.StringVector;
+import uk.ac.sanger.artemis.sequence.Bases;
import java.awt.*;
import java.awt.event.*;
@@ -40,7 +42,7 @@ import javax.swing.border.Border;
* Base class that creates a generic "Splash Screen"
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: Splash.java,v 1.1 2004-06-09 09:47:48 tjc Exp $
+ * @version $Id: Splash.java,v 1.2 2004-11-17 13:19:43 tjc Exp $
**/
abstract public class Splash extends JFrame
@@ -80,6 +82,8 @@ abstract public class Splash extends JFrame
protected JMenu options_menu;
+ private String geneticCode;
+
/**
* Create a new JFrame for a Splash screen.
* @param program_name The full name of the program.
@@ -187,13 +191,14 @@ abstract public class Splash extends JFrame
}
// return the program name and the program mode in one String
- private String getNameString()
- {
- if(Options.getOptions().isEukaryoticMode())
- return program_name + " [Eukaryotic mode]";
- else
- return program_name + " [Prokaryotic mode]";
- }
+// private String getNameString()
+// {
+// if(Options.getOptions().isEukaryoticMode())
+// return program_name + " [Eukaryotic mode]";
+// else
+// return program_name + " [Prokaryotic mode]";
+// return geneticCode;
+// }
/**
* Draws the splash screen text.
@@ -209,13 +214,16 @@ abstract public class Splash extends JFrame
helix_width + left_margin, font_height);
g.drawString(program_version,
helix_width + left_margin, font_height * 2);
- if(Options.getOptions().isEukaryoticMode())
- g.drawString("[Eukaryotic mode]",
+// if(Options.getOptions().isEukaryoticMode())
+// g.drawString("[Eukaryotic mode]",
+// helix_width + left_margin, font_height * 3);
+// else
+// g.drawString("[Prokaryotic mode]",
+// helix_width + left_margin, font_height * 3);
+ g.drawString(geneticCode,
helix_width + left_margin, font_height * 3);
- else
- g.drawString("[Prokaryotic mode]",
- helix_width + left_margin, font_height * 3);
- g.drawString("Copyright 1998 - 2003",
+
+ g.drawString("Copyright 1998 - 2004",
helix_width + left_margin, font_height * 9 / 2);
g.drawString("Genome Research Limited",
helix_width + left_margin, font_height * 11 / 2);
@@ -388,20 +396,115 @@ abstract public class Splash extends JFrame
});
options_menu.add(enable_direct_edit_item);
- final JCheckBoxMenuItem enable_euk_mode_item = new JCheckBoxMenuItem(
- "Eukaryotic Mode");
- enable_euk_mode_item.setState(Options.getOptions().isEukaryoticMode());
- enable_euk_mode_item.addItemListener(new ItemListener()
+
+ // available genetic codes
+ String gcodes[] = Options.getOptions().getOptionValues("genetic_codes").getArray();
+
+ ButtonGroup gcodeGroup = new ButtonGroup();
+ options_menu.addSeparator();
+ options_menu.add(new JLabel(" --- Genetic Codes Tables ---"));
+ for(int i = 0; i< gcodes.length; i++)
{
- public void itemStateChanged(ItemEvent event)
+ if(gcodes[i].equals("-"))
+ continue;
+
+ int ind1;
+ while((ind1 = gcodes[i].indexOf("_")) > -1)
+ gcodes[i] = gcodes[i].substring(0,ind1) + " " +
+ gcodes[i].substring(ind1+1,gcodes[i].length());
+
+ String num = Integer.toString(i+1);
+ final String gc_name = num+". "+gcodes[i];
+ final JCheckBoxMenuItem geneCode = new JCheckBoxMenuItem(gc_name);
+ gcodeGroup.add(geneCode);
+ geneCode.setActionCommand(num);
+
+ geneCode.addItemListener(new ItemListener()
{
- final boolean item_state = enable_euk_mode_item.getState();
- Options.getOptions().setEukaryoticMode(item_state);
+ public void itemStateChanged(ItemEvent event)
+ {
+ if(geneCode.getState())
+ {
+ geneticCode = gc_name;
+ String tab = "translation_table_"+geneCode.getActionCommand();
+ String startCodons = "start_codons_"+geneCode.getActionCommand();
+
+ StringVector options_file_table =
+ Options.getOptions().getOptionValues(tab);
+
+ if(options_file_table != null)
+ {
+ if(options_file_table.size() == 64)
+ {
+ StringBuffer sbuff = new StringBuffer();
+ for(int i = 0; i < 64; ++i)
+ sbuff.append(options_file_table.elementAt(i)+" ");
+
+ Options.getOptions().setGeneticCode(sbuff.toString());
+ }
+ else
+ {
+ StringVector table = Options.getOptions().getOptionValues("translation_table_1");
+
+ for(int i = 0; i < options_file_table.size(); ++i)
+ {
+ String cod_plus_aa = options_file_table.elementAt(i);
+// System.out.println(cod_plus_aa);
+ final int codon_index = Bases.getIndexOfBase(cod_plus_aa.charAt(0)) * 16 +
+ Bases.getIndexOfBase(cod_plus_aa.charAt(1)) * 4 +
+ Bases.getIndexOfBase(cod_plus_aa.charAt(2));
+
+// System.out.println(cod_plus_aa.substring(3)+" "+codon_index+" "+
+// table.elementAt(codon_index));
+ table.setElementAt(cod_plus_aa.substring(3), codon_index);
+ }
+
+ StringBuffer sbuff = new StringBuffer();
+ for(int i = 0; i < 64; ++i)
+ sbuff.append(table.elementAt(i)+" ");
+
+ Options.getOptions().setGeneticCode(sbuff.toString());
+ }
+
+ options_file_table =
