net.maizegenetics.plugindef.PluginParameter Maven / Gradle / Ivy
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TASSEL 6 is a software package to evaluate traits association. Feature Tables are at the heart of the package where, a feature is a range of positions or a single position. Row in the that table are taxon.
package net.maizegenetics.plugindef;
import com.google.common.collect.Range;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
import java.util.ArrayList;
import java.util.List;
import static net.maizegenetics.plugindef.AbstractPlugin.convert;
/**
* Defines the attributes of parameters to be used in the plugins
*
* @param
*
* @author Ed Buckler
* @author Terry Casstevens
*/
public final class PluginParameter {
private static final Logger myLogger = LogManager.getLogger(PluginParameter.class);
private final String myGuiName;
private final String myUnits;
private final String myCmdLineName;
private final String myDescription;
private final List>> myRanges;
private final T myDefaultValue;
private final T myValue;
private final boolean myRequired;
private final Class myClass;
private final PluginParameter myDependentOnParameter;
private final Object[] myDependentOnParameterValue;
private final List myPossibleValues;
private final boolean myIsNullable;
public enum PARAMETER_TYPE {
NA, IN_FILE, OUT_FILE, IN_DIR, OUT_DIR, GENOTYPE_TABLE, SITE_NAME_LIST,
OBJECT_LIST_SINGLE_SELECT, POSITION_LIST, DISTANCE_MATRIX,
LABEL, PASSWORD
}
private final PARAMETER_TYPE myParameterType;
private PluginParameter(String guiName, String guiUnits, String cmdLineName,
String description, List>> ranges, T defaultValue,
T value, boolean required, PARAMETER_TYPE fileType,
PluginParameter dependentOnParameter, Object[] dependentOnParameterValue,
List possibleValues, boolean isNullable, Class type) {
myGuiName = guiName;
myUnits = guiUnits;
myCmdLineName = cmdLineName;
myDescription = description;
myRanges = ranges;
myDefaultValue = defaultValue;
if (value == null) {
myValue = defaultValue;
} else {
myValue = value;
}
if ((hasRange()) && (myValue != null)) {
if (!acceptsValue(myValue)) {
StringBuilder builder = new StringBuilder();
builder.append("PluginParameter: init: " + myCmdLineName + " value: " + myValue.toString() + " outside range: ");
builder.append(rangeToString());
throw new IllegalArgumentException(builder.toString());
}
}
myRequired = required;
if ((myDefaultValue != null) && (myRequired)) {
throw new IllegalArgumentException("PluginParameter: init: " + myCmdLineName + " shouldn't have default value and be required.");
}
myClass = type;
myParameterType = fileType;
myDependentOnParameter = dependentOnParameter;
myDependentOnParameterValue = dependentOnParameterValue;
if ((possibleValues != null) && (possibleValues.isEmpty())) {
myPossibleValues = null;
} else {
myPossibleValues = possibleValues;
}
myIsNullable = isNullable;
}
/**
* Use these to change the value of an existing parameter, e.g. after a user
* changes the value. Otherwise use the Builder to create the parameter
*
* @param oldParameter
* @param newValue
*/
public PluginParameter(PluginParameter oldParameter, T newValue) {
this(oldParameter.myGuiName, oldParameter.myUnits, oldParameter.myCmdLineName,
oldParameter.myDescription, oldParameter.myRanges, oldParameter.myDefaultValue, newValue,
oldParameter.myRequired, oldParameter.myParameterType, oldParameter.dependentOnParameter(),
oldParameter.dependentOnParameterValue(), oldParameter.possibleValues(), oldParameter.myIsNullable, oldParameter.myClass);
}
/**
* Use this to change the possible values of a PluginParameter built as
* objectListSingleSelect().
