Merge branch 'develop' into features/JAL-250_hideredundantseqs

[jalview.git] / src / jalview / schemes / ScoreMatrix.java

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
deleted file mode 100644 (file)
index 5e5fa8d..0000000
--- a/src/jalview/schemes/ScoreMatrix.java
+++ /dev/null
@@ -1,173 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3
- * of the License, or (at your option) any later version.
- *  
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License
- * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.schemes;
-
-import jalview.analysis.scoremodels.PairwiseSeqScoreModel;
-import jalview.api.analysis.ScoreModelI;
-
-public class ScoreMatrix extends PairwiseSeqScoreModel implements
-        ScoreModelI
-{
-  String name;
-
-  @Override
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * reference to integer score matrix
-   */
-  int[][] matrix;
-
-  /**
-   * 0 for Protein Score matrix. 1 for dna score matrix
-   */
-  int type;
-
-  /**
-   * 
-   * @param name
-   *          Unique, human readable name for the matrix
-   * @param matrix
-   *          Pairwise scores indexed according to appropriate symbol alphabet
-   * @param type
-   *          0 for Protein, 1 for NA
-   */
-  ScoreMatrix(String name, int[][] matrix, int type)
-  {
-    this.matrix = matrix;
-    this.type = type;
-    this.name = name;
-  }
-
-  @Override
-  public boolean isDNA()
-  {
-    return type == 1;
-  }
-
-  @Override
-  public boolean isProtein()
-  {
-    return type == 0;
-  }
-
-  @Override
-  public int[][] getMatrix()
-  {
-    return matrix;
-  }
-
-  /**
-   * 
-   * @param A1
-   * @param A2
-   * @return score for substituting first char in A1 with first char in A2
-   */
-  public int getPairwiseScore(String A1, String A2)
-  {
-    return getPairwiseScore(A1.charAt(0), A2.charAt(0));
-  }
-
-  public int getPairwiseScore(char c, char d)
-  {
-    int pog = 0;
-
-    try
-    {
-      int a = (type == 0) ? ResidueProperties.aaIndex[c]
-              : ResidueProperties.nucleotideIndex[c];
-      int b = (type == 0) ? ResidueProperties.aaIndex[d]
-              : ResidueProperties.nucleotideIndex[d];
-
-      pog = matrix[a][b];
-    } catch (Exception e)
-    {
-      // System.out.println("Unknown residue in " + A1 + " " + A2);
-    }
-
-    return pog;
-  }
-
-  /**
-   * pretty print the matrix
-   */
-  public String toString()
-  {
-    return outputMatrix(false);
-  }
-
-  public String outputMatrix(boolean html)
-  {
-    StringBuffer sb = new StringBuffer();
-    int[] symbols = (type == 0) ? ResidueProperties.aaIndex
-            : ResidueProperties.nucleotideIndex;
-    int symMax = (type == 0) ? ResidueProperties.maxProteinIndex
-            : ResidueProperties.maxNucleotideIndex;
-    boolean header = true;
-    if (html)
-    {
-      sb.append("<table border=\"1\">");
-    }
-    for (char sym = 'A'; sym <= 'Z'; sym++)
-    {
-      if (symbols[sym] >= 0 && symbols[sym] < symMax)
-      {
-        if (header)
-        {
-          sb.append(html ? "<tr><td></td>" : "");
-          for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
-          {
-            if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
-            {
-              sb.append((html ? "<td>&nbsp;" : "\t") + sym2
-                      + (html ? "&nbsp;</td>" : ""));
-            }
-          }
-          header = false;
-          sb.append(html ? "</tr>\n" : "\n");
-        }
-        if (html)
-        {
-          sb.append("<tr>");
-        }
-        sb.append((html ? "<td>" : "") + sym + (html ? "</td>" : ""));
-        for (char sym2 = 'A'; sym2 <= 'Z'; sym2++)
-        {
-          if (symbols[sym2] >= 0 && symbols[sym2] < symMax)
-          {
-            sb.append((html ? "<td>" : "\t")
-                    + matrix[symbols[sym]][symbols[sym2]]
-                    + (html ? "</td>" : ""));
-          }
-        }
-        sb.append(html ? "</tr>\n" : "\n");
-      }
-    }
-    if (html)
-    {
-      sb.append("</table>");
-    }
-    return sb.toString();
-  }
-}