From 066a8f6082d220728f486c753f2260171e4861a0 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 23 Dec 2004 10:19:05 +0000
Subject: [PATCH] use char[] for getting at seq stop codons
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2156 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/FeatureDisplay.java | 31 +++++++++----------
uk/ac/sanger/artemis/io/BioJavaSequence.java | 9 ++++++
uk/ac/sanger/artemis/io/CorbaSequence.java | 13 ++++++--
uk/ac/sanger/artemis/io/Sequence.java | 6 ++--
uk/ac/sanger/artemis/io/StreamSequence.java | 12 +++++--
uk/ac/sanger/artemis/sequence/Bases.java | 10 ++++--
6 files changed, 55 insertions(+), 26 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index 195804790..fb681cc78 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 1.17 2004-12-22 13:28:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.18 2004-12-23 10:19:05 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 1.17 2004-12-22 13:28:31 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.18 2004-12-23 10:19:05 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -2128,6 +2128,11 @@ public class FeatureDisplay extends EntryGroupPanel
// used to remember the position of the previously drawn codon
int last_x_position = -1;
+ if(height_percent < 100)
+ g.setColor(start_codon_colour);
+ else
+ g.setColor(Color.black);
+
for(int i = 0 ; i < codon_positions.length ; ++i)
{
final int codon_base_start = codon_positions[i];
@@ -2150,12 +2155,8 @@ public class FeatureDisplay extends EntryGroupPanel
// draw only if we haven't drawn on the position already
if(last_x_position == -1 || draw_x_position != last_x_position)
{
- if(height_percent < 100)
- drawOneCodonMark(g, draw_x_position, draw_y_position,
- direction, mark_height, start_codon_colour);
- else
- drawOneCodonMark(g, draw_x_position, draw_y_position,
- direction, mark_height, Color.black);
+ drawOneCodonMark(g, draw_x_position, draw_y_position,
+ direction, mark_height);
last_x_position = draw_x_position;
}
@@ -2195,32 +2196,28 @@ public class FeatureDisplay extends EntryGroupPanel
* @param direction If this is FORWARD the line is draw from the y position
* to the right, otherwise it is drawn to the left.
* @param height The height in pixels of the codon mark.
- * @param colour The colour to use when drawing the mark.
**/
private void drawOneCodonMark(final Graphics g,
final int x_pos, final int y_pos,
final int direction,
- final int height,
- final Color colour)
+ final int height)
{
- g.setColor(colour);
-
if(getScaleFactor() == 1)
{
// draw a line three pixels/bases wide
if(direction == FORWARD)
{
g.drawLine(x_pos + 1, y_pos,
- x_pos + 1, y_pos + height - 1);
+ x_pos + 1, y_pos + height - 1);
g.drawLine(x_pos + 2, y_pos,
- x_pos + 2, y_pos + height - 1);
+ x_pos + 2, y_pos + height - 1);
}
else
{
g.drawLine(x_pos - 1, y_pos,
- x_pos - 1, y_pos + height - 1);
+ x_pos - 1, y_pos + height - 1);
g.drawLine(x_pos - 2, y_pos,
- x_pos - 2, y_pos + height - 1);
+ x_pos - 2, y_pos + height - 1);
}
}
g.drawLine(x_pos, y_pos, x_pos, y_pos + height - 1);
diff --git a/uk/ac/sanger/artemis/io/BioJavaSequence.java b/uk/ac/sanger/artemis/io/BioJavaSequence.java
index 26c61d2cc..2ef57069a 100644
--- a/uk/ac/sanger/artemis/io/BioJavaSequence.java
+++ b/uk/ac/sanger/artemis/io/BioJavaSequence.java
@@ -99,6 +99,15 @@ public class BioJavaSequence implements Sequence
return subSeq;
}
+ public char[] getCharSubSequence (int start, int end)
+ {
+ char[] dst = new char[end-start];
+ StringBuffer buff = new StringBuffer(getSubSequence(start,end));
+ buff.getChars(start, end, dst, 0);
+ return dst;
+ }
+
+
public void setFromString(String seqString)
throws ReadOnlyException, IllegalSymbolException
{
diff --git a/uk/ac/sanger/artemis/io/CorbaSequence.java b/uk/ac/sanger/artemis/io/CorbaSequence.java
index ecac29609..de196f82d 100644
--- a/uk/ac/sanger/artemis/io/CorbaSequence.java
+++ b/uk/ac/sanger/artemis/io/CorbaSequence.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/io/CorbaSequence.java,v 1.1 2004-06-09 09:49:01 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/CorbaSequence.java,v 1.2 2004-12-23 10:19:05 tjc Exp $
**/
package uk.ac.sanger.artemis.io;
@@ -34,7 +34,7 @@ import java.io.IOException;
* object.
