From bac273a1ea308a183dcc8ddb4d7385442ec017d8 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 23 Dec 2004 15:33:46 +0000
Subject: [PATCH] speed up
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2157 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/FeatureDisplay.java | 59 +++++++++++--------
uk/ac/sanger/artemis/io/StreamSequence.java | 8 +--
uk/ac/sanger/artemis/sequence/Bases.java | 38 ++++++------
3 files changed, 57 insertions(+), 48 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/FeatureDisplay.java b/uk/ac/sanger/artemis/components/FeatureDisplay.java
index fb681cc78..074137286 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 1.18 2004-12-23 10:19:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/FeatureDisplay.java,v 1.19 2004-12-23 15:33:46 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 1.18 2004-12-23 10:19:05 tjc Exp $
+ * @version $Id: FeatureDisplay.java,v 1.19 2004-12-23 15:33:46 tjc Exp $
**/
public class FeatureDisplay extends EntryGroupPanel
@@ -60,21 +60,21 @@ public class FeatureDisplay extends EntryGroupPanel
final static public int SCROLLBAR_AT_TOP = 1;
final static public int SCROLLBAR_AT_BOTTOM = 2;
- final static public int NO_SCROLLBAR = 3;
+ final static private int NO_SCROLLBAR = 3;
- public final static int FORWARD = Bases.FORWARD;
- public final static int REVERSE = Bases.REVERSE;
+ private final static int FORWARD = Bases.FORWARD;
+ private final static int REVERSE = Bases.REVERSE;
- public final static int NO_FRAME = FeatureSegment.NO_FRAME;
- public final static int FORWARD_STRAND = FeatureSegment.FORWARD_STRAND;
- public final static int REVERSE_STRAND = FeatureSegment.REVERSE_STRAND;
- public final static int FORWARD_FRAME_1 = FeatureSegment.FORWARD_FRAME_1;
- public final static int FORWARD_FRAME_2 = FeatureSegment.FORWARD_FRAME_2;
- public final static int FORWARD_FRAME_3 = FeatureSegment.FORWARD_FRAME_3;
- public final static int REVERSE_FRAME_3 = FeatureSegment.REVERSE_FRAME_3;
- public final static int REVERSE_FRAME_2 = FeatureSegment.REVERSE_FRAME_2;
- public final static int REVERSE_FRAME_1 = FeatureSegment.REVERSE_FRAME_1;
- public final static int SCALE_LINE = FeatureSegment.SCALE_LINE;
+ private final static int NO_FRAME = FeatureSegment.NO_FRAME;
+ private final static int FORWARD_STRAND = FeatureSegment.FORWARD_STRAND;
+ private final static int REVERSE_STRAND = FeatureSegment.REVERSE_STRAND;
+ private final static int FORWARD_FRAME_1 = FeatureSegment.FORWARD_FRAME_1;
+ private final static int FORWARD_FRAME_2 = FeatureSegment.FORWARD_FRAME_2;
+ private final static int FORWARD_FRAME_3 = FeatureSegment.FORWARD_FRAME_3;
+ private final static int REVERSE_FRAME_3 = FeatureSegment.REVERSE_FRAME_3;
+ private final static int REVERSE_FRAME_2 = FeatureSegment.REVERSE_FRAME_2;
+ private final static int REVERSE_FRAME_1 = FeatureSegment.REVERSE_FRAME_1;
+ private final static int SCALE_LINE = FeatureSegment.SCALE_LINE;
/**
@@ -2133,7 +2133,13 @@ public class FeatureDisplay extends EntryGroupPanel
else
g.setColor(Color.black);
- for(int i = 0 ; i < codon_positions.length ; ++i)
+
+ int length = 0;
+ if(direction != FORWARD)
+ length = getBases().getLength();
+
+ final int codon_positions_length = codon_positions.length;
+ for(int i = 0; i < codon_positions_length; ++i)
{
final int codon_base_start = codon_positions[i];
@@ -2147,13 +2153,14 @@ public class FeatureDisplay extends EntryGroupPanel
draw_x_position = getLowXPositionOfBase(codon_base_start);
else
{
- final int raw_base_position =
- getBases().getComplementPosition(codon_base_start);
+ final int raw_base_position = length - codon_base_start + 1;
+// final int raw_base_position =
+// getBases().getComplementPosition(codon_base_start);
draw_x_position = getLowXPositionOfBase(raw_base_position);
}
// draw only if we haven't drawn on the position already
- if(last_x_position == -1 || draw_x_position != last_x_position)
+ if(draw_x_position != last_x_position || last_x_position == -1)
{
drawOneCodonMark(g, draw_x_position, draw_y_position,
direction, mark_height);
@@ -4316,7 +4323,7 @@ public class FeatureDisplay extends EntryGroupPanel
* than or equal to zero than controls the number of bases that can appear
* on screen. See getScaleValue().
**/
- public int getScaleFactor()
+ protected int getScaleFactor()
{
return scale_factor;
}
@@ -4427,7 +4434,7 @@ public class FeatureDisplay extends EntryGroupPanel
* the sequence length. If hard_left_edge is true this method will always
* return the same as getForwardBaseAtLeftEdge*(.
**/
- public int getFirstVisibleForwardBase()
+ protected int getFirstVisibleForwardBase()
{
if(left_edge_base < 1)
return 1;
@@ -4442,7 +4449,7 @@ public class FeatureDisplay extends EntryGroupPanel
* being display in the forward direction will be the reverse strand if
* rev_comp_display is true.
