public class Annotator
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
protected boolean |
GENERATE_AAMIMAGE |
protected boolean |
GENERATE_IMAGE |
protected java.lang.String |
PREFIX |
protected boolean |
REMAP |
protected boolean |
REPORT_ALL_MAPPINGS |
protected boolean |
REPORT_MMP |
protected boolean |
REPORT_PATTERNS |
Modifier and Type | Method and Description |
---|---|
protected void |
annotateReactionAsText(ReactionMechanismTool rmt,
java.lang.String reactionID,
java.lang.StringBuilder sb) |
protected void |
annotateReactionAsXML(ReactionMechanismTool rmt,
java.lang.String reactionID,
org.w3c.dom.Document doc,
org.w3c.dom.Element rootElement) |
protected void |
compareRXNText(ReactionMechanismTool annotateRXNQ,
java.lang.String reactionQID,
ReactionMechanismTool annotateRXNT,
java.lang.String reactionTID,
java.lang.StringBuilder sb) |
protected void |
compareRXNXML(ReactionMechanismTool annotateRXNQ,
java.lang.String reactionQID,
ReactionMechanismTool annotateRXNT,
java.lang.String reactionTID,
org.w3c.dom.Document doc,
org.w3c.dom.Element rootElement) |
protected static void |
displayBlankLines(int numberBlankLines,
java.io.OutputStream out)
WreactionWithLayoutite the preactionWithLayoutovided
numbereactionWithLayout of blank lineheaderString to the
preactionWithLayoutovided OutputStreactionWithLayouteam.
|
protected java.io.File |
generateAAMImage(java.lang.String canonicalRootPath,
org.openscience.cdk.interfaces.IReaction mappedReaction,
java.lang.String reactionID) |
protected java.io.File |
generateImage(java.lang.String canonicalRootPath,
org.openscience.cdk.interfaces.IReaction mappedReaction,
java.lang.String reactionID) |
protected static void |
getHeader() |
protected ReactionMechanismTool |
getReactionMechanismTool(org.openscience.cdk.interfaces.IReaction cdkReaction,
boolean reMap) |
protected org.openscience.cdk.interfaces.IReaction |
parseCML(java.lang.String input) |
protected org.openscience.cdk.interfaces.IReaction |
parseMOL2(java.lang.String input) |
protected java.util.List<org.openscience.cdk.interfaces.IReaction> |
parseReactionSMILES(java.lang.String reactionSmiles) |
protected java.util.List<org.openscience.cdk.interfaces.IReaction> |
parseRXN(java.lang.String fileNames) |
protected org.openscience.cdk.interfaces.IReaction |
parseSDF(java.lang.String input) |
protected org.openscience.cdk.interfaces.IReaction |
parseSMILES(java.lang.String smiles) |
protected static void |
printHelp(java.util.Map<java.lang.String,org.apache.commons.cli.Options> optionsMap,
int printedRowWidth,
java.lang.String header,
java.lang.String footer,
int spacesBeforeOption,
int spacesBeforeOptionDescription,
boolean displayUsage,
java.io.OutputStream out) |
protected static void |
printHelp(java.io.OutputStream out,
org.apache.commons.cli.Options options) |
protected java.lang.String |
printUsageExamples() |
protected java.util.Map<java.lang.String,java.lang.String> |
similarityReactions(ReactionMechanismTool annotateRXNQ,
java.lang.String reactionQID,
ReactionMechanismTool annotateRXNT,
java.lang.String reactionTID) |
protected boolean |
writeFiles(java.lang.String reactionID,
ReactionMechanismTool mech) |
protected java.io.File |
writeRXNMappedFile(java.lang.String canonicalRootPath,
org.openscience.cdk.interfaces.IReaction mappedReaction,
java.lang.String name) |
protected void |
writeSimilarityMatrix(java.util.List<SimilarityResult> results,
java.lang.String jobID) |
protected boolean REPORT_ALL_MAPPINGS
protected boolean GENERATE_IMAGE
protected boolean GENERATE_AAMIMAGE
protected boolean REPORT_MMP
protected boolean REPORT_PATTERNS
protected boolean REMAP
protected java.lang.String PREFIX
protected ReactionMechanismTool getReactionMechanismTool(org.openscience.cdk.interfaces.IReaction cdkReaction, boolean reMap) throws java.lang.Exception
cdkReaction
- reMap
- remap the reactionjava.lang.Exception
protected boolean writeFiles(java.lang.String reactionID, ReactionMechanismTool mech) throws java.io.IOException, org.openscience.cdk.exception.CDKException, java.lang.Exception
