s_mart: smart_toolShed/SMART/Java/Sav/ProgramOption.java comparison

comparison smart_toolShed/SMART/Java/Sav/ProgramOption.java @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

author	yufei-luo
date	Thu, 17 Jan 2013 10:52:14 -0500
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+:e0f8dcca02ed
+/**
+*
+* Copyright INRA-URGI 2009-2010
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software. You can use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty and the software's author, the holder of the
+* economic rights, and the successive licensors have only limited
+* liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading, using, modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean that it is complicated to manipulate, and that also
+* therefore means that it is reserved for developers and experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and, more generally, to use and operate it in the
+* same conditions as regards security.
+*
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+*/
+import java.util.*;
+import java.awt.*;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.io.*;
+import javax.swing.*;
+import javax.swing.filechooser.*;
+import javax.swing.border.*;
+import javax.swing.SwingUtilities;
+public class ProgramOption {
+boolean       input;
+String        identifier;
+String        type;
+String        comment;
+boolean       compulsory;
+String[]      format;
+String        formatIdentifier;
+ProgramOption associatedOption;
+String        defaultValue;
+String[]      choices;
+JComponent    component;
+JPanel        panel;
+public ProgramOption() {
+this.input            = true;
+this.identifier       = null;
+this.type             = null;
+this.comment          = null;
+this.compulsory       = false;
+this.format           = null;
+this.formatIdentifier = null;
+this.associatedOption = null;
+this.defaultValue     = "";
+this.choices          = null;
+this.component        = null;
+this.panel            = null;
+}
+public void setInput(boolean input) {
+this.input = input;
+}
+public void setIdentifier(String identifier) {
+this.identifier = identifier;
+}
+public void setType(String type) {
+this.type = type;
+}
+public void setComment(String comment) {
+this.comment = comment;
+}
+public void setCompulsory(boolean compulsory) {
+this.compulsory = compulsory;
+}
+public void setFormat(String[] format) {
+this.format = format;
+}
+public void setFormat(String format) {
+this.format    = new String[1];
+this.format[0] = format;
+}
+public void setFormatIdentifier(String formatIdentifier) {
+this.formatIdentifier = formatIdentifier;
+}
+public void setAssociatedOption(ProgramOption option) {
+this.associatedOption = option;
+}
+public void setChoices(String[] choices) {
+this.choices = choices;
+}
+public void setDefault(String defaultValue) {
+this.defaultValue = defaultValue;
+}
+public boolean isInput() {
+return this.input;
+}
+public JPanel getPanel() {
+if (this.panel != null) {
+return this.panel;
+}
+String comment = this.comment;
+if (this.compulsory) {
+comment += " [*]";
+}
+GridLayout horizontalLayout = new GridLayout(1, 0);
+this.panel = new JPanel(false);
+this.panel.setLayout(horizontalLayout);
+JLabel label = new JLabel(comment);
+if (this.type == null) {
+System.out.println("Error! Option '" + this.identifier + "' is not set!");
+}
+if (("int".compareToIgnoreCase(this.type) == 0) || ("float".compareToIgnoreCase(this.type) == 0) || ("string".compareToIgnoreCase(this.type) == 0) || (("file".compareToIgnoreCase(this.type) == 0) && (!this.input))) {
+this.component = new JTextField();
+if (this.defaultValue != null) {
+((JTextField) this.component).setText(this.defaultValue);
+}
+label.setLabelFor(this.component);
+this.panel.add(label);
+this.panel.add(this.component);
+}
+else if ("file".compareToIgnoreCase(this.type) == 0) {
+this.component = new JList(Global.fileNames);
+((JList) this.component).setVisibleRowCount(1);
+JScrollPane scroll = new JScrollPane(this.component);
+Box box = Box.createHorizontalBox();
+box.add(Box.createRigidArea(new Dimension(0, 100)));
+box.add(scroll);
+label.setLabelFor(this.component);
+this.panel.add(label);
+this.panel.add(box);
+}
+else if ("boolean".compareToIgnoreCase(this.type) == 0) {
+this.component = new JCheckBox();
+if ((this.defaultValue != null) && (this.defaultValue.compareToIgnoreCase("true") == 0)) {
+((JCheckBox) this.component).setSelected(true);
