net.maizegenetics.plugindef.AbstractPlugin Maven / Gradle / Ivy
/*
* AbstractPlugin.java
*
* Created on December 22, 2006, 5:03 PM
*
*/
package net.maizegenetics.plugindef;
import net.maizegenetics.dna.map.PositionList;
import net.maizegenetics.dna.snp.GenotypeTable;
import net.maizegenetics.dna.snp.ImportUtils;
import net.maizegenetics.dna.snp.io.JSONUtils;
import net.maizegenetics.dna.snp.io.ReadBedfile;
import net.maizegenetics.gui.DialogUtils;
import net.maizegenetics.gui.SelectFromAvailableDialog;
import net.maizegenetics.gui.SiteNamesAvailableListModel;
import net.maizegenetics.gui.TaxaAvailableListModel;
import net.maizegenetics.phenotype.GenotypePhenotype;
import net.maizegenetics.prefs.TasselPrefs;
import net.maizegenetics.taxa.TaxaList;
import net.maizegenetics.taxa.TaxaListBuilder;
import net.maizegenetics.taxa.distance.DistanceMatrix;
import net.maizegenetics.taxa.distance.ReadDistanceMatrix;
import net.maizegenetics.util.ExceptionUtils;
import net.maizegenetics.util.Utils;
import org.apache.log4j.Logger;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.FocusAdapter;
import java.awt.event.FocusEvent;
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.awt.event.WindowEvent;
import java.io.BufferedReader;
import java.io.File;
import java.lang.reflect.Field;
import java.math.BigDecimal;
import java.net.URI;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
import java.time.LocalDateTime;
import java.time.format.DateTimeFormatter;
import java.util.*;
import java.util.List;
import java.util.regex.Pattern;
/**
* @author Terry Casstevens
*/
abstract public class AbstractPlugin implements Plugin {
private static final Logger myLogger = Logger.getLogger(AbstractPlugin.class);
public static final String DEFAULT_CITATION = "Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.";
public static final String POSITION_LIST_NONE = "None";
public static final String TAXA_LIST_NONE = "None";
private final List myListeners = new ArrayList<>();
private final List myInputs = new ArrayList<>();
private DataSet myCurrentInputData = null;
private final Frame myParentFrame;
private final boolean myIsInteractive;
private boolean myTrace = false;
private boolean myThreaded = false;
protected boolean myWasCancelled = false;
/**
* Creates a new instance of AbstractPlugin
*/
public AbstractPlugin() {
this(null, true);
}
/**
* Creates a new instance of AbstractPlugin
*/
public AbstractPlugin(Frame parentFrame, boolean isInteractive) {
myParentFrame = parentFrame;
myIsInteractive = isInteractive;
}
@Override
public DataSet performFunction(DataSet input) {
LocalDateTime time = LocalDateTime.now();
String timeStr = time.format(DateTimeFormatter.ofPattern("MMM d, uuuu H:mm:s"));
myLogger.info("Starting " + getClass().getName() + ": time: " + timeStr);
myCurrentInputData = input;
try {
preProcessParameters(input);
if (isInteractive()) {
if (!setParametersViaGUI()) {
return null;
}
}
checkRequiredParameters();
postProcessParameters();
printParameterValues();
checkParameters();
DataSet output = processData(input);
time = LocalDateTime.now();
timeStr = time.format(DateTimeFormatter.ofPattern("MMM d, uuuu H:mm:s"));
myLogger.info("Finished " + getClass().getName() + ": time: " + timeStr);
fireDataSetReturned(new PluginEvent(output, getClass()));
return output;
} catch (Exception e) {
if (isInteractive()) {
myLogger.debug(e.getMessage(), e);
DialogUtils.showError(e.getMessage() + "\n", getParentFrame());
} else {
myLogger.debug(e.getMessage(), e);
printUsage();
myLogger.error(e.getMessage());
if (!getListeners().isEmpty()) {
System.exit(1);
}
}
return null;
} finally {
fireProgress(100);
}
}
protected void preProcessParameters(DataSet input) {
// do nothing
}
protected void postProcessParameters() {
// do nothing
}
@Override
public DataSet processData(DataSet input) {
throw new UnsupportedOperationException();
}
protected List getParameterFields() {
List result = new ArrayList<>();
Field[] fields = getClass().getDeclaredFields();
for (Field current : fields) {
if (current.getType().isAssignableFrom(PluginParameter.class)) {
current.setAccessible(true);
result.add(current);
}
}
return result;
}
private List> getParameterInstances() {
List> result = new ArrayList<>();
Field[] fields = getClass().getDeclaredFields();
for (Field current : fields) {
if (current.getType().isAssignableFrom(PluginParameter.class)) {
current.setAccessible(true);
try {
PluginParameter parameter = (PluginParameter) current.get(this);
result.add(parameter);
} catch (Exception e) {
e.printStackTrace();
throw new IllegalArgumentException("AbstractPlugin: getParameterInstances: problem getting parameter instances");
}
}
}
return result;
}
private Field getParameterField(String key) {
Field[] fields = getClass().getDeclaredFields();
for (Field current : fields) {
if (current.getType().isAssignableFrom(PluginParameter.class)) {
try {
current.setAccessible(true);
PluginParameter parameter = (PluginParameter) current.get(this);
if (parameter.cmdLineName().equals(key)) {
return current;
}
} catch (Exception e) {
e.printStackTrace();
throw new IllegalArgumentException("AbstractPlugin: getParameterField: problem with key: " + key);
}
}
}
throw new IllegalArgumentException("AbstractPlugin: getParameterField: unknown key: " + key);
}
private PluginParameter getParameterInstance(String key) {
try {
Field field = getParameterField(key);
return (PluginParameter) field.get(this);
} catch (Exception e) {
return null;
}
}
public boolean isPluginParameter(String key) {
if (getParameterInstance(key) == null) {
return false;
} else {
return true;
}
}
public static T convert(String input, Class outputClass) {
try {
if ((input == null) || (input.length() == 0)) {
return null;
} else if (outputClass.isEnum()) {
return (T) Enum.valueOf((Class) outputClass, input);
} else if (outputClass.isAssignableFrom(String.class)) {
return (T) input;
} else if (outputClass.isAssignableFrom(Integer.class)) {
char groupingSeparator = DecimalFormatSymbols.getInstance(Locale.getDefault()).getGroupingSeparator();
input = input.replace(String.valueOf(groupingSeparator), "");
char decimalSeparator = DecimalFormatSymbols.getInstance(Locale.getDefault()).getDecimalSeparator();
input = input.replace(String.valueOf(decimalSeparator), ".");
return (T) new Integer(new BigDecimal(input).intValueExact());
} else if (outputClass.isAssignableFrom(Double.class)) {
char groupingSeparator = DecimalFormatSymbols.getInstance(Locale.getDefault()).getGroupingSeparator();
input = input.replace(String.valueOf(groupingSeparator), "");
char decimalSeparator = DecimalFormatSymbols.getInstance(Locale.getDefault()).getDecimalSeparator();
input = input.replace(String.valueOf(decimalSeparator), ".");
return (T) new Double(new BigDecimal(input).doubleValue());
} else if (outputClass.isAssignableFrom(Float.class)) {
