diff --git a/uk/ac/sanger/artemis/plot/BaseAlgorithm.java b/uk/ac/sanger/artemis/plot/BaseAlgorithm.java
index 20cd71a29e55bae851b7414dc8b3772855a89f27..36136f881ee296b1b5a16068a5ab393ebc60a11a 100644
--- a/uk/ac/sanger/artemis/plot/BaseAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/BaseAlgorithm.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/plot/BaseAlgorithm.java,v 1.6 2004-12-02 16:52:54 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/BaseAlgorithm.java,v 1.7 2006-06-23 10:40:14 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -38,7 +38,7 @@ import java.awt.BasicStroke;
* Strand of DNA, meaning the algorithm can't change strand part way along.
*
* @author Kim Rutherford
- * @version $Id: BaseAlgorithm.java,v 1.6 2004-12-02 16:52:54 tjc Exp $
+ * @version $Id: BaseAlgorithm.java,v 1.7 2006-06-23 10:40:14 tjc Exp $
**/
public abstract class BaseAlgorithm extends Algorithm
@@ -117,7 +117,8 @@ public abstract class BaseAlgorithm extends Algorithm
FontMetrics fm = g2d.getFontMetrics();
int lineHgt = 3 * font_height/4;
- if(strand.isForwardStrand())
+ if( (strand.isForwardStrand() && !isRevCompDisplay()) ||
+ (!strand.isForwardStrand() && isRevCompDisplay()))
{
g2d.setColor(Color.black);
g2d.drawString("1",0,font_height);
@@ -138,13 +139,19 @@ public abstract class BaseAlgorithm extends Algorithm
}
else
{
+
+ /*
+ int frame = strand.getSequenceLength() % 3;
g2d.setColor(Color.black);
+
g2d.drawString("4",0,font_height);
g2d.drawString("5",font_width*5,font_height);
g2d.drawString("6",font_width*10,font_height);
BasicStroke stroke = (BasicStroke)g2d.getStroke();
g2d.setStroke(new BasicStroke(3.f));
+
+
g2d.setColor(frameColour[0]);
g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
@@ -154,6 +161,50 @@ public abstract class BaseAlgorithm extends Algorithm
g2d.setColor(frameColour[1]);
g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
g2d.setStroke(stroke);
+ */
+
+ g2d.setColor(Color.black);
+ g2d.drawString("4",0,font_height);
+ g2d.drawString("5",font_width*5,font_height);
+ g2d.drawString("6",font_width*10,font_height);
+
+ BasicStroke stroke = (BasicStroke)g2d.getStroke();
+ g2d.setStroke(new BasicStroke(3.f));
+ int frame = strand.getSequenceLength() % 3;
+
+ //System.out.println("FRAME "+frame+" length="+strand.getSequenceLength());
+ Color col4 = null;
+ Color col5 = null;
+ Color col6 = null;
+
+ switch(frame)
+ {
+ case 0:
+ col4 = frameColour[1];
+ col5 = frameColour[2];
+ col6 = frameColour[0];
+ break;
+ case 1:
+ col4 = frameColour[2];
+ col5 = frameColour[0];
+ col6 = frameColour[1];
+ break;
+ case 2:
+ col4 = frameColour[0];
+ col5 = frameColour[1];
+ col6 = frameColour[2];
+ break;
+ }
+
+ g2d.setColor(col4);
+ g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
+
+ g2d.setColor(col5);
+ g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
+
+ g2d.setColor(col6);
+ g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
+ g2d.setStroke(stroke);
}
}
diff --git a/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java b/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java
index d0359ea34e9ce545e35e4188c2a687e975c049d1..d88e8202043544e727e0a128a3d068a4843ab048 100644
--- a/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.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/plot/Codon12CorrelationAlgorithm.java,v 1.3 2004-12-02 16:52:55 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java,v 1.4 2006-06-23 10:40:14 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -38,7 +38,7 @@ import java.awt.*;
* the given strand. The Strand to use is set in the constructor.
*
* @author Kim Rutherford
- * @version $Id: Codon12CorrelationAlgorithm.java,v 1.3 2004-12-02 16:52:55 tjc Exp $
+ * @version $Id: Codon12CorrelationAlgorithm.java,v 1.4 2006-06-23 10:40:14 tjc Exp $
**/
public class Codon12CorrelationAlgorithm extends BaseAlgorithm
{
@@ -101,24 +101,21 @@ public class Codon12CorrelationAlgorithm extends BaseAlgorithm
else
start += (end - start + 1) % 3;
- final String sub_sequence;
+ final char[] sub_sequence_raw;
try
{
- sub_sequence = getStrand().getRawSubSequence(new Range(start, end));
+ sub_sequence_raw = getStrand().getRawSubSequenceC(new Range(start, end));
}
catch(OutOfRangeException e)
{
throw new Error("internal error - unexpected exception: " + e);
}
- final char[] sub_sequence_raw = sub_sequence.toCharArray();
-
final float gc_counts[] = new float[3];
// the first index is the position the second is the base (t,c,a,g)
final int[][] positional_base_counts = new int[4][3];
-
final int sub_sequence_length = sub_sequence_raw.length;
if(getStrand().isForwardStrand())
@@ -132,10 +129,7 @@ public class Codon12CorrelationAlgorithm extends BaseAlgorithm
}
else
{
- final String complement_string = Bases.complement(sub_sequence);
-
- final char [] complement_sub_sequence_raw =
- complement_string.toCharArray();
+ final char[] complement_sub_sequence_raw = Bases.complement(sub_sequence_raw);
for(int i = 0 ; i < sub_sequence_length ; ++i)
{
@@ -149,6 +143,9 @@ public class Codon12CorrelationAlgorithm extends BaseAlgorithm
}
}
+ final int whole_sequence_length = getStrand().getSequenceLength();
+ final int whole_sequence_length_mod3 = whole_sequence_length % 3;
+
for(int frame = 0 ; frame < 3 ; ++frame)
{
final double cor1_2_score =
@@ -181,10 +178,26 @@ public class Codon12CorrelationAlgorithm extends BaseAlgorithm
correlation_score_factors_2[3]) +
0.5; // add 0.5 because that is what the old uk.ac.sanger.artemis did
- values [(start + frame) % 3] = (float)cor1_2_score;
+ // add 2 brings the frame colouring in-line with codon usage
+ if(getStrand().isForwardStrand())
+ values [(start + frame + 2) % 3] = (float)cor1_2_score;
+ else
+ values [(start + frame + whole_sequence_length_mod3 + 2) % 3] = (float)cor1_2_score;
+ }
+
+ /*
+ for(int frame = 0 ; frame < 3 ; ++frame)
+ {
+ if(getStrand().isForwardStrand())
+ System.out.println("FWD "+frame+" "+((start + frame + 2) % 3));
+ else
+ System.out.println("BWD "+frame+" "+((start + frame + whole_sequence_length_mod3 -1) % 3)+
+ " "+whole_sequence_length_mod3);
}
+ */
}
+
/**
* Return the number of values a call to getValues () will return - three
* in this case.
diff --git a/uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java b/uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java
index cda00e027eb870c9ff48e1f1fc029be1fb97fc79..c5016fd6e89a90a58063e11be10868d3ec8f3284 100644
--- a/uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java
@@ -20,11 +20,17 @@
* 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/plot/CodonUsageAlgorithm.java,v 1.1 2004-06-09 09:51:19 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/CodonUsageAlgorithm.java,v 1.2 2006-06-23 10:40:14 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
+import java.awt.BasicStroke;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
@@ -39,7 +45,7 @@ import uk.ac.sanger.artemis.io.Range;
* See Gribskov et al. (Nucl. Acids Res. 12(1); 539-549 (1984)).
*
* @author Kim Rutherford
- * @version $Id: CodonUsageAlgorithm.java,v 1.1 2004-06-09 09:51:19 tjc Exp $
+ * @version $Id: CodonUsageAlgorithm.java,v 1.2 2006-06-23 10:40:14 tjc Exp $
**/
public class CodonUsageAlgorithm extends BaseAlgorithm {
@@ -68,8 +74,10 @@ public class CodonUsageAlgorithm extends BaseAlgorithm {
* this array. There is one value for each frame and the value is the
* the average of the weightings for the codons in the range.
