X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FScoreMatrix.java;h=e2aa232fba0f2e2733b69d651f5e5ce328f6a054;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=93415096e204476e1ed20a56903f6c4e5a30c9a6;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git

diff --git a/src/jalview/schemes/ScoreMatrix.java b/src/jalview/schemes/ScoreMatrix.java
index 9341509..e2aa232 100644
--- a/src/jalview/schemes/ScoreMatrix.java
+++ b/src/jalview/schemes/ScoreMatrix.java
@@ -1,147 +1,173 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
- * 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/>.
- */
-package jalview.schemes;
-
-public class ScoreMatrix
-{
-  String name;
-
-  /**
-   * reference to integer score matrix
-   */
-  int[][] matrix;
-
-  /**
-   * 0 for Protein Score matrix. 1 for dna score matrix
-   */
-  int type;
-
-  ScoreMatrix(String name, int[][] matrix, int type)
-  {
-    this.matrix = matrix;
-    this.type = type;
-  }
-
-  public boolean isDNA()
-  {
-    return type == 1;
-  }
-
-  public boolean isProtein()
-  {
-    return type == 0;
-  }
-
-  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>");
-    }
-    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();
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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();
+  }
+}