char groupingSeparator = DecimalFormatSymbols.getInstance(Locale.getDefault()).getGroupingSeparator();
input = input.replace(String.valueOf(groupingSeparator), "");
char decimalSeparator = DecimalFormatSymbols.getInstance(Locale.getDefault()).getDecimalSeparator();
input = input.replace(String.valueOf(decimalSeparator), ".");
return (T) new Double(new BigDecimal(input).floatValue());
} else if (outputClass.isAssignableFrom(List.class)) {
return (T) getListFromString(input);
} else if (outputClass.isAssignableFrom(SortedSet.class)) {
return (T) getSortedSet(input);
} else if (outputClass.isAssignableFrom(PositionList.class)) {
String test = input.trim().substring(Math.max(0, input.length() - 8)).toLowerCase();
if ((test.endsWith(".bed")) || (test.endsWith(".bed.gz"))) {
return (T) ReadBedfile.getPositionList(input);
} else if (test.endsWith(".json") || test.endsWith(".json.gz")) {
return (T) JSONUtils.importPositionListFromJSON(input);
} else {
try {
GenotypeTable temp = ImportUtils.read(input);
return (T) temp.positions();
} catch (Exception e) {
myLogger.debug(e.getMessage(), e);
throw new IllegalArgumentException("AbstractPlugin: convert: don't know who to covert: " + input + " to postion list");
}
}
} else if (outputClass.isAssignableFrom(TaxaList.class)) {
String test = input.trim().substring(Math.max(0, input.length() - 8)).toLowerCase();
if (test.endsWith(".json") || test.endsWith(".json.gz")) {
return (T) JSONUtils.importTaxaListFromJSON(input);
} else if (test.endsWith(".txt")) {
TaxaListBuilder builder = new TaxaListBuilder();
try (BufferedReader br = Utils.getBufferedReader(input)) {
String line = br.readLine();
Pattern sep = Pattern.compile("[\\s,]+");
while (line != null) {
line = line.trim();
String[] parsedline = sep.split(line);
for (int i = 0; i < parsedline.length; i++) {
if ((parsedline[i] != null) || (parsedline[i].length() != 0)) {
builder.add(parsedline[i]);
}
}
line = br.readLine();
}
}
return (T) builder.build();
} else {
String[] taxa = input.trim().split(",");
return (T) new TaxaListBuilder().addAll(taxa).build();
}
} else if (outputClass.isAssignableFrom(DistanceMatrix.class)) {
return (T) ReadDistanceMatrix.readDistanceMatrix(input);
} else if (outputClass.isAssignableFrom(Character.class)) {
if (input.length() != 1) {
throw new IllegalArgumentException("Should be one character");
}
return (T) new Character(input.charAt(0));
} else {
return outputClass.getConstructor(String.class).newInstance(input);
}
} catch (Exception nfe) {
myLogger.debug(nfe.getMessage(), nfe);
String message = nfe.getMessage();
if (message == null) {
throw new IllegalArgumentException("Problem converting: " + input + " to " + Utils.getBasename(outputClass.getName()));
} else {
throw new IllegalArgumentException(message + " Problem converting: " + input + " to " + Utils.getBasename(outputClass.getName()));
}
}
}
private static List getListFromString(String str) {
if ((str == null) || (str.length() == 0) || str.equalsIgnoreCase("null")) {
return null;
}
String[] tokens = str.split(",");
List result = new ArrayList<>();
for (String current : tokens) {
current = current.trim();
if (current.length() != 0) {
result.add(current);
}
}
return result;
}
private static SortedSet getSortedSet(String str) {
if ((str == null) || (str.length() == 0) || str.equalsIgnoreCase("null")) {
return null;
}
String[] tokens = str.split(",");
SortedSet result = new TreeSet<>();
for (String current : tokens) {
current = current.trim();
if (current.length() != 0) {
result.add(Integer.valueOf(current));
}
}
return result;
}
@Override
public void setParameters(String[] args) {
if (args != null) {
for (int i = 0; i < args.length; i++) {
String arg = args[i];
if (args[i].startsWith("-")) {
arg = arg.substring(1);
PluginParameter parameter = getParameterInstance(arg);
if (parameter == null) {
myLogger.error("Unrecognized argument: " + args[i]);
printUsage();
System.exit(1);
}
if ((i == args.length - 1) || (args[i + 1]).startsWith("-")) {
if (parameter.valueType().isAssignableFrom(Boolean.class)) {
setParameter(arg, Boolean.TRUE);
} else if (Number.class.isAssignableFrom(parameter.valueType())) {
setParameter(arg, args[i + 1]);
i++;
} else {
myLogger.error("Parameter requires a value: " + args[i]);
printUsage();
System.exit(1);
}
} else {
setParameter(arg, args[i + 1]);
i++;
}
} else {
myLogger.error("Argument expected to start with dash(-): " + args[i]);
printUsage();
System.exit(1);
}
}
}
}
private void setFieldsToConfigParameters(Map parameterFields) {
final List> parameterInstances = getParameterInstances();
if (parameterInstances.isEmpty()) {
return;
}
for (final PluginParameter current : parameterInstances) {
JComponent component = parameterFields.get(current.cmdLineName());
setFieldToConfigParameters(component, current);
}
}
private void setFieldToConfigParameters(JComponent component, PluginParameter parameter) {
Optional configValue = ParameterCache.value(this, parameter.cmdLineName());
if (!configValue.isPresent()) {
return;
}
try {
if (component instanceof JTextField) {
((JTextField) component).setText(configValue.get());
} else if (component instanceof JCheckBox) {
Boolean value = convert(configValue.get(), Boolean.class);
((JCheckBox) component).setSelected(value);
} else if (component instanceof JComboBox) {
Object value = convert(configValue.get(), parameter.valueType());
((JComboBox) component).setSelectedItem(value);
}
} catch (Exception e) {
myLogger.warn("setFieldToConfigParameters: problem with configuration key: " + this.getClass().getName() + "." + parameter.cmdLineName() + " value: " + configValue.get() + "\n" + e.getMessage());
}
}
public void setConfigParameters() {
if (ParameterCache.hasValues()) {
for (PluginParameter parameter : getParameterInstances()) {
Optional value = ParameterCache.value(this, parameter.cmdLineName());
if (value.isPresent()) {
try {
setParameter(parameter, value.get());
} catch (Exception e) {
myLogger.warn("setConfigParameters: problem with configuration key: " + this.getClass().getName() + "." + parameter.cmdLineName() + " value: " + value.get() + "\n" + e.getMessage());
}
}
}
}
}
private void checkRequiredParameters() {
List cmdLineNames = new ArrayList<>();
for (PluginParameter current : getParameterInstances()) {
if (cmdLineNames.contains(current.cmdLineName())) {
if (isInteractive()) {
throw new IllegalStateException(current.cmdLineName() + " exist multiple times for this plugin.");
} else {
myLogger.error("-" + current.cmdLineName() + " exist multiple times for this plugin.\n");
printUsage();
System.exit(1);
}
} else {
cmdLineNames.add(current.cmdLineName());
}
if (current.required()) {
if (current.isEmpty()) {
if (isInteractive()) {
throw new IllegalStateException(current.guiName() + " must be defined.");
} else {
myLogger.error("-" + current.cmdLineName() + " is required.\n");
printUsage();
System.exit(1);
}
}
}
}
}
/**
* Verification checks of parameters.
