From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 30 Oct 2017 13:48:16 +0000 (+0000)
Subject: JAL-2795 added comments links from ForesterMatrix to MatrixI
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=eeb51330a8c0ad188e7b07597e66cbe090d9d160;p=jalview.git

JAL-2795 added comments links from ForesterMatrix to MatrixI
---

diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index f8b68d0..daeec3b 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -21,7 +21,6 @@ public class ForesterMatrix implements DistanceMatrix
 
   private Sequence[] sequences;
 
-
   private String[] identifiers;
 
   public ForesterMatrix(MatrixI jalviewInputMatrix,
@@ -66,12 +65,19 @@ public class ForesterMatrix implements DistanceMatrix
     return 0;
   }
 
+  /**
+   * Returns the length of whichever is longest, columns or rows
+   */
   @Override
   public int getSize()
   {
-    return jalviewMatrix.width();
+    return jalviewMatrix.getValues().length;
   }
 
+  /**
+   * See {@link MatrixI#getValue(int,int)} except that the order of column, row
+   * in the parameters is inverted here
+   */
   @Override
   public double getValue(int col, int row)
   {
@@ -85,6 +91,10 @@ public class ForesterMatrix implements DistanceMatrix
 
   }
 
+  /**
+   * See {@link MatrixI#setValue()} except that the order of column, row in the
+   * parameters is inverted here
+   */
   @Override
   public void setValue(int col, int row, double distance)
   {
@@ -99,6 +109,9 @@ public class ForesterMatrix implements DistanceMatrix
     return null;
   }
 
+  /**
+   * See {@link MatrixI#getValues()}
+   */
   @Override
   public double[][] getValues()
   {
diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 21c5a4d..5c264a8 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -996,6 +996,7 @@ public class Matrix implements MatrixI
     }
   }
 
+
   @Override
   public double[][] getValues()
   {
diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index f4d5030..840e93b 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -48,7 +48,7 @@ public interface MatrixI
   double getValue(int i, int j);
 
   /**
-   * Sets the value at row i, colum j
+   * Sets the value at row i, column j
    * 
    * @param i
    * @param j
@@ -63,6 +63,12 @@ public interface MatrixI
    */
   double[] getRow(int i);
 
+  /**
+   * Answers all values present in the Matrix ordered by row,column
+   * 
+   * @return the double array containing the values ordered in {row values} per
+   *         column
+   */
   double[][] getValues();