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[Cdk-commits] CVS: cdk/src/org/openscience/cdk/io CIFReader.java,1.18,1.19 INChIReader.java,1.10,1.11 MACiEReader.java,1.38,1.39 MDLRXNReader.java,1.22,1.23 MDLRXNV3000Reader.java,1.18,1.19 MDLReader.java,1.72,1.73 MDLV3000Reader.java,1.21,1.22 MDLWriter.java,1.45,1.46 PDBReader.java,1.26,1.27 PMPReader.java,1.25,1.26 SMILESWriter.java,1.18,1.19 SVGWriter.java,1.22,1.23 ShelXReader.java,1.25,1.26 VASPReader.java,1.20,1.21
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From: Egon W. <eg...@us...> - 2005-01-13 09:40:45
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/io In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17593/src/org/openscience/cdk/io Modified Files: CIFReader.java INChIReader.java MACiEReader.java MDLRXNReader.java MDLRXNV3000Reader.java MDLReader.java MDLV3000Reader.java MDLWriter.java PDBReader.java PMPReader.java SMILESWriter.java SVGWriter.java ShelXReader.java VASPReader.java Log Message: Removed use of deprecated LoggingTool methods (and added a new contructor for easier use in static classes) Index: CIFReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/CIFReader.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- CIFReader.java 12 Jan 2005 15:21:10 -0000 1.18 +++ CIFReader.java 13 Jan 2005 09:39:48 -0000 1.19 @@ -46,11 +46,12 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.*; import org.openscience.cdk.geometry.CrystalGeometryTools; - +import org.openscience.cdk.tools.LoggingTool; /** * This is not a reader for the CIF and mmCIF crystallographic formats. - * It is able, however, to extract some content from it. It's very ad hoc, not written + * It is able, however, to extract some content from such files. + * It's very ad hoc, not written * using any dictionary. So please complain if something is not working. * In addition, the things it does read are considered experimental. * @@ -68,7 +69,7 @@ public class CIFReader extends DefaultChemObjectReader { private BufferedReader input; - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; private Crystal crystal = null; // cell parameters @@ -86,7 +87,7 @@ */ public CIFReader(Reader input) { this.input = new BufferedReader(input); - this.logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + this.logger = new LoggingTool(this); } public CIFReader() { Index: INChIReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/INChIReader.java,v retrieving revision 1.10 retrieving revision 1.11 diff -u -r1.10 -r1.11 --- INChIReader.java 12 Jan 2005 15:21:11 -0000 1.10 +++ INChIReader.java 13 Jan 2005 09:39:48 -0000 1.11 @@ -37,6 +37,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.*; import org.openscience.cdk.io.inchi.INChIHandler; +import org.openscience.cdk.tools.LoggingTool; import org.xml.sax.InputSource; import org.xml.sax.SAXException; import org.xml.sax.XMLReader; @@ -65,7 +66,7 @@ private XMLReader parser; private Reader input; - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; /** * Construct a INChI reader from a Reader object. @@ -94,7 +95,7 @@ * Initializes this reader. */ private void init() { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); boolean success = false; // If JAXP is prefered (comes with Sun JVM 1.4.0 and higher) if (!success) { Index: MACiEReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MACiEReader.java,v retrieving revision 1.38 retrieving revision 1.39 diff -u -r1.38 -r1.39 --- MACiEReader.java 12 Jan 2005 15:21:11 -0000 1.38 +++ MACiEReader.java 13 Jan 2005 09:39:48 -0000 1.39 @@ -90,7 +90,7 @@ public final static String EnzymeName = "org.openscience.cdk.io.MACiE.EnzymeName"; private LineNumberReader input = null; - private org.openscience.cdk.tools.LoggingTool logger = null; + private LoggingTool logger = null; private IntegerIOSetting selectedEntry; private BooleanIOSetting readSecondaryFiles; Index: MDLRXNReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLRXNReader.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- MDLRXNReader.java 12 Jan 2005 15:21:11 -0000 1.22 +++ MDLRXNReader.java 13 Jan 2005 09:39:48 -0000 1.23 @@ -45,6 +45,7 @@ import org.openscience.cdk.SetOfReactions; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.*; +import org.openscience.cdk.tools.LoggingTool; /** * Reads a molecule from an MDL RXN file {@cdk.cite DAL92}. @@ -59,7 +60,7 @@ public class MDLRXNReader extends DefaultChemObjectReader { BufferedReader input = null; - private org.openscience.cdk.tools.LoggingTool logger = null; + private LoggingTool logger = null; /** * Contructs a new MDLReader that can read Molecule from a given Reader. @@ -67,7 +68,7 @@ * @param in The Reader to read from */ public MDLRXNReader(Reader in) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); input = new BufferedReader(in); } Index: MDLRXNV3000Reader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLRXNV3000Reader.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- MDLRXNV3000Reader.java 12 Jan 2005 15:21:11 -0000 1.18 +++ MDLRXNV3000Reader.java 13 Jan 2005 09:39:48 -0000 1.19 @@ -60,7 +60,7 @@ private LoggingTool logger = null; public MDLRXNV3000Reader(Reader in) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); input = new BufferedReader(in); initIOSettings(); } Index: MDLReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLReader.java,v retrieving revision 1.72 retrieving revision 1.73 diff -u -r1.72 -r1.73 --- MDLReader.java 12 Jan 2005 15:21:11 -0000 1.72 +++ MDLReader.java 13 Jan 2005 09:39:48 -0000 1.73 @@ -80,7 +80,7 @@ public class MDLReader extends DefaultChemObjectReader { BufferedReader input = null; - private org.openscience.cdk.tools.LoggingTool logger = null; + private LoggingTool logger = null; private IsotopeFactory isotopeFactory = null; private BooleanIOSetting forceReadAs3DCoords; Index: MDLV3000Reader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLV3000Reader.java,v retrieving revision 1.21 retrieving revision 1.22 diff -u -r1.21 -r1.22 --- MDLV3000Reader.java 12 Jan 2005 15:21:11 -0000 1.21 +++ MDLV3000Reader.java 13 Jan 2005 09:39:48 -0000 1.22 @@ -79,7 +79,7 @@ private Pattern keyValueTuple2; public MDLV3000Reader(Reader in) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); input = new BufferedReader(in); initIOSettings(); try { Index: MDLWriter.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/MDLWriter.java,v retrieving revision 1.45 retrieving revision 1.46 diff -u -r1.45 -r1.46 --- MDLWriter.java 12 Jan 2005 15:21:11 -0000 1.45 +++ MDLWriter.java 13 Jan 2005 09:39:48 -0000 1.46 @@ -46,6 +46,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.*; import org.openscience.cdk.config.IsotopeFactory; +import org.openscience.cdk.tools.LoggingTool; @@ -67,7 +68,7 @@ public class MDLWriter extends DefaultChemObjectWriter { private BufferedWriter writer; - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; private IsotopeFactory isotopeFactory = null; /** @@ -92,7 +93,7 @@ */ public MDLWriter(Writer out) { writer = new BufferedWriter(out); - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); try { isotopeFactory = IsotopeFactory.getInstance(); } catch (Exception exception) { Index: PDBReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/PDBReader.java,v retrieving revision 1.26 retrieving revision 1.27 diff -u -r1.26 -r1.27 --- PDBReader.java 12 Jan 2005 15:21:11 -0000 1.26 +++ PDBReader.java 13 Jan 2005 09:39:48 -0000 1.27 @@ -66,7 +66,7 @@ */ public class PDBReader extends DefaultChemObjectReader { - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; private BufferedReader _oInput; // The internal used BufferedReader /** @@ -90,7 +90,7 @@ * */ public PDBReader(Reader oIn) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); _oInput = new BufferedReader(oIn); } Index: PMPReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/PMPReader.