public PeptidesTableLayout(
final int validPep,
final int totalPep,
final String desc,
final Map<Integer, PeptideBean> pepProtList,
final String accession,
final String expName) {
// for peptides information (table) view
MarginInfo m = new MarginInfo(false, false, true, false);
this.setMargin(m);
this.setSpacing(false);
this.setWidth("100%");
final HorizontalLayout headerLayout = new HorizontalLayout();
headerLayout.setHeight("45px");
headerLayout.setSpacing(true);
show = new ShowLabel(true);
headerLayout.addComponent(show);
headerLayout.setComponentAlignment(show, Alignment.BOTTOM_LEFT);
stat = true;
final Label pepLabel =
new Label(
"<h4 style='font-family:verdana;color:black;'>Peptides ("
+ validPep
+ ") "
+ desc
+ "</h4>");
// new Label("<h4 style='font-family:verdana;color:black;'>Peptides (" + validPep + "/" +
// totalPep + ") " + desc + "</h4>");
pepLabel.setContentMode(Label.CONTENT_XHTML);
pepLabel.setHeight("45px");
headerLayout.addComponent(pepLabel);
headerLayout.setComponentAlignment(pepLabel, Alignment.TOP_RIGHT);
this.addComponent(headerLayout);
mainLayout = new VerticalLayout();
mainLayout.setWidth("100%");
this.addComponent(mainLayout);
mainLayout.addComponent(pepTableLayout);
mainLayout.setComponentAlignment(pepTableLayout, Alignment.MIDDLE_CENTER);
Map<Integer, PeptideBean> vPepProtList = getValidatedList(pepProtList);
vt = new PeptideTable(vPepProtList, null, false);
pepTableLayout.addComponent(vt);
if (trs != null) {
PepSize = trs.getCurrentSize();
}
vt.setHeight(PepSize);
HorizontalLayout lowerLayout = new HorizontalLayout();
lowerLayout.setWidth("100%");
lowerLayout.setHeight("25px");
lowerLayout.setSpacing(false);
// Panel toolbar = new Panel(lowerLayout);
// toolbar.setStyleName(Reindeer.PANEL_LIGHT);
// toolbar.setHeight("35px");
mainLayout.addComponent(lowerLayout);
mainLayout.setComponentAlignment(lowerLayout, Alignment.TOP_CENTER);
HorizontalLayout lowerLeftLayout = new HorizontalLayout();
lowerLayout.addComponent(lowerLeftLayout);
lowerLeftLayout.setSpacing(true);
lowerLeftLayout.setMargin(new MarginInfo(false, false, false, false));
lowerLayout.setComponentAlignment(lowerLeftLayout, Alignment.MIDDLE_LEFT);
// lowerLayout.setExpandRatio(lowerLeftLayout, 0.4f);
HorizontalLayout lowerRightLayout = new HorizontalLayout();
// lowerRightLayout.setSpacing(true);
lowerRightLayout.setWidth("450px");
lowerLayout.addComponent(lowerRightLayout);
lowerLayout.setComponentAlignment(lowerRightLayout, Alignment.BOTTOM_RIGHT);
// lowerLayout.setExpandRatio(lowerRightLayout, 0.5f);
final OptionGroup selectionType = new OptionGroup();
selectionType.setMultiSelect(true);
selectionType.addItem("\t\tShow Validated Peptides Only");
selectionType.select("\t\tShow Validated Peptides Only");
selectionType.setHeight("15px");
lowerLeftLayout.addComponent(selectionType);
lowerLeftLayout.setComponentAlignment(selectionType, Alignment.BOTTOM_LEFT);
final TableResizeSet trs1 = new TableResizeSet(vt, PepSize); // resize tables
lowerLeftLayout.addComponent(trs1);
lowerLeftLayout.setComponentAlignment(trs1, Alignment.BOTTOM_LEFT);
exportPepLayout.setWidth("300px");
lowerRightLayout.addComponent(exportPepLayout);
lowerRightLayout.setComponentAlignment(exportPepLayout, Alignment.BOTTOM_RIGHT);