+ Options.getOptions().getOptionValues(startCodons);
+
+ if(options_file_table != null)
+ {
+ StringBuffer sbuff = new StringBuffer();
+ for(int i = 0; i < options_file_table.size(); ++i)
+ sbuff.append(options_file_table.elementAt(i)+" ");
+
+ Options.getOptions().setProperty("start_codons",sbuff.toString());
+ }
+ }
+
+ if(helix_canvas != null)
+ helix_canvas.repaint();
+ }
+ }
+ });
+ options_menu.add(geneCode);
- helix_canvas.repaint();
- }
- });
- options_menu.add(enable_euk_mode_item);
+ if(i == 0)
+ geneCode.setState(true);
+ }
+ options_menu.addSeparator();
+
+
+// final JCheckBoxMenuItem enable_euk_mode_item = new JCheckBoxMenuItem(
+// "Eukaryotic Mode");
+// enable_euk_mode_item.setState(Options.getOptions().isEukaryoticMode());
+// enable_euk_mode_item.addItemListener(new ItemListener()
+// {
+// public void itemStateChanged(ItemEvent event)
+// {
+// final boolean item_state = enable_euk_mode_item.getState();
+// Options.getOptions().setEukaryoticMode(item_state);
+// helix_canvas.repaint();
+// }
+// });
+// options_menu.add(enable_euk_mode_item);
final JCheckBoxMenuItem highlight_active_entry_item =
new JCheckBoxMenuItem("Highlight Active Entry");
diff --git a/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java b/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java
index 2a1b859ff..31aa792f3 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 1.1 2004-06-09 09:52:11 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/AminoAcidSequence.java,v 1.2 2004-11-17 13:20:10 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
@@ -33,16 +33,18 @@ import uk.ac.sanger.artemis.util.*;
* Objects of this class represent a string of amino acids.
*
* @author Kim Rutherford
- * @version $Id: AminoAcidSequence.java,v 1.1 2004-06-09 09:52:11 tjc Exp $
+ * @version $Id: AminoAcidSequence.java,v 1.2 2004-11-17 13:20:10 tjc Exp $
**/
-public class AminoAcidSequence {
+public class AminoAcidSequence
+{
/**
* Create a new AminoAcidSequence object from a string containing single
* character amino acids symbols.
**/
- public AminoAcidSequence (String amino_acid_string) {
- this.amino_acid_string = amino_acid_string.toLowerCase ();
+ public AminoAcidSequence(String amino_acid_string)
+ {
+ this.amino_acid_string = amino_acid_string.toLowerCase();
}
/**
@@ -56,24 +58,25 @@ public class AminoAcidSequence {
* translated as '.'
* @return The translated sequence in one letter abbreviated form.
**/
- public static AminoAcidSequence getTranslation (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) {
+ public static AminoAcidSequence getTranslation(final String bases,
+ final boolean unknown_is_x)
+ {
+ setGeneCode();
+ 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 {
+ else
aa_buffer.append (aa);
- }
}
- return new AminoAcidSequence (aa_buffer.toString ());
+ return new AminoAcidSequence(aa_buffer.toString());
}
/**
@@ -86,13 +89,14 @@ public class AminoAcidSequence {
* contains more or less than three letters or the letters aren't from
* "CTAG")
**/
- public static char getCodonTranslation (String codon_string) {
- if (codon_string.length () < 3) {
+ public static char getCodonTranslation(String codon_string)
+ {
+ if(codon_string.length() < 3)
return '.';
- }
- return getCodonTranslation (codon_string.charAt (0),
- codon_string.charAt (1),
- codon_string.charAt (2));
+
+ return getCodonTranslation(codon_string.charAt(0),
+ codon_string.charAt(1),
+ codon_string.charAt(2));
}
/**
@@ -104,75 +108,82 @@ public class AminoAcidSequence {
* @return The translated sequence in one letter abbreviated form. The
* return value will be '.' if the letters do not form a codon.
**/
- public static char getCodonTranslation (char first_letter,
- char second_letter,
- char third_letter) {
- final int first_index = Bases.getIndexOfBase (first_letter);
-
- if (first_index >= 4) {
+ public static char getCodonTranslation(char first_letter,
+ char second_letter,
+ char third_letter)
+ {
+ final int first_index = Bases.getIndexOfBase(first_letter);
+ if(first_index >= 4)
return '.';
- }
- final int second_index = Bases.getIndexOfBase (second_letter);
-
- if (second_index >= 4) {
+ final int second_index = Bases.getIndexOfBase(second_letter);
+ if(second_index >= 4)
return '.';
- }
-
- final int third_index = Bases.getIndexOfBase (third_letter);
- if (third_index >= 4) {
+ final int third_index = Bases.getIndexOfBase(third_letter);
+ if(third_index >= 4)
return '.';
- }
final int codon_index = first_index * 16 + second_index * 4 + third_index;
+// char[] codon = { first_letter,
+// second_letter,
+// third_letter,
+// codon_translation_array[codon_index] };
+// System.out.println(new String(codon));
return codon_translation_array[codon_index];
}
+
/**
* Return the number of units in this amino acid sequence.
