if ( !isEqual( matrix_0.getValue( 0, 0 ), 0.0 ) ) { return false; if ( !isEqual( matrix_0.getValue( 3, 3 ), 0.0 ) ) { return false; if ( !isEqual( matrix_0.getValue( 0, 1 ), 0.00001 ) ) { return false; if ( !isEqual( matrix_0.getValue( 0, 2 ), 0.0000009 ) ) { return false; if ( !isEqual( matrix_0.getValue( 0, 3 ), 3 ) ) { return false; if ( !isEqual( matrix_0.getValue( 1, 0 ), 0.00001 ) ) { return false; if ( !isEqual( matrix_0.getValue( 1, 2 ), 4 ) ) { return false; if ( !isEqual( matrix_0.getValue( 1, 3 ), 5 ) ) { return false; if ( !isEqual( matrix_0.getValue( 2, 0 ), 0.0000009 ) ) { return false; if ( !isEqual( matrix_0.getValue( 2, 1 ), 4 ) ) { return false;
if ( !isEqual( ma0[ 0 ].getValue( 0, 0 ), 0 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 1, 0 ), 1 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 2, 0 ), 2 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 3, 0 ), 3 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 0, 1 ), 1 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 1, 1 ), 0 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 2, 1 ), 4 ) ) { return false; if ( !isEqual( ma0[ 0 ].getValue( 3, 1 ), 5 ) ) { return false; if ( !isEqual( ma0[ 1 ].getValue( 0, 0 ), 0 ) ) { return false; if ( !isEqual( ma0[ 1 ].getValue( 1, 0 ), 11 ) ) { return false;
String nodeName2 = matrix.getIdentifier(col); PhylogenyNode node2 = externalNodesHashMap.get(nodeName2); double distance = matrix.getValue(col, row); averageMatrixDistance = averageMatrixDistance + distance; PhylogenyNode commonParent = findCommonParent(node2, path);
String nodeName2 = matrix.getIdentifier(col); PhylogenyNode node2 = externalNodesHashMap.get(nodeName2); double distance = matrix.getValue(col, row); averageMatrixDistance = averageMatrixDistance + distance; PhylogenyNode commonParent = findCommonParent(node2, path);
String nodeName2 = matrix.getIdentifier(col); PhylogenyNode node2 = externalNodesHashMap.get(nodeName2); double distance = matrix.getValue(col, row); averageMatrixDistance = averageMatrixDistance + distance; PhylogenyNode commonParent = findCommonParent(node2, path);
distance.setValue(i, j, 100 - Comparison.PID( sequenceString[i], sequenceString[j])); distance.setValue(j, i, distance.getValue(i, j));
DM.setValue(i, j, 0.0); else { double dS = Math.max(maxscore - DM.getValue(i, j), 0); DM.setValue(i, j, dS); DM.setValue(j, i, dS);
DM.setValue(i, j, 0.0); else { double dS = Math.max(maxscore - DM.getValue(i, j), 0); DM.setValue(i, j, dS); DM.setValue(j, i, dS);
DM.setValue(i, j, 0.0); else { double dS = Math.max(maxscore - DM.getValue(i, j), 0); DM.setValue(i, j, dS); DM.setValue(j, i, dS);
distance.setValue(i, j, 100 - Comparison.PID( sequenceString[i], sequenceString[j])); distance.setValue(j, i, distance.getValue(i, j));
distance.setValue(i, j, 100 - Comparison.PID( sequenceString[i], sequenceString[j])); distance.setValue(j, i, distance.getValue(i, j));