/*
Part of the CircDesigNA Project - http://cssb.utexas.edu/circdesigna
Copyright (c) 2010-11 Ben Braun
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation, version 2.1.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General
Public License along with this library; if not, write to the
Free Software Foundation, Inc., 59 Temple Place, Suite 330,
Boston, MA 02111-1307 USA
*/
package circdesignagui;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.Point;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import javax.swing.BorderFactory;
import javax.swing.DefaultListModel;
import javax.swing.JComponent;
import javax.swing.JList;
import javax.swing.JPanel;
import javax.swing.JScrollPane;
import javax.swing.JTextArea;
import javax.swing.JTextField;
import javax.swing.ListSelectionModel;
import javax.swing.OverlayLayout;
import javax.swing.event.CaretEvent;
import javax.swing.event.CaretListener;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import circdesigna.AbstractDomainDesignTarget;
import circdesigna.CircDesigNAOptions;
import circdesigna.DesignIntermediateReporter;
import circdesigna.DomainDefinitions;
import circdesigna.DomainPolymerGraph;
import circdesigna.CircDesigNA.ScorePenalty;
import circdesigna.abstractpolymer.DnaDefinition;
import circdesigna.config.CircDesigNAConfig;
import circdesigna.energy.ConstraintsNAFoldingImpl;
import circdesigna.energy.OneMatrixNAFolding;
import circdesigna.impl.CircDesigNAImpl;
import circdesigna.impl.SequencePenaltiesImpl;
/**
* Displays a window which allows for debugging of the individual components of the objective function,
* Score.
*/
public class FoldingImplTestGui extends ThemedApplet{
ScaleUtils su;
public FoldingImplTestGui(){
su = new ScaleUtils();
}
boolean started = false;
public void start(){
if (started){
return;
}
started = true;
parseThemeColors();
setBackground(Color.white);
new Thread(){
public void run(){
runStartRoutine();
}
}.start();
}
private CircDesigNAConfig config;
private ConstraintsNAFoldingImpl fil;
private StructurePenaltyTriangle triangleApplet;
private JPanel triangleAppletProxy;
private JList possibleViews;
private int[][] domain_sequences;
private DefaultListModel possibleViews_model;
private JTextArea domainDefs,errText,penaltyScore;
private JTextField moleculeInput1, moleculeInput2;
private String molAtextLatch = "", molBtextLatch = "", domainDefsTextLatch = "";
private void updateViewTriangle() {
PenaltyObject cur = (PenaltyObject)possibleViews.getSelectedValue();
if (cur!=null && domain_sequences!=null){
int[][] nullMarkings = new int[domain_sequences.length][];
for(int k = 0; k < nullMarkings.length; k++){
nullMarkings[k] = new int[domain_sequences[k].length];
}
triangleApplet.setPenalty(cur.sp, domain_sequences, nullMarkings, fil);
double score = triangleApplet.getEvalScore();
penaltyScore.setText(String.format("%.3f",score));
}
}
private void runStartRoutine() {
//Logic
config = new CircDesigNAConfig();
//fil = new CircDesigNAMCSFolder(config);
fil = new ConstraintsNAFoldingImpl(config);
//Gui
JPanel mainPanel = new JPanel();
mainPanel.setLayout(new BorderLayout());
JPanel leftPanel = skinPanel(new JPanel());
final CaretListener cl = new CaretListener(){
public void caretUpdate(CaretEvent e) {
updatepossibleViews();
}
};
float leftProportion = .5f;
{
domainDefs = new JTextArea("");
JScrollPane domainDefsScroll = new JScrollPane(domainDefs);
moleculeInput1 = new JTextField("");
moleculeInput2 = new JTextField("");
leftPanel.setLayout(new FlowLayout());
final JComponent domainDefsHolder = skinGroup(domainDefsScroll, "Domain Definition");
leftPanel.add(domainDefsHolder);
final JComponent molIn1Holder = skinGroup(moleculeInput1, "Molecule A Input");
leftPanel.add(molIn1Holder);
final JComponent molIn2Holder = skinGroup(moleculeInput2, "Molecule B Input");
leftPanel.add(molIn2Holder);
su.addPreferredSize(leftPanel, leftProportion, 1f);
int texHeight = 50;
possibleViews = new JList();
possibleViews.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
//possibleViews.setBorder(BorderFactory.createEtchedBorder());
possibleViews.addListSelectionListener(new ListSelectionListener(){
public void valueChanged(ListSelectionEvent e) {
updateViewTriangle();
}
});
JScrollPane possibleViewScroll = new JScrollPane(possibleViews);
possibleViews_model = new DefaultListModel();
JComponent possibleViewsInHolder = skinGroup(possibleViewScroll, "Computed Constraints");
leftPanel.add(possibleViewsInHolder);
float sumH = 0f;
int sumHD = 0;
su.addPreferredSize(domainDefsHolder, leftProportion, .3f, 0, -18); sumH += .3f;
su.addPreferredSize(domainDefsScroll, leftProportion, .3f, -9, -18);
su.addPreferredSize(molIn1Holder, leftProportion, 0, 0, texHeight); sumHD+= texHeight;
su.addPreferredSize(molIn2Holder, leftProportion, 0, 0, texHeight); sumHD+= texHeight;
su.addPreferredSize(moleculeInput1, leftProportion, 0, -9, texHeight*2/3);
su.addPreferredSize(moleculeInput2, leftProportion, 0, -9, texHeight*2/3);
