From: Egon W. <eg...@us...> - 2003-04-11 10:01:06
|
Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/geometry In directory sc8-pr-cvs1:/tmp/cvs-serv4608/src/org/openscience/cdk/geometry Modified Files: GeometryTools.java Log Message: Added some debug information Index: GeometryTools.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/geometry/GeometryTools.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- GeometryTools.java 10 Apr 2003 15:14:12 -0000 1.14 +++ GeometryTools.java 11 Apr 2003 10:00:55 -0000 1.15 @@ -29,6 +29,7 @@ import javax.vecmath.*; import org.openscience.cdk.*; +import org.openscience.cdk.tools.LoggingTool; import java.awt.Dimension; import java.util.Vector; @@ -38,6 +39,12 @@ */ public class GeometryTools { + private static LoggingTool logger = null; + + static { + if (logger == null) logger = new LoggingTool("org.openscience.cdk.geometry.GeometryTools"); + } + /** * Adds an automatically calculated offset to the coordinates of all atoms * such that all coordinates are positive and the smallest x or y coordinate @@ -45,25 +52,23 @@ * * @param molecule for which all the atoms are translated to positive coordinates */ - public static void translateAllPositive(AtomContainer atomCon) - { - double transX = Double.MAX_VALUE, transY = Double.MAX_VALUE; - for (int i = 0; i < atomCon.getAtomCount(); i++) - { - if (atomCon.getAtomAt(i).getPoint2D() != null) - { - if (atomCon.getAtomAt(i).getPoint2D().x < transX) - { - transX = atomCon.getAtomAt(i).getPoint2D().x; - } - if (atomCon.getAtomAt(i).getPoint2D().y < transY) - { - transY = atomCon.getAtomAt(i).getPoint2D().y; - } - } - } - translate2D(atomCon,transX * -1,transY * -1); - } + public static void translateAllPositive(AtomContainer atomCon) { + double minX = Double.MAX_VALUE, + minY = Double.MAX_VALUE; + Atom[] atoms = atomCon.getAtoms(); + for (int i = 0; i < atoms.length; i++) { + if (atoms[i].getPoint2D() != null) { + if (atoms[i].getPoint2D().x < minX) { + minX = atoms[i].getPoint2D().x; + } + if (atoms[i].getPoint2D().y < minY) { + minY = atoms[i].getPoint2D().y; + } + } + } + logger.debug("Translating: minx=" + minX + ", minY=" + minY); + translate2D(atomCon, minX * -1, minY * -1); + } /** @@ -192,16 +197,16 @@ * @param atomCon molecule to be translated * @param vector dimension that represents the translation vector */ - public static void translate2D(AtomContainer atomCon, Vector2d vector) - { - for (int i = 0; i < atomCon.getAtomCount(); i++) - { - if (atomCon.getAtomAt(i).getPoint2D() != null) - { - atomCon.getAtomAt(i).getPoint2D().add(vector); - } - } - } + public static void translate2D(AtomContainer atomCon, Vector2d vector) { + Atom[] atoms = atomCon.getAtoms(); + for (int i = 0; i < atoms.length; i++) { + if (atoms[i].getPoint2D() != null) { + atoms[i].getPoint2D().add(vector); + } else { + logger.warn("Could not translate atom in 2D space"); + } + } + } /** * Translates a molecule from the origin to a new point denoted by a vector. |