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Commit 20dc5418 authored by tjc's avatar tjc
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speed up for drawing stop codons 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2158 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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uk/ac/sanger/artemis/sequence/Bases.java
+ 150
− 126
View file @ 20dc5418
......@@ -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 1.7 2004-12-23 15:33:46 tjc Exp $
* $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/sequence/Bases.java,v 1.8 2004-12-23 17:01:15 tjc Exp $
*/
package uk.ac.sanger.artemis.sequence;
......@@ -45,9 +45,10 @@ import java.util.Iterator;
* non-base letter returns '@'.
*
* @author Kim Rutherford
* @version $Id: Bases.java,v 1.7 2004-12-23 15:33:46 tjc Exp $ */
* @version $Id: Bases.java,v 1.8 2004-12-23 17:01:15 tjc Exp $ */
public class Bases {
public class Bases
{
/**
* Indicates the bases should be read in the forward direction for a
* particular operation.
......@@ -79,25 +80,26 @@ public class Bases {
* Create a new Bases object.
* @param sequence The raw sequence that the new object will use.
**/
public Bases (final Sequence sequence) {
public Bases(final Sequence sequence)
{
this.embl_sequence = sequence;
forward_stop_codon_cache = null;
reverse_stop_codon_cache = null;
forward_strand = new Strand (this, FORWARD);
reverse_strand = new Strand (this, REVERSE);
forward_strand = new Strand(this, FORWARD);
reverse_strand = new Strand(this, REVERSE);
for (int i = 0 ; i < listener_hash_map_array.length ; ++i) {
listener_hash_map_array [i] = new WeakHashMap ();
}
for(int i = 0 ; i < listener_hash_map_array.length ; ++i)
listener_hash_map_array [i] = new WeakHashMap();
}
/**
* Return the object representing the forward sequence of bases for this
* object.
**/
public Strand getForwardStrand () {
public Strand getForwardStrand()
{
return forward_strand;
}
......@@ -105,22 +107,25 @@ public class Bases {
* Return the object representing the reverse complemented sequence of
* bases for this Bases objects.
**/
public Strand getReverseStrand () {
public Strand getReverseStrand()
{
return reverse_strand;
}
/**
* Returns the length of the sequence in bases.
**/
public int getLength () {
return embl_sequence.length ();
public int getLength()
{
return embl_sequence.length();
}
/**
* Return a String representation of the sequence.
**/
public String toString () {
return embl_sequence.toString ();
public String toString()
{
return embl_sequence.toString();
}
/**
......@@ -128,8 +133,9 @@ public class Bases {
* reverse complementing the sequence).
* @exception ReadOnlyException If the Bases cannot be changed.
**/
public void reverseComplement ()
throws ReadOnlyException {
public void reverseComplement()
throws ReadOnlyException
{
forward_stop_codon_cache = null;
reverse_stop_codon_cache = null;
......@@ -138,7 +144,7 @@ public class Bases {
reverse_strand = temp;
final String new_sequence =
reverseComplement (getSequence ().getSubSequence (1, getLength ()));
reverseComplement(getSequence().getSubSequence(1, getLength()));
try {
getSequence ().setFromString (new_sequence);
......@@ -482,140 +488,159 @@ public class Bases {
* @return An array containing the positions of the first base of the stop
* codons. This array is padded with zeros at the end.
**/
public int [] getStopCodons (final Range range, final int direction) {
public int[] getStopCodons(final Range range, final int direction)
{
final Range real_range;
if (direction == FORWARD) {
if(direction == FORWARD)
real_range = range;
} else {
else
real_range = complementRange (range);
}
// guess the number of stop codons in getCount () bases - there are 3
// guess the number of stop codons in getCount() bases - there are 3
// stop codons in every 64 codons if G+C is 50% and we have getCount()/3
// codons to look at.
float at_content = (100 - getAverageGCPercent ()) / 100;
float at_content = (100 - getAverageGCPercent()) / 100;
int array_start_size =
(int) (range.getCount () *
(int)(range.getCount() *
at_content * at_content * (2-at_content) * 3 / 64);
if (array_start_size < 20) {
if(array_start_size < 20)
array_start_size = 20;
}
// this array will be resized as necessary
int [] return_positions = new int [array_start_size];
int[] return_positions = new int[array_start_size];
int current_return_array_index = 0;
final String sequence_string =
getSequence().getSubSequence(1, getLength());
// final char sequence_string[] =
// 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;
final byte [] forward_stop_codon_flags = getForwardStopCodonCache ();
final byte [] reverse_stop_codon_flags = getReverseStopCodonCache ();
if (direction == FORWARD) {
for (int i = range_start_index ; i < range_end_index - 2 ; i += 3) {
if (i < 0 || i >= sequence_string_length - 2) {
int range_start_index = real_range.getStart();
int range_end_index = real_range.getEnd();
final int sequence_string_length = getLength();
if(range_start_index < 1)
range_start_index = 1;
if(range_end_index > sequence_string_length)
range_end_index = sequence_string_length;
final char sequence_string[] =
getSequence().getCharSubSequence(range_start_index, range_end_index);
range_start_index--;
range_end_index--;
final byte[] forward_stop_codon_flags = getForwardStopCodonCache();
final byte[] reverse_stop_codon_flags = getReverseStopCodonCache();
if(direction == FORWARD)
{
for(int i = range_start_index; i < range_end_index - 2; i += 3)
{
if(i < 0 || i >= sequence_string_length - 2)
continue;
}