su.addPreferredSize(possibleViewScroll, leftProportion, 1f-sumH, -9, -sumHD - 18);
su.addPreferredSize(possibleViewsInHolder, leftProportion, 1f-sumH, 0, -sumHD - 18);
updatepossibleViews();
moleculeInput1.addCaretListener(cl);
moleculeInput2.addCaretListener(cl);
domainDefs.addCaretListener(cl);
}
JPanel rightPanel = skinPanel(new JPanel());
{
errText = new JTextArea("");
errText.setEditable(false);
errText.setBorder(BorderFactory.createEtchedBorder());
JComponent errTexH = skinGroup(errText, "Errors");
penaltyScore = new JTextArea("");
penaltyScore.setEditable(false);
penaltyScore.setBorder(BorderFactory.createEtchedBorder());
JComponent penaltyScoreH = skinGroup(penaltyScore, "Penalty Evaluation");
triangleAppletProxy = skinPanel(new JPanel(){
public void setPreferredSize(Dimension dim){
super.setPreferredSize(dim);
Point loc = getLocation();
loc.translate(8, 8);
Container parent = getParent();
for(int k = 0; k < 3; k++){
loc.translate(parent.getLocation().x,parent.getLocation().y);
parent = parent.getParent();
}
triangleApplet.setLocation(loc);
}
});
triangleApplet = new StructurePenaltyTriangle(this,config){
public void draw(){
triangleApplet.setSize(new Dimension(triangleAppletProxy.getPreferredSize().width -16, triangleAppletProxy.getPreferredSize().height -16));
super.draw();
}
};
triangleAppletProxy.setBorder(BorderFactory.createLineBorder(Color.black, 8));
JComponent triangleproxyGroup = skinGroup(triangleAppletProxy, "Structure analysis, displaying MFE");
rightPanel.add(errTexH);
rightPanel.add(penaltyScoreH);
rightPanel.add(triangleproxyGroup);
su.addPreferredSize(errText, 1f-leftProportion, .2f, -9, -9);
su.addPreferredSize(errTexH, 1f-leftProportion, .2f);
su.addPreferredSize(penaltyScore, 1f-leftProportion, .1f, -9, -9);
su.addPreferredSize(penaltyScoreH, 1f-leftProportion, .1f);
su.addPreferredSize(triangleAppletProxy, 1f-leftProportion, 0, -8, 0, 1f);
su.addPreferredSize(triangleproxyGroup, 1f-leftProportion, 0, 0, 18, 1f);
su.addPreferredSize(rightPanel, 1-leftProportion, 1f);
}
mainPanel.add(leftPanel, BorderLayout.WEST);
mainPanel.add(rightPanel, BorderLayout.CENTER);
su.addPreferredSize(mainPanel, 1f, 1f);
setLayout(new OverlayLayout(this));
add(triangleApplet);
add(mainPanel);
triangleApplet.init();
triangleApplet.start();
validate();
}
private void updatepossibleViews() {
boolean changed = !(molAtextLatch.equals(moleculeInput1.getText()) && molBtextLatch.equals(moleculeInput2.getText()) && domainDefs.getText().equals(domainDefsTextLatch));
if (changed){
molAtextLatch = moleculeInput1.getText();
molBtextLatch = moleculeInput2.getText();
domainDefsTextLatch = domainDefs.getText();
//Build new model
Collection<PenaltyObject> penalties = getPenalties();
possibleViews_model.clear();
for(PenaltyObject q : penalties){
possibleViews_model.addElement(q);
}
possibleViews.setModel(possibleViews_model);
}
}
private Collection<PenaltyObject> getPenalties() {
ArrayList<PenaltyObject> penalties = new ArrayList();
try {
CircDesigNAImpl ddi = new CircDesigNAImpl(fil,new SequencePenaltiesImpl(config),config);
DomainDefinitions dsd = new DomainDefinitions(config);
DomainDefinitions.readDomainDefs(domainDefs.getText(), dsd);
DomainPolymerGraph dsg = new DomainPolymerGraph(dsd);
AbstractDomainDesignTarget target = new AbstractDomainDesignTarget(dsd,config);
for(int whichMolecule = 0; whichMolecule <= 1; whichMolecule++){
if (whichMolecule==0){
target.addTargetStructure(moleculeInput1.getText());
} else {
target.addTargetStructure(moleculeInput2.getText());
}
}
DesignIntermediateReporter dir = new DesignIntermediateReporter();
//Make domain array
int[] domainLengths = dsd.domainLengths;
int[][] domain = new int[domainLengths.length][];
for(int i = 0; i < domain.length; i++){
domain[i] = new int[domainLengths[i]];
String constraint = dsd.getConstraint(i);
for(int j = 0; j < domain[i].length; j++){
domain[i][j] = config.monomer.decodeConstraintChar(constraint.charAt(j));
if (config.monomer.noFlags(domain[i][j])==DnaDefinition.NOBASE){
throw new RuntimeException("Invalid sequence given for "+dsd.getDomainName(i));
}
}
}
List<ScorePenalty> listPenalties = ddi.listPenalties(target, dir, domain, CircDesigNAOptions.getDefaultOptions(config), dsd);
for(ScorePenalty sp : listPenalties){
penalties.add(new PenaltyObject(sp, dsd));
}
domain_sequences = domain;
errText.setText("No problems here");
} catch (Throwable e){
errText.setText(e.getMessage());
}
return penalties;
}
private class PenaltyObject {
public String myString;
private ScorePenalty sp;
public PenaltyObject(ScorePenalty sp, DomainDefinitions dsd){
myString = sp.toString(dsd);
this.sp = sp;
}
public String toString(){
return myString;
}
}
public void invalidate(){
//Good time as any.
int w = getWidth();
int h = getHeight();
float ar = 550f/480f;
w = (int) Math.min(w,h*ar);
su.pushSizes(w,h);
super.invalidate();
}
public void addModalScale(Runnable runnable) {
}
public JPanel getModalPanel() {
return null;
}
public void removeAllModalScale() {
}
public boolean modalPanelIsOccupied() {
return false;
}
}