diff --git a/uk/ac/sanger/artemis/sequence/Bases.java b/uk/ac/sanger/artemis/sequence/Bases.java
index 278c12a73152589b33fb9cf0a64e04bf7cd89eda..c888e3d5ec093c89df11635dedc7d72d191bba7e 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 1.7 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;
- }
}