*
* @param oldParameter old plugin parameter
* @param possibleValues new values
*/
public PluginParameter(PluginParameter oldParameter, List possibleValues) {
this(oldParameter.myGuiName, oldParameter.myUnits, oldParameter.myCmdLineName,
oldParameter.myDescription, oldParameter.myRanges, oldParameter.myDefaultValue, oldParameter.value(),
oldParameter.myRequired, oldParameter.myParameterType, oldParameter.dependentOnParameter(),
oldParameter.dependentOnParameterValue(), possibleValues, oldParameter.myIsNullable, oldParameter.myClass);
}
public static PluginParameter getLabelInstance(String label) {
return new PluginParameter<>(label, null, label, "label", null, null, null, false, PARAMETER_TYPE.LABEL, null, null, null, false, String.class);
}
public String guiName() {
return myGuiName;
}
public String units() {
return myUnits;
}
public String cmdLineName() {
return myCmdLineName;
}
public String description() {
return myDescription;
}
public boolean hasRange() {
if ((myRanges == null) || myRanges.isEmpty()) {
return false;
} else {
return true;
}
}
public String rangeToString() {
return rangeToString(false);
}
public String rangeToString(boolean friendly) {
if (hasRange()) {
StringBuilder builder = new StringBuilder();
if (myRanges.size() == 1) {
Range> current = myRanges.get(0);
if ((current.hasLowerBound() && current.hasUpperBound())
&& (current.lowerEndpoint().equals(current.upperEndpoint()))) {
builder.append("[");
if (!friendly && (current.lowerEndpoint() instanceof Enum)) {
builder.append(((Enum) current.lowerEndpoint()).name());
} else {
builder.append(current.lowerEndpoint().toString());
}
builder.append("]");
} else {
builder.append(current.toString());
}
} else {
boolean first = true;
builder.append("[");
for (Range> current : myRanges) {
if (!first) {
builder.append(", ");
} else {
first = false;
}
if ((current.hasLowerBound() && current.hasUpperBound())
&& (current.lowerEndpoint().equals(current.upperEndpoint()))) {
if (!friendly && (current.lowerEndpoint() instanceof Enum)) {
builder.append(((Enum) current.lowerEndpoint()).name());
} else {
builder.append(current.lowerEndpoint().toString());
}
} else {
builder.append(current.toString());
}
}
builder.append("]");
}
return builder.toString();
} else {
return "";
}
}
public String possibleValuesString(boolean friendly) {
if (hasPossibleValues()) {
StringBuilder builder = new StringBuilder();
if (myPossibleValues.size() == 1) {
T current = myPossibleValues.get(0);
builder.append("[");
if (!friendly && (current instanceof Enum)) {
builder.append(((Enum) current).name());
} else {
builder.append(current.toString());
}
builder.append("]");
} else {
boolean first = true;
builder.append("[");
for (T current : myPossibleValues) {
if (!first) {
builder.append(", ");
} else {
first = false;
}
if (!friendly && (current instanceof Enum)) {
builder.append(((Enum) current).name());
} else {
builder.append(current.toString());
}
}
builder.append("]");
}
return builder.toString();
} else {
return "";
}
}
public boolean acceptsValue(Object value) {
try {
if (value == null && myIsNullable) {
return true;
}
if (hasRange()) {
for (Range> current : myRanges) {
if (current.contains((Comparable) value)) {
return true;
}
}
return false;
} else {
return true;
}
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
return false;
}
}
public boolean acceptsValue(String input) {
Comparable value = (Comparable) convert(input, valueType());
return acceptsValue(value);
}
public T value() {
return myValue;
}
public T defaultValue() {
return myDefaultValue;
}
public boolean required() {
return myRequired;
}
public Class valueType() {
return myClass;
}
public PARAMETER_TYPE parameterType() {
return myParameterType;
}
public PluginParameter dependentOnParameter() {
return myDependentOnParameter;
}
public Object[] dependentOnParameterValue() {
return myDependentOnParameterValue;
}
public boolean hasPossibleValues() {
return myPossibleValues != null;
}
public List possibleValues() {