mainLayout.setSpacing(true);
headerLayout.addListener(
new com.vaadin.event.LayoutEvents.LayoutClickListener() {
@Override
public void layoutClick(LayoutEvents.LayoutClickEvent event) {
if (stat) {
stat = false;
show.updateIcon(false);
mainLayout.setVisible(false);
} else {
stat = true;
show.updateIcon(true);
mainLayout.setVisible(true);
}
}
});
selectionType.setImmediate(true);
selectionType.addListener(
new Property.ValueChangeListener() {
@Override
public void valueChange(Property.ValueChangeEvent event) {
if (selectionType.isSelected("\t\tShow Validated Peptides Only")) {
headerLayout.removeAllComponents();
headerLayout.addComponent(show);
headerLayout.setComponentAlignment(show, Alignment.BOTTOM_LEFT);
// Label pepLabel = new Label("<h4 style='font-family:verdana;color:black;'>Peptides
// (" + validPep + ") " + desc + "</h4>");
pepLabel.setContentMode(Label.CONTENT_XHTML);
pepLabel.setHeight("45px");
headerLayout.addComponent(pepLabel);
headerLayout.setComponentAlignment(pepLabel, Alignment.TOP_RIGHT);
// Map<Integer, PeptideBean> vPepProtList = getValidatedList(pepProtList);
pepTableLayout.removeAllComponents();
// vt = new PeptideTable(vPepProtList, null);
pepTableLayout.addComponent(vt);
trs1.setTable(vt);
vt.setHeight(pepTable.getHeight() + "");
} else {
headerLayout.removeAllComponents();
headerLayout.addComponent(show);
headerLayout.setComponentAlignment(show, Alignment.BOTTOM_LEFT);
Label pepLabel =
new Label(
"<h4 style='font-family:verdana;color:black;'>Peptides ("
+ validPep
+ "/"
+ totalPep
+ ") "
+ desc
+ "</h4>");
pepLabel.setContentMode(Label.CONTENT_XHTML);
headerLayout.addComponent(pepLabel);
headerLayout.setComponentAlignment(pepLabel, Alignment.TOP_RIGHT);
pepTableLayout.removeAllComponents();
pepTable = new PeptideTable(pepProtList, null, false);
pepTableLayout.addComponent(pepTable);
trs1.setTable(pepTable);
pepTable.setHeight(vt.getHeight() + "");
}
}
});
}
public FractionsLayout(
final String accession,
final double mw,
Map<Integer, ProteinBean> proteinFractionAvgList,
List<StandardProteinBean> standardProtPlotList,
final String expName) {
this.setSpacing(false);
this.setWidth("100%");
this.setMargin(new MarginInfo(false, false, false, true));
final HorizontalLayout headerLayout = new HorizontalLayout();
headerLayout.setHeight("45px");
headerLayout.setSpacing(true);
final HorizontalLayout clickableheaderLayout = new HorizontalLayout();
clickableheaderLayout.setHeight("45px");
clickableheaderLayout.setSpacing(true);
headerLayout.addComponent(clickableheaderLayout);
headerLayout.setComponentAlignment(clickableheaderLayout, Alignment.BOTTOM_LEFT);
show = new ShowLabel(true);
clickableheaderLayout.addComponent(show);
clickableheaderLayout.setComponentAlignment(show, Alignment.BOTTOM_LEFT);
stat = true;
Label fractionLabel =
new Label(
"<h4 style='font-family:verdana;color:black;'>Fractions (Protein: "
+ accession
+ " MW: "
+ mw
+ " kDa)</h4>");
fractionLabel.setContentMode(Label.CONTENT_XHTML);
fractionLabel.setHeight("45px");
clickableheaderLayout.addComponent(fractionLabel);
clickableheaderLayout.setComponentAlignment(fractionLabel, Alignment.TOP_RIGHT);
// Label infoLable = new Label("<center style='background-color:#E6E6FA;'><p