**/
- public int length () {
- return amino_acid_string.length ();
+ public int length()
+ {
+ return amino_acid_string.length();
}
/**
* Return the one letter codon code of the codon at the given index
* (counting from zero).
**/
- public char elementAt (final int index) {
- return amino_acid_string.charAt (index);
+ public char elementAt(final int index)
+ {
+ return amino_acid_string.charAt(index);
}
/**
* Return the total molecular weight of the amino acids in this
* AminoAcidSequence..
**/
- public float getMolecularWeight () {
+ public float getMolecularWeight()
+ {
float return_weight = 0;
- for (int i = 0 ; i < amino_acid_string.length () ; ++i) {
- final char this_char = amino_acid_string.charAt (i);
+ for(int i = 0 ; i < amino_acid_string.length() ; ++i)
+ {
+ final char this_char = amino_acid_string.charAt(i);
return_weight +=
- molecular_weights[getSymbolIndex (this_char)];
+ molecular_weights[getSymbolIndex(this_char)];
}
- if (amino_acid_string.length () > 1) {
+ if(amino_acid_string.length() > 1)
+ {
// need to take off the weight of a water molecule for each peptide bond
return return_weight -
molecular_weight_of_water * (amino_acid_string.length () - 1);
- } else {
- return return_weight;
}
+ else
+ return return_weight;
}
/**
* Return a string representation of this object. This string will contain
* the one character amino acid codes for each acid in sequence.
**/
- public String toString () {
+ public String toString()
+ {
return amino_acid_string;
}
@@ -180,31 +191,31 @@ public class AminoAcidSequence {
* Search the subject_sequence for this AminoAcidSequence as a substring.
* 'X' AAs are treated as wildcards in both sequences.
**/
- public boolean checkForMatch (final AminoAcidSequence subject_sequence) {
- final String subject_sequence_string = subject_sequence.toString ();
+ public boolean checkForMatch(final AminoAcidSequence subject_sequence)
+ {
+ final String subject_sequence_string = subject_sequence.toString();
- for (int subject_index = 0 ;
- subject_index < subject_sequence_string.length () -
- toString ().length () + 1 ;
- ++subject_index) {
+ for(int subject_index = 0;
+ subject_index < subject_sequence_string.length() -
+ toString ().length () + 1;
+ ++subject_index)
+ {
int query_index = 0;
boolean is_matching = true;
- for (;
- query_index < toString ().length () ;
- ++query_index) {
+ for(; query_index < toString().length();
+ ++query_index)
+ {
final char this_query_char =
- toString ().charAt (query_index);
+ toString().charAt(query_index);
final char this_subject_char =
- subject_sequence_string.charAt (subject_index + query_index);
- if (!aminoAcidMatches (this_subject_char,
- this_query_char)) {
+ subject_sequence_string.charAt(subject_index + query_index);
+ if(!aminoAcidMatches(this_subject_char,
+ this_query_char))
break;
- }
}
- if (query_index == toString ().length ()) {
+ if(query_index == toString().length())
return true;
- }
}
return false;
@@ -214,16 +225,17 @@ public class AminoAcidSequence {
* Return true if and only if the two argument are the same AA or if one is
* an X.
**/
- private static boolean aminoAcidMatches (final char aa_char1,
- final char aa_char2) {
- if (aa_char1 == aa_char2) {
+ private static boolean aminoAcidMatches(final char aa_char1,
+ final char aa_char2)
+ {
+ if (aa_char1 == aa_char2)
return true;
- } else {
- if (aa_char1 == 'x' || aa_char2 == 'x') {
+ else
+ {
+ if(aa_char1 == 'x' || aa_char2 == 'x')
return true;
- } else {
+ else
return false;
- }
}
}
@@ -245,10 +257,11 @@ public class AminoAcidSequence {
* @return A MarkerRange covering the matching bases or null if there is no
* match in the given range.
