public abstract class IteratingFilesWithHeaderReader<COLUMN>
extends org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader
Modifier and Type | Field and Description |
---|---|
static String |
defaultSMILESHeader |
protected ArrayList<COLUMN> |
header |
protected org.openscience.cdk.inchi.InChIGeneratorFactory |
inchiFactory |
protected int |
inchiIndex |
protected static Logger |
logger |
protected int |
numberOfHeaderLines |
String |
optionalSMILESHeader |
protected int |
smilesIndex |
protected SmilesParserWrapper |
sp |
protected long |
timeout |
Constructor and Description |
---|
IteratingFilesWithHeaderReader() |
Modifier and Type | Method and Description |
---|---|
protected void |
addHeaderColumn(String name) |
protected abstract ArrayList<COLUMN> |
createHeader() |
protected abstract COLUMN |
createPropertyByColumnName(String name) |
protected COLUMN |
getHeaderColumn(int index) |
protected int |
getNumberOfColumns() |
int |
getNumberOfHeaderLines() |
String |
getOptionalSMILESHeader() |
protected abstract LiteratureEntry |
getReference() |
long |
getTimeout() |
protected boolean |
isHeaderEmpty() |
protected void |
setHeaderColumn(int index,
String name) |
void |
setNumberOfHeaderLines(int numberOfHeaderLines) |
void |
setOptionalSMILESHeader(String optionalSMILESHeader) |
void |
setTimeout(long timeout) |
protected void |
updateHeaderColumn(int index,
COLUMN value) |
accepts, handleError, handleError, handleError, handleError, remove, setErrorHandler, setReaderMode
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addChemObjectIOListener, addSetting, addSettings, close, getFormat, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
forEachRemaining, hasNext, next
protected static Logger logger
protected SmilesParserWrapper sp
protected org.openscience.cdk.inchi.InChIGeneratorFactory inchiFactory
public static final String defaultSMILESHeader
protected int smilesIndex
protected int inchiIndex
protected long timeout
protected int numberOfHeaderLines
public String optionalSMILESHeader
public String getOptionalSMILESHeader()
public void setOptionalSMILESHeader(String optionalSMILESHeader)
public long getTimeout()
public void setTimeout(long timeout)
public int getNumberOfHeaderLines()
public void setNumberOfHeaderLines(int numberOfHeaderLines)
protected abstract LiteratureEntry getReference()
protected void addHeaderColumn(String name)
protected void setHeaderColumn(int index, String name)
protected COLUMN getHeaderColumn(int index)
protected void updateHeaderColumn(int index, COLUMN value)
protected int getNumberOfColumns()
protected boolean isHeaderEmpty()
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