package PDVGUI.gui.utils.Export;
import PDVGUI.gui.PDVMainClass;
import PDVGUI.gui.SpectrumLibDisplay;
import PDVGUI.utils.Export;
import com.compomics.util.enumeration.ImageType;
import com.compomics.util.experiment.biology.Ion;
import com.compomics.util.experiment.biology.Peptide;
import com.compomics.util.experiment.biology.ions.PeptideFragmentIon;
import com.compomics.util.experiment.biology.ions.TagFragmentIon;
import com.compomics.util.experiment.identification.SpectrumIdentificationAssumption;
import com.compomics.util.experiment.identification.identification_parameters.PtmSettings;
import com.compomics.util.experiment.identification.matches.IonMatch;
import com.compomics.util.experiment.identification.spectrum_annotation.AnnotationSettings;
import com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationSettings;
import com.compomics.util.experiment.identification.spectrum_annotation.SpectrumAnnotator;
import com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.PeptideSpectrumAnnotator;
import com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators.TagSpectrumAnnotator;
import com.compomics.util.experiment.identification.spectrum_assumptions.PeptideAssumption;
import com.compomics.util.experiment.identification.spectrum_assumptions.TagAssumption;
import com.compomics.util.experiment.massspectrometry.MSnSpectrum;
import com.compomics.util.experiment.massspectrometry.Peak;
import com.compomics.util.experiment.massspectrometry.Precursor;
import com.compomics.util.gui.JOptionEditorPane;
import com.compomics.util.gui.spectrum.SequenceFragmentationPanel;
import com.compomics.util.gui.spectrum.SpectrumPanel;
import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX;
import com.compomics.util.preferences.SequenceMatchingPreferences;
import com.compomics.util.preferences.UtilitiesUserPreferences;
import com.jgoodies.forms.layout.FormLayout;
import org.apache.batik.transcoder.TranscoderException;
import javax.swing.*;
import java.awt.*;
import java.awt.event.WindowEvent;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashMap;
import java.util.regex.Pattern;
/**
* Real time export batch spectrum
* Created by Ken on 8/9/2017.
*/
public class RealTimeExportJDialog extends JDialog {
private JPanel secondarySpectrumPlotsJPanel;
private JPanel spectrumJPanel;
private JPanel resizeJPanel;
private JSplitPane spectrumSplitPane;
/**
* Forward ions searched for (a, b or c)
*/
private Integer forwardIon;
/**
* Reward ions searched for (x, y or z)
*/
private Integer rewindIon;
/**
* SpectrumPanel to paint spectrum import from utilities
*/
private SpectrumPanel spectrumPanel;
/**
* Utilities user preferences
*/
private UtilitiesUserPreferences utilitiesUserPreferences;
/**
* Annotation setting
*/
private AnnotationSettings annotationSettings;
/**
* Spectrum annotator
*/
private PeptideSpectrumAnnotator peptideSpectrumAnnotator;
/**
* Spectrum tagSpectrumAnnotator
*/
private TagSpectrumAnnotator tagSpectrumAnnotator = new TagSpectrumAnnotator();
/**
* SpecificAnnotationSettings
*/
private SpecificAnnotationSettings specificAnnotationSettings;
/**
* Delta mass map
*/
private HashMap<Double, String> deltaMassMap;
/**
* PTM settings
*/
private PtmSettings ptmSettings;
/**
* Image type
*/
private ImageType imageType;
/**
* Output path
*/
private String outputPath;
/**
* Parent class
*/
private PDVMainClass pdvMainClass;
/**
* Parent class
*/
private SpectrumLibDisplay spectrumLibDisplay;
/**
* Spectrum panel height
*/
private Integer height;
/**
* Spectrum panel width
*/
private Integer width;
/**
* The length unit
*/
