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Open Source Chemistry Library
/*
* Copyright (c) 1997 - 2016
* Actelion Pharmaceuticals Ltd.
* Gewerbestrasse 16
* CH-4123 Allschwil, Switzerland
*
* All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice, this
* list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
* 3. Neither the name of the the copyright holder nor the
* names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
* ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
* ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*
*/
package com.actelion.research.gui;
import com.actelion.research.chem.ExtendedMolecule;
import com.actelion.research.chem.Molecule;
import info.clearthought.layout.TableLayout;
import javax.swing.*;
import java.awt.*;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
@Deprecated
public class JAtomLabelDialog extends JDialog implements ActionListener {
public static final long serialVersionUID = 0x20080213;
private static final String[] RADICAL_STATES = { "None", "One electron (duplet)", "Two electrons (triplet)", "Two electrons (singulet)" };
private Frame mOwner;
private ExtendedMolecule mMol;
private int mAtom;
private JTextField mTextFieldLabel,mTextFieldMass,mTextFieldValence;
private JComboBox mComboBoxRadical;
protected JAtomLabelDialog(Frame owner, ExtendedMolecule mol, int atom) {
super(owner, true);
mOwner = owner;
mMol = mol;
mAtom = atom;
init();
}
private void init() {
JPanel p1 = new JPanel();
double[][] size = { {8, TableLayout.PREFERRED, 8, TableLayout.PREFERRED, 8 },
{8, TableLayout.PREFERRED, 4, TableLayout.PREFERRED,
12, TableLayout.PREFERRED, 4, TableLayout.PREFERRED,
12, TableLayout.PREFERRED, 4, TableLayout.PREFERRED,
12, TableLayout.PREFERRED, 8} };
p1.setLayout(new TableLayout(size));
mTextFieldLabel = new JTextField(1);
mTextFieldLabel.addActionListener(this);
p1.add(new JLabel("Atom Label:", JLabel.RIGHT), "1,1");
p1.add(mTextFieldLabel, "3,1");
p1.add(new JLabel("(examples: 'D', 'Li', 'Cys', 'R12', 'R3@C')", JLabel.RIGHT), "1,3,3,3");
mTextFieldMass = new JTextField(1);
mTextFieldMass.addActionListener(this);
p1.add(new JLabel("Atom Mass:", JLabel.RIGHT), "1,5");
p1.add(mTextFieldMass, "3,5");
p1.add(new JLabel("(empty for natural abundance)", JLabel.RIGHT), "1,7,3,7");
mTextFieldValence = new JTextField(1);
mTextFieldValence.addActionListener(this);
p1.add(new JLabel("Abnormal Valence:", JLabel.RIGHT), "1,9");
p1.add(mTextFieldValence, "3,9");
p1.add(new JLabel("(empty for default valence)", JLabel.RIGHT), "1,11,3,11");
if (mAtom != -1) {
String label = mMol.getAtomLabel(mAtom);
String customLabel = mMol.getAtomCustomLabel(mAtom);
mTextFieldLabel.setText(customLabel == null ? label : customLabel+"@"+label);
if (mMol.getAtomMass(mAtom) != 0)
mTextFieldMass.setText(""+mMol.getAtomMass(mAtom));
if (mMol.getAtomAbnormalValence(mAtom) != -1)
mTextFieldValence.setText(""+mMol.getAtomAbnormalValence(mAtom));
}
mComboBoxRadical = new JComboBox(RADICAL_STATES);
if (mAtom != -1) {
int state = mMol.getAtomRadical(mAtom);
mComboBoxRadical.setSelectedIndex(state == Molecule.cAtomRadicalStateD ? 1 :
state == Molecule.cAtomRadicalStateT ? 2 :
state == Molecule.cAtomRadicalStateS ? 3 : 0);
}
p1.add(new JLabel("Radical State:", JLabel.RIGHT), "1,13");
p1.add(mComboBoxRadical, "3,13");
JPanel p2 = new JPanel();
p2.setBorder(BorderFactory.createEmptyBorder(12, 8, 8, 8));
p2.setLayout(new BorderLayout());
JPanel ibp = new JPanel();
ibp.setLayout(new GridLayout(1, 2, 8, 0));
JButton bcancel = new JButton("Cancel");
bcancel.addActionListener(this);
ibp.add(bcancel);
JButton bok = new JButton("OK");
bok.addActionListener(this);
ibp.add(bok);
p2.add(ibp, BorderLayout.EAST);
getContentPane().add(p1, BorderLayout.CENTER);
getContentPane().add(p2, BorderLayout.SOUTH);
getRootPane().setDefaultButton(bok);
pack();
setLocationRelativeTo(mOwner);
setVisible(true);
}
public void actionPerformed(ActionEvent e) {
if (e.getSource() instanceof JTextField)
processAtomLabel();
else if (e.getActionCommand() == "Cancel")
dispose();
else if (e.getActionCommand() == "OK")
processAtomLabel();
}
private void processAtomLabel() {
String text = mTextFieldLabel.getText();
String customLabel = null;
if (text.length() != 0) {
int index = text.indexOf('@');
if (index != -1) {
customLabel = text.substring(0, index);
text = text.substring(index+1);
}
}
if (text.length() != 0) {
int atomicNo = Molecule.getAtomicNoFromLabel(text);
if (atomicNo != 0 || text.equals("?")) {
int mass = 0;
if (mTextFieldMass.getText().length() != 0) {
try {
mass = Integer.parseInt(mTextFieldMass.getText());
if (mass < Molecule.cRoundedMass[atomicNo] - 18
|| mass > Molecule.cRoundedMass[atomicNo] + 12) {
JOptionPane.showMessageDialog(mOwner, "Your mass is out of range!");
return;
}
}
catch (NumberFormatException nfe) {
JOptionPane.showMessageDialog(mOwner, "Your mass is not a number!");
return;
}
}
int valence = -1;
if (mTextFieldValence.getText().length() != 0) {
try {
valence = Integer.parseInt(mTextFieldValence.getText());
if (valence < 0 || valence > 15) {
JOptionPane.showMessageDialog(mOwner, "Your valence is out of range!");
return;
}
}
catch (NumberFormatException nfe) {
JOptionPane.showMessageDialog(mOwner, "Your valence is not a number!");
return;
}
}
int radical = mComboBoxRadical.getSelectedIndex() == 1 ? Molecule.cAtomRadicalStateD :
mComboBoxRadical.getSelectedIndex() == 2 ? Molecule.cAtomRadicalStateT :
mComboBoxRadical.getSelectedIndex() == 3 ? Molecule.cAtomRadicalStateS : 0;
mMol.changeAtom(mAtom, atomicNo, mass, valence, radical);
if (customLabel != null)
mMol.setAtomCustomLabel(mAtom, customLabel);
dispose();
}
}
}
}