/** Sets the visibility of the column with the specified name. */
public void setColumnVisible(String name, boolean visible) {
// Get column and set visibility.
TableColumnExt column = getColumnExt(name);
column.setVisible(visible);
// Get column title.
String columnTitle = column.getTitle();
// Find checkbox menu item with matching title.
JCheckBoxMenuItem matchingItem = null;
int itemCount = headerPopup.getComponentCount();
for (int i = 0; i < itemCount; i++) {
Component menuComponent = headerPopup.getComponent(i);
if (menuComponent instanceof JCheckBoxMenuItem) {
JCheckBoxMenuItem item = (JCheckBoxMenuItem) menuComponent;
String itemTitle = item.getText();
if (itemTitle.equals(columnTitle)) {
matchingItem = item;
break;
}
}
}
// Select matching menu item.
if (matchingItem != null) {
matchingItem.setSelected(visible);
}
}
public StockTableColumnModel(List<String> columns) {
for (int i = 0; i < columns.size(); i++) {
TableColumnExt tableColumn = new TableColumnExt(i);
tableColumn.setCellRenderer(stockTableColumnCellRenderer);
tableColumn.setHeaderValue(TextToHtmlSplitter.instance.split(columns.get(i)));
addColumn(tableColumn);
}
}
@Override
public void actionPerformed(ActionEvent e) {
// Get table column.
String name = e.getActionCommand();
TableColumnExt selectedColumn = getColumnExt(name);
// Toggle column visibility.
boolean visible = selectedColumn.isVisible();
selectedColumn.setVisible(!visible);
// Update popup menu.
updateHeaderPopup();
// Resize table columns to fit.
packAll();
}
/**
* Create a table for showing a ParamTableModel
*
* @param paramTableModel given param table model
* @return JTable param table
*/
private static JTable createParamTable(ParamTableModel paramTableModel) {
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable paramTable = new DefaultPrideTable(paramTableModel, columnModel);
// hyperlink ontology accessions
String accColumnHeader = ParamTableModel.TableHeader.ACCESSION.getHeader();
TableColumnExt accColumn = (TableColumnExt) paramTable.getColumn(accColumnHeader);
accColumn.setCellRenderer(new HyperLinkCellRenderer());
// add mouse motion listener
paramTable.addMouseMotionListener(
new TableCellMouseMotionListener(paramTable, accColumnHeader));
paramTable.addMouseListener(
new HyperLinkCellMouseClickListener(
paramTable, accColumnHeader, new PrefixedHyperLinkGenerator(Constants.OLS_URL_PREFIX)));
return paramTable;
}
/**
* Create a table for showing contacts
*
* @param contacts given list of contacts
* @return JTable contact table
*/
public static JTable createContactTable(Collection<ParamGroup> contacts) {
ContactTableModel tableModel = new ContactTableModel(contacts);
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable contactTable = new DefaultPrideTable(tableModel, columnModel);
// hyperlink contact emails
String infoColumnHeader = ContactTableModel.TableHeader.INFORMATION.getHeader();
TableColumnExt infoColumn = (TableColumnExt) contactTable.getColumn(infoColumnHeader);
infoColumn.setCellRenderer(new HyperLinkCellRenderer());
// add mouse motion listener
contactTable.addMouseMotionListener(
new TableCellMouseMotionListener(contactTable, infoColumnHeader));
contactTable.addMouseListener(
new HyperLinkCellMouseClickListener(
contactTable, infoColumnHeader, new EmailHyperLinkGenerator()));
return contactTable;
}
/**
* Build a table to display PTM related details.
*
* @return JTable ptm table
*/
public static JTable createPTMTable() {
PTMTableModel tableModel = new PTMTableModel();
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable table = new DefaultPrideTable(tableModel, columnModel);
// add hyper link click listener
String modAccColumnHeader = PTMTableModel.TableHeader.PTM_ACCESSION.getHeader();
table.addMouseMotionListener(new TableCellMouseMotionListener(table, modAccColumnHeader));
table.addMouseListener(
new HyperLinkCellMouseClickListener(
table, modAccColumnHeader, new PTMHyperLinkGenerator()));
// ptm accession hyperlink
TableColumnExt ptmColumn =
(TableColumnExt) table.getColumn(PTMTableModel.TableHeader.PTM_ACCESSION.getHeader());
ptmColumn.setCellRenderer(new HyperLinkCellRenderer());
return table;
}
/**
* Updates the header popup menu by enabling/disabling menu items based on the number of visible
* columns.
*/
private void updateHeaderPopup() {
// Get number of visible columns.
int visibleColumnCount = getColumnCount(false);
// If only one visible column, then disable its menu item.
if (visibleColumnCount == 1) {
// Find the only visible column.
int allColumnCount = getColumnCount(true);
TableColumnExt column = null;
for (int i = 0; i < allColumnCount; i++) {
column = getColumnExt(i);
if (column.isVisible()) {
break;
}
}
// Get menu item name from column title.
assert column != null;
String headerName = column.getTitle();
// Find matching menu item, and disable so user cannot hide column.