// style='background-color:#E6E6FA;font-family:verdana;color:black;font-weight:bold;'>Bar charts
// showing the distribution of the protein in the fractions cut from the gel.<br/>Three charts
// show number of peptides, number of spectra and average precursor intensity.<br/>The fraction
// number represents the gel pieces cut from top to bottom.<br/>Protein standards (dark blue
// bars) indicate the molecular weight range of each fraction. Darker blue bars mark the area
// where the protein's theoretical mass suggests the protein should occur. </p></center>");
// infoLable.setContentMode(Label.CONTENT_XHTML);
// infoLable.setWidth("300px");
// infoLable.setStyleName(Reindeer.LAYOUT_BLUE);
//
// Help help = new Help();
// HorizontalLayout infoIco = help.getInfoNote(infoLable);
// infoIco.setMargin(new MarginInfo(false, false, false, true));
// headerLayout.addComponent(infoIco);
// headerLayout.setComponentAlignment(infoIco, Alignment.MIDDLE_LEFT);
this.addComponent(headerLayout);
mainLayout = new VerticalLayout();
this.addComponent(mainLayout);
FractionPlotLayout plotsLayout =
new FractionPlotLayout(proteinFractionAvgList, mw, standardProtPlotList);
mainLayout.addComponent(plotsLayout);
mainLayout.setComponentAlignment(plotsLayout, Alignment.MIDDLE_CENTER);
HorizontalLayout lowerLayout = new HorizontalLayout();
lowerLayout.setWidth("100%");
lowerLayout.setHeight("25px");
lowerLayout.setMargin((new MarginInfo(false, true, false, true)));
lowerLayout.setSpacing(false);
// Panel toolbar = new Panel(lowerLayout);
// toolbar.setStyleName(Reindeer.PANEL_LIGHT);
//// toolbar.setHeight("35px");
// toolbar.setWidth("100%");
mainLayout.addComponent(lowerLayout);
mainLayout.setComponentAlignment(lowerLayout, Alignment.TOP_CENTER);
exportFracLayout.setWidth("300px");
lowerLayout.addComponent(exportFracLayout);
lowerLayout.setComponentAlignment(exportFracLayout, Alignment.MIDDLE_RIGHT);
lowerLayout.setExpandRatio(exportFracLayout, 0.1f);
final Table fractTable = getFractionTable(proteinFractionAvgList);
fractTable.setVisible(false);
this.addComponent(fractTable);
expBtnFracTable =
new PopupView(
"Export Fractions from Selected Dataset for ( " + accession + " )",
new CustomExportBtnLayout(
null,
"fractions",
0,
expName,
accession,
accession,
null,
null,
0,
null,
fractTable,
null));
expBtnFracTable.setDescription(
"Export Fractions from ( " + expName + " ) Dataset for ( " + accession + " )");
// expBtnFracTable = new Help().getExpIcon(new CustomExportBtnLayout(null, "fractions", 0,
// expName, accession, accession, null, null, 0, null, fractTable, null), "Export CSF-PR /
// "+expName+" / Fractions", "Export CSF-PR / "+expName+" / Fractions");
exportFracLayout.addComponent(expBtnFracTable);
exportFracLayout.setMargin(new MarginInfo(false, true, false, false));
exportFracLayout.setComponentAlignment(expBtnFracTable, Alignment.BOTTOM_RIGHT);
clickableheaderLayout.addListener(
new com.vaadin.event.LayoutEvents.LayoutClickListener() {
@Override
public void layoutClick(LayoutEvents.LayoutClickEvent event) {
if (stat) {
stat = false;
show.updateIcon(false);
mainLayout.setVisible(false);
} else {
stat = true;
show.updateIcon(true);
mainLayout.setVisible(true);
}
}
});
}
