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Added @cdk.iooptions to all IO classes

Change-Id: I7e81241212d1b734fb6df9cdf460ba0cb5c76b6a
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1 parent 1dc58bf commit 086b8c88fee0e426e19b3b05cebadc7bc6f886ac @egonw egonw committed Aug 6, 2012
Showing with 49 additions and 1 deletion.
  1. +1 −0 src/main/org/openscience/cdk/io/CDKSourceCodeWriter.java
  2. +1 −0 src/main/org/openscience/cdk/io/CIFReader.java
  3. +1 −0 src/main/org/openscience/cdk/io/CMLReader.java
  4. +1 −0 src/main/org/openscience/cdk/io/CTXReader.java
  5. +1 −0 src/main/org/openscience/cdk/io/CrystClustReader.java
  6. +1 −0 src/main/org/openscience/cdk/io/CrystClustWriter.java
  7. +1 −0 src/main/org/openscience/cdk/io/GamessReader.java
  8. +1 −0 src/main/org/openscience/cdk/io/Gaussian03Reader.java
  9. +1 −0 src/main/org/openscience/cdk/io/Gaussian98Reader.java
  10. +1 −0 src/main/org/openscience/cdk/io/GhemicalMMReader.java
  11. +1 −0 src/main/org/openscience/cdk/io/HINReader.java
  12. +1 −0 src/main/org/openscience/cdk/io/HINWriter.java
  13. +1 −0 src/main/org/openscience/cdk/io/INChIPlainTextReader.java
  14. +1 −0 src/main/org/openscience/cdk/io/INChIReader.java
  15. +1 −0 src/main/org/openscience/cdk/io/MDLRXNReader.java
  16. +2 −1 src/main/org/openscience/cdk/io/MDLRXNV2000Reader.java
  17. +1 −0 src/main/org/openscience/cdk/io/MDLRXNV3000Reader.java
  18. +1 −0 src/main/org/openscience/cdk/io/MDLRXNWriter.java
  19. +1 −0 src/main/org/openscience/cdk/io/MDLReader.java
  20. +1 −0 src/main/org/openscience/cdk/io/MDLV2000Reader.java
  21. +1 −0 src/main/org/openscience/cdk/io/MDLV2000Writer.java
  22. +1 −0 src/main/org/openscience/cdk/io/MDLV3000Reader.java
  23. +1 −0 src/main/org/openscience/cdk/io/MoSSOutputReader.java
  24. +1 −0 src/main/org/openscience/cdk/io/Mol2Reader.java
  25. +1 −0 src/main/org/openscience/cdk/io/Mol2Writer.java
  26. +1 −0 src/main/org/openscience/cdk/io/PCCompoundASNReader.java
  27. +1 −0 src/main/org/openscience/cdk/io/PCCompoundXMLReader.java
  28. +1 −0 src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java
  29. +1 −0 src/main/org/openscience/cdk/io/PDBReader.java
  30. +1 −0 src/main/org/openscience/cdk/io/PDBWriter.java
  31. +1 −0 src/main/org/openscience/cdk/io/PMPReader.java
  32. +1 −0 src/main/org/openscience/cdk/io/RGroupQueryReader.java
  33. +1 −0 src/main/org/openscience/cdk/io/RGroupQueryWriter.java
  34. +1 −0 src/main/org/openscience/cdk/io/RssWriter.java
  35. +1 −0 src/main/org/openscience/cdk/io/SDFWriter.java
  36. +1 −0 src/main/org/openscience/cdk/io/SMILESReader.java
  37. +1 −0 src/main/org/openscience/cdk/io/SMILESWriter.java
  38. +1 −0 src/main/org/openscience/cdk/io/ShelXReader.java
  39. +1 −0 src/main/org/openscience/cdk/io/ShelXWriter.java
  40. +1 −0 src/main/org/openscience/cdk/io/VASPReader.java
  41. +1 −0 src/main/org/openscience/cdk/io/XYZReader.java
  42. +1 −0 src/main/org/openscience/cdk/io/XYZWriter.java
  43. +1 −0 src/main/org/openscience/cdk/io/ZMatrixReader.java
  44. +1 −0 src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java
  45. +1 −0 src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java
  46. +1 −0 src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReader.java
  47. +1 −0 src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
  48. +1 −0 src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
@@ -70,6 +70,7 @@
* @cdk.created 2003-10-01
*
* @cdk.keyword file format, CDK source code
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.CDKSourceCodeWriterTest")
public class CDKSourceCodeWriter extends DefaultChemObjectWriter {
@@ -72,6 +72,7 @@
*
* @author E.L. Willighagen
* @cdk.created 2003-10-12
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.CIFReaderTest")
public class CIFReader extends DefaultChemObjectReader {
@@ -61,6 +61,7 @@
* @cdk.githash
* @cdk.keyword file format, CML
* @cdk.bug 1544406
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.CMLReaderTest")
public class CMLReader extends DefaultChemObjectReader {
@@ -55,6 +55,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.CTXReaderTest")
public class CTXReader extends DefaultChemObjectReader {
@@ -48,6 +48,7 @@
/**
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.CrystClustReaderTest")
public class CrystClustReader extends DefaultChemObjectReader {
@@ -50,6 +50,7 @@
*
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.CrystClustWriterTest")
public class CrystClustWriter extends DefaultChemObjectWriter {
@@ -88,6 +88,7 @@
* @cdk.keyword file format
* @cdk.keyword output
* @cdk.keyword log file
+ * @cdk.iooptions
*
* @author Bradley A. Smith
*
@@ -70,6 +70,7 @@
* @author Egon Willighagen
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*/
public class Gaussian03Reader extends DefaultChemObjectReader {
@@ -74,6 +74,7 @@
* @author Christoph Steinbeck
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.Gaussian98ReaderTest")
public class Gaussian98Reader extends DefaultChemObjectReader {
@@ -58,6 +58,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen <egonw@sci.kun.nl>
*/
@@ -57,6 +57,7 @@
* @cdk.created 2004-01-27
*
* @cdk.keyword file format, HIN
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.HINReaderTest")
public class HINReader extends DefaultChemObjectReader {
@@ -53,6 +53,7 @@
* @cdk.module io
* @cdk.githash
* @cdk.created 2004-01-27
+ * @cdk.iooptions
*/
@TestClass("org.openscience.cdk.io.HINWriterTest")
public class HINWriter extends DefaultChemObjectWriter {
@@ -64,6 +64,7 @@
*
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen <egonw@sci.kun.nl>
* @cdk.created 2004-08-01
@@ -57,6 +57,7 @@
*
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen <egonw@sci.kun.nl>
* @cdk.created 2004-05-17
@@ -61,6 +61,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen
* @cdk.created 2003-07-24
@@ -59,7 +59,8 @@
* Reads a molecule from an MDL RXN file {@cdk.cite DAL92}.