+}
+label.setLabelFor(this.component);
+this.panel.add(label);
+this.panel.add(this.component);
+}
+else if ("format".compareToIgnoreCase(this.type) == 0) {
+Vector < String > formats = new Vector < String > ();
+for (String format: this.format) {
+formats.addAll(Global.formats.getFormats(format).getFormats());
+}
+this.component = new JComboBox(formats);
+label.setLabelFor(this.component);
+this.panel.add(label);
+this.panel.add(this.component);
+}
+else if ("files".compareToIgnoreCase(this.type) == 0) {
+JButton button = new JButton("file...");
+this.component = new JTextField();
+label.setLabelFor(this.component);
+this.panel.add(label);
+this.panel.add(this.component);
+this.panel.add(button);
+Global.otherFileConcatenationChooser.put(button, (JTextField) this.component);
+}
+else if ("directory".compareToIgnoreCase(this.type) == 0) {
+JButton button = new JButton("directory...");
+this.component = new JTextField();
+label.setLabelFor(this.component);
+this.panel.add(label);
+JPanel rightPanel = new JPanel(false);
+rightPanel.setLayout(new BoxLayout(rightPanel, BoxLayout.LINE_AXIS));
+rightPanel.add(this.component);
+rightPanel.add(button);
+this.panel.add(rightPanel);
+Global.otherDirectoriesChooser.put(button, (JTextField) this.component);
+}
+else if ("choice".compareToIgnoreCase(this.type) == 0) {
+this.component = new JComboBox(this.choices);
+label.setLabelFor(this.component);
+this.panel.add(label);
+this.panel.add(this.component);
+}
+else {
+System.out.println("Do not know how to read type " + this.type);
+}
+return this.panel;
+}
+public JComponent getComponent() {
+if (component == null) {
+this.getPanel();
+}
+return this.component;
+}
+private String getValue() {
+if (("int".equals(this.type)) || ("float".equals(this.type)) || ("string".equals(this.type)) || (("file".equals(this.type)) && (! this.input)) || ("directory".equals(this.type)) || ("files".equals(this.type)))  {
+String s = ((JTextField) this.component).getText();
+if ("None".equals(s)) {
+return "";
+}
+return s;
+}
+if ("file".equals(this.type)) {
+return (String) ((JList) this.component).getSelectedValue();
+}
+if ("boolean".equals(this.type)) {
+return ((JCheckBox) this.component).isSelected()? "true": "false";
+}
+if ("format".equals(this.type)) {
+return (String) ((JComboBox) this.component).getSelectedItem();
+}
+return null;
+}
+public String checkValue() {
+String value = this.getValue();
+if ((this.compulsory) && ((value == null) || ("".equals(value)))) {
+return "Option '" + this.comment + "' has no value... Please specify it.\n";
+}
+if ("int".equals(this.type)) {
+if ((value != null) && (! "".equals(value)) && (! "None".equals(value))) {
+try {
+int i = Integer.parseInt(value);
+}
+catch (NumberFormatException e) {
+return "Option '" + this.comment + "' should be an integer... Please correct it.\n";
+}
+}
+}
+else if ("float".equals(this.type)) {
+if ((value != null) && (! "".equals(value))) {
+try {
+float i = Float.parseFloat(value);
+}
+catch (NumberFormatException e) {
+return "Option '" + this.comment + "' should be a float... Please correct it.\n";
+}
+}
+}
+return null;
+}
+public LinkedList <String> getCommand() {
+LinkedList <String> list = new LinkedList <String> ();
+if (("int".equals(this.type)) || ("float".equals(this.type)) || ("string".equals(this.type)) || (("file".equals(this.type)) && (! this.input)) || ("format".equals(this.type)) || ("directory".equals(this.type)) || ("files".equals(this.type))) {
+String value = this.getValue();
+if (value.length() == 0) {
+return list;
+}
+list.add(this.identifier);
+list.add(value);
+return list;
+}
+if ("file".equals(this.type)) {
+String fileName = (String) ((JList) this.component).getSelectedValue();
+if (fileName == null) {
+return list;
+}
+list.add(this.identifier);
+list.add(this.getValue());
+return list;
+}
+if ("boolean".equals(this.type)) {
+if ("true".equals(this.getValue())) {
+list.add(this.identifier);
+}
+return list;
+}
+return null;
+}
+public File getOutputFile() {
+if (this.input) return null;
+String format = "";
+if (this.format != null) {
+format = this.format[0];
+}
+if (this.associatedOption != null) {
+format = this.associatedOption.getValue();
+}
+return new File(this.getValue() + "." + format, Global.formats.getFormatType(format), format);
+}
+}

Mercurial > repos > yufei-luo > s_mart

comparison smart_toolShed/SMART/Java/Sav/ProgramOption.java @ 0:e0f8dcca02ed