in progress (special coloring is still true)

[jalview.git] / forester / java / src / org / forester / development / neTest.java

diff --git a/forester/java/src/org/forester/development/neTest.java b/forester/java/src/org/forester/development/neTest.java
index 7e96d04..9b02188 100644 (file)
--- a/forester/java/src/org/forester/development/neTest.java
+++ b/forester/java/src/org/forester/development/neTest.java
@@ -37,7 +37,7 @@ public class neTest {
     //    }  /* coeffs */
     // compute cosine and sine of theta
     void coeffs( final double x, final double y, final DoublePointer c, final DoublePointer s, final double accuracy ) {
-        final double root = Math.sqrt( x * x + y * y );
+        final double root = Math.sqrt( ( x * x ) + ( y * y ) );
         if ( root < accuracy ) {
             c.setValue( 1.0 );
             s.setValue( 0.0 );
@@ -66,8 +66,8 @@ public class neTest {
     void tridiag( final double a[][], final int n, final double accuracy ) {
         int i, j;
         double s, c;
-        DoublePointer sp = new DoublePointer( 0 );
-        DoublePointer cp = new DoublePointer( 0 );
+        final DoublePointer sp = new DoublePointer( 0 );
+        final DoublePointer cp = new DoublePointer( 0 );
         for( i = 2; i < n; i++ ) {
             for( j = i + 1; j <= n; j++ ) {
                 coeffs( a[ i - 2 ][ i - 1 ], a[ i - 2 ][ j - 1 ], cp, sp, accuracy );
@@ -113,8 +113,8 @@ public class neTest {
     void shiftqr( final double a[][], final int n, final double accuracy ) {
         int i, j;
         double approx;
-        DoublePointer sp = new DoublePointer( 0 );
-        DoublePointer cp = new DoublePointer( 0 );
+        final DoublePointer sp = new DoublePointer( 0 );
+        final DoublePointer cp = new DoublePointer( 0 );
         double s;
         double c;
         double d;
@@ -124,7 +124,7 @@ public class neTest {
             do {
                 TEMP = a[ i - 2 ][ i - 2 ] - a[ i - 1 ][ i - 1 ];
                 TEMP1 = a[ i - 1 ][ i - 2 ];
-                d = Math.sqrt( TEMP * TEMP + TEMP1 * TEMP1 );
+                d = Math.sqrt( ( TEMP * TEMP ) + ( TEMP1 * TEMP1 ) );
                 approx = a[ i - 2 ][ i - 2 ] + a[ i - 1 ][ i - 1 ];
                 if ( a[ i - 1 ][ i - 1 ] < a[ i - 2 ][ i - 2 ] ) {
                     approx = ( approx - d ) / 2.0;
@@ -181,13 +181,13 @@ public class neTest {
         double d;
         for( k = 0; k < n; k++ ) {
             if ( left ) {
-                d = ctheta * a[ i - 1 ][ k ] + stheta * a[ j - 1 ][ k ];
-                a[ j - 1 ][ k ] = ctheta * a[ j - 1 ][ k ] - stheta * a[ i - 1 ][ k ];
+                d = ( ctheta * a[ i - 1 ][ k ] ) + ( stheta * a[ j - 1 ][ k ] );
+                a[ j - 1 ][ k ] = ( ctheta * a[ j - 1 ][ k ] ) - ( stheta * a[ i - 1 ][ k ] );
                 a[ i - 1 ][ k ] = d;
             }
             else {
-                d = ctheta * a[ k ][ i - 1 ] + stheta * a[ k ][ j - 1 ];
-                a[ k ][ j - 1 ] = ctheta * a[ k ][ j - 1 ] - stheta * a[ k ][ i - 1 ];
+                d = ( ctheta * a[ k ][ i - 1 ] ) + ( stheta * a[ k ][ j - 1 ] );
+                a[ k ][ j - 1 ] = ( ctheta * a[ k ][ j - 1 ] ) - ( stheta * a[ k ][ i - 1 ] );
                 a[ k ][ i - 1 ] = d;
             }
         }