**/
- public void getValues (int start, int end, final float [] values) {
- if (isRevCompDisplay ()) {
+ public void getValues(int start, int end, final float[] values)
+ {
+ if (isRevCompDisplay ())
+ {
final int new_end =
getStrand ().getBases ().getComplementPosition (start);
final int new_start =
@@ -80,74 +88,78 @@ public class CodonUsageAlgorithm extends BaseAlgorithm {
}
// add 1 or 2 if necessary to make the range a multiple of 3
- if (getStrand ().isForwardStrand ()) {
+ if(getStrand ().isForwardStrand ())
end -= (end - start + 1) % 3;
- } else {
+ else
start += (end - start + 1) % 3;
- }
- final String sequence;
+ final char[] sequence;
- try {
- sequence = getStrand ().getRawSubSequence (new Range (start, end));
- } catch (OutOfRangeException e) {
+ try
+ {
+ sequence = getStrand ().getRawSubSequenceC(new Range (start, end));
+ }
+ catch (OutOfRangeException e)
+ {
throw new Error ("internal error - unexpected exception: " + e);
}
- float [] totals = { 0, 0, 0 };
+ float[] totals = { 0, 0, 0 };
// a count of the number of codons we have seen
int codon_count = 0;
- final int sub_sequence_length = sequence.length ();
+ final int sub_sequence_length = sequence.length;
- if (getStrand ().isForwardStrand ()) {
-
- for (int frame = 0 ; frame < 3 ; ++frame) {
- for (int i = frame ; i < sub_sequence_length - 3 ; i += 3) {
-
- final char base1 = sequence.charAt (i);
- final char base2 = sequence.charAt (i + 1);
- final char base3 = sequence.charAt (i + 2);
+ if(getStrand ().isForwardStrand ())
+ {
+ for (int frame = 0 ; frame < 3 ; ++frame)
+ {
+ final int real_frame = (frame + start + 2) % 3;
+ for (int i = frame ; i < sub_sequence_length - 3 ; i += 3)
+ {
+ final char base1 = sequence[i];
+ final char base2 = sequence[i + 1];
+ final char base3 = sequence[i + 2];
final float this_weight =
- usage_data.getCodonValue (base1, base2, base3);
-
- final int real_frame = (frame + start + 2) % 3;
+ usage_data.getCodonValue(base1, base2, base3);
++codon_count;
- totals[real_frame] += Math.log (this_weight);
+ totals[real_frame] += Math.log(this_weight);
}
}
- } else {
- for (int frame = 2 ; frame >= 0 ; --frame) {
- for (int i = frame ; i < sub_sequence_length - 3 ; i += 3) {
-
- final char base1 = Bases.complement (sequence.charAt (i + 2));
- final char base2 = Bases.complement (sequence.charAt (i + 1));
- final char base3 = Bases.complement (sequence.charAt (i));
+ }
+ else
+ {
+ for(int frame = 2; frame >= 0 ; --frame)
+ {
+ final int real_frame = (frame + start + 2) % 3;
+ for (int i = frame ; i < sub_sequence_length - 3 ; i += 3)
+ {
+ final char base1 = Bases.complement(sequence[i + 2]);
+ final char base2 = Bases.complement(sequence[i + 1]);
+ final char base3 = Bases.complement(sequence[i]);
final float this_weight =
- usage_data.getCodonValue (base1, base2, base3);
-
- final int real_frame = (frame + start + 2) % 3;
+ usage_data.getCodonValue(base1, base2, base3);
++codon_count;
- totals[real_frame] += Math.log (this_weight);
-
+ totals[real_frame] += Math.log(this_weight);
}
}
}
- for (int frame = 0 ; frame < 3 ; ++frame) {
- if (codon_count == 0) {
+ for (int frame = 0 ; frame < 3 ; ++frame)
+ {
+ if (codon_count == 0)
values[frame] = 0;
- } else {
- values[frame] = (float) Math.exp (totals[frame] / codon_count);
- }
+ else
+ values[frame] = (float)Math.exp(totals[frame] / codon_count);
}
}
+
/**
* Return the number of values a call to getValues () will return - three
* in this case.
diff --git a/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java b/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java
index ff965f5f8a4d668057842154ab7e58ef930c844e..74db76dd1ef99a56b6a424f1a29666dea919d133 100644
--- a/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.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/plot/GCFrameAlgorithm.java,v 1.5 2006-06-21 10:06:08 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java,v 1.6 2006-06-23 10:40:14 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -38,7 +38,7 @@ import java.awt.*;
* constructor.