* This MDL RXN reader uses the MDLV2000 reader to read each mol file
* @cdk.module io
- * @cdk.githash
+ * @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen
* @author Thomas Kuhn
@@ -51,6 +51,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen <egonw@sci.kun.nl>
* @cdk.created 2003-10-05
@@ -71,6 +71,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, MDL RXN file
*/
@@ -75,6 +75,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author steinbeck
* @author Egon Willighagen
@@ -90,6 +90,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author steinbeck
* @author Egon Willighagen
@@ -89,6 +89,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
* @cdk.keyword file format, MDL molfile
*/
@TestClass("org.openscience.cdk.io.MDLV2000WriterTest")
@@ -60,6 +60,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen <egonw@users.sf.net>
* @cdk.created 2006
@@ -58,6 +58,7 @@
*
* @cdk.module smiles
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword MoSS
*/
@@ -61,6 +61,7 @@
* @author Egon Willighagen
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
* @cdk.created 2003-08-21
* @cdk.keyword file format, Mol2
*/
@@ -49,6 +49,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen
*/
@@ -57,6 +57,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, PubChem Compound ASN
*/
@@ -49,6 +49,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, PubChem Compound XML
*/
@@ -49,6 +49,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, PubChem Compound ASN
*/
@@ -77,6 +77,7 @@
*
* @cdk.module pdb
* @cdk.githash
+ * @cdk.iooptions
*
* @author Edgar Luttmann
* @author Bradley Smith <bradley@baysmith.com>
@@ -62,6 +62,7 @@
*
* @author Gilleain Torrance <gilleain.torrance@gmail.com>
* @cdk.module io
+ * @cdk.iooptions
* @cdk.githash
*/
@TestClass("org.openscience.cdk.io.PDBWriterTest")
@@ -65,6 +65,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, Polymorph Predictor (tm)
*
@@ -66,6 +66,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword Rgroup
* @cdk.keyword R group
@@ -57,6 +57,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
* @cdk.keyword Rgroup
* @cdk.keyword R group
* @cdk.keyword R-group
@@ -48,6 +48,7 @@
*
* @cdk.module libiocml
* @cdk.githash
+ * @cdk.iooptions
* @cdk.builddepends xom-1.0.jar
*
* @author Stefan Kuhn
@@ -62,6 +62,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
* @cdk.keyword file format, MDL SD file
*/
@TestClass("org.openscience.cdk.io.SDFWriterTest")
@@ -66,6 +66,7 @@
*
* @cdk.module smiles
* @cdk.githash
+ * @cdk.iooptions
* @cdk.keyword file format, SMILES
*
* @see org.openscience.cdk.io.iterator.IteratingSMILESReader
@@ -55,6 +55,7 @@
*
* @cdk.module smiles
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, SMILES
*/
@@ -66,6 +66,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, ShelXL
* @author E.L. Willighagen
@@ -55,6 +55,7 @@
*
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen
*
@@ -57,6 +57,7 @@
*
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*
* @author Fabian Dortu <Fabian.Dortu@wanadoo.be>
*/
@@ -61,6 +61,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, XYZ
*/
@@ -48,6 +48,7 @@
/**
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Bradley A. Smith <bradley@baysmith.com>
* @author J. Daniel Gezelter
@@ -48,6 +48,7 @@
*
* @cdk.module extra
* @cdk.githash
+ * @cdk.iooptions
*
* @cdk.keyword file format, Z-matrix
*/
@@ -85,6 +85,7 @@
*
* @cdk.keyword file format, MDL molfile
* @cdk.keyword file format, SDF
+ * @cdk.iooptions
*/
public class IteratingMDLReader extends DefaultIteratingChemObjectReader<IAtomContainer>
implements IChemObjectIOListener {
@@ -49,6 +49,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @see org.openscience.cdk.io.PCCompoundASNReader
*
@@ -47,6 +47,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @see org.openscience.cdk.io.PCCompoundASNReader
*
@@ -47,6 +47,7 @@
*
* @cdk.module io
* @cdk.githash
+ * @cdk.iooptions
*
* @author Egon Willighagen <egonw@users.sf.net>
* @cdk.created 2008-05-05
@@ -57,6 +57,7 @@
*
* @cdk.module smiles
* @cdk.githash
+ * @cdk.iooptions
*
* @see org.openscience.cdk.io.SMILESReader
*

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