private String unit;
/**
* Remove illegal pattern
*/
private static Pattern FilePattern = Pattern.compile("[\\\\/:*?\"<>|]");
/**
* The resize panel width
*/
private Integer resizeJPanelWidth;
/**
* The resize panel length
*/
private Integer resizeJPanelHeight;
/**
* Parent jFrame
*/
private JFrame parentFrame;
/**
* Current peptide sequence
*/
private String currentPeptide;
/**
* Constructor
*@param forwardIon Forward Ion
* @param rewindIon Rewind Ion
* @param height Height
* @param width Width
* @param unit Unit
* @param peptideSpectrumAnnotator Peptide spectrum annotator
* @param specificAnnotationSettings specificAnnotationSettings
* @param pdvMainClass Parent class
* @param deltaMassMap deltaMassMap
* @param ptmSettings ptmSettings
* @param imageType imageType
* @param outputPath outputPath
*/
public RealTimeExportJDialog(Integer forwardIon, Integer rewindIon, Integer height, Integer width, String unit
, PeptideSpectrumAnnotator peptideSpectrumAnnotator, SpecificAnnotationSettings specificAnnotationSettings, PDVMainClass pdvMainClass
, HashMap<Double, String> deltaMassMap, PtmSettings ptmSettings, ImageType imageType, String outputPath){
this.forwardIon = forwardIon;
this.rewindIon = rewindIon;
this.pdvMainClass = pdvMainClass;
this.parentFrame = pdvMainClass;
this.utilitiesUserPreferences = pdvMainClass.utilitiesUserPreferences;
this.annotationSettings = pdvMainClass.getAnnotationSettings();
this.peptideSpectrumAnnotator = peptideSpectrumAnnotator;
this.specificAnnotationSettings = specificAnnotationSettings;
this.deltaMassMap = deltaMassMap;
this.ptmSettings = ptmSettings;
this.imageType = imageType;
this.outputPath = outputPath;
this.height = height;
this.width = width;
this.unit = unit;
initComponent();
this.setVisible(true);
}
/**
* Constructor
* @param forwardIon Forward Ion
* @param rewindIon Rewind Ion
* @param height Height
* @param width Width
* @param unit Unit
* @param peptideSpectrumAnnotator Peptide spectrum annotator
* @param specificAnnotationSettings specificAnnotationSettings
* @param spectrumLibDisplay Parent class
* @param deltaMassMap deltaMassMap
* @param ptmSettings ptmSettings
* @param imageType imageType
* @param outputPath outputPath
*/
public RealTimeExportJDialog(Integer forwardIon, Integer rewindIon, Integer height, Integer width, String unit
, PeptideSpectrumAnnotator peptideSpectrumAnnotator, SpecificAnnotationSettings specificAnnotationSettings, SpectrumLibDisplay spectrumLibDisplay
, HashMap<Double, String> deltaMassMap, PtmSettings ptmSettings, ImageType imageType, String outputPath){
this.forwardIon = forwardIon;
this.rewindIon = rewindIon;
this.spectrumLibDisplay = spectrumLibDisplay;
this.parentFrame = spectrumLibDisplay;
this.utilitiesUserPreferences = spectrumLibDisplay.utilitiesUserPreferences;
this.annotationSettings = spectrumLibDisplay.annotationSettings;
this.peptideSpectrumAnnotator = peptideSpectrumAnnotator;
this.specificAnnotationSettings = specificAnnotationSettings;
this.deltaMassMap = deltaMassMap;
this.ptmSettings = ptmSettings;
this.imageType = imageType;
this.outputPath = outputPath;
this.height = height;
this.width = width;
this.unit = unit;
initComponent();
this.setVisible(true);
}
/**
* Init all GUI component
*/
private void initComponent(){
spectrumJPanel = new JPanel();
secondarySpectrumPlotsJPanel = new JPanel();
spectrumSplitPane = new JSplitPane();
resizeJPanel = new JPanel();
JPanel spectrumOuterJPanel = new JPanel();
setDefaultCloseOperation(javax.swing.WindowConstants.DO_NOTHING_ON_CLOSE);
setTitle("PDV - Export");
setBackground(new java.awt.Color(255, 255, 255));