return myPossibleValues;
}
public boolean isEmpty() {
return (myValue == null || ((myValue instanceof String) && ((String) myValue).trim().isEmpty()));
}
public static class Builder {
private String myGuiName;
private String myUnits = "";
private final String myCmdLineName;
private String myDescription = "";
private List>> myRanges = new ArrayList<>();
private final T myDefaultValue;
private boolean myIsRequired = false;
private final Class myClass;
private PARAMETER_TYPE myParameterType = PARAMETER_TYPE.NA;
private PluginParameter myDependentOnParameter = null;
private Object[] myDependentOnParameterValue = null;
private List myPossibleValues = null;
private boolean myIsNullable = false;
public Builder(String cmdLineName, T defaultValue, Class type) {
myCmdLineName = cmdLineName;
myDefaultValue = defaultValue;
myClass = type;
}
public Builder units(String units) {
myUnits = units;
return this;
}
public Builder description(String description) {
myDescription = description;
return this;
}
public Builder range(Range> range) {
if (range != null) {
myRanges.add(range);
}
return this;
}
public Builder range(Comparable[] values) {
if (values != null) {
for (Comparable current : values) {
myRanges.add(Range.singleton(current));
}
}
return this;
}
public Builder required(boolean required) {
myIsRequired = required;
return this;
}
public Builder guiName(String guiName) {
myGuiName = guiName;
return this;
}
public Builder inFile() {
myParameterType = PARAMETER_TYPE.IN_FILE;
return this;
}
public Builder outFile() {
myParameterType = PARAMETER_TYPE.OUT_FILE;
return this;
}
public Builder inDir() {
myParameterType = PARAMETER_TYPE.IN_DIR;
return this;
}
public Builder outDir() {
myParameterType = PARAMETER_TYPE.OUT_DIR;
return this;
}
public Builder genotypeTable() {
myParameterType = PARAMETER_TYPE.GENOTYPE_TABLE;
return this;
}
public Builder distanceMatrix() {
myParameterType = PARAMETER_TYPE.DISTANCE_MATRIX;
return this;
}
public Builder siteNameList() {
myParameterType = PARAMETER_TYPE.SITE_NAME_LIST;
return this;
}
public Builder positionList() {
myParameterType = PARAMETER_TYPE.POSITION_LIST;
return this;
}
public Builder objectListSingleSelect() {
myParameterType = PARAMETER_TYPE.OBJECT_LIST_SINGLE_SELECT;
return this;
}
public Builder password() {
myParameterType = PARAMETER_TYPE.PASSWORD;
return this;
}
public Builder dependentOnParameter(PluginParameter parameter) {
if (Boolean.class.isAssignableFrom(parameter.valueType())) {
return dependentOnParameter(parameter, true);
} else {
throw new IllegalArgumentException("PluginParameter: dependentOnParameter: no default value for: " + parameter.valueType().getName());
}
}
public Builder dependentOnParameter(PluginParameter parameter, Object value) {
myDependentOnParameter = parameter;
myDependentOnParameterValue = new Object[]{value};
return this;
}
public Builder dependentOnParameter(PluginParameter parameter, Object[] values) {
myDependentOnParameter = parameter;
Object[] result = new Object[values.length];
System.arraycopy(values, 0, result, 0, values.length);
myDependentOnParameterValue = result;
return this;
}
public Builder possibleValues(List possibleValues) {
myPossibleValues = possibleValues;
return this;
}
public Builder nullable() {
myIsNullable = true;
return this;
}
public PluginParameter build() {
if ((myGuiName == null) || (myGuiName.isEmpty())) {
StringBuilder builder = new StringBuilder();
builder.append(Character.toUpperCase(myCmdLineName.charAt(0)));
for (int i = 1; i < myCmdLineName.length(); i++) {
char current = myCmdLineName.charAt(i);
if (Character.isUpperCase(current)) {
builder.append(" ");
}
builder.append(current);
}
myGuiName = builder.toString();
}
if (myDescription.isEmpty()) {
myDescription = myGuiName;
}
return new PluginParameter<>(myGuiName, myUnits, myCmdLineName,
myDescription, myRanges, myDefaultValue, null, myIsRequired,
myParameterType, myDependentOnParameter,
myDependentOnParameterValue, myPossibleValues, myIsNullable, myClass);
}
}
}