Added @cdk.iooptions to all IO classes

Change-Id: I7e81241212d1b734fb6df9cdf460ba0cb5c76b6a
cdk · Aug 6, 2012 · 086b8c8 · 086b8c8
1 parent 1dc58bf
commit 086b8c8
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Showing 48 changed files with 49 additions and 1 deletion.
diff --git a/src/main/org/openscience/cdk/io/CDKSourceCodeWriter.java b/src/main/org/openscience/cdk/io/CDKSourceCodeWriter.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 {

diff --git a/src/main/org/openscience/cdk/io/CIFReader.java b/src/main/org/openscience/cdk/io/CIFReader.java
@@ -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 {

diff --git a/src/main/org/openscience/cdk/io/CMLReader.java b/src/main/org/openscience/cdk/io/CMLReader.java
@@ -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 {

diff --git a/src/main/org/openscience/cdk/io/CTXReader.java b/src/main/org/openscience/cdk/io/CTXReader.java
@@ -55,6 +55,7 @@
  * 
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  */
 @TestClass("org.openscience.cdk.io.CTXReaderTest")
 public class CTXReader extends DefaultChemObjectReader {

diff --git a/src/main/org/openscience/cdk/io/CrystClustReader.java b/src/main/org/openscience/cdk/io/CrystClustReader.java
@@ -48,6 +48,7 @@
 /**
  * @cdk.module extra
  * @cdk.githash
+ * @cdk.iooptions
  */
 @TestClass("org.openscience.cdk.io.CrystClustReaderTest")
 public class CrystClustReader extends DefaultChemObjectReader {

diff --git a/src/main/org/openscience/cdk/io/CrystClustWriter.java b/src/main/org/openscience/cdk/io/CrystClustWriter.java
@@ -50,6 +50,7 @@
  *
  * @cdk.module extra
  * @cdk.githash
+ * @cdk.iooptions
  */
 @TestClass("org.openscience.cdk.io.CrystClustWriterTest")
 public class CrystClustWriter extends DefaultChemObjectWriter {

diff --git a/src/main/org/openscience/cdk/io/GamessReader.java b/src/main/org/openscience/cdk/io/GamessReader.java
@@ -88,6 +88,7 @@
  * @cdk.keyword file format
  * @cdk.keyword output
  * @cdk.keyword log file
+ * @cdk.iooptions
  * 
  * @author Bradley A. Smith
  * 

diff --git a/src/main/org/openscience/cdk/io/Gaussian03Reader.java b/src/main/org/openscience/cdk/io/Gaussian03Reader.java
@@ -70,6 +70,7 @@
  * @author Egon Willighagen
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  */
 public class Gaussian03Reader extends DefaultChemObjectReader {
 

diff --git a/src/main/org/openscience/cdk/io/Gaussian98Reader.java b/src/main/org/openscience/cdk/io/Gaussian98Reader.java
@@ -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 {

diff --git a/src/main/org/openscience/cdk/io/GhemicalMMReader.java b/src/main/org/openscience/cdk/io/GhemicalMMReader.java
@@ -58,6 +58,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author Egon Willighagen <egonw@sci.kun.nl>
  */

diff --git a/src/main/org/openscience/cdk/io/HINReader.java b/src/main/org/openscience/cdk/io/HINReader.java
@@ -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 {

diff --git a/src/main/org/openscience/cdk/io/HINWriter.java b/src/main/org/openscience/cdk/io/HINWriter.java
@@ -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 {

diff --git a/src/main/org/openscience/cdk/io/INChIPlainTextReader.java b/src/main/org/openscience/cdk/io/INChIPlainTextReader.java
@@ -64,6 +64,7 @@
  *
  * @cdk.module extra
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author      Egon Willighagen <egonw@sci.kun.nl>
  * @cdk.created 2004-08-01

diff --git a/src/main/org/openscience/cdk/io/INChIReader.java b/src/main/org/openscience/cdk/io/INChIReader.java
@@ -57,6 +57,7 @@
  *
  * @cdk.module extra
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author      Egon Willighagen <egonw@sci.kun.nl>
  * @cdk.created 2004-05-17

diff --git a/src/main/org/openscience/cdk/io/MDLRXNReader.java b/src/main/org/openscience/cdk/io/MDLRXNReader.java
@@ -61,6 +61,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author     Egon Willighagen
  * @cdk.created    2003-07-24