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
formWindowClosing(evt);
}
});
spectrumSplitPane.setBackground(Color.WHITE);
spectrumSplitPane.setBorder(null);
spectrumSplitPane.setDividerLocation(90);
spectrumSplitPane.setDividerSize(0);
spectrumSplitPane.setOrientation(JSplitPane.VERTICAL_SPLIT);
secondarySpectrumPlotsJPanel.setMinimumSize(new Dimension(0, 80));
secondarySpectrumPlotsJPanel.setOpaque(false);
secondarySpectrumPlotsJPanel.setLayout(new BoxLayout(secondarySpectrumPlotsJPanel, BoxLayout.LINE_AXIS));
spectrumSplitPane.setTopComponent(secondarySpectrumPlotsJPanel);
spectrumOuterJPanel.setBackground(new Color(255, 255, 255));
spectrumJPanel.setBackground(new Color(255, 255, 255));
spectrumJPanel.setLayout(new BorderLayout());
GroupLayout spectrumOuterJPanelLayout = new GroupLayout(spectrumOuterJPanel);
spectrumOuterJPanel.setLayout(spectrumOuterJPanelLayout);
spectrumOuterJPanelLayout.setHorizontalGroup(
spectrumOuterJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(spectrumJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE, Short.MAX_VALUE)
);
spectrumOuterJPanelLayout.setVerticalGroup(
spectrumOuterJPanelLayout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addGroup(spectrumOuterJPanelLayout.createSequentialGroup()
.addComponent(spectrumJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.PREFERRED_SIZE, Short.MAX_VALUE))
);
spectrumSplitPane.setRightComponent(spectrumOuterJPanel);
resizeJPanel.add(spectrumSplitPane);
GroupLayout layout = new GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(resizeJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(GroupLayout.Alignment.LEADING)
.addComponent(resizeJPanel, GroupLayout.DEFAULT_SIZE, GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
);
pack();
}
/**
* Closes the dialog
* @param evt window event
*/
private void formWindowClosing(WindowEvent evt) {
this.dispose();
}
/**
* Parsing all spectrum
* @param allSpectrums All spectrum keys
*/
public void readAllSpectrums(ArrayList<ArrayList<String>> allSpectrums){
ProgressDialogX progressDialog = new ProgressDialogX(parentFrame,
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMassWait.png")),
true);
progressDialog.setPrimaryProgressCounterIndeterminate(false);
progressDialog.setTitle("Export Selected spectrum. Please Wait...");
progressDialog.setUnstoppable(true);
new Thread(new Runnable() {
public void run() {
progressDialog.setVisible(true);
}
}, "ProgressDialog").start();
int size = 0;
for(ArrayList<String> countSize:allSpectrums){
size = size + countSize.size();
}
progressDialog.setMaxPrimaryProgressCounter(size);
new Thread("Export") {
@Override
public void run() {
try {
FormLayout formLayout = new FormLayout(width + unit, height + unit);
resizeJPanel.setLayout(formLayout);
resizeJPanel.revalidate();
resizeJPanel.repaint();
resizeJPanelWidth = Math.toIntExact(Math.round(resizeJPanel.getPreferredSize().getWidth()));
resizeJPanelHeight = Math.toIntExact(Math.round(resizeJPanel.getPreferredSize().getHeight()));
if (resizeJPanelWidth <= 200 || resizeJPanelHeight<= 200) {
JOptionPane.showMessageDialog(null, "Please set a bigger size", "Warning", JOptionPane.WARNING_MESSAGE);
progressDialog.setRunFinished();
} else {
spectrumSplitPane.setBounds(0, 0, resizeJPanelWidth, resizeJPanelHeight);
spectrumSplitPane.setPreferredSize(new Dimension(resizeJPanelWidth, resizeJPanelHeight));
for (ArrayList<String> eachPage : allSpectrums) {
for (String spectrumKey : eachPage) {
if (!progressDialog.isRunCanceled()) {
MSnSpectrum mSnSpectrum;
SpectrumIdentificationAssumption spectrumIdentificationAssumption;