*/
private void checkParameters() {
for (PluginParameter current : getParameterInstances()) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.IN_FILE) {
if (!current.isEmpty()) {
String filename = current.value().toString();
File theFile = new File(filename);
if (!theFile.exists()) {
if (isInteractive()) {
throw new IllegalStateException(current.guiName() + ": " + filename + " doesn't exist.");
} else {
myLogger.error("-" + current.cmdLineName() + ": " + filename + " doesn't exist\n");
printUsage();
System.exit(1);
}
}
if (!theFile.isFile()) {
if (isInteractive()) {
throw new IllegalStateException(current.guiName() + ": " + filename + " isn't a file.");
} else {
myLogger.error("-" + current.cmdLineName() + ": " + filename + " isn't a file\n");
printUsage();
System.exit(1);
}
}
}
}
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.OUT_FILE) {
if (!current.isEmpty()) {
String filename = current.value().toString();
String outFolder = Utils.getDirectory(filename);
File outDir = new File(outFolder);
if (!outDir.isDirectory()) {
if (isInteractive()) {
throw new IllegalStateException(current.guiName() + ": Output Directory: " + outFolder + " doesn't exist.");
} else {
myLogger.error("-" + current.cmdLineName() + ": Output Directory: " + outFolder + " doesn't exist\n");
printUsage();
System.exit(1);
}
}
}
}
if ((current.parameterType() == PluginParameter.PARAMETER_TYPE.IN_DIR)
|| (current.parameterType() == PluginParameter.PARAMETER_TYPE.OUT_DIR)) {
if (!current.isEmpty()) {
String dirname = current.value().toString();
File directory = new File(dirname);
if (!directory.isDirectory()) {
if (isInteractive()) {
throw new IllegalStateException(current.guiName() + ": Directory: " + dirname + " doesn't exist.");
} else {
myLogger.error("-" + current.cmdLineName() + ": Directory: " + dirname + " doesn't exist\n");
printUsage();
System.exit(1);
}
}
}
}
}
}
protected void printParameterValues() {
List> parameters = getParameterInstances();
if ((parameters == null) || (parameters.isEmpty())) {
return;
}
StringBuilder builder = new StringBuilder();
builder.append("\n");
builder.append(Utils.getBasename(getClass().getName()));
builder.append(" Parameters\n");
for (PluginParameter current : parameters) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
continue;
}
builder.append(current.cmdLineName());
builder.append(": ");
Object value = current.value();
if (value instanceof PositionList) {
builder.append(((PositionList) value).numberOfSites());
builder.append(" positions");
} else if (value instanceof List) {
builder.append((Arrays.toString(((List) value).toArray())));
} else if (value instanceof DistanceMatrix) {
DistanceMatrix temp = (DistanceMatrix) value;
builder.append(temp.getColumnCount());
builder.append(" columns x ");
builder.append(temp.getRowCount());
builder.append(" rows");
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.PASSWORD) {
builder.append("?????");
} else {
builder.append(value);
}
builder.append("\n");
}
myLogger.info(builder.toString());
}
private void printUsage() {
StringBuilder builder = new StringBuilder();
String description = pluginDescription();
if (description != null) {
builder.append("\n");
builder.append(Utils.getBasename(getClass().getName())).append(" Description...\n");
builder.append(description);
builder.append("\n");
}
builder.append("\nUsage:\n");
builder.append(Utils.getBasename(getClass().getName())).append(" \n");
for (PluginParameter current : getParameterInstances()) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
continue;
}
builder.append("-");
builder.append(current.cmdLineName());
builder.append(" ");
if (current.valueType().isAssignableFrom(Boolean.class)) {
builder.append("");
} else {
builder.append("<");
builder.append(current.guiName());
builder.append(">");
}
builder.append(" : ");
builder.append(current.description());
if (current.hasRange()) {
builder.append(" ");
builder.append(current.rangeToString());
}
if (current.defaultValue() != null) {
builder.append(" (Default: ");
builder.append(current.defaultValue());
builder.append(")");
}
if (current.required()) {
builder.append(" (required)");
}
builder.append("\n");
}
myLogger.info(builder.toString());
}
@Override
public String getUsage() {
StringBuilder builder = new StringBuilder();
builder.append(Utils.getBasename(getClass().getName()));
builder.append("\n");
String description = pluginDescription();
if (description != null) {
builder.append("\nDescription: ");
builder.append(description);
builder.append("\n\n");
}
for (PluginParameter current : getParameterInstances()) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
continue;
}
builder.append("\n");
builder.append(current.guiName());
builder.append(" : ");
builder.append(current.description());
if (current.hasRange()) {
builder.append(" ");
builder.append(current.rangeToString());
}
if (current.defaultValue() != null) {
builder.append(" (Default: ");
builder.append(current.defaultValue());
builder.append(")");
}
if (current.required()) {
builder.append(" (required)");
}
builder.append("\n");
}
return builder.toString();
}
public Map> usageParameters() {
Map> result = new HashMap<>();
for (PluginParameter current : getParameterInstances()) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
continue;
}
Map temp = new HashMap<>();
temp.put(PARAMETER_PROPERTIES.Required, Boolean.toString(current.required()));
String defaultValue = (current.defaultValue() == null) ? null : current.defaultValue().toString();
temp.put(PARAMETER_PROPERTIES.Default, defaultValue);
temp.put(PARAMETER_PROPERTIES.Description, current.description());
result.put(current.cmdLineName(), temp);
}
return result;
}
@Override
public Map pluginParameters() {
Map result = new HashMap<>();
for (PluginParameter current : getParameterInstances()) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
continue;
}
result.put(current.cmdLineName(), (current.value() == null)? null : current.value().toString());
}
return result;
}
@Override
public Object getParameter(Enum key) {
return getParameterInstance(key.toString()).value();
}
@Override
public Object getParameter(String key) {
return getParameterInstance(key).value();
}
@Override
public Plugin setParameter(PluginParameter param, Object value) {
if (value == null) {
setParameter(param.cmdLineName(), value);
} else if (value instanceof String) {
setParameter(param.cmdLineName(), (String) value);
} else {
setParameter(param.cmdLineName(), value);
}
return this;
}
@Override
public Plugin setParameter(String key, Object value) {
try {
Field field = getParameterField(key);
PluginParameter parameter = (PluginParameter) field.get(this);
if (parameter == null) {
throw new IllegalArgumentException("setParameter: Unknown Parameter: " + key);
}
if ((parameter.hasRange()) && (!parameter.acceptsValue(value))) {
throw new IllegalArgumentException("setParameter: " + parameter.cmdLineName() + " value: " + value.toString() + " outside range: " + parameter.rangeToString());
}
PluginParameter newParameter = new PluginParameter<>(parameter, value);
field.set(this, newParameter);
} catch (Exception e) {
if (isInteractive()) {
try {
throw e;
} catch (IllegalAccessException ex) {
myLogger.error(ex.getMessage(), ex);
}
} else {
myLogger.error(key + ": " + e.getMessage());
printUsage();
myLogger.debug(e.getMessage(), e);
System.exit(1);
}
}
return this;
}
@Override
public Plugin setParameter(String key, String value) {
try {
PluginParameter parameter = getParameterInstance(key);
return setParameter(key, convert(value, parameter.valueType()));
} catch (Exception e) {
if (isInteractive()) {
throw new IllegalArgumentException(getParameterInstance(key).guiName() + ": " + e.getMessage());
} else {
myLogger.error(key + ": " + e.getMessage());
printUsage();
System.exit(1);
}
}
return this;
}
private static final int TEXT_FIELD_WIDTH = 25;
private boolean parametersAreSet = true;
/**
* Generates dialog based on this plugins define parameters.