*
* @author Kim Rutherford
- * @version $Id: CorbaSequence.java,v 1.1 2004-06-09 09:49:01 tjc Exp $
+ * @version $Id: CorbaSequence.java,v 1.2 2004-12-23 10:19:05 tjc Exp $
**/
public class CorbaSequence implements Sequence {
@@ -73,6 +73,15 @@ public class CorbaSequence implements Sequence {
}
}
+ public char[] getCharSubSequence (int start, int end)
+ {
+ char[] dst = new char[end-start+1];
+ StringBuffer buff = new StringBuffer(sequence);
+ buff.getChars(start-1, end, dst, 0);
+ return dst;
+ }
+
+
/**
* Set this sequence to hold the bases in the given String - throws
* ReadOnlyException for CorbaSequence objects.
diff --git a/uk/ac/sanger/artemis/io/Sequence.java b/uk/ac/sanger/artemis/io/Sequence.java
index 8a5b09572..6699f31a3 100644
--- a/uk/ac/sanger/artemis/io/Sequence.java
+++ b/uk/ac/sanger/artemis/io/Sequence.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/io/Sequence.java,v 1.1 2004-06-09 09:50:27 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/Sequence.java,v 1.2 2004-12-23 10:19:05 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -32,7 +32,7 @@ import org.biojava.bio.symbol.IllegalSymbolException;
* Sequence interface
*
* @author Kim Rutherford
- * @version $Id: Sequence.java,v 1.1 2004-06-09 09:50:27 tjc Exp $
+ * @version $Id: Sequence.java,v 1.2 2004-12-23 10:19:05 tjc Exp $
*
*/
@@ -45,6 +45,8 @@ public interface Sequence
**/
String getSubSequence(int start, int end);
+ char[] getCharSubSequence(int start, int end);
+
/**
* Set this sequence to hold the bases in the given String.
* @exception ReadOnlyException If this Sequence cannot be changed.
diff --git a/uk/ac/sanger/artemis/io/StreamSequence.java b/uk/ac/sanger/artemis/io/StreamSequence.java
index 3479a8569..3ab163826 100644
--- a/uk/ac/sanger/artemis/io/StreamSequence.java
+++ b/uk/ac/sanger/artemis/io/StreamSequence.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/io/StreamSequence.java,v 1.1 2004-06-09 09:50:37 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/StreamSequence.java,v 1.2 2004-12-23 10:19:05 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -33,7 +33,7 @@ import java.io.Writer;
* stream.
*
* @author Kim Rutherford
- * @version $Id: StreamSequence.java,v 1.1 2004-06-09 09:50:37 tjc Exp $
+ * @version $Id: StreamSequence.java,v 1.2 2004-12-23 10:19:05 tjc Exp $
**/
public abstract class StreamSequence
@@ -91,6 +91,14 @@ public abstract class StreamSequence
}
}
+ public char[] getCharSubSequence (int start, int end)
+ {
+ char[] dst = new char[end-start+1];
+ StringBuffer buff = new StringBuffer(sequence);
+ buff.getChars(start-1, end, dst, 0);
+ return dst;
+ }
+
/**
* Set this sequence to hold the bases in the given String.
**/
diff --git a/uk/ac/sanger/artemis/sequence/Bases.java b/uk/ac/sanger/artemis/sequence/Bases.java
index 4cfbc69b8..5bf37e03a 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 1.5 2004-12-22 18:39:17 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.6 2004-12-23 10:19:05 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 1.5 2004-12-22 18:39:17 tjc Exp $ */
+ * @version $Id: Bases.java,v 1.6 2004-12-23 10:19:05 tjc Exp $ */
public class Bases {
/**
@@ -510,8 +510,12 @@ public class Bases {
int current_return_array_index = 0;
+// final char sequence_string[] =
+// getSequence().getSubSequence(1, getLength()).toCharArray();
+
final char sequence_string[] =
- getSequence().getSubSequence(1, getLength()).toCharArray();
+ getSequence().getCharSubSequence(1, getLength());
+
final int sequence_string_length = sequence_string.length;
final int range_start_index = real_range.getStart () - 1;
final int range_end_index = real_range.getEnd () - 1;
--
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