if (pdvMainClass != null) {
mSnSpectrum = pdvMainClass.getSpectrum(spectrumKey);
spectrumIdentificationAssumption = pdvMainClass.getspectrumIdentificationAssumption();
} else {
mSnSpectrum = spectrumLibDisplay.getSpectrum(Integer.valueOf(spectrumKey));
spectrumIdentificationAssumption = spectrumLibDisplay.getSpectrumIdentificationAssumption();
}
Thread.sleep(100);
updateSpectrum(spectrumKey, mSnSpectrum, spectrumIdentificationAssumption);
String outputPathName = outputPath + PDVMainClass.FILE_SEPARATOR + FilePattern.matcher(mSnSpectrum.getSpectrumTitle()).replaceAll("") + "_" + currentPeptide + imageType.getExtension();
exportFigure(outputPathName);
progressDialog.increasePrimaryProgressCounter();
} else {
break;
}
}
}
}
} catch (Exception e){
progressDialog.setRunFinished();
JOptionPane.showMessageDialog(parentFrame, JOptionEditorPane.getJOptionEditorPane(
"Failed to export.<br>"
+ "Please <a href=\"https://github.com/wenbostar/PDV\">contact the developers</a>."),
"Export Error", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
}
progressDialog.setRunFinished();
formWindowClosing(null);
}
}.start();
}
/**
* Reading all selections
* @param allSelections All selections
*/
public void readAllSelections(ArrayList<String> allSelections){
ProgressDialogX progressDialog = new ProgressDialogX(parentFrame,
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMass.png")),
Toolkit.getDefaultToolkit().getImage(getClass().getResource("/icons/SeaGullMassWait.png")),
true);
progressDialog.setPrimaryProgressCounterIndeterminate(false);
progressDialog.setTitle("Export Selected spectrum. Please Wait...");
progressDialog.setUnstoppable(true);
new Thread(new Runnable() {
public void run() {
progressDialog.setVisible(true);
}
}, "ProgressDialog").start();
progressDialog.setMaxPrimaryProgressCounter(allSelections.size());
new Thread("Export") {
@Override
public void run() {
try {
FormLayout formLayout = new FormLayout(width+unit, height+unit);
resizeJPanel.setLayout(formLayout);
resizeJPanel.revalidate();
resizeJPanel.repaint();
resizeJPanelWidth = Math.toIntExact(Math.round(resizeJPanel.getPreferredSize().getWidth()));
resizeJPanelHeight = Math.toIntExact(Math.round(resizeJPanel.getPreferredSize().getHeight()));
if(resizeJPanelWidth < 200){
JOptionPane.showMessageDialog(null, "The width must be bigger than 200 pixels or "+200/Toolkit.getDefaultToolkit().getScreenResolution()+" inch.", "Warning", JOptionPane.WARNING_MESSAGE);
progressDialog.setRunFinished();
} else {
spectrumSplitPane.setBounds(0, 0, resizeJPanelWidth, resizeJPanelHeight);
spectrumSplitPane.setPreferredSize(new Dimension(resizeJPanelWidth, resizeJPanelHeight));
for (String eachKey : allSelections) {
if (!progressDialog.isRunCanceled()) {
MSnSpectrum mSnSpectrum;
SpectrumIdentificationAssumption spectrumIdentificationAssumption;
if (pdvMainClass != null) {
mSnSpectrum = pdvMainClass.getSpectrum(eachKey);
spectrumIdentificationAssumption = pdvMainClass.getspectrumIdentificationAssumption();
} else {
mSnSpectrum = spectrumLibDisplay.getSpectrum(Integer.valueOf(eachKey));
spectrumIdentificationAssumption = spectrumLibDisplay.getSpectrumIdentificationAssumption();
}
updateSpectrum(eachKey, mSnSpectrum, spectrumIdentificationAssumption);
if (allSelections.indexOf(eachKey) == 0){
Thread.sleep(200);
}
Thread.sleep(100);
String outputPathName = outputPath + PDVMainClass.FILE_SEPARATOR + FilePattern.matcher(mSnSpectrum.getSpectrumTitle()).replaceAll("") + "_" + currentPeptide + imageType.getExtension();
exportFigure(outputPathName);