*
* @return true if OK clicked, false if canceled
*/
private boolean setParametersViaGUI() {
final List> parameterInstances = getParameterInstances();
if (parameterInstances.isEmpty()) {
return true;
}
final JDialog dialog = new JDialog(getParentFrame(), null, true);
dialog.addWindowListener(new java.awt.event.WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
parametersAreSet = false;
dialog.setVisible(false);
}
});
final Map parameterFields = new HashMap<>();
parametersAreSet = true;
JButton okButton = new JButton();
okButton.setActionCommand("Ok");
okButton.setText("Ok");
okButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try {
for (final PluginParameter current : parameterInstances) {
JComponent component = parameterFields.get(current.cmdLineName());
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
// do nothing
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.GENOTYPE_TABLE) {
GenotypeWrapper input = (GenotypeWrapper) ((JComboBox) component).getSelectedItem();
if (input != null) {
setParameter(current.cmdLineName(), input.myObj);
}
} else if (PositionList.class.isAssignableFrom(current.valueType())) {
if (component instanceof JComboBox) {
Object temp = ((JComboBox) component).getSelectedItem();
if (temp == POSITION_LIST_NONE) {
setParameter(current.cmdLineName(), null);
} else {
setParameter(current.cmdLineName(), ((Datum) temp).getData());
}
} else {
String input = ((JTextField) component).getText().trim();
setParameter(current.cmdLineName(), input);
}
} else if (TaxaList.class.isAssignableFrom(current.valueType())) {
if (component instanceof JComboBox) {
Object temp = ((JComboBox) component).getSelectedItem();
if (temp == TAXA_LIST_NONE) {
setParameter(current.cmdLineName(), null);
} else {
setParameter(current.cmdLineName(), ((Datum) temp).getData());
}
} else {
String input = ((JTextField) component).getText().trim();
setParameter(current.cmdLineName(), input);
}
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.DISTANCE_MATRIX) {
if (component instanceof JComboBox) {
Object temp = ((JComboBox) component).getSelectedItem();
if (temp == null) {
throw new IllegalArgumentException("setParametersViaGUI: must specify a distance matrix.");
} else {
setParameter(current.cmdLineName(), ((Datum) temp).getData());
}
} else {
String input = ((JTextField) component).getText().trim();
setParameter(current.cmdLineName(), input);
}
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.OBJECT_LIST_SINGLE_SELECT) {
Object selectedObjects = ((JComboBox) component).getSelectedItem();
setParameter(current.cmdLineName(), selectedObjects);
} else if (component instanceof JTextField) {
String input = ((JTextField) component).getText().trim();
setParameter(current.cmdLineName(), input);
} else if (component instanceof JCheckBox) {
if (((JCheckBox) component).isSelected()) {
setParameter(current.cmdLineName(), Boolean.TRUE);
} else {
setParameter(current.cmdLineName(), Boolean.FALSE);
}
} else if (component instanceof JComboBox) {
Enum temp = (Enum) ((JComboBox) component).getSelectedItem();
setParameter(current.cmdLineName(), temp);
}
}
} catch (Exception ex) {
myLogger.debug(ex.getMessage(), ex);
StringBuilder builder = new StringBuilder();
builder.append("Problem Setting Parameters: ");
builder.append("\n");
builder.append(Utils.shortenStrLineLen(ExceptionUtils.getExceptionCauses(ex), 50));
String str = builder.toString();
DialogUtils.showError(str, getParentFrame());
return;
}
dialog.setVisible(false);
}
});
JButton cancelButton = new JButton();
cancelButton.setText("Cancel");
cancelButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
parametersAreSet = false;
dialog.setVisible(false);
}
});
JButton defaultsButton = new JButton();
defaultsButton.setText("Defaults");
defaultsButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
setFieldsToDefault(parameterFields);
setFieldsToConfigParameters(parameterFields);
}
});
JButton userManualButton = new JButton();
userManualButton.setText("User Manual");
userManualButton.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
try {
Desktop desktop = Desktop.getDesktop();
URI uri = new URI(pluginUserManualURL());
desktop.browse(uri);
} catch (Exception ex) {
myLogger.debug(ex.getMessage(), ex);
}
}
});
JPanel panel = new JPanel();
panel.setLayout(new BoxLayout(panel, BoxLayout.Y_AXIS));
panel.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
boolean show_citation = !DEFAULT_CITATION.equals(getCitation());
JTextPane citationText = null;
if (show_citation) {
citationText = new JTextPane();
citationText.setContentType("text/html");
citationText.setMargin(new Insets(5, 5, 5, 5));
citationText.setEditable(false);
JScrollPane scroll = new JScrollPane(citationText);
scroll.setHorizontalScrollBarPolicy(ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER);
scroll.setVerticalScrollBarPolicy(ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED);
scroll.setPreferredSize(new Dimension(scroll.getWidth(), 45));
panel.add(scroll);
}
for (final PluginParameter current : getParameterInstances()) {
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.GENOTYPE_TABLE) {
Datum datum = getGenotypeTable();
JComboBox menu = new JComboBox();
if (datum != null) {
String name = datum.getName();
GenotypeTable table;
if (datum.getData() instanceof GenotypeTable) {
table = (GenotypeTable) datum.getData();
} else if (datum.getData() instanceof GenotypePhenotype) {
table = ((GenotypePhenotype) datum.getData()).genotypeTable();
} else {
throw new IllegalStateException("AbstractPlugin: setParametersViaGUI: unknown GenotypeTable type: " + datum.getData().getClass().getName());
}
if (current.acceptsValue(GenotypeTable.GENOTYPE_TABLE_COMPONENT.Genotype) && table.hasGenotype()) {
menu.addItem(new GenotypeWrapper(GenotypeTable.GENOTYPE_TABLE_COMPONENT.Genotype, "Genotype (" + name + ")"));
}
if (current.acceptsValue(GenotypeTable.GENOTYPE_TABLE_COMPONENT.ReferenceProbability) && table.hasReferenceProbablity()) {
menu.addItem(new GenotypeWrapper(GenotypeTable.GENOTYPE_TABLE_COMPONENT.ReferenceProbability, "Reference Probability (" + name + ")"));
}
if (current.acceptsValue(GenotypeTable.GENOTYPE_TABLE_COMPONENT.AlleleProbability) && table.hasAlleleProbabilities()) {
menu.addItem(new GenotypeWrapper(GenotypeTable.GENOTYPE_TABLE_COMPONENT.AlleleProbability, "Allele Probability (" + name + ")"));
}
if (current.acceptsValue(GenotypeTable.GENOTYPE_TABLE_COMPONENT.Depth) && table.hasDepth()) {
menu.addItem(new GenotypeWrapper(GenotypeTable.GENOTYPE_TABLE_COMPONENT.Depth, "Depth (" + name + ")"));
}
if (current.acceptsValue(GenotypeTable.GENOTYPE_TABLE_COMPONENT.Dosage) && table.hasDosage()) {
menu.addItem(new GenotypeWrapper(GenotypeTable.GENOTYPE_TABLE_COMPONENT.Dosage, "Dosage (" + name + ")"));
}
menu.setSelectedIndex(0);
}
createEnableDisableAction(current, parameterFields, menu);
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
temp.add(new JLabel(current.guiName()));
temp.add(menu);
temp.setToolTipText(getToolTip(current));
panel.add(temp);
parameterFields.put(current.cmdLineName(), menu);
} else if (PositionList.class.isAssignableFrom(current.valueType())) {
Datum datum = getPositionList();
if (datum != null) {
JComboBox menu = new JComboBox();
menu.addItem(POSITION_LIST_NONE);
menu.addItem(datum);
menu.setSelectedIndex(0);
createEnableDisableAction(current, parameterFields, menu);
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
temp.add(new JLabel(current.guiName()));
temp.add(menu);
temp.setToolTipText(getToolTip(current));
panel.add(temp);
parameterFields.put(current.cmdLineName(), menu);
} else {