**/
- public MarkerRange findMatch (final Bases bases,
- final Marker search_start_marker,
- final boolean search_backwards) {
- final String bases_string = bases.toString ();
+ public MarkerRange findMatch(final Bases bases,
+ final Marker search_start_marker,
+ final boolean search_backwards)
+ {
+ final String bases_string = bases.toString();
// search the bases_string forward for the pattern_string and its
// complement
@@ -261,84 +274,108 @@ public class AminoAcidSequence {
// for the reverse complement of this position
final int complement_search_start_index;
- if (search_backwards) {
- if (search_start_marker == null) {
+ if(search_backwards)
+ {
+ if(search_start_marker == null)
+ {
forward_search_start_index = bases.getLength () - 1;
complement_search_start_index = bases.getLength () - 1;
- } else {
+ }
+ else
+ {
complement_search_start_index =
- search_start_marker.getRawPosition () - 2;
- if (search_start_marker.getStrand ().isForwardStrand ()) {
+ search_start_marker.getRawPosition() - 2;
+ if(search_start_marker.getStrand().isForwardStrand())
+ {
forward_search_start_index =
- search_start_marker.getRawPosition () - 2;
- } else {
+ search_start_marker.getRawPosition() - 2;
+ }
+ else
+ {
forward_search_start_index =
- search_start_marker.getRawPosition () - 1;
+ search_start_marker.getRawPosition() - 1;
}
}
- } else {
- if (search_start_marker == null) {
+ }
+ else
+ {
+ if(search_start_marker == null)
+ {
forward_search_start_index = 0;
complement_search_start_index = 0;
- } else {
- forward_search_start_index = search_start_marker.getRawPosition ();
- if (search_start_marker.getStrand ().isForwardStrand ()) {
+ }
+ else
+ {
+ forward_search_start_index = search_start_marker.getRawPosition();
+ if(search_start_marker.getStrand().isForwardStrand())
+ {
complement_search_start_index =
- search_start_marker.getRawPosition () - 1;
- } else {
+ search_start_marker.getRawPosition() - 1;
+ }
+ else
+ {
complement_search_start_index =
- search_start_marker.getRawPosition ();
+ search_start_marker.getRawPosition();
}
}
}
final int forward_search_result =
- searchFor (bases_string,
- forward_search_start_index,
- search_backwards);
+ searchFor(bases_string,
+ forward_search_start_index,
+ search_backwards);
final int complement_search_result =
- reverseComplementSearchFor (bases_string,
- complement_search_start_index,
- search_backwards);
+ reverseComplementSearchFor(bases_string,
+ complement_search_start_index,
+ search_backwards);
final int match_first_base;
final int match_last_base;
final Strand match_strand;
- if (forward_search_result == -1) {
- if (complement_search_result == -1) {
- // no match
+ if(forward_search_result == -1)
+ {
+ // no match
+ if(complement_search_result == -1)
return null;
- }
}
- if (search_backwards) {
+ if(search_backwards)
+ {
// take the match that is closest to the end, or the complement match if
// there is a tie
- if (complement_search_result != -1 &&
- (forward_search_result == -1 ||
- complement_search_result >= forward_search_result)) {
+ if(complement_search_result != -1 &&
+ (forward_search_result == -1 ||
+ complement_search_result >= forward_search_result))
+ {
match_first_base =
bases.getComplementPosition (complement_search_result + 1);
match_last_base = match_first_base - (length () * 3 - 1);
match_strand = bases.getReverseStrand ();
- } else {
+ }
+ else
+ {
match_first_base = forward_search_result + 1;
match_last_base = match_first_base + length () * 3 - 1;
match_strand = bases.getForwardStrand ();
}
- } else {
+ }
+ else
+ {
// take the match that is closest to base 1, or the forward match if
// there is a tie
- if (forward_search_result != -1 &&
- (complement_search_result == -1 ||
- forward_search_result <= complement_search_result)) {
+ if(forward_search_result != -1 &&
+ (complement_search_result == -1 ||
+ forward_search_result <= complement_search_result))
+ {
match_first_base = forward_search_result + 1;
match_last_base = match_first_base + length () * 3 - 1;
match_strand = bases.getForwardStrand ();
- } else {
+ }
+ else
+ {
match_first_base =
bases.getComplementPosition (complement_search_result + 1);
match_last_base = match_first_base - (length () * 3 - 1);
@@ -346,12 +383,15 @@ public class AminoAcidSequence {
}
}
- try {
- return new MarkerRange (match_strand,
- match_first_base,
- match_last_base);
- } catch (OutOfRangeException e) {
- throw new Error ("internal error - unexpected exception: " + e);
+ try
+ {
+ return new MarkerRange(match_strand,
+ match_first_base,
+ match_last_base);
+ }
+ catch (OutOfRangeException e)
+ {
+ throw new Error("internal error - unexpected exception: " + e);
}
}
@@ -366,14 +406,14 @@ public class AminoAcidSequence {
* first base, otherwise first to last.
* @return The index of the match or -1 if there is no match.
**/
- public int searchFor (final String bases_string,
- final int start_index,
- final boolean search_backwards) {
- if (search_backwards) {
- return searchBackwardFor (bases_string, start_index);
- } else {
- return searchForwardFor (bases_string, start_index);
- }
+ public int searchFor(final String bases_string,
+ final int start_index,
+ final boolean search_backwards)
+ {
+ if(search_backwards)
+ return searchBackwardFor(bases_string, start_index);
+ else
+ return searchForwardFor(bases_string, start_index);
}
/**
@@ -385,37 +425,38 @@ public class AminoAcidSequence {
* should start.
* @return The index of the match or -1 if there is no match.
