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[jalview.git]
/
src
/
jalview
/
datamodel
/
BinarySequence.java
diff --git
a/src/jalview/datamodel/BinarySequence.java
b/src/jalview/datamodel/BinarySequence.java
index
062f6ba
..
62171f7
100755
(executable)
--- a/
src/jalview/datamodel/BinarySequence.java
+++ b/
src/jalview/datamodel/BinarySequence.java
@@
-42,7
+42,8
@@
public class BinarySequence extends Sequence
double[] dbinary;
double[] dbinary;
- boolean isNa=false;
+ boolean isNa = false;
+
/**
* Creates a new BinarySequence object.
*
/**
* Creates a new BinarySequence object.
*
@@
-52,16
+53,18
@@
public class BinarySequence extends Sequence
public BinarySequence(String s, boolean isNa)
{
super("", s, 0, s.length());
public BinarySequence(String s, boolean isNa)
{
super("", s, 0, s.length());
- this.isNa=isNa;
+ this.isNa = isNa;
}
/**
}
/**
- * clear the dbinary matrix
+ * clear the dbinary matrix
+ *
* @return nores - dimension of sequence symbol encoding for this sequence
*/
private int initMatrixGetNoRes()
{
* @return nores - dimension of sequence symbol encoding for this sequence
*/
private int initMatrixGetNoRes()
{
- int nores=(isNa) ? ResidueProperties.maxNucleotideIndex : ResidueProperties.maxProteinIndex;
+ int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
// Set all matrix to 0
dbinary = new double[getSequence().length * nores];
// Set all matrix to 0
dbinary = new double[getSequence().length * nores];
@@
-71,32
+74,35
@@
public class BinarySequence extends Sequence
}
return nores;
}
}
return nores;
}
+
private int[] getSymbolmatrix()
{
private int[] getSymbolmatrix()
{
- return (isNa) ? ResidueProperties.nucleotideIndex : ResidueProperties.aaIndex;
+ return (isNa) ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex;
}
}
+
/**
* DOCUMENT ME!
*/
public void encode()
{
/**
* DOCUMENT ME!
*/
public void encode()
{
- 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 < getSequence().length; i++)
{
- int aanum = nores-1;
+ int aanum = nores - 1;
try
{
aanum = sindex[getCharAt(i)];
} catch (NullPointerException e)
{
try
{
aanum = sindex[getCharAt(i)];
} catch (NullPointerException e)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
if (aanum >= nores)
{
}
if (aanum >= nores)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
dbinary[(i * nores) + aanum] = 1.0;
}
dbinary[(i * nores) + aanum] = 1.0;
@@
-108,9
+114,10
@@
public class BinarySequence extends Sequence
*
* @param matrix
*/
*
* @param matrix
*/
- public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException
+ public void matrixEncode(final ScoreMatrix matrix)
+ throws InvalidSequenceTypeException
{
{
- if (isNa!=matrix.isDNA())
+ if (isNa != matrix.isDNA())
{
throw new InvalidSequenceTypeException("matrix "
+ matrix.getClass().getCanonicalName()
{
throw new InvalidSequenceTypeException("matrix "
+ matrix.getClass().getCanonicalName()
@@
-131,21
+138,21
@@
public class BinarySequence extends Sequence
// for (int i = 0; i < dbinary.length; i++) {
// dbinary[i] = 0.0;
// }
// for (int i = 0; i < dbinary.length; i++) {
// dbinary[i] = 0.0;
// }
- for (int i = 0,iSize=getSequence().length; i<iSize; i++)
+ for (int i = 0, iSize = getSequence().length; i < iSize; i++)
{
{
- int aanum = nores-1;
+ int aanum = nores - 1;
try
{
aanum = aaIndex[getCharAt(i)];
} catch (NullPointerException e)
{
try
{
aanum = aaIndex[getCharAt(i)];
} catch (NullPointerException e)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
}
- if (aanum >=nores)
+ if (aanum >= nores)
{
{
- aanum = nores-1;
+ aanum = nores - 1;
}
// Do the blosum^H^H^H^H^H score matrix summation thing
}
// Do the blosum^H^H^H^H^H score matrix summation thing