JTextField field = new JTextField(TEXT_FIELD_WIDTH - 8);
JButton browse = getOpenFile(dialog, field);
JPanel line = getLine(current.guiName(), field, browse, getToolTip(current));
createEnableDisableAction(current, parameterFields, new JComponent[]{field, browse}, field);
panel.add(line);
parameterFields.put(current.cmdLineName(), field);
}
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.DISTANCE_MATRIX) {
List matrices = getDistanceMatrices();
if (!matrices.isEmpty()) {
JComboBox menu = new JComboBox();
for (Datum matrix : matrices) {
menu.addItem(matrix);
}
menu.setSelectedIndex(0);
createEnableDisableAction(current, parameterFields, menu);
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
temp.add(new JLabel(current.guiName()));
temp.add(menu);
temp.setToolTipText(getToolTip(current));
panel.add(temp);
parameterFields.put(current.cmdLineName(), menu);
} else {
JTextField field = new JTextField(TEXT_FIELD_WIDTH - 8);
JButton browse = getOpenFile(dialog, field);
JPanel line = getLine(current.guiName(), field, browse, getToolTip(current));
createEnableDisableAction(current, parameterFields, new JComponent[]{field, browse}, field);
panel.add(line);
parameterFields.put(current.cmdLineName(), field);
}
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.OBJECT_LIST_SINGLE_SELECT) {
JPanel listPanel = new JPanel(new FlowLayout(FlowLayout.CENTER));
listPanel.add(new JLabel(current.guiName()));
JComboBox list = new JComboBox<>(current.possibleValues().toArray());
list.setSelectedIndex(0);
createEnableDisableAction(current, parameterFields, list);
listPanel.add(list);
listPanel.setToolTipText(getToolTip(current));
panel.add(listPanel);
parameterFields.put(current.cmdLineName(), list);
} else if (current.valueType().isEnum()) {
JComboBox menu = new JComboBox();
Object[] values = current.valueType().getEnumConstants();
for (Object item : values) {
menu.addItem(item);
}
menu.setSelectedItem(current.value());
createEnableDisableAction(current, parameterFields, menu);
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
temp.add(new JLabel(current.guiName()));
temp.add(menu);
temp.setToolTipText(getToolTip(current));
panel.add(temp);
parameterFields.put(current.cmdLineName(), menu);
} else if (Boolean.class.isAssignableFrom(current.valueType())) {
JCheckBox check = new JCheckBox(current.guiName());
check.setToolTipText(getToolTip(current));
if (current.value() == Boolean.TRUE) {
check.setSelected(true);
} else {
check.setSelected(false);
}
createEnableDisableAction(current, parameterFields, check);
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
temp.add(check);
panel.add(temp);
parameterFields.put(current.cmdLineName(), check);
} else if (TaxaList.class.isAssignableFrom(current.valueType())) {
List datums = getTaxaListDatum();
if (datums != null) {
JComboBox menu = new JComboBox();
menu.addItem(TAXA_LIST_NONE);
for (Datum datum : datums) {
menu.addItem(datum);
}
menu.setSelectedIndex(0);
createEnableDisableAction(current, parameterFields, menu);
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
temp.add(new JLabel(current.guiName()));
temp.add(menu);
temp.setToolTipText(getToolTip(current));
panel.add(temp);
parameterFields.put(current.cmdLineName(), menu);
} else {
TaxaList taxa = getTaxaList();
JTextField field;
if (taxa == null) {
field = new JTextField(TEXT_FIELD_WIDTH);
} else {
field = new JTextField(TEXT_FIELD_WIDTH - 7);
}
if (current.value() != null) {
field.setText(current.value().toString());
}
JPanel taxaPanel = getTaxaListPanel(current.guiName(), field, current.description(), dialog, taxa);
panel.add(taxaPanel);
parameterFields.put(current.cmdLineName(), field);
}
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.SITE_NAME_LIST) {
PositionList positions = getSiteNameList();
JTextField field;
if (positions == null) {
field = new JTextField(TEXT_FIELD_WIDTH);
} else {
field = new JTextField(TEXT_FIELD_WIDTH - 7);
}
if (current.value() != null) {
field.setText(current.value().toString());
}
JPanel positionsPanel = getPositionListPanel(current.guiName(), field, current.description(), dialog, positions);
List componentList = new ArrayList<>();
for (Component component : positionsPanel.getComponents()) {
if (component instanceof JComponent) {
componentList.add((JComponent) component);
}
}
createEnableDisableAction(current, parameterFields, componentList.toArray(new JComponent[0]), field);
panel.add(positionsPanel);
parameterFields.put(current.cmdLineName(), field);
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.LABEL) {
JPanel temp = new JPanel(new FlowLayout(FlowLayout.CENTER));
JLabel label = new JLabel(current.guiName());
label.setFont(new Font("Dialog", Font.BOLD, 14));
temp.add(label);
panel.add(temp);
} else {
final JTextField field;
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.PASSWORD) {
field = new JPasswordField(TEXT_FIELD_WIDTH);
} else if (current.parameterType() != PluginParameter.PARAMETER_TYPE.NA) {
field = new JTextField(TEXT_FIELD_WIDTH - 8);
} else {
field = new JTextField(TEXT_FIELD_WIDTH);
}
if (current.value() != null) {
setFieldToValue(field, current, current.value());
}
field.addFocusListener(new FocusAdapter() {
@Override
public void focusLost(FocusEvent e) {
String input = field.getText().trim();
try {
PluginParameter parameter = getParameterInstance(current.cmdLineName());
if (!current.acceptsValue(input)) {
JOptionPane.showMessageDialog(dialog, current.guiName() + " range: " + current.rangeToString());
setFieldToValue(field, parameter, parameter.value());
} else {
setFieldToValue(field, parameter, convert(input, parameter.valueType()));
}
} catch (Exception ex) {
myLogger.debug(ex.getMessage(), ex);
JOptionPane.showMessageDialog(dialog, current.guiName() + ": " + ex.getMessage());
field.setText(getParameterInstance(current.cmdLineName()).value().toString());
}
}
});
String label = null;
if (current.required()) {
label = current.guiName() + "*";
} else {
label = current.guiName();
}
JPanel line = null;
if (current.parameterType() == PluginParameter.PARAMETER_TYPE.IN_FILE) {
JButton browse = getOpenFile(dialog, field);
line = getLine(label, field, browse, getToolTip(current));
createEnableDisableAction(current, parameterFields, new JComponent[]{field, browse}, field);
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.OUT_FILE) {
JButton browse = getSaveFile(dialog, field);
line = getLine(label, field, browse, getToolTip(current));
createEnableDisableAction(current, parameterFields, new JComponent[]{field, browse}, field);
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.IN_DIR) {
JButton browse = getOpenDir(dialog, field);
line = getLine(label, field, browse, getToolTip(current));
createEnableDisableAction(current, parameterFields, new JComponent[]{field, browse}, field);
} else if (current.parameterType() == PluginParameter.PARAMETER_TYPE.OUT_DIR) {
JButton browse = getSaveDir(dialog, field);
line = getLine(label, field, browse, getToolTip(current));
createEnableDisableAction(current, parameterFields, new JComponent[]{field, browse}, field);
} else {
line = getLine(label, field, null, getToolTip(current));
createEnableDisableAction(current, parameterFields, field);
}
panel.add(line);
parameterFields.put(current.cmdLineName(), field);
}
}
JTabbedPane tabbedPane = new JTabbedPane();
tabbedPane.add(new JScrollPane(panel, ScrollPaneConstants.VERTICAL_SCROLLBAR_AS_NEEDED, ScrollPaneConstants.HORIZONTAL_SCROLLBAR_NEVER), getButtonName());
JPanel pnlButtons = new JPanel();
pnlButtons.setLayout(new FlowLayout());
pnlButtons.add(okButton);
pnlButtons.add(cancelButton);
pnlButtons.add(defaultsButton);
