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JAL-3446 no actual changes; just using meaningful frame options
[jalview.git]
/
src
/
jalview
/
datamodel
/
BinarySequence.java
diff --git
a/src/jalview/datamodel/BinarySequence.java
b/src/jalview/datamodel/BinarySequence.java
index
53bffa9
..
cea9de7
100755
(executable)
--- a/
src/jalview/datamodel/BinarySequence.java
+++ b/
src/jalview/datamodel/BinarySequence.java
@@
-70,7
+70,7
@@
public class BinarySequence extends Sequence
int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
: ResidueProperties.maxProteinIndex;
int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
: ResidueProperties.maxProteinIndex;
- dbinary = new double[getSequence().length * nores];
+ dbinary = new double[getLength() * nores];
return nores;
}
return nores;
}
@@
-88,7
+88,7
@@
public class BinarySequence extends Sequence
{
int nores = initMatrixGetNoRes();
final int[] sindex = getSymbolmatrix();
{
int nores = initMatrixGetNoRes();
final int[] sindex = getSymbolmatrix();
- for (int i = 0; i < getSequence().length; i++)
+ for (int i = 0; i < getLength(); i++)
{
int aanum = nores - 1;
{
int aanum = nores - 1;
@@
-132,7
+132,7
@@
public class BinarySequence extends Sequence
{
int nores = initMatrixGetNoRes();
{
int nores = initMatrixGetNoRes();
- for (int i = 0, iSize = getSequence().length; i < iSize; i++)
+ for (int i = 0, iSize = getLength(); i < iSize; i++)
{
int aanum = nores - 1;
{
int aanum = nores - 1;
@@
-169,7
+169,7
@@
public class BinarySequence extends Sequence
for (int i = 0; i < binary.length; i++)
{
for (int i = 0; i < binary.length; i++)
{
- out += (new Integer(binary[i])).toString();
+ out += (Integer.valueOf(binary[i])).toString();
if (i < (binary.length - 1))
{
if (i < (binary.length - 1))
{