JAL-1632 first cut of Tree chooser dialog and ScoreModels singleton

[jalview.git] / src / jalview / analysis / scoremodels / ScoreMatrix.java

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
similarity index 96%
rename from src/jalview/schemes/ScoreMatrix.java
rename to src/jalview/analysis/scoremodels/ScoreMatrix.java
index 5e5fa8d..41aef82 100644 (file)
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -18,10 +18,10 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-package jalview.schemes;
+package jalview.analysis.scoremodels;
 
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
 import jalview.api.analysis.ScoreModelI;
+import jalview.schemes.ResidueProperties;
 
 public class ScoreMatrix extends PairwiseSeqScoreModel implements
         ScoreModelI
@@ -53,7 +53,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
    * @param type
    *          0 for Protein, 1 for NA
    */
-  ScoreMatrix(String name, int[][] matrix, int type)
+  public ScoreMatrix(String name, int[][] matrix, int type)
   {
     this.matrix = matrix;
     this.type = type;
@@ -89,6 +89,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
     return getPairwiseScore(A1.charAt(0), A2.charAt(0));
   }
 
+  @Override
   public int getPairwiseScore(char c, char d)
   {
     int pog = 0;
@@ -112,6 +113,7 @@ public class ScoreMatrix extends PairwiseSeqScoreModel implements
   /**
    * pretty print the matrix
    */
+  @Override
   public String toString()
   {
     return outputMatrix(false);