pnlButtons.add(userManualButton);
dialog.getContentPane().add(tabbedPane, BorderLayout.CENTER);
dialog.getContentPane().add(pnlButtons, BorderLayout.SOUTH);
JTextPane helpText = new JTextPane();
helpText.setMargin(new Insets(10, 10, 10, 10));
helpText.setEditable(false);
helpText.setContentType("text/html");
tabbedPane.add(new JScrollPane(helpText), "Help");
dialog.pack();
if (show_citation) {
citationText.setText(getCitationHTML(dialog.getWidth() / 9));
dialog.setMinimumSize(null);
dialog.pack();
}
helpText.setText(getUsageHTML());
Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
if (screenSize.getHeight() - 125 < dialog.getHeight()) {
dialog.setSize(Math.max(dialog.getWidth(), 550), (int) screenSize.getHeight() - 125);
} else {
dialog.setSize(Math.max(dialog.getWidth(), 550), Math.max(dialog.getHeight(), 250));
}
dialog.setResizable(false);
dialog.setLocationRelativeTo(getParentFrame());
dialog.setVisible(true);
return parametersAreSet;
}
/**
* This sets the GUI field text to appropriate formatting for integers, doubles, floats, strings, etc. for the
* user's default locale.
*
* @param field text field
* @param parameter associated plugin parameter
* @param value value to format
*/
private void setFieldToValue(JTextField field, PluginParameter parameter, Object value) {
if (value == null) {
field.setText(null);
} else if (Integer.class.isAssignableFrom(parameter.valueType())) {
field.setText(NumberFormat.getInstance().format(value));
} else if ((Double.class.isAssignableFrom(parameter.valueType())) ||
(Float.class.isAssignableFrom(parameter.valueType()))) {
DecimalFormat temp = new DecimalFormat();
temp.setMaximumFractionDigits(5);
temp.setMinimumFractionDigits(1);
field.setText(temp.format(value));
} else {
field.setText(value.toString());
}
}
private void setFieldsToDefault(Map parameterFields) {
final List> parameterInstances = getParameterInstances();
if (parameterInstances.isEmpty()) {
return;
}
for (final PluginParameter current : parameterInstances) {
JComponent component = parameterFields.get(current.cmdLineName());
setFieldToDefault(component, current);
}
}
private void setFieldToDefault(JComponent component, PluginParameter current) {
if (component instanceof JTextField) {
Object defaultValue = current.defaultValue();
setFieldToValue((JTextField) component, current, defaultValue);
setParameter(current.cmdLineName(), defaultValue);
} else if (component instanceof JCheckBox) {
Boolean value = (Boolean) current.defaultValue();
((JCheckBox) component).setSelected(value);
setParameter(current.cmdLineName(), value);
} else if (component instanceof JComboBox) {
((JComboBox) component).setSelectedItem(current.defaultValue());
setParameter(current.cmdLineName(), current.defaultValue());
}
}
@Override
public void setParametersToDefault() {
final List> parameterInstances = getParameterInstances();
if (parameterInstances.isEmpty()) {
return;
}
for (final PluginParameter current : parameterInstances) {
setParameter(current.cmdLineName(), current.defaultValue());
}
}
private String getCitationHTML(int lineWidth) {
String citation = getCitation();
int count = 10;
StringBuilder builder = new StringBuilder();
builder.append("Citation: ");
for (int i = 0, n = citation.length(); i < n; i++) {
count++;
if (citation.charAt(i) == '\n') {
builder.append("
");
count = 0;
} else if ((count > lineWidth) && (citation.charAt(i) == ' ')) {
builder.append("
");
count = 0;
} else {
builder.append(citation.charAt(i));
}
}
builder.append(" ");
return builder.toString();
}
public String getUsageHTML() {
StringBuilder builder = new StringBuilder();
builder.append("");
builder.append(Utils.getBasename(getClass().getName()));
builder.append("");
String description = pluginDescription();
if (description != null) {
builder.append("
Description: ");
builder.append(description);
}
builder.append("
");
builder.append("");
builder.append("Parameter Description Values Default ");
builder.append("");
if (current.required()) {
builder.append("");
}
builder.append(current.guiName());
if (current.required()) {
builder.append("");
}
builder.append(" ");
builder.append("");
builder.append(current.description());
builder.append(" ");
builder.append("");
if (current.hasPossibleValues()) {
String range = current.possibleValuesString(true);
if ((range.charAt(0) == '[') && (range.charAt(range.length() - 1) == ']')) {
range = range.substring(1, range.length() - 1);
}
StringBuilder buildRange = new StringBuilder();
for (char rangeChr : range.toCharArray()) {
if (rangeChr == '_') {
buildRange.append("\n");
}
buildRange.append(rangeChr);
}
builder.append(buildRange.toString());
} else if (current.hasRange()) {
String range = current.rangeToString(true);
if ((range.charAt(0) == '[') && (range.charAt(range.length() - 1) == ']')) {
range = range.substring(1, range.length() - 1);
}
StringBuilder buildRange = new StringBuilder();
for (char rangeChr : range.toCharArray()) {
if (rangeChr == '_') {
buildRange.append("\n");
}
buildRange.append(rangeChr);
}
builder.append(buildRange.toString());
} else if (current.valueType().isAssignableFrom(Boolean.class)) {
builder.append("true, false");
}
builder.append(" ");
builder.append("");
if (current.defaultValue() != null) {
String defaultValue = current.defaultValue().toString();
StringBuilder buildDefault = new StringBuilder();
for (char defaultChr : defaultValue.toCharArray()) {
if (defaultChr == '_') {
buildDefault.append("\n");
}
buildDefault.append(defaultChr);
}
builder.append(buildDefault.toString());
}
builder.append(" ");
builder.append(" ");
}
builder.append("
");
builder.append(" ");
builder.append("
* parameters in red are required");
builder.append("");
return builder.toString();
}
private void createEnableDisableAction(PluginParameter current, Map parameterFields, final JComponent component) {
createEnableDisableAction(current, parameterFields, new JComponent[]{component}, component);
}
private void createEnableDisableAction(final PluginParameter current, Map parameterFields, final JComponent[] components, final JComponent input) {
if (current.dependentOnParameter() != null) {
JComponent depends = parameterFields.get(current.dependentOnParameter().cmdLineName());
if (depends instanceof JCheckBox) {
final JCheckBox checkBox = (JCheckBox) depends;
for (JComponent component : components) {
if (checkBox.isSelected() == (Boolean) current.dependentOnParameterValue()[0]) {
component.setEnabled(true);
} else {
component.setEnabled(false);
}
}
checkBox.addItemListener(new ItemListener() {
@Override
public void itemStateChanged(ItemEvent e) {
for (JComponent component : components) {
if (checkBox.isSelected() == (Boolean) current.dependentOnParameterValue()[0]) {
component.setEnabled(true);
} else {
component.setEnabled(false);
}
}
}
});
} else if (depends instanceof JComboBox) {
final JComboBox comboBox = (JComboBox) depends;
for (JComponent component : components) {
Object[] values = current.dependentOnParameterValue();
component.setEnabled(false);
for (Object value : values) {
if (comboBox.getSelectedItem() == value) {
component.setEnabled(true);
break;
}
}
}
comboBox.addItemListener((ItemEvent e) -> {
for (JComponent component : components) {
Object[] values = current.dependentOnParameterValue();
component.setEnabled(false);
for (Object value : values) {
if (comboBox.getSelectedItem() == value) {
component.setEnabled(true);
break;
}
}
}
});
}
}
}
private static final int DEFAULT_TOOL_TIP_LINE_LENGTH = 50;
private String getToolTip(PluginParameter parameter) {
String description = parameter.description();
int count = 0;
