From 22b4c26b5d96f5f7a90e3de0eb1057cc3877ca83 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 2 Dec 2004 16:52:55 +0000
Subject: [PATCH] fix colour legend
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2093 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/plot/BaseAlgorithm.java | 51 +++----------
.../plot/Codon12CorrelationAlgorithm.java | 59 +--------------
.../sanger/artemis/plot/GCFrameAlgorithm.java | 74 ++++++++++++++++++-
uk/ac/sanger/artemis/plot/MRIAlgorithm.java | 9 +--
4 files changed, 86 insertions(+), 107 deletions(-)
diff --git a/uk/ac/sanger/artemis/plot/BaseAlgorithm.java b/uk/ac/sanger/artemis/plot/BaseAlgorithm.java
index e83516fa6..20cd71a29 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 1.5 2004-11-30 11:27:50 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/BaseAlgorithm.java,v 1.6 2004-12-02 16:52:54 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 1.5 2004-11-30 11:27:50 tjc Exp $
+ * @version $Id: BaseAlgorithm.java,v 1.6 2004-12-02 16:52:54 tjc Exp $
**/
public abstract class BaseAlgorithm extends Algorithm
@@ -138,9 +138,6 @@ public abstract class BaseAlgorithm extends Algorithm
}
else
{
- int frame = strand.getSequenceLength() % 3;
-
-// System.out.println("MOD "+frame);
g2d.setColor(Color.black);
g2d.drawString("4",0,font_height);
g2d.drawString("5",font_width*5,font_height);
@@ -148,43 +145,15 @@ public abstract class BaseAlgorithm extends Algorithm
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);
- switch(frame)
- {
- case 0:
- g2d.setColor(frameColour[0]);
- g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
-
- g2d.setColor(frameColour[2]);
- g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
-
- g2d.setColor(frameColour[1]);
- g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
- g2d.setStroke(stroke);
- return;
- case 1:
- g2d.setColor(frameColour[2]);
- g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
-
- g2d.setColor(frameColour[1]);
- g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
-
- g2d.setColor(frameColour[0]);
- g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
- g2d.setStroke(stroke);
- return;
- case 2:
- g2d.setColor(frameColour[1]);
- g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
-
- g2d.setColor(frameColour[0]);
- g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
-
- g2d.setColor(frameColour[2]);
- g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
- g2d.setStroke(stroke);
- return;
- }
+ g2d.setColor(frameColour[2]);
+ g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
+
+ g2d.setColor(frameColour[1]);
+ 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 74b894a74..d0359ea34 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 1.2 2004-11-30 10:52:38 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/Codon12CorrelationAlgorithm.java,v 1.3 2004-12-02 16:52:55 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 1.2 2004-11-30 10:52:38 tjc Exp $
+ * @version $Id: Codon12CorrelationAlgorithm.java,v 1.3 2004-12-02 16:52:55 tjc Exp $
**/
public class Codon12CorrelationAlgorithm extends BaseAlgorithm
{
@@ -185,61 +185,6 @@ public class Codon12CorrelationAlgorithm extends BaseAlgorithm
}
}
- /**
- *
- * Override as reverse strand is not sequence length dependent
- *
- */
- public void drawLegend(Graphics g, int font_height,
- int font_width, Color[] frameColour)
- {
- Graphics2D g2d = (Graphics2D)g;
-
- FontMetrics fm = g2d.getFontMetrics();
- int lineHgt = 3 * font_height/4;
-
- Strand strand = getStrand();
- if(strand.isForwardStrand())
- {
- g2d.setColor(Color.black);
- g2d.drawString("1",0,font_height);
- g2d.drawString("2",font_width*5,font_height);
- g2d.drawString("3",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);
-
- g2d.setColor(frameColour[1]);
- g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
-
- g2d.setColor(frameColour[2]);
- g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
- g2d.setStroke(stroke);
- }
- else
- {
-// int frame = strand.getSequenceLength() % 3;
-// System.out.println("MOD "+frame);
- 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);
-
- g2d.setColor(frameColour[2]);
- g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
-
- g2d.setColor(frameColour[1]);
- g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
- g2d.setStroke(stroke);
- }
- }
/**
* 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 d03f66d0a..92b82bcb7 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 1.2 2004-11-30 11:08:55 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/GCFrameAlgorithm.java,v 1.3 2004-12-02 16:52:55 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -29,6 +29,8 @@ import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.Range;
+import java.awt.*;
+
/**
* Objects of this class have one useful method - getValues (), which takes a
* range of bases and returns three floating point numbers, which are the
@@ -36,7 +38,7 @@ import uk.ac.sanger.artemis.io.Range;
* constructor.