**/
- public int searchForwardFor (final String bases_string,
- final int start_index) {
- final int pattern_base_length = length () * 3;
-
- for (int base_index = start_index ;
- base_index <= bases_string.length () - pattern_base_length ;
- ++base_index) {
+ public int searchForwardFor(final String bases_string,
+ final int start_index)
+ {
+ final int pattern_base_length = length() * 3;
+ for(int base_index = start_index;
+ base_index <= bases_string.length() - pattern_base_length ;
+ ++base_index)
+ {
boolean matched = true;
- for (int offset = 0 ; offset < length () ; ++offset) {
- final char search_aa = amino_acid_string.charAt (offset);
+ for(int offset = 0 ; offset < length(); ++offset)
+ {
+ final char search_aa = amino_acid_string.charAt(offset);
- if (search_aa == 'x') {
- // X matches any AA
+ // X matches any AA
+ if(search_aa == 'x')
continue;
- }
- final char base1 = bases_string.charAt (base_index + offset * 3 + 0);
- final char base2 = bases_string.charAt (base_index + offset * 3 + 1);
- final char base3 = bases_string.charAt (base_index + offset * 3 + 2);
+ final char base1 = bases_string.charAt(base_index + offset * 3 + 0);
+ final char base2 = bases_string.charAt(base_index + offset * 3 + 1);
+ final char base3 = bases_string.charAt(base_index + offset * 3 + 2);
- if (getCodonTranslation (base1, base2, base3) != search_aa) {
+ if(getCodonTranslation(base1, base2, base3) != search_aa)
+ {
matched = false;
break;
}
}
- if (matched) {
+ if(matched)
return base_index;
- }
}
return -1;
@@ -430,39 +471,38 @@ public class AminoAcidSequence {
* should start.
* @return The index of the match or -1 if there is no match.
**/
- public int searchBackwardFor (final String bases_string,
- int start_index) {
- if (bases_string.length () - start_index < length () * 3) {
- start_index = bases_string.length () - length () * 3;
- }
-
- for (int base_index = start_index ;
- base_index >= 0 ;
- --base_index) {
+ public int searchBackwardFor(final String bases_string,
+ int start_index)
+ {
+ if(bases_string.length() - start_index < length() * 3)
+ start_index = bases_string.length() - length() * 3;
+ for(int base_index = start_index; base_index >= 0;
+ --base_index)
+ {
boolean matched = true;
- for (int offset = 0 ; offset < length () ; ++offset) {
- final char search_aa = amino_acid_string.charAt (offset);
+ for(int offset = 0 ; offset < length() ; ++offset)
+ {
+ final char search_aa = amino_acid_string.charAt(offset);
- if (search_aa == 'x') {
- // X matches any AA
+ // X matches any AA
+ if(search_aa == 'x')
continue;
- }
- final char base1 = bases_string.charAt (base_index + offset * 3 + 0);
- final char base2 = bases_string.charAt (base_index + offset * 3 + 1);
- final char base3 = bases_string.charAt (base_index + offset * 3 + 2);
+ final char base1 = bases_string.charAt(base_index + offset * 3 + 0);
+ final char base2 = bases_string.charAt(base_index + offset * 3 + 1);
+ final char base3 = bases_string.charAt(base_index + offset * 3 + 2);
- if (getCodonTranslation (base1, base2, base3) != search_aa) {
+ if(getCodonTranslation(base1, base2, base3) != search_aa)
+ {
matched = false;
break;
}
}
- if (matched) {
+ if(matched)
return base_index;
- }
}
return -1;
@@ -479,14 +519,14 @@ public class AminoAcidSequence {
* first base, otherwise first to last.
* @return The index of the match or -1 if there is no match.
**/
- public int reverseComplementSearchFor (final String bases_string,
- final int start_index,
- final boolean search_backwards) {
- if (search_backwards) {
- return reverseComplementSearchBackwardFor (bases_string, start_index);
- } else {
- return reverseComplementSearchForwardFor (bases_string, start_index);
- }
+ public int reverseComplementSearchFor(final String bases_string,
+ final int start_index,
+ final boolean search_backwards)
+ {
+ if(search_backwards)
+ return reverseComplementSearchBackwardFor(bases_string, start_index);
+ else
+ return reverseComplementSearchForwardFor(bases_string, start_index);
}
/**
@@ -499,41 +539,43 @@ public class AminoAcidSequence {
* should start.
* @return The index of the match or -1 if there is no match.
**/
- public int reverseComplementSearchForwardFor (final String bases_string,
- final int start_index) {
- final int pattern_base_length = length () * 3;
-
- for (int base_index = start_index ;
- base_index <= bases_string.length () - pattern_base_length ;
- ++base_index) {
+ public int reverseComplementSearchForwardFor(final String bases_string,
+ final int start_index)
+ {
+ final int pattern_base_length = length() * 3;
+ for(int base_index = start_index ;
+ base_index <= bases_string.length() - pattern_base_length ;
+ ++base_index)
+ {
boolean matched = true;
- for (int offset = 0 ; offset < length () ; ++offset) {
+ for(int offset = 0; offset < length (); ++offset)
+ {
final char base1 =
- Bases.complement (bases_string.charAt (base_index + offset * 3 + 0));
+ Bases.complement(bases_string.charAt(base_index + offset * 3 + 0));
final char base2 =
- Bases.complement (bases_string.charAt (base_index + offset * 3 + 1));
+ Bases.complement(bases_string.charAt(base_index + offset * 3 + 1));
final char base3 =
- Bases.complement (bases_string.charAt (base_index + offset * 3 + 2));
+ Bases.complement(bases_string.charAt(base_index + offset * 3 + 2));
final char amino_acid_char =
- amino_acid_string.charAt (amino_acid_string.length () - offset - 1);
+ amino_acid_string.charAt(amino_acid_string.length() - offset - 1);
- if (amino_acid_char == 'x') {
+ // X matches any AA
+ if(amino_acid_char == 'x')
// X matches any AA
continue;
- }
- if (getCodonTranslation (base3, base2, base1) != amino_acid_char) {
+ if(getCodonTranslation(base3, base2, base1) != amino_acid_char)
+ {
matched = false;
break;
}
}
- if (matched) {
+ if(matched)
return base_index;
- }
}
return -1;
@@ -549,44 +591,42 @@ public class AminoAcidSequence {
* should start.