StringBuilder builder = new StringBuilder();
builder.append("");
for (int i = 0, n = description.length(); i < n; i++) {
count++;
if (description.charAt(i) == '\n') {
builder.append("
");
count = 0;
} else if ((count > DEFAULT_TOOL_TIP_LINE_LENGTH) && (description.charAt(i) == ' ')) {
builder.append("
");
count = 0;
} else {
builder.append(description.charAt(i));
}
}
builder.append("");
return builder.toString();
}
private JPanel getLine(String label, JTextField ref, JButton button, String description) {
JPanel result = new JPanel(new FlowLayout(FlowLayout.RIGHT));
result.setToolTipText(description);
result.add(new JLabel(label));
ref.setEditable(true);
ref.setHorizontalAlignment(JTextField.LEFT);
ref.setAlignmentX(JTextField.CENTER_ALIGNMENT);
ref.setAlignmentY(JTextField.CENTER_ALIGNMENT);
ref.setMaximumSize(ref.getPreferredSize());
result.add(ref);
if (button != null) {
result.add(button);
}
return result;
}
private JPanel getTaxaListPanel(String label, final JTextField ref, String description, final JDialog parent, final TaxaList taxa) {
JPanel result = new JPanel(new FlowLayout(FlowLayout.RIGHT));
result.setToolTipText(description);
result.add(new JLabel(label));
ref.setEditable(true);
ref.setHorizontalAlignment(JTextField.LEFT);
ref.setAlignmentX(JTextField.CENTER_ALIGNMENT);
ref.setAlignmentY(JTextField.CENTER_ALIGNMENT);
ref.setMaximumSize(ref.getPreferredSize());
result.add(ref);
if (taxa != null) {
final SelectFromAvailableDialog dialog = new SelectFromAvailableDialog(getParentFrame(), "Taxa Filter", new TaxaAvailableListModel(taxa));
JButton taxaButton = new JButton(new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
dialog.setLocationRelativeTo(parent);
dialog.setVisible(true);
if (!dialog.isCanceled()) {
int[] indicesToKeep = dialog.getDesiredIndices();
StringBuilder builder = new StringBuilder();
for (int i = 0; i < indicesToKeep.length; i++) {
if (i != 0) {
builder.append(",");
}
builder.append(taxa.taxaName(indicesToKeep[i]));
}
ref.setText(builder.toString());
}
dialog.setVisible(false);
}
});
taxaButton.setText("Select");
result.add(taxaButton);
}
JButton browse = getOpenFile(parent, ref);
result.add(browse);
return result;
}
private JPanel getPositionListPanel(String label, final JTextField ref, String description, final JDialog parent, final PositionList positions) {
JPanel result = new JPanel(new FlowLayout(FlowLayout.RIGHT));
result.setToolTipText(description);
result.add(new JLabel(label));
ref.setEditable(true);
ref.setHorizontalAlignment(JTextField.LEFT);
ref.setAlignmentX(JTextField.CENTER_ALIGNMENT);
ref.setAlignmentY(JTextField.CENTER_ALIGNMENT);
ref.setMaximumSize(ref.getPreferredSize());
result.add(ref);
if (positions != null) {
final SelectFromAvailableDialog dialog = new SelectFromAvailableDialog(getParentFrame(), "Site Name Filter", new SiteNamesAvailableListModel(positions));
JButton siteNamesButton = new JButton(new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
dialog.setLocationRelativeTo(parent);
dialog.setVisible(true);
if (!dialog.isCanceled()) {
int[] indicesToKeep = dialog.getDesiredIndices();
StringBuilder builder = new StringBuilder();
for (int i = 0; i < indicesToKeep.length; i++) {
if (i != 0) {
builder.append(",");
}
builder.append(positions.siteName(indicesToKeep[i]));
}
ref.setText(builder.toString());
}
dialog.setVisible(false);
}
});
siteNamesButton.setText("Select");
result.add(siteNamesButton);
}
return result;
}
private JButton getOpenFile(final JDialog parent, final JTextField textField) {
final JFileChooser fileChooser = new JFileChooser(TasselPrefs.getOpenDir());
JButton result = new JButton("Browse");
result.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (fileChooser.showOpenDialog(parent) == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
textField.setText(file.getPath());
TasselPrefs.putOpenDir(fileChooser.getCurrentDirectory().getPath());
}
}
});
return result;
}
private JButton getSaveFile(final JDialog parent, final JTextField textField) {
final JFileChooser fileChooser = new JFileChooser(TasselPrefs.getSaveDir());
JButton result = new JButton("Browse");
result.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (fileChooser.showSaveDialog(parent) == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
textField.setText(file.getPath());
TasselPrefs.putSaveDir(fileChooser.getCurrentDirectory().getPath());
}
}
});
return result;
}
private JButton getOpenDir(final JDialog parent, final JTextField textField) {
final JFileChooser fileChooser = new JFileChooser(Utils.getDirectory(TasselPrefs.getOpenDir()));
fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
JButton result = new JButton("Browse");
result.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (fileChooser.showOpenDialog(parent) == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
textField.setText(file.getPath());
TasselPrefs.putOpenDir(file.getPath());
}
}
});
return result;
}
private JButton getSaveDir(final JDialog parent, final JTextField textField) {
final JFileChooser fileChooser = new JFileChooser(Utils.getDirectory(TasselPrefs.getSaveDir()));
fileChooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
JButton result = new JButton("Browse");
result.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
if (fileChooser.showOpenDialog(parent) == JFileChooser.APPROVE_OPTION) {
File file = fileChooser.getSelectedFile();
textField.setText(file.getPath());
TasselPrefs.putSaveDir(file.getPath());
}
}
});
return result;
}
private class GenotypeWrapper {
private final Object myObj;
private final String myName;
public GenotypeWrapper(Object obj, String name) {
myObj = obj;
myName = name;
}
@Override
public String toString() {
return myName;
}
public Object getObject() {
return myObj;
}
}
private Datum getGenotypeTable() {
if (myCurrentInputData == null) {
return null;
}
List genotypeTables = myCurrentInputData.getDataOfType(GenotypeTable.class);
if (!genotypeTables.isEmpty()) {
return genotypeTables.get(0);
}
genotypeTables = myCurrentInputData.getDataOfType(GenotypePhenotype.class);
if (!genotypeTables.isEmpty()) {
return genotypeTables.get(0);
}
return null;
}
private TaxaList getTaxaList() {
if (myCurrentInputData == null) {
return null;
}
List taxaList = myCurrentInputData.getDataOfType(GenotypeTable.class);
if (!taxaList.isEmpty()) {
return ((GenotypeTable) taxaList.get(0).getData()).taxa();
}
taxaList = myCurrentInputData.getDataOfType(TaxaList.class);
if (!taxaList.isEmpty()) {
return (TaxaList) taxaList.get(0).getData();
}
return null;
}
private List getTaxaListDatum() {
if (myCurrentInputData == null) {
return null;
}
List taxaList = myCurrentInputData.getDataOfType(TaxaList.class);
if (!taxaList.isEmpty()) {
return taxaList;
}
return null;
}
private PositionList getSiteNameList() {
if (myCurrentInputData == null) {
return null;
}
List positionList = myCurrentInputData.getDataOfType(GenotypeTable.class);
if (!positionList.isEmpty()) {
return ((GenotypeTable) positionList.get(0).getData()).positions();
}
positionList = myCurrentInputData.getDataOfType(PositionList.class);
if (!positionList.isEmpty()) {
return (PositionList) positionList.get(0).getData();
}
return null;
}
private Datum getPositionList() {
if (myCurrentInputData == null) {
return null;
}
List positionList = myCurrentInputData.getDataOfType(PositionList.class);
if (!positionList.isEmpty()) {
return positionList.get(0);
}
return null;
}
private List getDistanceMatrices() {
if (myCurrentInputData != null) {
return myCurrentInputData.getDataOfType(DistanceMatrix.class);
} else {
return null;
}
}
/**
* Returns menu that can be added to main menu bar.
