From: <eg...@us...> - 2006-05-10 05:06:08
|
Revision: 6206 Author: egonw Date: 2006-05-09 22:05:30 -0700 (Tue, 09 May 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6206&view=rev Log Message: ----------- Fixed compile errors: updated for new IO API. Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/io/CDKSourceCodeWriter.java trunk/cdk/src/org/openscience/cdk/io/CIFReader.java trunk/cdk/src/org/openscience/cdk/io/CMLReader.java trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java trunk/cdk/src/org/openscience/cdk/io/CrystClustReader.java trunk/cdk/src/org/openscience/cdk/io/CrystClustWriter.java trunk/cdk/src/org/openscience/cdk/io/GamessReader.java trunk/cdk/src/org/openscience/cdk/io/Gaussian03Reader.java trunk/cdk/src/org/openscience/cdk/io/Gaussian98Reader.java trunk/cdk/src/org/openscience/cdk/io/GhemicalMMReader.java trunk/cdk/src/org/openscience/cdk/io/HINReader.java trunk/cdk/src/org/openscience/cdk/io/HINWriter.java trunk/cdk/src/org/openscience/cdk/io/INChIPlainTextReader.java trunk/cdk/src/org/openscience/cdk/io/INChIReader.java trunk/cdk/src/org/openscience/cdk/io/JMEReader.java trunk/cdk/src/org/openscience/cdk/io/MACiEReader.java trunk/cdk/src/org/openscience/cdk/io/MDLRXNReader.java trunk/cdk/src/org/openscience/cdk/io/MDLRXNV3000Reader.java trunk/cdk/src/org/openscience/cdk/io/MDLRXNWriter.java trunk/cdk/src/org/openscience/cdk/io/MDLReader.java trunk/cdk/src/org/openscience/cdk/io/MDLV3000Reader.java trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java trunk/cdk/src/org/openscience/cdk/io/Mol2Writer.java trunk/cdk/src/org/openscience/cdk/io/PDBReader.java trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java trunk/cdk/src/org/openscience/cdk/io/PMPReader.java trunk/cdk/src/org/openscience/cdk/io/RssWriter.java trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java trunk/cdk/src/org/openscience/cdk/io/ShelXReader.java trunk/cdk/src/org/openscience/cdk/io/ShelXWriter.java trunk/cdk/src/org/openscience/cdk/io/VASPReader.java trunk/cdk/src/org/openscience/cdk/io/XYZReader.java trunk/cdk/src/org/openscience/cdk/io/XYZWriter.java trunk/cdk/src/org/openscience/cdk/io/ZMatrixReader.java trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingMDLReader.java trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java trunk/cdk/src/org/openscience/cdk/io/iterator/event/EventCMLReader.java trunk/cdk/src/org/openscience/cdk/io/program/GaussianInputWriter.java Modified: trunk/cdk/src/org/openscience/cdk/io/CDKSourceCodeWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CDKSourceCodeWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/CDKSourceCodeWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -43,6 +43,7 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.CDKSourceCodeFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.IDCreator; import org.openscience.cdk.tools.LoggingTool; @@ -92,7 +93,7 @@ public CDKSourceCodeWriter() { this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CDKSourceCodeFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/CIFReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CIFReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/CIFReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -50,6 +50,7 @@ import org.openscience.cdk.geometry.CrystalGeometryTools; import org.openscience.cdk.io.formats.CIFFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.LoggingTool; /** @@ -102,7 +103,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CIFFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/CMLReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CMLReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/CMLReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -46,6 +46,7 @@ import org.openscience.cdk.io.cml.cdopi.IChemicalDocumentObject; import org.openscience.cdk.io.formats.CMLFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.ringsearch.AllRingsFinder; import org.openscience.cdk.tools.DeAromatizationTool; import org.openscience.cdk.tools.LoggingTool; @@ -113,7 +114,7 @@ this.url = url; } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CMLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/CMLWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -54,6 +54,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.CMLFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.io.setting.StringIOSetting; @@ -144,7 +145,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CMLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/CrystClustReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CrystClustReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/CrystClustReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -46,6 +46,7 @@ import org.openscience.cdk.geometry.CrystalGeometryTools; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.CrystClustFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.math.FortranFormat; import org.openscience.cdk.tools.LoggingTool; @@ -74,7 +75,7 @@ this(new InputStreamReader(input)); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CrystClustFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/CrystClustWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/CrystClustWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/CrystClustWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -46,6 +46,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.CrystClustFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.LoggingTool; /** @@ -87,7 +88,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CrystClustFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/GamessReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/GamessReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/GamessReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -48,6 +48,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.GamessFormat; +import org.openscience.cdk.io.formats.IResourceFormat; /** @@ -157,7 +158,7 @@ */ //TODO Update comment with appropriate information to comply Constructor's documentation. - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new GamessFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/Gaussian03Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/Gaussian03Reader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/Gaussian03Reader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -51,6 +51,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.Gaussian03Format; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.LoggingTool; /** @@ -96,7 +97,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new Gaussian03Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/Gaussian98Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/Gaussian98Reader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/Gaussian98Reader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -53,6 +53,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.Gaussian98Format; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.tools.LoggingTool; @@ -103,7 +104,7 @@ this(new InputStreamReader(input)); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new Gaussian98Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/GhemicalMMReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/GhemicalMMReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/GhemicalMMReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -48,6 +48,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.GhemicalMMFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.LoggingTool; /** @@ -77,7 +78,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new GhemicalMMFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/HINReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/HINReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/HINReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -50,6 +50,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.HINFormat; +import org.openscience.cdk.io.formats.IResourceFormat; /** * Reads an object from HIN formated input. @@ -82,7 +83,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new HINFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/HINWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/HINWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/HINWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -47,6 +47,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.HINFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.tools.LoggingTool; /** @@ -86,7 +87,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new HINFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/INChIPlainTextReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/INChIPlainTextReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/INChIPlainTextReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -50,6 +50,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.INChIPlainTextFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.inchi.INChIContentProcessorTool; /** @@ -99,7 +100,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new INChIPlainTextFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/INChIReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/INChIReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/INChIReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -47,6 +47,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; import org.openscience.cdk.io.formats.INChIFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.inchi.INChIHandler; import org.openscience.cdk.tools.LoggingTool; import org.xml.sax.InputSource; @@ -104,7 +105,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new INChIFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/JMEReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/JMEReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/JMEReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -41,6 +41,7 @@ import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.JMEFormat; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.libio.jmol.Convertor; @@ -79,7 +80,7 @@ } } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new JMEFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MACiEReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MACiEReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MACiEReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -61,6 +61,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MACiEFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; @@ -147,7 +148,7 @@ initIOSettings(); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MACiEFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MDLRXNReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLRXNReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MDLRXNReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -50,6 +50,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLRXNFormat; import org.openscience.cdk.tools.LoggingTool; @@ -86,7 +87,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLRXNFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MDLRXNV3000Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLRXNV3000Reader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MDLRXNV3000Reader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -45,6 +45,7 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLRXNV3000Format; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.tools.LoggingTool; @@ -82,7 +83,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLRXNV3000Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MDLRXNWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLRXNWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MDLRXNWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -51,6 +51,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; import org.openscience.cdk.tools.LoggingTool; @@ -110,7 +111,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MDLReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MDLReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -44,6 +44,7 @@ import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; @@ -96,7 +97,7 @@ this(new InputStreamReader(in)); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MDLV3000Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLV3000Reader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MDLV3000Reader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -56,6 +56,7 @@ import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLV3000Format; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.tools.LoggingTool; @@ -104,7 +105,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLV3000Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MDLWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -60,6 +60,7 @@ import org.openscience.cdk.interfaces.IReaction; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.ChemFileManipulator; @@ -137,7 +138,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/MOPAC97Reader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -35,6 +35,7 @@ import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MOPAC97Format; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.libio.jmol.Convertor; @@ -66,7 +67,7 @@ } } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MOPAC97Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/Mol2Reader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -53,6 +53,7 @@ import org.openscience.cdk.config.AtomTypeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.Mol2Format; import org.openscience.cdk.tools.LoggingTool; @@ -90,7 +91,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new Mol2Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/Mol2Writer.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/Mol2Writer.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/Mol2Writer.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -43,6 +43,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.Mol2Format; import org.openscience.cdk.tools.LoggingTool; @@ -80,7 +81,7 @@ this(new OutputStreamWriter(output)); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new Mol2Format(); } Modified: trunk/cdk/src/org/openscience/cdk/io/PDBReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/PDBReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/PDBReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -52,6 +52,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.IStrand; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PDBFormat; import org.openscience.cdk.protein.data.PDBAtom; import org.openscience.cdk.protein.data.PDBMonomer; @@ -110,7 +111,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new PDBFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/PDBWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -44,6 +44,7 @@ import org.openscience.cdk.interfaces.ICrystal; import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PDBFormat; import org.openscience.cdk.tools.FormatStringBuffer; import