* @return The index of the match or -1 if there is no match.
**/
- public int reverseComplementSearchBackwardFor (final String bases_string,
- int start_index) {
-
- if (bases_string.length () - start_index < length () * 3) {
- start_index = bases_string.length () - length () * 3;
- }
-
- for (int base_index = start_index ;
- base_index >= 0 ;
- --base_index) {
+ public int reverseComplementSearchBackwardFor(final String bases_string,
+ int start_index)
+ {
+ if(bases_string.length() - start_index < length() * 3)
+ start_index = bases_string.length() - length() * 3;
+ for(int base_index = start_index; base_index >= 0;
+ --base_index)
+ {
boolean matched = true;
- for (int offset = 0 ; offset < length () ; ++offset) {
+ for(int offset = 0 ; offset < length() ; ++offset)
+ {
final char base1 =
- Bases.complement (bases_string.charAt (base_index + offset * 3 + 0));
+ Bases.complement(bases_string.charAt(base_index + offset * 3 + 0));
final char base2 =
- Bases.complement (bases_string.charAt (base_index + offset * 3 + 1));
+ Bases.complement(bases_string.charAt(base_index + offset * 3 + 1));
final char base3 =
- Bases.complement (bases_string.charAt (base_index + offset * 3 + 2));
+ Bases.complement(bases_string.charAt(base_index + offset * 3 + 2));
final char amino_acid_char =
- amino_acid_string.charAt (amino_acid_string.length () - offset - 1);
+ amino_acid_string.charAt(amino_acid_string.length() - offset - 1);
- if (amino_acid_char == 'x') {
- // X matches any AA
+ // X matches any AA
+ if(amino_acid_char == 'x')
continue;
- }
- if (getCodonTranslation (base3, base2, base1) != amino_acid_char) {
+ if(getCodonTranslation(base3, base2, base1) != amino_acid_char)
+ {
matched = false;
break;
}
}
- if (matched) {
+ if(matched)
return base_index;
- }
}
return -1;
@@ -595,13 +635,14 @@ public class AminoAcidSequence {
/**
* Return true if and only if this sequence contains a stop codon.
**/
- public boolean containsStopCodon () {
- for (int i = 0 ; i < amino_acid_string.length () ; ++i) {
- final char this_char = amino_acid_string.charAt (i);
+ public boolean containsStopCodon()
+ {
+ for(int i = 0 ; i < amino_acid_string.length() ; ++i)
+ {
+ final char this_char = amino_acid_string.charAt(i);
- if (isStopCodon (this_char)) {
+ if(isStopCodon (this_char))
return true;
- }
}
return false;
@@ -611,35 +652,37 @@ public class AminoAcidSequence {
* Return true if and only if the given amino acid symbol is the
* translation of a stop codon. ie #, * or +.
**/
- public static boolean isStopCodon (final char amino_acid_char) {
- if (amino_acid_char == '#' ||
- amino_acid_char == '*' ||
- amino_acid_char == '+') {
+ public static boolean isStopCodon(final char amino_acid_char)
+ {
+ if(amino_acid_char == '#' ||
+ amino_acid_char == '*' ||
+ amino_acid_char == '+')
return true;
- } else {
+ else
return false;
- }
}
/**
* Return true if and only if the given one letter code symbol is the a
* legal amino acid or stop symbol.
**/
- public static boolean isLegalCodon (final char one_letter_code) {
- switch (one_letter_code) {
- case 'a': case 'r': case 'n': case 'd': case 'c': case 'q': case 'e':
- case 'g': case 'h': case 'i': case 'l': case 'k': case 'm': case 'f':
- case 'p': case 's': case 't': case 'w': case 'y': case 'v': case '*':
- case '#': case '+':
- return true;
- default:
- return false;
+ public static boolean isLegalCodon(final char one_letter_code)
+ {
+ switch(one_letter_code)
+ {
+ case 'a': case 'r': case 'n': case 'd': case 'c': case 'q': case 'e':
+ case 'g': case 'h': case 'i': case 'l': case 'k': case 'm': case 'f':
+ case 'p': case 's': case 't': case 'w': case 'y': case 'v': case '*':
+ case '#': case '+':
+ return true;
+ default:
+ return false;
}
}
/**
* This table is used for fast lookup of codon translations by
- * getCodonTranslation (). There is one entry for each codon and the
+ * getCodonTranslation(). There is one entry for each codon and the
* entries are in this order: TTT, TTC, TTA, TTG, TCT, TCC, ...