diff --git a/src/main/org/openscience/cdk/io/MDLRXNV2000Reader.java b/src/main/org/openscience/cdk/io/MDLRXNV2000Reader.java
@@ -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

diff --git a/src/main/org/openscience/cdk/io/MDLRXNV3000Reader.java b/src/main/org/openscience/cdk/io/MDLRXNV3000Reader.java
@@ -51,6 +51,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author  Egon Willighagen <egonw@sci.kun.nl>
  * @cdk.created 2003-10-05

diff --git a/src/main/org/openscience/cdk/io/MDLRXNWriter.java b/src/main/org/openscience/cdk/io/MDLRXNWriter.java
@@ -71,6 +71,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, MDL RXN file
  */

diff --git a/src/main/org/openscience/cdk/io/MDLReader.java b/src/main/org/openscience/cdk/io/MDLReader.java
@@ -75,6 +75,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author     steinbeck
  * @author     Egon Willighagen

diff --git a/src/main/org/openscience/cdk/io/MDLV2000Reader.java b/src/main/org/openscience/cdk/io/MDLV2000Reader.java
@@ -90,6 +90,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author     steinbeck
  * @author     Egon Willighagen

diff --git a/src/main/org/openscience/cdk/io/MDLV2000Writer.java b/src/main/org/openscience/cdk/io/MDLV2000Writer.java
@@ -89,6 +89,7 @@
  *
  * @cdk.module  io
  * @cdk.githash
+ * @cdk.iooptions
  * @cdk.keyword file format, MDL molfile
  */
 @TestClass("org.openscience.cdk.io.MDLV2000WriterTest")

diff --git a/src/main/org/openscience/cdk/io/MDLV3000Reader.java b/src/main/org/openscience/cdk/io/MDLV3000Reader.java
@@ -60,6 +60,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author      Egon Willighagen <egonw@users.sf.net>
  * @cdk.created 2006

diff --git a/src/main/org/openscience/cdk/io/MoSSOutputReader.java b/src/main/org/openscience/cdk/io/MoSSOutputReader.java
@@ -58,6 +58,7 @@
  *
  * @cdk.module  smiles
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword MoSS
  */

diff --git a/src/main/org/openscience/cdk/io/Mol2Reader.java b/src/main/org/openscience/cdk/io/Mol2Reader.java
@@ -61,6 +61,7 @@
  * @author Egon Willighagen
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  * @cdk.created 2003-08-21
  * @cdk.keyword file format, Mol2
  */

diff --git a/src/main/org/openscience/cdk/io/Mol2Writer.java b/src/main/org/openscience/cdk/io/Mol2Writer.java
@@ -49,6 +49,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author     Egon Willighagen
  */

diff --git a/src/main/org/openscience/cdk/io/PCCompoundASNReader.java b/src/main/org/openscience/cdk/io/PCCompoundASNReader.java
@@ -57,6 +57,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, PubChem Compound ASN
  */

diff --git a/src/main/org/openscience/cdk/io/PCCompoundXMLReader.java b/src/main/org/openscience/cdk/io/PCCompoundXMLReader.java
@@ -49,6 +49,7 @@
  *
  * @cdk.module  io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, PubChem Compound XML
  */

diff --git a/src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java b/src/main/org/openscience/cdk/io/PCSubstanceXMLReader.java
@@ -49,6 +49,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, PubChem Compound ASN
  */

diff --git a/src/main/org/openscience/cdk/io/PDBReader.java b/src/main/org/openscience/cdk/io/PDBReader.java
@@ -77,6 +77,7 @@
  *
  * @cdk.module  pdb
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author      Edgar Luttmann
  * @author      Bradley Smith <bradley@baysmith.com>

diff --git a/src/main/org/openscience/cdk/io/PDBWriter.java b/src/main/org/openscience/cdk/io/PDBWriter.java
@@ -62,6 +62,7 @@
  * 
  * @author      Gilleain Torrance <gilleain.torrance@gmail.com>
  * @cdk.module io
+ * @cdk.iooptions
  * @cdk.githash
  */
 @TestClass("org.openscience.cdk.io.PDBWriterTest")

diff --git a/src/main/org/openscience/cdk/io/PMPReader.java b/src/main/org/openscience/cdk/io/PMPReader.java
@@ -65,6 +65,7 @@
  *
  * @cdk.module  io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, Polymorph Predictor (tm)
  *

