diff --git a/uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java b/uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java
index a900194fb7be4c8ca115c9d2c98f8d65d02a3b70..98d6d99a0b71ed729895a63887cb66de516d654a 100644
--- a/uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/AGWindowAlgorithm.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/AGWindowAlgorithm.java,v 1.3 2009-03-13 20:39:37 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/AGWindowAlgorithm.java,v 1.4 2009-03-17 17:47:42 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -37,7 +37,7 @@ import uk.ac.sanger.artemis.sequence.*;
* constructor.
*
* @author Kim Rutherford
- * @version $Id: AGWindowAlgorithm.java,v 1.3 2009-03-13 20:39:37 tjc Exp $
+ * @version $Id: AGWindowAlgorithm.java,v 1.4 2009-03-17 17:47:42 tjc Exp $
**/
public class AGWindowAlgorithm extends BaseAlgorithm {
@@ -59,18 +59,18 @@ public class AGWindowAlgorithm extends BaseAlgorithm {
* this array.
**/
public void getValues (int start, int end, final float [] values) {
- final char[] sequence;
+ final String sequence;
try {
- sequence = getStrand ().getBases().getSubSequenceC (new Range (start, end), getStrand().getDirection());
+ sequence = getStrand ().getSubSequence (new Range (start, end));
} catch (OutOfRangeException e) {
throw new Error ("internal error - unexpected exception: " + e);
}
float gc_count = 0;
- for (int i = 0 ; i < sequence.length ; ++i) {
- final char this_char = sequence[i];
+ for (int i = 0 ; i < sequence.length () ; ++i) {
+ final char this_char = sequence.charAt (i);
// System.out.println (this_char);
if (this_char == 'g' || this_char == 'a') {
@@ -80,7 +80,7 @@ public class AGWindowAlgorithm extends BaseAlgorithm {
// System.out.println ("start: " + start + " end: " + end + " returning: " + gc_count/sequence.length ());
- values[0] = gc_count/sequence.length * 100;
+ values[0] = gc_count/sequence.length () * 100;
}
/**
diff --git a/uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java b/uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java
index 70ae4e9bd84b8b4ac6cad11f59df65540e02272b..7b08e0d2aabf3ad13031d0d2599c6ed20d52ba17 100644
--- a/uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.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/GCSDWindowAlgorithm.java,v 1.3 2009-03-13 20:39:37 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/GCSDWindowAlgorithm.java,v 1.4 2009-03-17 17:47:42 tjc Exp $
*/
package uk.ac.sanger.artemis.plot;
@@ -39,7 +39,7 @@ import uk.ac.sanger.artemis.sequence.*;
* to use is set in the constructor.
*
* @author Kim Rutherford
- * @version $Id: GCSDWindowAlgorithm.java,v 1.3 2009-03-13 20:39:37 tjc Exp $
+ * @version $Id: GCSDWindowAlgorithm.java,v 1.4 2009-03-17 17:47:42 tjc Exp $
**/
public class GCSDWindowAlgorithm extends BaseAlgorithm {
@@ -82,18 +82,18 @@ public class GCSDWindowAlgorithm extends BaseAlgorithm {
}
}
- final char[] sequence;
+ final String sequence;
try {
- sequence = getStrand ().getBases().getSubSequenceC (new Range (start, end), getStrand().getDirection());
+ sequence = getStrand ().getSubSequence (new Range (start, end));
} catch (OutOfRangeException e) {
throw new Error ("internal error - unexpected exception: " + e);
}
float gc_count = 0;
- for (int i = 0 ; i < sequence.length ; ++i) {
- final char this_char = sequence[i];
+ for (int i = 0 ; i < sequence.length () ; ++i) {
+ final char this_char = sequence.charAt (i);
// System.out.println (this_char);
if (this_char == 'g' || this_char == 'c') {
@@ -101,7 +101,7 @@ public class GCSDWindowAlgorithm extends BaseAlgorithm {
}
}
- final float gc_content = gc_count/sequence.length * 100;
+ final float gc_content = gc_count/sequence.length () * 100;
final float gc_average =
getStrand ().getBases ().getAverageGCPercent ();
@@ -122,17 +122,8 @@ public class GCSDWindowAlgorithm extends BaseAlgorithm {
final int sequence_length = getStrand ().getBases ().getLength ();
- //final String bases = getStrand ().getBases ().toString ();
- char[] bases = null;
- try
- {
- bases = getStrand ().getBases ().getSubSequenceC(new Range(1,sequence_length), Strand.FORWARD);
- }
- catch(OutOfRangeException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
+ final String bases = getStrand ().getBases ().toString ();
+
// the number of windows to search
final int window_count = sequence_length - window_size;
@@ -150,14 +141,14 @@ public class GCSDWindowAlgorithm extends BaseAlgorithm {
for (int i = - window_size ; i < window_count ; ++i) {
if (i > 0) {
- final char previous_char = bases[i - 1];
+ final char previous_char = bases.charAt (i - 1);
if (previous_char == 'g' || previous_char == 'c') {
--current_gc_count;
}
}
- final char new_char = bases[i + window_size];
+ final char new_char = bases.charAt (i + window_size);
if (new_char == 'g' || new_char == 'c') {
++current_gc_count;
diff --git a/uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java b/uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java
index a608deab7cbb303fe5579a036e6346575e467774..a4b5bd362a74949a23d88db85bcb15c56d6939b3 100644
--- a/uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java
+++ b/uk/ac/sanger/artemis/plot/GCWindowAlgorithm.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/GCWindowAlgorithm.java,v 1.3 2009-03-13 20:39:37 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/plot/GCWindowAlgorithm.java,v 1.4 2009-03-17 17:47:42 tjc Exp $
**/
package uk.ac.sanger.artemis.plot;
@@ -37,7 +37,7 @@ import uk.ac.sanger.artemis.sequence.*;
* constructor.
*
* @author Kim Rutherford
- * @version $Id: GCWindowAlgorithm.java,v 1.3 2009-03-13 20:39:37 tjc Exp $
+ * @version $Id: GCWindowAlgorithm.java,v 1.4 2009-03-17 17:47:42 tjc Exp $
**/
public class GCWindowAlgorithm extends BaseAlgorithm {
@@ -59,27 +59,28 @@ public class GCWindowAlgorithm extends BaseAlgorithm {
* this array.
**/
public void getValues (int start, int end, final float [] values) {
- final char[] sequence;
+ final String sequence;
try {
- sequence = getStrand ().getBases().getSubSequenceC(
- new Range (start, end), getStrand ().getDirection());
+ sequence = getStrand ().getSubSequence (new Range (start, end));
} catch (OutOfRangeException e) {
throw new Error ("internal error - unexpected exception: " + e);
}
float gc_count = 0;
- final int sequence_length = sequence.length;
- for (int i = 0 ; i < sequence_length ; ++i)
- {
- if (sequence[i] == 'g' || sequence[i] == 'c')
+ for (int i = 0 ; i < sequence.length () ; ++i) {
+ final char this_char = sequence.charAt (i);
+// System.out.println (this_char);
+
+ if (this_char == 'g' || this_char == 'c') {
++gc_count;
+ }
}
// System.out.println ("start: " + start + " end: " + end + " returning: " + gc_count/sequence.length ());
- values[0] = gc_count/sequence_length * 100;
+ values[0] = gc_count/sequence.length () * 100;
}
/**