progressDialog.increasePrimaryProgressCounter();
} else {
break;
}
}
}
}catch (Exception e){
progressDialog.setRunFinished();
JOptionPane.showMessageDialog(parentFrame, JOptionEditorPane.getJOptionEditorPane(
"Failed to export.<br>"
+ "Please <a href=\"https://github.com/wenbostar/PDV\">contact the developers</a>."),
"Export Error", JOptionPane.ERROR_MESSAGE);
e.printStackTrace();
}
progressDialog.setRunFinished();
formWindowClosing(null);
}
}.start();
}
/**
* Update spectrum
* @param spectrumKey Spectrum key
* @param mSnSpectrum Msn spectrum
* @param spectrumIdentificationAssumption Peptide assumption
*/
private void updateSpectrum(String spectrumKey, MSnSpectrum mSnSpectrum, SpectrumIdentificationAssumption spectrumIdentificationAssumption){
try {
if (mSnSpectrum != null) {
Collection<Peak> peaks = mSnSpectrum.getPeakList();
if (peaks == null || peaks.isEmpty()) {
// do nothing, peaks list not found
} else {
boolean newMax = false;
double lastMzMaximum = 0;
try {
lastMzMaximum = mSnSpectrum.getMaxMz()*1.05;
newMax = true;
} catch (InterruptedException e) {
e.printStackTrace();
}
double lowerMzZoomRange = 0;
double upperMzZoomRange = lastMzMaximum;
if (spectrumPanel != null && spectrumPanel.getXAxisZoomRangeLowerValue() != 0 && !newMax) {
lowerMzZoomRange = spectrumPanel.getXAxisZoomRangeLowerValue();
upperMzZoomRange = spectrumPanel.getXAxisZoomRangeUpperValue();
}
Precursor precursor = mSnSpectrum.getPrecursor();
spectrumPanel = new SpectrumPanel(
mSnSpectrum.getMzValuesAsArray(), mSnSpectrum.getIntensityValuesNormalizedAsArray(),
precursor.getMz(), spectrumIdentificationAssumption.getIdentificationCharge().toString(),
"", 40, false, false, false, 2, false);
spectrumPanel.setFont(new Font("Arial", Font.PLAIN, 13));
spectrumPanel.setBounds(0, 0, resizeJPanelWidth, resizeJPanelHeight - 90);
spectrumPanel.setKnownMassDeltas(deltaMassMap);
spectrumPanel.setDeltaMassWindow(annotationSettings.getFragmentIonAccuracy());
spectrumPanel.setBorder(null);
spectrumPanel.setDataPointAndLineColor(utilitiesUserPreferences.getSpectrumAnnotatedPeakColor(), 0);
spectrumPanel.setPeakWaterMarkColor(utilitiesUserPreferences.getSpectrumBackgroundPeakColor());
spectrumPanel.setPeakWidth(utilitiesUserPreferences.getSpectrumAnnotatedPeakWidth());
spectrumPanel.setBackgroundPeakWidth(utilitiesUserPreferences.getSpectrumBackgroundPeakWidth());
specificAnnotationSettings = annotationSettings.getSpecificAnnotationPreferences(spectrumKey, spectrumIdentificationAssumption, SequenceMatchingPreferences.defaultStringMatching, SequenceMatchingPreferences.defaultStringMatching);
specificAnnotationSettings.setNeutralLossesAuto(false);
specificAnnotationSettings.clearNeutralLosses();
specificAnnotationSettings.addIonType(Ion.IonType.PEPTIDE_FRAGMENT_ION, PeptideFragmentIon.B_ION);
specificAnnotationSettings.addIonType(Ion.IonType.TAG_FRAGMENT_ION, PeptideFragmentIon.B_ION);
specificAnnotationSettings.addIonType(Ion.IonType.PEPTIDE_FRAGMENT_ION, PeptideFragmentIon.Y_ION);
specificAnnotationSettings.addIonType(Ion.IonType.TAG_FRAGMENT_ION, PeptideFragmentIon.Y_ION);
specificAnnotationSettings.addIonType(Ion.IonType.PRECURSOR_ION);
specificAnnotationSettings.addIonType(Ion.IonType.IMMONIUM_ION);
specificAnnotationSettings.addIonType(Ion.IonType.RELATED_ION);
String modSequence;
ArrayList<IonMatch> annotations;
if (spectrumIdentificationAssumption instanceof TagAssumption) {
TagAssumption tagAssumption = (TagAssumption) spectrumIdentificationAssumption;
modSequence = tagAssumption.getTag().getTaggedModifiedSequence(ptmSettings, false, false, false, false);