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- PMPReader.java 12 Jan 2005 15:21:12 -0000 1.25 +++ PMPReader.java 13 Jan 2005 09:39:48 -0000 1.26 @@ -52,6 +52,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.*; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; +import org.openscience.cdk.tools.LoggingTool; /** * Reads an frames from a PMP formated input. @@ -68,7 +69,7 @@ private BufferedReader input; - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; /* Keep a copy of the PMP model */ private SetOfMolecules som; @@ -91,7 +92,7 @@ */ public PMPReader(Reader input) { this.input = new BufferedReader(input); - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); /* compile patterns */ objHeader = Pattern.compile(".*\\((\\d+)\\s(\\w+)$"); Index: SMILESWriter.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/SMILESWriter.java,v retrieving revision 1.18 retrieving revision 1.19 diff -u -r1.18 -r1.19 --- SMILESWriter.java 12 Jan 2005 15:21:12 -0000 1.18 +++ SMILESWriter.java 13 Jan 2005 09:39:48 -0000 1.19 @@ -40,6 +40,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.*; import org.openscience.cdk.smiles.SmilesGenerator; +import org.openscience.cdk.tools.LoggingTool; /** * Writes the SMILES strings to a plain text file. @@ -50,7 +51,7 @@ */ public class SMILESWriter extends DefaultChemObjectWriter { - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; static BufferedWriter writer; /** @@ -59,7 +60,7 @@ * @param out The Writer to write to */ public SMILESWriter(Writer out) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); try { writer = new BufferedWriter(out); } catch (Exception exc) { Index: SVGWriter.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/SVGWriter.java,v retrieving revision 1.22 retrieving revision 1.23 diff -u -r1.22 -r1.23 --- SVGWriter.java 12 Jan 2005 15:21:12 -0000 1.22 +++ SVGWriter.java 13 Jan 2005 09:39:48 -0000 1.23 @@ -48,6 +48,7 @@ import org.openscience.cdk.io.formats.*; import org.openscience.cdk.geometry.GeometryTools; import org.openscience.cdk.renderer.Renderer2D; +import org.openscience.cdk.tools.LoggingTool; import org.w3c.dom.DOMImplementation; import org.w3c.dom.Document; @@ -74,7 +75,7 @@ */ public class SVGWriter extends DefaultChemObjectWriter { - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; static BufferedWriter writer; /** @@ -83,7 +84,7 @@ * @param out The Writer to write to */ public SVGWriter(Writer out) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); try { writer = new BufferedWriter(out); } catch (Exception exc) { Index: ShelXReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/ShelXReader.java,v retrieving revision 1.25 retrieving revision 1.26 diff -u -r1.25 -r1.26 --- ShelXReader.java 12 Jan 2005 15:21:12 -0000 1.25 +++ ShelXReader.java 13 Jan 2005 09:39:48 -0000 1.26 @@ -47,6 +47,7 @@ import org.openscience.cdk.io.formats.*; import org.openscience.cdk.geometry.CrystalGeometryTools; import org.openscience.cdk.math.FortranFormat; +import org.openscience.cdk.tools.LoggingTool; /** @@ -68,7 +69,7 @@ public class ShelXReader extends DefaultChemObjectReader { private BufferedReader input; - private org.openscience.cdk.tools.LoggingTool logger; + private LoggingTool logger; /** * Create an ShelX file reader. @@ -77,7 +78,7 @@ */ public ShelXReader(Reader input) { this.input = new BufferedReader(input); - this.logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + this.logger = new LoggingTool(this); } public ShelXReader() { Index: VASPReader.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/io/VASPReader.java,v retrieving revision 1.20 retrieving revision 1.21 diff -u -r1.20 -r1.21 --- VASPReader.java 12 Jan 2005 15:21:12 -0000 1.20 +++ VASPReader.java 13 Jan 2005 09:39:48 -0000 1.21 @@ -83,7 +83,7 @@ * @param input a <code>Reader</code> value */ public VASPReader(Reader input) { - logger = new org.openscience.cdk.tools.LoggingTool(this.getClass().getName()); + logger = new LoggingTool(this); try { isotopeFac = IsotopeFactory.getInstance(); } catch (Exception exception) { |