final boolean is_stop_codon;
if (forward_stop_codon_flags[i] == 0) {
if(forward_stop_codon_flags[i] == 0)
{
// not cached yet
if (isStopCodon (sequence_string, i, direction)) {
if(isStopCodon (sequence_string, i-range_start_index, direction))
{
forward_stop_codon_flags[i] = 2;
is_stop_codon = true;
} else {
}
else
{
forward_stop_codon_flags[i] = 1;
is_stop_codon = false;
}
} else {
}
else
{
// used the cached value
if (forward_stop_codon_flags[i] == 2) {
if(forward_stop_codon_flags[i] == 2)
is_stop_codon = true;
} else {
else
is_stop_codon = false;
}
}
if (is_stop_codon) {
if (current_return_array_index == return_positions.length) {
if(is_stop_codon)
{
if(current_return_array_index == return_positions.length)
{
// first reallocate the array
final int [] new_array =
new int [return_positions.length * 3 / 2 + 1];
final int[] new_array =
new int[return_positions.length * 3 / 2 + 1];
System.arraycopy (return_positions, 0,
new_array, 0,
return_positions.length);
System.arraycopy(return_positions, 0,
new_array, 0,
return_positions.length);
return_positions = new_array;
}
if (is_stop_codon) {
// negative position marks an illegal codon
if(is_stop_codon)
return_positions[current_return_array_index] = i + 1;
} else {
// negative position marks an illegal codon
else
return_positions[current_return_array_index] = -(i + 1);
}
++current_return_array_index;
}
}
} else {
for (int i = range_end_index ; i > range_start_index + 2 ; i -= 3) {
if (i < 2 || i >= sequence_string_length) {
}
else
{
for (int i = range_end_index ; i > range_start_index + 2 ; i -= 3)
{
if(i < 2 || i >= sequence_string_length)
continue;
}
final boolean is_stop_codon;
if (reverse_stop_codon_flags[i] == 0) {
if (isStopCodon (sequence_string, i, direction)) {
if(reverse_stop_codon_flags[i] == 0)
{
if(isStopCodon(sequence_string, i-range_start_index, direction))
{
reverse_stop_codon_flags[i] = 2;
is_stop_codon = true;
} else {
}
else
{
reverse_stop_codon_flags[i] = 1;
is_stop_codon = false;
}
} else {
if (reverse_stop_codon_flags[i] == 2) {
}
else
{
if(reverse_stop_codon_flags[i] == 2)
is_stop_codon = true;
} else {
else
is_stop_codon = false;
}
}
if (is_stop_codon) {
if (current_return_array_index == return_positions.length) {
if(is_stop_codon)
{
if(current_return_array_index == return_positions.length)
{
// first reallocate the array
final int [] new_array =
new int [return_positions.length * 3 / 2 + 1];
final int[] new_array =
new int[return_positions.length * 3 / 2 + 1];
System.arraycopy (return_positions, 0,
new_array, 0,
return_positions.length);
System.arraycopy(return_positions, 0,
new_array, 0,
return_positions.length);
return_positions = new_array;
}
if (is_stop_codon) {
// return the complemented base position
// return the complemented base position
if(is_stop_codon)
return_positions[current_return_array_index] =
sequence_string_length - i;
} else {
// return the complemented base position
else
return_positions[current_return_array_index] =
- (sequence_string_length - i);
}
++current_return_array_index;
}
}
......@@ -628,14 +653,15 @@ public class Bases {
* Return the base at the given position.
**/
public char getBaseAt (final int position)
throws OutOfRangeException {
if (position > getLength ()) {
throw new OutOfRangeException (position + " > " + getLength ());
}
if (position < 1) {
throw new OutOfRangeException (position + " < " + 1);
}
return toString ().charAt (position - 1);
throws OutOfRangeException
{
if(position > getLength())
throw new OutOfRangeException(position + " > " + getLength());
if(position < 1)
throw new OutOfRangeException(position + " < " + 1);
return toString().charAt(position - 1);
}
/**
......@@ -997,47 +1023,45 @@ 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 String sequence_string,
final int start_index,
final int direction) {
private static boolean isStopCodon(final char[] sequence,
final int start_index,
final int direction)
{
final char translation;
if (direction == FORWARD) {
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(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];
if (first_letter == 'x' || second_letter == 'x' || third_letter == 'x') {
// codons that contain an X are considered to be stop codons.
// codons that contain an X are considered to be stop codons.
if(first_letter == 'x' || second_letter == 'x' || third_letter == 'x')
return true;
}
translation = AminoAcidSequence.getCodonTranslation (first_letter,
second_letter,
third_letter);
} else {
final char first_letter =
complement (sequence_string.charAt (start_index - 2));
final char second_letter =
complement (sequence_string.charAt (start_index - 1));
final char third_letter =
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.
translation = AminoAcidSequence.getCodonTranslation(first_letter,
second_letter,
third_letter);
}
else
{
final char first_letter = complement(sequence[start_index - 2]);
final char second_letter = complement(sequence[start_index - 1]);
final char third_letter = complement(sequence[start_index]);
// codons that contain an X are considered to be stop codons.
if (first_letter == 'x' || second_letter == 'x' || third_letter == 'x')
return true;
}
translation = AminoAcidSequence.getCodonTranslation (third_letter,
second_letter,
first_letter);
translation = AminoAcidSequence.getCodonTranslation(third_letter,
second_letter,
first_letter);
}
if (translation == '+' || translation == '*' || translation == '#') {
if(translation == '+' || translation == '*' || translation == '#')
return true;
} else {
else
return false;
}
}
......
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