org.openscience.cdk.tools.LoggingTool; @@ -81,7 +82,7 @@ this(new OutputStreamWriter(output)); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new PDBFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/PMPReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/PMPReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/PMPReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -56,6 +56,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.PMPFormat; import org.openscience.cdk.tools.LoggingTool; import org.openscience.cdk.tools.manipulator.ChemModelManipulator; @@ -117,7 +118,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new PMPFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/RssWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/RssWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/RssWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -40,6 +40,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.CMLRSSFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.libio.cml.Convertor; /** @@ -82,7 +83,7 @@ writer.close(); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CMLRSSFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/SMILESReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -48,6 +48,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.LoggingTool; @@ -94,7 +95,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new SMILESFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/SMILESWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -49,6 +49,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.smiles.SmilesGenerator; import org.openscience.cdk.tools.LoggingTool; @@ -90,7 +91,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new SMILESFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/ShelXReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/ShelXReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/ShelXReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -52,6 +52,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.CrystalGeometryTools; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.ShelXFormat; import org.openscience.cdk.math.FortranFormat; import org.openscience.cdk.tools.LoggingTool; @@ -96,7 +97,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new ShelXFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/ShelXWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/ShelXWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/ShelXWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -50,6 +50,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.ShelXFormat; import org.openscience.cdk.tools.FormatStringBuffer; import org.openscience.cdk.tools.LoggingTool; @@ -96,7 +97,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new ShelXFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/VASPReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/VASPReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/VASPReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -49,6 +49,7 @@ import org.openscience.cdk.config.IsotopeFactory; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.VASPFormat; import org.openscience.cdk.math.FortranFormat; import org.openscience.cdk.tools.LoggingTool; @@ -104,7 +105,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new VASPFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/XYZReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/XYZReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/XYZReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -52,6 +52,7 @@ import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.XYZFormat; import org.openscience.cdk.tools.LoggingTool; @@ -87,7 +88,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new XYZFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/XYZWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/XYZWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/XYZWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -46,6 +46,7 @@ import org.openscience.cdk.interfaces.ISetOfMolecules; import org.openscience.cdk.interfaces.ISetOfReactions; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.XYZFormat; import org.openscience.cdk.tools.LoggingTool; @@ -85,7 +86,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new XYZFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/ZMatrixReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/ZMatrixReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/ZMatrixReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -53,6 +53,7 @@ import org.openscience.cdk.exception.CDKException; import org.openscience.cdk.geometry.ZMatrixTools; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.ZMatrixFormat; /** @@ -86,7 +87,7 @@ this(new StringReader("")); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new ZMatrixFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingMDLReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingMDLReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingMDLReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -39,6 +39,7 @@ import org.openscience.cdk.interfaces.IMolecule; import org.openscience.cdk.io.MDLReader; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.MDLFormat; import org.openscience.cdk.tools.LoggingTool; @@ -93,7 +94,7 @@ this(new InputStreamReader(in), builder); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new MDLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/iterator/IteratingSMILESReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -36,6 +36,7 @@ import org.openscience.cdk.Molecule; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.formats.SMILESFormat; import org.openscience.cdk.smiles.SmilesParser; import org.openscience.cdk.tools.LoggingTool; @@ -91,7 +92,7 @@ this(new InputStreamReader(in)); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new SMILESFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/iterator/event/EventCMLReader.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/iterator/event/EventCMLReader.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/iterator/event/EventCMLReader.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -39,6 +39,7 @@ import org.openscience.cdk.io.cml.CMLResolver; import org.openscience.cdk.io.formats.CMLFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.listener.IReaderListener; import org.openscience.cdk.tools.LoggingTool; import org.xml.sax.InputSource; @@ -83,7 +84,7 @@ this.addChemObjectIOListener(listener); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new CMLFormat(); } Modified: trunk/cdk/src/org/openscience/cdk/io/program/GaussianInputWriter.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/io/program/GaussianInputWriter.java 2006-05-09 19:54:03 UTC (rev 6205) +++ trunk/cdk/src/org/openscience/cdk/io/program/GaussianInputWriter.java 2006-05-10 05:05:30 UTC (rev 6206) @@ -43,6 +43,7 @@ import org.openscience.cdk.io.DefaultChemObjectWriter; import org.openscience.cdk.io.formats.GaussianInputFormat; import org.openscience.cdk.io.formats.IChemFormat; +import org.openscience.cdk.io.formats.IResourceFormat; import org.openscience.cdk.io.setting.BooleanIOSetting; import org.openscience.cdk.io.setting.IOSetting; import org.openscience.cdk.io.setting.IntegerIOSetting; @@ -96,7 +97,7 @@ this(new StringWriter()); } - public IChemFormat getFormat() { + public IResourceFormat getFormat() { return new GaussianInputFormat(); } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |