UserArgumentProcessor
CeUserArgumentProcessor
, FatCatUserArgumentProcessor
, SmithWatermanUserArgumentProcessor
public abstract class AbstractUserArgumentProcessor extends java.lang.Object implements UserArgumentProcessor
To add a new StructureAlignment with a CLI similar to CE or FATCAT,
Note that reflection is used in a number of places, so the CLI argument names must match the get/set functions in both parameter beans.
Modifier and Type | Field | Description |
---|---|---|
static java.util.List<java.lang.String> |
mandatoryArgs |
|
static java.lang.String |
newline |
|
protected StartupParameters |
params |
Modifier | Constructor | Description |
---|---|---|
protected |
AbstractUserArgumentProcessor() |
Modifier and Type | Method | Description |
---|---|---|
abstract StructureAlignment |
getAlgorithm() |
|
abstract java.lang.String |
getDbSearchLegend() |
|
java.lang.String |
getDbSearchResult(AFPChain afpChain) |
|
abstract java.lang.Object |
getParameters() |
|
protected abstract StartupParameters |
getStartupParametersInstance() |
StartupParameters is a bean to store all the possible
command line parameters.
|
static void |
printAboutMe() |
|
java.lang.String |
printHelp() |
Print help about the arguments
|
void |
process(java.lang.String[] argv) |
Process user arguments that have been provided from the command line
|
public static java.lang.String newline
protected StartupParameters params
public static final java.util.List<java.lang.String> mandatoryArgs
protected abstract StartupParameters getStartupParametersInstance()
public abstract StructureAlignment getAlgorithm()
public abstract java.lang.Object getParameters()
public abstract java.lang.String getDbSearchLegend()
public void process(java.lang.String[] argv)
UserArgumentProcessor
process
in interface UserArgumentProcessor
public static void printAboutMe()
public java.lang.String getDbSearchResult(AFPChain afpChain)
public java.lang.String printHelp()
UserArgumentProcessor
printHelp
in interface UserArgumentProcessor