**/
final public static char [] codon_translation_array = {
@@ -665,35 +708,35 @@ public class AminoAcidSequence {
};
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int POLAR_UNCHARGED_AA = 0;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int POSITIVELY_CHARGED_AA = 1;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int NEGATIVELY_CHARGED_AA = 2;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int HYDROPHOBIC_AA = 3;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int SPECIAL_AA = 4;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int STOP_AA = 5;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int UNKNOWN_AA = 6;
/**
- * Used by getAminoAcidType ().
+ * Used by getAminoAcidType().
**/
public final static int ILLEGAL_AA = 7;
@@ -702,29 +745,31 @@ public class AminoAcidSequence {
* NEGATIVELY_CHARGED_AA, HYDROPHOBIC_AA, SPECIAL_AA or STOP_AA depending
* on the aa_char argument.
**/
- public static int getAminoAcidType (final char aa_char) {
- switch (aa_char) {
- case 'S': case 'T': case 'N': case 'Q':
- return POLAR_UNCHARGED_AA;
+ public static int getAminoAcidType(final char aa_char)
+ {
+ switch (aa_char)
+ {
+ case 'S': case 'T': case 'N': case 'Q':
+ return POLAR_UNCHARGED_AA;
- case 'K': case 'R': case 'H':
- return POSITIVELY_CHARGED_AA;
+ case 'K': case 'R': case 'H':
+ return POSITIVELY_CHARGED_AA;
- case 'E': case 'D':
- return NEGATIVELY_CHARGED_AA;
+ case 'E': case 'D':
+ return NEGATIVELY_CHARGED_AA;
- case 'A': case 'I': case 'L': case 'M': case 'F': case 'W': case 'V':
- case 'Y':
- return HYDROPHOBIC_AA;
+ case 'A': case 'I': case 'L': case 'M': case 'F': case 'W': case 'V':
+ case 'Y':
+ return HYDROPHOBIC_AA;
- case 'C': case 'G': case 'P':
- return SPECIAL_AA;
+ case 'C': case 'G': case 'P':
+ return SPECIAL_AA;
- case '#': case '*': case '+':
- return STOP_AA;
+ case '#': case '*': case '+':
+ return STOP_AA;
- default:
- return ILLEGAL_AA;
+ default:
+ return ILLEGAL_AA;
}
}
@@ -734,15 +779,16 @@ public class AminoAcidSequence {
* name.
* @return A one letter code or -1 if three_letter_code can't be understood.
**/
- public static char getOneLetterCode (final String three_letter_code) {
+ public static char getOneLetterCode(final String three_letter_code)
+ {
final String real_code =
- three_letter_code.substring (0, 1).toUpperCase () +
- three_letter_code.substring (1).toLowerCase ();
+ three_letter_code.substring(0, 1).toUpperCase() +
+ three_letter_code.substring(1).toLowerCase();
- for (int i = 0 ; i < amino_acid_one_letter_names.length ; ++i) {
- if (real_code.equals (amino_acid_abbreviated_names[i])) {
+ for(int i = 0 ; i < amino_acid_one_letter_names.length ; ++i)
+ {
+ if(real_code.equals(amino_acid_abbreviated_names[i]))
return amino_acid_one_letter_names[i];
- }
}
return (char) -1;
@@ -752,20 +798,22 @@ public class AminoAcidSequence {
* Return the three letter abbreviation for the given one letter amino acid
* code.
**/
- public static String getThreeLetterAbbreviation (char one_letter_code) {
- for (int i = 0 ; i < amino_acid_one_letter_names.length ; ++i) {
- if (one_letter_code == amino_acid_one_letter_names[i]) {
+ public static String getThreeLetterAbbreviation(char one_letter_code)
+ {
+ for(int i = 0 ; i < amino_acid_one_letter_names.length ; ++i)
+ {
+ if(one_letter_code == amino_acid_one_letter_names[i])
return amino_acid_abbreviated_names[i];
- }
}
- throw new Error ("internal error - illegal one letter amino acid code");
+ throw new Error("internal error - illegal one letter amino acid code");
}
/**
* Return the three letter abbreviation for the given index code.
**/
- public static String getThreeLetterAbbreviation (final int index) {
+ public static String getThreeLetterAbbreviation(final int index)
+ {
return amino_acid_abbreviated_names[index];
}
@@ -773,45 +821,48 @@ public class AminoAcidSequence {
* Return an integer from 0 to 22 representing the index of a codon
* symbol.