reactionID
- mech
- java.io.IOException
org.openscience.cdk.exception.CDKException
java.lang.Exception
protected void writeSimilarityMatrix(java.util.List<SimilarityResult> results, java.lang.String jobID) throws java.io.IOException
results
- jobID
- java.io.IOException
protected void annotateReactionAsText(ReactionMechanismTool rmt, java.lang.String reactionID, java.lang.StringBuilder sb) throws java.lang.CloneNotSupportedException
rmt
- reactionID
- sb
- java.lang.CloneNotSupportedException
protected void annotateReactionAsXML(ReactionMechanismTool rmt, java.lang.String reactionID, org.w3c.dom.Document doc, org.w3c.dom.Element rootElement)
rmt
- reactionID
- doc
- rootElement
- protected void compareRXNXML(ReactionMechanismTool annotateRXNQ, java.lang.String reactionQID, ReactionMechanismTool annotateRXNT, java.lang.String reactionTID, org.w3c.dom.Document doc, org.w3c.dom.Element rootElement) throws java.lang.Exception
annotateRXNQ
- reactionQID
- annotateRXNT
- reactionTID
- doc
- rootElement
- java.lang.Exception
protected java.util.Map<java.lang.String,java.lang.String> similarityReactions(ReactionMechanismTool annotateRXNQ, java.lang.String reactionQID, ReactionMechanismTool annotateRXNT, java.lang.String reactionTID) throws java.lang.Exception
annotateRXNQ
- reactionQID
- annotateRXNT
- reactionTID
- java.lang.Exception
protected void compareRXNText(ReactionMechanismTool annotateRXNQ, java.lang.String reactionQID, ReactionMechanismTool annotateRXNT, java.lang.String reactionTID, java.lang.StringBuilder sb) throws java.lang.Exception
annotateRXNQ
- reactionQID
- annotateRXNT
- reactionTID
- sb
- StreactionWithLayouting buildereactionWithLayoutjava.lang.Exception
protected static void getHeader()
protected static void displayBlankLines(int numberBlankLines, java.io.OutputStream out)
numberBlankLines
- NumbereactionWithLayout of blank lineheaderString
to wreactionWithLayoutite.out
- OutputStreactionWithLayouteam to which to
wreactionWithLayoutite the blank lineheaderString.protected static void printHelp(java.io.OutputStream out, org.apache.commons.cli.Options options)
protected static void printHelp(java.util.Map<java.lang.String,org.apache.commons.cli.Options> optionsMap, int printedRowWidth, java.lang.String header, java.lang.String footer, int spacesBeforeOption, int spacesBeforeOptionDescription, boolean displayUsage, java.io.OutputStream out)
protected java.io.File generateImage(java.lang.String canonicalRootPath, org.openscience.cdk.interfaces.IReaction mappedReaction, java.lang.String reactionID) throws java.lang.Exception
java.lang.Exception
protected java.io.File generateAAMImage(java.lang.String canonicalRootPath, org.openscience.cdk.interfaces.IReaction mappedReaction, java.lang.String reactionID) throws java.lang.Exception
java.lang.Exception
protected java.io.File writeRXNMappedFile(java.lang.String canonicalRootPath, org.openscience.cdk.interfaces.IReaction mappedReaction, java.lang.String name) throws java.io.IOException, org.openscience.cdk.exception.CDKException
java.io.IOException
org.openscience.cdk.exception.CDKException
protected java.lang.String printUsageExamples()
protected org.openscience.cdk.interfaces.IReaction parseCML(java.lang.String input) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
protected java.util.List<org.openscience.cdk.interfaces.IReaction> parseRXN(java.lang.String fileNames)
protected java.util.List<org.openscience.cdk.interfaces.IReaction> parseReactionSMILES(java.lang.String reactionSmiles)
protected org.openscience.cdk.interfaces.IReaction parseSMILES(java.lang.String smiles)
protected org.openscience.cdk.interfaces.IReaction parseMOL2(java.lang.String input) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException
protected org.openscience.cdk.interfaces.IReaction parseSDF(java.lang.String input) throws java.io.FileNotFoundException, org.openscience.cdk.exception.CDKException
java.io.FileNotFoundException
org.openscience.cdk.exception.CDKException