*
* @author Kim Rutherford
- * @version $Id: GCFrameAlgorithm.java,v 1.5 2006-06-21 10:06:08 tjc Exp $
+ * @version $Id: GCFrameAlgorithm.java,v 1.6 2006-06-23 10:40:14 tjc Exp $
**/
public class GCFrameAlgorithm extends BaseAlgorithm
{
@@ -149,6 +149,8 @@ public class GCFrameAlgorithm extends BaseAlgorithm
public void drawLegend(Graphics g, int font_height,
int font_width, Color[] frameColour)
{
+ return;
+ /*
final Strand strand = getStrand();
if(strand.isForwardStrand())
super.drawLegend(g,font_height,font_width,frameColour);
@@ -182,7 +184,7 @@ public class GCFrameAlgorithm extends BaseAlgorithm
g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
g2d.setStroke(stroke);
return;
- /* case 1:
+ case 1:
g2d.setColor(frameColour[2]);
g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
@@ -204,8 +206,8 @@ public class GCFrameAlgorithm extends BaseAlgorithm
g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
g2d.setStroke(stroke);
return;
- } */
- }
+ }
+ } */
}
diff --git a/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.java b/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.java
index 792be5c0426a17d65333011a4d919fc6d582ca25..9dee5bf5cf2c37f94a821e07f07761f8b335343b 100644
--- a/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.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/plot/KarlinSigAlgorithm.java,v 1.1 2004-06-09 09:51:36 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/KarlinSigAlgorithm.java,v 1.2 2006-06-23 10:40:14 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -42,7 +42,7 @@ import uk.ac.sanger.artemis.sequence.*;
* constructor.
*
* @author Kim Rutherford
- * @version $Id: KarlinSigAlgorithm.java,v 1.1 2004-06-09 09:51:36 tjc Exp $
+ * @version $Id: KarlinSigAlgorithm.java,v 1.2 2006-06-23 10:40:14 tjc Exp $
**/
public class KarlinSigAlgorithm extends BaseAlgorithm {
@@ -69,10 +69,10 @@ public class KarlinSigAlgorithm extends BaseAlgorithm {
// add 1 or 2 if necessary to make the range a multiple of 3
end -= (end - start + 1) % 3;
- final String sub_sequence;
+ final char[] sub_sequence;
try {
- sub_sequence = getStrand ().getSubSequence (new Range (start, end));
+ sub_sequence = getStrand().getRawSubSequenceC(new Range (start, end));
} catch (OutOfRangeException e) {
throw new Error ("internal error - unexpected exception: " + e);
}
@@ -194,12 +194,11 @@ public class KarlinSigAlgorithm extends BaseAlgorithm {
* dinucleotide "TT" is stored in global_signature[0][0], "TC" is stored in
* [0][1], etc.
**/
- private float [][] getRelativeAbundance (final String sequence) {
+ private float [][] getRelativeAbundance (final char [] sequence_forward_raw) {
final float [][] return_value = new float [4][4];
- final char [] sequence_forward_raw = sequence.toCharArray ();
final char [] sequence_reverse_raw =
- Bases.reverseComplement (sequence).toCharArray ();
+ Bases.reverseComplement (sequence_forward_raw);
final int [] base_counts = new int [4];
final int [][] dinucleotide_base_counts = new int [4][4];
@@ -287,8 +286,8 @@ public class KarlinSigAlgorithm extends BaseAlgorithm {
try {
final Range whole_range =
new Range (1, getStrand ().getSequenceLength ());
- final String sequence =
- getStrand ().getSubSequence (whole_range);
+ final char[] sequence =
+ getStrand().getRawSubSequenceC(whole_range);
global_relative_abundance_values = getRelativeAbundance (sequence);
} catch (OutOfRangeException e) {
throw new Error ("internal error - unexpected exception: " + e);