*
* @return menu
*/
@Override
public JMenu getMenu() {
return null;
}
/**
* Sets up this plugin to receive input from another plugin.
*
* @param input input
*/
@Override
public void receiveInput(Plugin input) {
if (input == null) {
throw new IllegalArgumentException("AbstractPlugin: receiveInput: input can not be null.");
}
if (!myInputs.contains(input)) {
myInputs.add(input);
}
input.addListener(this);
}
/**
* GUI Panel for this plugin.
*
* @return panel
*/
@Override
public JPanel getPanel() {
return null;
}
/**
* If interactive = true, the plugin will create dialogs and panels to interacts with the user
*
* @return boolean
*/
@Override
public boolean isInteractive() {
return myIsInteractive;
}
/**
* Parent Frame for this plugin. Can be null.
*
* @return frame
*/
@Override
public Frame getParentFrame() {
return myParentFrame;
}
/**
* Adds listener to this plugin.
*
* @param listener listener to add
*/
@Override
public void addListener(PluginListener listener) {
synchronized (myListeners) {
if ((listener != null) && (!myListeners.contains(listener))) {
myListeners.add(listener);
}
}
}
public List getListeners() {
return Collections.unmodifiableList(myListeners);
}
public boolean hasListeners() {
return !myListeners.isEmpty();
}
public List getInputs() {
return myInputs;
}
/**
* Returns data set after complete.
*
* @param event event
*/
protected void fireDataSetReturned(PluginEvent event) {
synchronized (myListeners) {
Iterator itr = myListeners.iterator();
while (itr.hasNext()) {
try {
if (myThreaded) {
PluginListener current = itr.next();
ThreadedPluginListener thread = new ThreadedPluginListener(current, event);
thread.start();
} else {
PluginListener current = itr.next();
current.dataSetReturned(event);
}
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
/**
* Returns data set after complete.
*
* @param data data set
*/
protected void fireDataSetReturned(DataSet data) {
fireDataSetReturned(new PluginEvent(data));
}
private static final List myPrintedCitations = new ArrayList<>();
/**
* Returns progress of execution.
*
* @param event event
*/
protected void fireProgress(PluginEvent event) {
synchronized (myListeners) {
Iterator itr = myListeners.iterator();
while (itr.hasNext()) {
PluginListener current = itr.next();
current.progress(event);
}
}
DataSet ds = (DataSet) event.getSource();
if (ds != null) {
List percentage = ds.getDataOfType(Integer.class);
if (percentage.size() > 0) {
Datum datum = percentage.get(0);
Integer percent = (Integer) datum.getData();
if (percent == 100) {
if (!myPrintedCitations.contains(getCitation())) {
myLogger.info(getClass().getName() + " Citation: " + getCitation());
myPrintedCitations.add(getCitation());
}
}
}
}
}
/**
* Returns progress of execution.
*
* @param percent percentage between 0 and 100 inclusive.
*/
protected void fireProgress(Integer percent) {
if ((percent < 0) || (percent > 100)) {
throw new IllegalArgumentException("AbstractPlugin: fireProgress: percent must be between 0 and 100 inclusive. arg: " + percent);
}
Datum percentage = new Datum("Percent", percent, null);
fireProgress(new PluginEvent(new DataSet(percentage, this)));
}
@Override
public String getCitation() {
return DEFAULT_CITATION;
}
@Override
public String pluginDescription() {
return null;
}
@Override
public String pluginUserManualURL() {
return "https://bitbucket.org/tasseladmin/tassel-5-source/wiki/UserManual";
}
//
// Methods for PluginListener.
//
/**
* Returns data set after complete.
*
* @param event event
*/
@Override
public void dataSetReturned(PluginEvent event) {
DataSet input = (DataSet) event.getSource();
performFunction(input);
}
/**
* No operation for this abstract class.
*/
@Override
public void progress(PluginEvent event) {
// The default action of a plugin is to do
// nothing when another plugin reports its
// progress. This is intended to be implemented
// by GUI applications to show the user the
// progress of an interactive action.
}
public void reverseTrace(int indent) {
if (myTrace) {
return;
}
indent(indent);
System.out.println(getClass().getName());
Iterator itr = myInputs.iterator();
while (itr.hasNext()) {
try {
AbstractPlugin current = (AbstractPlugin) itr.next();
current.reverseTrace(indent + 3);
} catch (Exception e) {
// do nothing
}
}
myTrace = true;
}
public void trace(int indent) {
if (myTrace) {
return;
}
indent(indent);
System.out.println(getClass().getName());
Iterator itr = myListeners.iterator();
while (itr.hasNext()) {
try {
AbstractPlugin current = (AbstractPlugin) itr.next();
current.trace(indent + 3);
} catch (Exception e) {
// do nothing
}
}
myTrace = true;
}
private void indent(int indent) {
for (int i = 0; i < indent; i++) {
System.out.print(" ");
}
}
@Override
public void setThreaded(boolean threaded) {
myThreaded = threaded;
}
@Override
public boolean cancel() {
return false;
}
@Override
public void run() {
performFunction(null);
}
@Override
public void progress(int percent, Object meta) {
fireProgress(percent);
}
@Override
public boolean wasCancelled() {
return myWasCancelled;
}
}
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