*
* @author Kim Rutherford
- * @version $Id: GCFrameAlgorithm.java,v 1.2 2004-11-30 11:08:55 tjc Exp $
+ * @version $Id: GCFrameAlgorithm.java,v 1.3 2004-12-02 16:52:55 tjc Exp $
**/
public class GCFrameAlgorithm extends BaseAlgorithm
{
@@ -137,6 +139,74 @@ public class GCFrameAlgorithm extends BaseAlgorithm
values[frame] = 1.0F * gc_counts[frame]/sub_sequence_length * 3 * 100;
}
+ /**
+ *
+ * Override drawLegend()
+ *
+ */
+ public void drawLegend(Graphics g, int font_height,
+ int font_width, Color[] frameColour)
+ {
+ final Strand strand = getStrand();
+ if(strand.isForwardStrand())
+ super.drawLegend(g,font_height,font_width,frameColour);
+ else
+ {
+ Graphics2D g2d = (Graphics2D)g;
+
+ FontMetrics fm = g2d.getFontMetrics();
+ int lineHgt = 3 * font_height/4;
+ int frame = strand.getSequenceLength() % 3;
+
+// System.out.println("MOD "+frame);
+ 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));
+
+ switch(frame)
+ {
+ case 0:
+ g2d.setColor(frameColour[0]);
+ g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
+
+ g2d.setColor(frameColour[1]);
+ g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
+
+ g2d.setColor(frameColour[2]);
+ g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
+ g2d.setStroke(stroke);
+ return;
+ case 1:
+ g2d.setColor(frameColour[2]);
+ g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
+
+ g2d.setColor(frameColour[0]);
+ g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
+
+ g2d.setColor(frameColour[1]);
+ g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
+ g2d.setStroke(stroke);
+ return;
+ case 2:
+ g2d.setColor(frameColour[1]);
+ g2d.drawLine(font_width*2, lineHgt, font_width*4, lineHgt);
+
+ g2d.setColor(frameColour[2]);
+ g2d.drawLine(font_width*7, lineHgt, font_width*9, lineHgt);
+
+ g2d.setColor(frameColour[0]);
+ g2d.drawLine(font_width*12, lineHgt, font_width*14, lineHgt);
+ g2d.setStroke(stroke);
+ return;
+ }
+ }
+ }
+
+
/**
* Return the number of values a call to getValues() will return - three
* in this case.
diff --git a/uk/ac/sanger/artemis/plot/MRIAlgorithm.java b/uk/ac/sanger/artemis/plot/MRIAlgorithm.java
index 619498766..3dce8278e 100644
--- a/uk/ac/sanger/artemis/plot/MRIAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/MRIAlgorithm.java
@@ -34,7 +34,7 @@ import uk.ac.sanger.artemis.sequence.*;
* Biol Int 43:107-14
*
* @author Derek Gatherer
- * @version $Id: MRIAlgorithm.java,v 1.2 2004-12-01 16:33:27 tjc Exp $
+ * @version $Id: MRIAlgorithm.java,v 1.3 2004-12-02 16:52:55 tjc Exp $
* original version 10-09-03
* revised 01-12-04
**/
@@ -61,11 +61,7 @@ public class MRIAlgorithm extends BaseAlgorithm
**/
public void getValues(int start, int end, final float [] values)
{
- if(getStrand().isForwardStrand()) // rather than isRevCompDisplay()
- {
-// System.out.println("isRevCompDisplay does not activate here");
- }
- else
+ if(!getStrand().isForwardStrand() || isRevCompDisplay())
{
final int new_end =
getStrand().getBases().getComplementPosition(start);
@@ -74,7 +70,6 @@ public class MRIAlgorithm extends BaseAlgorithm
end = new_end;
start = new_start;
-// System.out.println("Revcomp, so new start:"+start+"new end:"+end);
}
final String sub_sequence;
--
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