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JAL-2629 adjust placement and optionality of arguments/options
[jalview.git]
/
src
/
jalview
/
analysis
/
scoremodels
/
ScoreMatrix.java
diff --git
a/src/jalview/analysis/scoremodels/ScoreMatrix.java
b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index
efaeb43
..
6cdfacb
100644
(file)
--- a/
src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/
src/jalview/analysis/scoremodels/ScoreMatrix.java
@@
-36,8
+36,8
@@
import java.util.Arrays;
* symbols. Instances of this class are immutable and thread-safe, so the same
* object is returned from calls to getInstance().
*/
* symbols. Instances of this class are immutable and thread-safe, so the same
* object is returned from calls to getInstance().
*/
-public class ScoreMatrix extends SimilarityScoreModel implements
- PairwiseScoreModelI
+public class ScoreMatrix extends SimilarityScoreModel
+ implements PairwiseScoreModelI
{
private static final char GAP_CHARACTER = Comparison.GAP_DASH;
{
private static final char GAP_CHARACTER = Comparison.GAP_DASH;
@@
-98,7
+98,7
@@
public class ScoreMatrix extends SimilarityScoreModel implements
private float minValue;
private float maxValue;
private float minValue;
private float maxValue;
-
+
/**
* Constructor given a name, symbol alphabet, and matrix of scores for pairs
* of symbols. The matrix should be square and of the same size as the
/**
* Constructor given a name, symbol alphabet, and matrix of scores for pairs
* of symbols. The matrix should be square and of the same size as the
@@
-130,8
+130,8
@@
public class ScoreMatrix extends SimilarityScoreModel implements
* @param values
* Pairwise scores indexed according to the symbol alphabet
*/
* @param values
* Pairwise scores indexed according to the symbol alphabet
*/
- public ScoreMatrix(String theName, String theDescription,
- char[] alphabet, float[][] values)
+ public ScoreMatrix(String theName, String theDescription, char[] alphabet,
+ float[][] values)
{
if (alphabet.length != values.length)
{
{
if (alphabet.length != values.length)
{
@@
-454,7
+454,8
@@
public class ScoreMatrix extends SimilarityScoreModel implements
* @param params
* @return
*/
* @param params
* @return
*/
- protected MatrixI findSimilarities(String[] seqs, SimilarityParamsI params)
+ protected MatrixI findSimilarities(String[] seqs,
+ SimilarityParamsI params)
{
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)
{
double[][] values = new double[seqs.length][];
for (int row = 0; row < seqs.length; row++)