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added description of alignment quality scores and separated
[jalview.git]
/
src
/
jalview
/
math
/
Matrix.java
diff --git
a/src/jalview/math/Matrix.java
b/src/jalview/math/Matrix.java
index
81d520a
..
f9abbda
100755
(executable)
--- a/
src/jalview/math/Matrix.java
+++ b/
src/jalview/math/Matrix.java
@@
-804,13
+804,13
@@
public class Matrix
//symm.print(System.out);
\r
//System.out.println();
\r
// Copy the symmetric matrix for later
\r
//symm.print(System.out);
\r
//System.out.println();
\r
// Copy the symmetric matrix for later
\r
- Matrix origsymm = symm.copy();
\r
+ //Matrix origsymm = symm.copy();
\r
\r
// This produces the tridiagonal transformation matrix
\r
\r
// This produces the tridiagonal transformation matrix
\r
- long tstart = System.currentTimeMillis();
\r
+ //long tstart = System.currentTimeMillis();
\r
symm.tred();
\r
\r
symm.tred();
\r
\r
- long tend = System.currentTimeMillis();
\r
+ //long tend = System.currentTimeMillis();
\r
\r
//System.out.println("Time take for tred = " + (tend-tstart) + "ms");
\r
//System.out.println(" ---Tridiag transform matrix ---");
\r
\r
//System.out.println("Time take for tred = " + (tend-tstart) + "ms");
\r
//System.out.println(" ---Tridiag transform matrix ---");
\r
@@
-823,9
+823,9
@@
public class Matrix
//symm.printE(System.out);
\r
//System.out.println();
\r
// Now produce the diagonalization matrix
\r
//symm.printE(System.out);
\r
//System.out.println();
\r
// Now produce the diagonalization matrix
\r
- tstart = System.currentTimeMillis();
\r
+ //tstart = System.currentTimeMillis();
\r
symm.tqli();
\r
symm.tqli();
\r
- tend = System.currentTimeMillis();
\r
+ //tend = System.currentTimeMillis();
\r
\r
//System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
\r
//System.out.println(" --- New diagonalization matrix ---");
\r
\r
//System.out.println("Time take for tqli = " + (tend-tstart) + " ms");
\r
//System.out.println(" --- New diagonalization matrix ---");
\r