Added getRow() and getColumn() methods to SubstitutionMatrix.

dmyersturnbull · dmyersturnbull · commit edcdbc6a8177 · 2013-12-17T10:43:11.000-08:00
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSubstitutionMatrix.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/SimpleSubstitutionMatrix.java
@@ -31,7 +31,9 @@
 import java.io.Reader;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Scanner;
 import java.util.StringTokenizer;
 
@@ -273,4 +275,22 @@ public String toString() {
         return s.toString();
     }
 
+	public Map<C, Short> getRow(C row) {
+		int rowIndex = rows.indexOf(row);
+		Map<C, Short> map = new HashMap<C, Short>();
+		for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) {
+			map.put(cols.get(colIndex), matrix[rowIndex][colIndex]);
+		}
+		return map;
+	}
+
+	public Map<C, Short> getColumn(C column) {
+		int colIndex = cols.indexOf(column);
+		Map<C, Short> map = new HashMap<C, Short>();
+		for (int i = 0; i < matrix.length; i++) {
+			map.put(rows.get(i), matrix[i][colIndex]);
+		}
+		return map;
+	}
+
 }
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/ScaledSubstitutionMatrix.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/aaindex/ScaledSubstitutionMatrix.java
@@ -1,6 +1,8 @@
 package org.biojava3.alignment.aaindex;
 
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.StringTokenizer;
 
 import org.biojava3.alignment.template.SubstitutionMatrix;
@@ -185,6 +187,24 @@ public SubstitutionMatrix<AminoAcidCompound> normalizeMatrix(short scale) {
 		return null;
 	}
     
-    
+
+	public Map<AminoAcidCompound, Short> getRow(AminoAcidCompound row) {
+		int rowIndex = rows.indexOf(row);
+		Map<AminoAcidCompound, Short> map = new HashMap<AminoAcidCompound, Short>();
+		for (int colIndex = 0; colIndex < matrix[rowIndex].length; colIndex++) {
+			map.put(cols.get(colIndex), matrix[rowIndex][colIndex]);
+		}
+		return map;
+	}
+
+	public Map<AminoAcidCompound, Short> getColumn(AminoAcidCompound column) {
+		int colIndex = cols.indexOf(column);
+		Map<AminoAcidCompound, Short> map = new HashMap<AminoAcidCompound, Short>();
+		for (int i = 0; i < matrix.length; i++) {
+			map.put(rows.get(i), matrix[i][colIndex]);
+		}
+		return map;
+	}
+
 
 }
diff --git a/biojava3-alignment/src/main/java/org/biojava3/alignment/template/SubstitutionMatrix.java b/biojava3-alignment/src/main/java/org/biojava3/alignment/template/SubstitutionMatrix.java
@@ -23,6 +23,8 @@
 
 package org.biojava3.alignment.template;
 
+import java.util.Map;
+
 import org.biojava3.core.sequence.template.Compound;
 import org.biojava3.core.sequence.template.CompoundSet;
 
@@ -118,4 +120,8 @@ public interface SubstitutionMatrix<C extends Compound> {
      */
     void setName(String name);
 
+    Map<C, Short> getRow(C row);
+    
+    Map<C, Short> getColumn(C column);
+    
 }