**/
- public int getForwardBaseAtLeftEdge()
+ protected int getForwardBaseAtLeftEdge()
{
return left_edge_base;
}
@@ -4476,7 +4483,7 @@ public class FeatureDisplay extends EntryGroupPanel
* edge of the canvas. The number returned will always be > 1 and < the
* sequence length.
**/
- public int getLastVisibleForwardBase()
+ protected int getLastVisibleForwardBase()
{
final int possible_last_base =
(int)(getForwardBaseAtLeftEdge() + getMaxVisibleBases());
@@ -4558,7 +4565,7 @@ public class FeatureDisplay extends EntryGroupPanel
* Return the number of bases we can fit on screen at once, ie the number
* that will fit side by side on the canvas.
**/
- public int getMaxVisibleBases()
+ protected int getMaxVisibleBases()
{
return(int)(getWidth() / getScaleValue());
}
@@ -4590,7 +4597,7 @@ public class FeatureDisplay extends EntryGroupPanel
* Scroll and scale the display so that the given first base is at the left
* edge of the screen and the given last base is at the right edge.
**/
- public void setFirstAndLastBase(final int first, final int last)
+ protected void setFirstAndLastBase(final int first, final int last)
{
left_edge_base = first;
setScaleValue(1.0F * getWidth() /(last - first + 1));
@@ -4600,7 +4607,7 @@ public class FeatureDisplay extends EntryGroupPanel
* Scroll the display so that the given first base is at the left edge of
* the screen.
**/
- public void setFirstBase(int base_position)
+ protected void setFirstBase(int base_position)
{
if(base_position > getSequenceLength())
base_position = getSequenceLength();
diff --git a/uk/ac/sanger/artemis/io/StreamSequence.java b/uk/ac/sanger/artemis/io/StreamSequence.java
index 3ab163826..64d297df0 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 1.2 2004-12-23 10:19:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/StreamSequence.java,v 1.3 2004-12-23 15:33:46 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 1.2 2004-12-23 10:19:05 tjc Exp $
+ * @version $Id: StreamSequence.java,v 1.3 2004-12-23 15:33:46 tjc Exp $
**/
public abstract class StreamSequence
@@ -94,11 +94,11 @@ 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);
+ sequence.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 5bf37e03a..278c12a73 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 1.6 2004-12-23 10:19:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.7 2004-12-23 15:33:46 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 1.6 2004-12-23 10:19:05 tjc Exp $ */
+ * @version $Id: Bases.java,v 1.7 2004-12-23 15:33:46 tjc Exp $ */
public class Bases {
/**
@@ -167,15 +167,15 @@ public class Bases {
**/
public static int getIndexOfBase (final char base) {
switch (base) {
- case 't':
- case 'u':
- return 0;
case 'c':
return 1;
case 'a':
return 2;
case 'g':
return 3;
+ case 't':
+ case 'u':
+ return 0;
}
return 4;
@@ -510,13 +510,13 @@ public class Bases {
int current_return_array_index = 0;
-// final char sequence_string[] =
-// getSequence().getSubSequence(1, getLength()).toCharArray();
+ final String sequence_string =
+ getSequence().getSubSequence(1, getLength());
- final char sequence_string[] =
- getSequence().getCharSubSequence(1, getLength());
+// final char sequence_string[] =
+// getSequence().getCharSubSequence(1, getLength());
- final int sequence_string_length = sequence_string.length;
+ 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;
@@ -957,6 +957,7 @@ public class Bases {
* or 'x' (any base) is 'n'.
**/
public static char complement (final char base) {
+
switch (base) {
case 'a': case 'A': return 't';
case 't': case 'T': case 'u': case 'U': return 'a';
@@ -996,31 +997,31 @@ public class Bases {
* complement of those three bases is a stop codon.
* Codons that contain an X are considered to be stop codons.
**/
- private static boolean isStopCodon (final char[] sequence,
+ private static boolean isStopCodon (final String sequence_string,
final int start_index,
final int direction) {
final char translation;
if (direction == FORWARD) {
- final char first_letter = sequence[start_index];
- final char second_letter = sequence[start_index + 1];
- final char third_letter = sequence[start_index + 2];
+ final char first_letter = sequence_string.charAt (start_index);
+ final char second_letter = sequence_string.charAt (start_index + 1);
+ final char third_letter = sequence_string.charAt (start_index + 2);
if (first_letter == 'x' || second_letter == 'x' || third_letter == 'x') {
// codons that contain an X are considered to be stop codons.
return true;
}
-
+
translation = AminoAcidSequence.getCodonTranslation (first_letter,
second_letter,
third_letter);
} else {
final char first_letter =
- complement (sequence[start_index - 2]);
+ complement (sequence_string.charAt (start_index - 2));
final char second_letter =
- complement (sequence[start_index - 1]);
+ complement (sequence_string.charAt (start_index - 1));
final char third_letter =
- complement (sequence[start_index]);
+ complement (sequence_string.charAt (start_index));
if (first_letter == 'x' || second_letter == 'x' || third_letter == 'x') {
// codons that contain an X are considered to be stop codons.
@@ -1039,6 +1040,7 @@ public class Bases {
}
}
+
/**
* Check a three character substring and return true if and only if the
* three bases are legal (see isLegalBase ()).
--
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