diff --git a/src/main/org/openscience/cdk/io/RGroupQueryReader.java b/src/main/org/openscience/cdk/io/RGroupQueryReader.java
@@ -66,6 +66,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword Rgroup
  * @cdk.keyword R group

diff --git a/src/main/org/openscience/cdk/io/RGroupQueryWriter.java b/src/main/org/openscience/cdk/io/RGroupQueryWriter.java
@@ -57,6 +57,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  * @cdk.keyword Rgroup
  * @cdk.keyword R group
  * @cdk.keyword R-group

diff --git a/src/main/org/openscience/cdk/io/RssWriter.java b/src/main/org/openscience/cdk/io/RssWriter.java
@@ -48,6 +48,7 @@
  *
  * @cdk.module       libiocml
  * @cdk.githash
+ * @cdk.iooptions
  * @cdk.builddepends xom-1.0.jar
  *
  * @author Stefan Kuhn

diff --git a/src/main/org/openscience/cdk/io/SDFWriter.java b/src/main/org/openscience/cdk/io/SDFWriter.java
@@ -62,6 +62,7 @@
  *
  * @cdk.module  io
  * @cdk.githash
+ * @cdk.iooptions
  * @cdk.keyword file format, MDL SD file
  */
 @TestClass("org.openscience.cdk.io.SDFWriterTest")

diff --git a/src/main/org/openscience/cdk/io/SMILESReader.java b/src/main/org/openscience/cdk/io/SMILESReader.java
@@ -66,6 +66,7 @@
  *
  * @cdk.module  smiles
  * @cdk.githash
+ * @cdk.iooptions
  * @cdk.keyword file format, SMILES
  *
  * @see org.openscience.cdk.io.iterator.IteratingSMILESReader

diff --git a/src/main/org/openscience/cdk/io/SMILESWriter.java b/src/main/org/openscience/cdk/io/SMILESWriter.java
@@ -55,6 +55,7 @@
  *
  * @cdk.module  smiles
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, SMILES
  */

diff --git a/src/main/org/openscience/cdk/io/ShelXReader.java b/src/main/org/openscience/cdk/io/ShelXReader.java
@@ -66,6 +66,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, ShelXL
  * @author E.L. Willighagen

diff --git a/src/main/org/openscience/cdk/io/ShelXWriter.java b/src/main/org/openscience/cdk/io/ShelXWriter.java
@@ -55,6 +55,7 @@
  *
  * @cdk.module  extra
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author Egon Willighagen
  *

diff --git a/src/main/org/openscience/cdk/io/VASPReader.java b/src/main/org/openscience/cdk/io/VASPReader.java
@@ -57,6 +57,7 @@
  *
  * @cdk.module extra
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author  Fabian Dortu <Fabian.Dortu@wanadoo.be>
  */

diff --git a/src/main/org/openscience/cdk/io/XYZReader.java b/src/main/org/openscience/cdk/io/XYZReader.java
@@ -61,6 +61,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, XYZ
  */

diff --git a/src/main/org/openscience/cdk/io/XYZWriter.java b/src/main/org/openscience/cdk/io/XYZWriter.java
@@ -48,6 +48,7 @@
 /**
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @author  Bradley A. Smith <bradley@baysmith.com>
  * @author  J. Daniel Gezelter

diff --git a/src/main/org/openscience/cdk/io/ZMatrixReader.java b/src/main/org/openscience/cdk/io/ZMatrixReader.java
@@ -48,6 +48,7 @@
  *
  * @cdk.module extra
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @cdk.keyword file format, Z-matrix
  */

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingMDLReader.java
@@ -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 {

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundASNReader.java
@@ -49,6 +49,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @see org.openscience.cdk.io.PCCompoundASNReader
  * 

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingPCCompoundXMLReader.java
@@ -47,6 +47,7 @@
  *
  * @cdk.module io
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @see org.openscience.cdk.io.PCCompoundASNReader
  * 

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingPCSubstancesXMLReader.java
@@ -47,6 +47,7 @@
  *
  * @cdk.module   io
  * @cdk.githash
+ * @cdk.iooptions
  * 
  * @author       Egon Willighagen <egonw@users.sf.net>
  * @cdk.created  2008-05-05

diff --git a/src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java b/src/main/org/openscience/cdk/io/iterator/IteratingSMILESReader.java
@@ -57,6 +57,7 @@
  *
  * @cdk.module smiles
  * @cdk.githash
+ * @cdk.iooptions
  *
  * @see org.openscience.cdk.io.SMILESReader
  *