**/
- public static int getSymbolIndex (char one_letter_code) {
- switch (one_letter_code) {
- case 'a': return 0;
- case 'r': return 1;
- case 'n': return 2;
- case 'd': return 3;
- case 'c': return 4;
- case 'q': return 5;
- case 'e': return 6;
- case 'g': return 7;
- case 'h': return 8;
- case 'i': return 9;
- case 'l': return 10;
- case 'k': return 11;
- case 'm': return 12;
- case 'f': return 13;
- case 'p': return 14;
- case 's': return 15;
- case 't': return 16;
- case 'w': return 17;
- case 'y': return 18;
- case 'v': return 19;
- case '*': return 20;
- case '#': return 21;
- case '+': return 22;
- case '.': return 23;
- case 'x': return 23;
- case 'u': return 24;
- default:
- throw new Error ("Internal error - illegal one letter codon symbol: " +
- one_letter_code);
+ public static int getSymbolIndex(char one_letter_code)
+ {
+ switch(one_letter_code)
+ {
+ case 'a': return 0;
+ case 'r': return 1;
+ case 'n': return 2;
+ case 'd': return 3;
+ case 'c': return 4;
+ case 'q': return 5;
+ case 'e': return 6;
+ case 'g': return 7;
+ case 'h': return 8;
+ case 'i': return 9;
+ case 'l': return 10;
+ case 'k': return 11;
+ case 'm': return 12;
+ case 'f': return 13;
+ case 'p': return 14;
+ case 's': return 15;
+ case 't': return 16;
+ case 'w': return 17;
+ case 'y': return 18;
+ case 'v': return 19;
+ case '*': return 20;
+ case '#': return 21;
+ case '+': return 22;
+ case '.': return 23;
+ case 'x': return 23;
+ case 'u': return 24;
+ default:
+ throw new Error("Internal error - illegal one letter codon symbol: " +
+ one_letter_code);
}
}
/**
* Given an index return a one letter codon symbol. This method is the
- * inverse of getSymbolIndex ().
+ * inverse of getSymbolIndex().
**/
- public static char getSymbolFromIndex (final int index) {
+ public static char getSymbolFromIndex(final int index)
+ {
return amino_acid_one_letter_names[index];
}
@@ -825,7 +876,8 @@ public class AminoAcidSequence {
* The names here correspond to the letter codes at the same indices in
* amino_acid_one_letter_names.
**/
- private final static String [] amino_acid_abbreviated_names = {
+ private final static String [] amino_acid_abbreviated_names =
+ {
"Ala", "Arg", "Asn", "Asp", "Cys",
"Gln", "Glu", "Gly", "His", "Ile",
"Leu", "Lys", "Met", "Phe", "Pro",
@@ -839,7 +891,8 @@ public class AminoAcidSequence {
* The names here correspond to the three letter codes at the same indices
* in amino_acid_abbreviated_names.
**/
- private final static char [] amino_acid_one_letter_names = {
+ private final static char [] amino_acid_one_letter_names =
+ {
'a', 'r', 'n', 'd', 'c',
'q', 'e', 'g', 'h', 'i',
'l', 'k', 'm', 'f', 'p',
@@ -852,7 +905,8 @@ public class AminoAcidSequence {
* three letter codes at the same indices in amino_acid_abbreviated_names.
* For example "Met" corresponds to a weight of 149.22
**/
- private final static float [] molecular_weights = {
+ private final static float [] molecular_weights =
+ {
89.09F, 174.21F, 132.12F, 133.10F, 121.15F,
146.15F, 147.13F, 75.07F, 155.16F, 131.18F,
131.18F, 146.19F, 149.22F, 165.19F, 115.13F,
@@ -882,23 +936,26 @@ public class AminoAcidSequence {
public final static int amino_acid_symbol_count = 20;
- static {
+ private static void setGeneCode()
+ {
// if translation_table is in the options file use it to set
// codon_translation_array
final StringVector options_file_table =
- Options.getOptions ().getOptionValues ("translation_table");
-
- if (options_file_table != null) {
- if (options_file_table.size () == 64) {
- for (int i = 0 ; i < 64 ; ++i) {
+ Options.getOptions().getOptionValues("translation_table");
+
+ if(options_file_table != null)
+ {
+ if(options_file_table.size () == 64)
+ {
+ for(int i = 0 ; i < 64 ; ++i)
+ {
final char new_table_char =
- options_file_table.elementAt (i).charAt (0);
+ options_file_table.elementAt(i).charAt(0);
- if (isLegalCodon (new_table_char)) {
+ if(isLegalCodon (new_table_char))
codon_translation_array[i] = new_table_char;
- } else {
+ else
codon_translation_array[i] = '.';
- }
}
}
}
diff --git a/uk/ac/sanger/artemis/sequence/Bases.java b/uk/ac/sanger/artemis/sequence/Bases.java
index d3a1baea9..4a78d30ae 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 1.1 2004-06-09 09:52:15 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.2 2004-11-17 13:20:10 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 1.1 2004-06-09 09:52:15 tjc Exp $ */
+ * @version $Id: Bases.java,v 1.2 2004-11-17 13:20:10 tjc Exp $ */
public class Bases {
/**
@@ -451,6 +451,15 @@ public class Bases {
return reverse_stop_codon_cache;
}
+ /**
+ * Clear stop codon cache (forward and reverse).
+ **/
+ public void clearStopCodonCache()
+ {
+ forward_stop_codon_cache = null;
+ reverse_stop_codon_cache = null;
+ }
+
/**
* Return an array containing the positions of the stop codons. Only those
* codons that are in the same frame as the first base of the range are
--
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