annotations = tagSpectrumAnnotator.getSpectrumAnnotation(annotationSettings, specificAnnotationSettings, mSnSpectrum, tagAssumption.getTag());
} else if (spectrumIdentificationAssumption instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption = (PeptideAssumption) spectrumIdentificationAssumption;
Peptide currentPeptide = peptideAssumption.getPeptide();
modSequence = currentPeptide.getTaggedModifiedSequence(ptmSettings, false, false, false, false);
annotations = peptideSpectrumAnnotator.getSpectrumAnnotationFiter(annotationSettings, specificAnnotationSettings, mSnSpectrum, peptideAssumption.getPeptide(), null, true);
} else {
throw new UnsupportedOperationException("Operation not supported for spectrumIdentificationAssumption of type " + spectrumIdentificationAssumption.getClass() + ".");
}
spectrumPanel.setAnnotations(SpectrumAnnotator.getSpectrumAnnotation(annotations), annotationSettings.getTiesResolution() == SpectrumAnnotator.TiesResolution.mostAccurateMz);
spectrumPanel.rescale(lowerMzZoomRange, upperMzZoomRange);
spectrumPanel.showAnnotatedPeaksOnly(!annotationSettings.showAllPeaks());
spectrumPanel.setYAxisZoomExcludesBackgroundPeaks(false);
if (spectrumIdentificationAssumption instanceof TagAssumption) {
TagAssumption tagAssumption = (TagAssumption) spectrumIdentificationAssumption;
currentPeptide = tagAssumption.getTag().asSequence();
spectrumPanel.addAutomaticDeNovoSequencing(tagAssumption.getTag(), annotations,
TagFragmentIon.B_ION,
TagFragmentIon.Y_ION,
annotationSettings.getDeNovoCharge(),
annotationSettings.showForwardIonDeNovoTags(),
annotationSettings.showRewindIonDeNovoTags(), false);
} else if (spectrumIdentificationAssumption instanceof PeptideAssumption) {
PeptideAssumption peptideAssumption = (PeptideAssumption) spectrumIdentificationAssumption;
currentPeptide = peptideAssumption.getPeptide().getSequence();
spectrumPanel.addAutomaticDeNovoSequencing(peptideAssumption.getPeptide(), annotations,
PeptideFragmentIon.B_ION,
PeptideFragmentIon.Y_ION,
annotationSettings.getDeNovoCharge(),
annotationSettings.showForwardIonDeNovoTags(),
annotationSettings.showRewindIonDeNovoTags(), false);
} else {
throw new UnsupportedOperationException("Operation not supported for spectrumIdentificationAssumption of type " + spectrumIdentificationAssumption.getClass() + ".");
}
spectrumJPanel.removeAll();
spectrumJPanel.setBounds(0, 0, resizeJPanelWidth, resizeJPanelHeight - 90);
spectrumJPanel.setPreferredSize(new Dimension(resizeJPanelWidth, resizeJPanelHeight-90));
spectrumJPanel.add(spectrumPanel);
spectrumJPanel.revalidate();
spectrumJPanel.repaint();
secondarySpectrumPlotsJPanel.removeAll();
SequenceFragmentationPanel sequenceFragmentationPanel = new SequenceFragmentationPanel(
modSequence, annotations, true, ptmSettings, forwardIon, rewindIon);
sequenceFragmentationPanel.setMinimumSize(new Dimension(sequenceFragmentationPanel.getPreferredSize().width, sequenceFragmentationPanel.getHeight()));
sequenceFragmentationPanel.setOpaque(true);
sequenceFragmentationPanel.setBackground(Color.WHITE);
secondarySpectrumPlotsJPanel.add(sequenceFragmentationPanel);
secondarySpectrumPlotsJPanel.revalidate();
secondarySpectrumPlotsJPanel.repaint();
}
}
} catch (Exception e) {
System.err.println("Update error");
}
}
/**
* Export single pic
* @param outputPathName File name
*/
private void exportFigure(String outputPathName){
File imageFile = new File(outputPathName);
try {
Export.exportPic(spectrumSplitPane, spectrumSplitPane.getBounds(), imageFile, imageType);
} catch (IOException | TranscoderException e) {
e.printStackTrace();
}
}
}