Component[] components = headerPopup.getComponents();
for (Component component : components) {
if (component instanceof JMenuItem) {
JMenuItem item = (JMenuItem) component;
// Disable matching menu item.
if (item.getText().equals(headerName)) {
item.setEnabled(false);
disabledMenuItem = item;
break;
}
}
}
} else if (disabledMenuItem != null) {
// Re-enable previously disabled menu item because more than one
// column is visible.
disabledMenuItem.setEnabled(true);
}
}
/**
* Create a table to show a list of references
*
* @param references a list of input references
* @return JTable reference table
*/
public static JTable createReferenceTable(Collection<Reference> references) {
ReferenceTableModel tableModel = new ReferenceTableModel(references);
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable referenceTable = new DefaultPrideTable(tableModel, columnModel);
// pubmed
String pubMedColumnHeader = ReferenceTableModel.TableHeader.PUBMED.getHeader();
TableColumnExt pubMedColumn = (TableColumnExt) referenceTable.getColumn(pubMedColumnHeader);
Pattern pubmedPattern = Pattern.compile("[\\d,]+");
pubMedColumn.setCellRenderer(new HyperLinkCellRenderer(pubmedPattern));
pubMedColumn.setMaxWidth(100);
// doi
String doiColumnHeader = ReferenceTableModel.TableHeader.DOI.getHeader();
TableColumnExt doiColumn = (TableColumnExt) referenceTable.getColumn(doiColumnHeader);
doiColumn.setCellRenderer(new HyperLinkCellRenderer());
doiColumn.setMaxWidth(100);
// add mouse motion listener
referenceTable.addMouseMotionListener(
new TableCellMouseMotionListener(referenceTable, pubMedColumnHeader, doiColumnHeader));
referenceTable.addMouseListener(
new HyperLinkCellMouseClickListener(
referenceTable,
pubMedColumnHeader,
new PrefixedHyperLinkGenerator(Constants.PUBMED_URL_PERFIX),
pubmedPattern));
referenceTable.addMouseListener(
new HyperLinkCellMouseClickListener(
referenceTable, doiColumnHeader, new DOIHyperLinkGenerator(Constants.DOI_URL_PREFIX)));
return referenceTable;
}
/**
* Build a table to display database search summaries.
*
* @return JTable database search table
*/
public static JTable createDatabaseSearchTable() {
DatabaseSearchTableModel tableModel = new DatabaseSearchTableModel();
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable searchTable = new DefaultPrideTable(tableModel, columnModel);
// hide row number column
String rowNumHeader = DatabaseSearchTableModel.TableHeader.ROW_NUMBER_COLUMN.getHeader();
TableColumnExt rowColumn = (TableColumnExt) searchTable.getColumn(rowNumHeader);
rowColumn.setVisible(false);
// add cell renderer to view column
String viewColumnHeader = DatabaseSearchTableModel.TableHeader.VIEW.getHeader();
TableColumnExt viewColumn = (TableColumnExt) searchTable.getColumn(viewColumnHeader);
Icon icon =
GUIUtilities.loadIcon(
Desktop.getInstance().getDesktopContext().getProperty("add.experiment.small.icon"));
viewColumn.setCellRenderer(new IconRenderer(icon));
viewColumn.setMaxWidth(50);
// pubmed column
String pubmedHeader = DatabaseSearchTableModel.TableHeader.PUBMED_ID.getHeader();
TableColumnExt pubmedColumn = (TableColumnExt) searchTable.getColumn(pubmedHeader);
Pattern pubmedPattern = Pattern.compile("[\\d,]+");
pubmedColumn.setCellRenderer(new HyperLinkCellRenderer(pubmedPattern));
// add mouse motion listener
searchTable.addMouseMotionListener(
new TableCellMouseMotionListener(searchTable, viewColumnHeader, pubmedHeader));
searchTable.addMouseListener(new OpenExperimentMouseListener(searchTable, viewColumnHeader));
searchTable.addMouseListener(
new HyperLinkCellMouseClickListener(
searchTable,
pubmedHeader,
new PrefixedHyperLinkGenerator(Constants.PUBMED_URL_PERFIX),
pubmedPattern));
return searchTable;
}
/** Creates new form PanelUsuarios */
public PanelUsuarios() {
initComponents();
tabla.setDefaultEditor(GregorianCalendar.class, new DateCellEditor());
tabla.setDefaultRenderer(
GregorianCalendar.class,
new DefaultTableCellRenderer() {
@Override
public void setValue(Object val) {
if (val instanceof GregorianCalendar) {
setText(Fechas.format((GregorianCalendar) val));
} else {
setText("");
}
}
});
TableColumnExt colRoles = tabla.getColumnExt("Roles");
colRoles.setCellEditor(new EditorRoles());
colRoles.setCellRenderer(
new DefaultTableCellRenderer() {
@Override
public void setValue(Object val) {
setText(Rol.getTextoRoles(Num.getInt(val)));
}
});
TableColumnExt colTutor = tabla.getColumnExt("Profesor");
TableColumnExt colClave = tabla.getColumnExt("Clave");
colClave.setCellRenderer(
new DefaultTableCellRenderer() {
@Override
public void setValue(Object val) {
setText("*********");
}
});
colClave.setCellEditor(new DefaultCellEditor(new JPasswordField()));
JComboBox comboTutores = new JComboBox(Profesor.getProfesores().toArray());
comboTutores.insertItemAt("Sin profesor asignado", 0);
DefaultCellEditor dceTutor =
new DefaultCellEditor(comboTutores) {
@Override
public Object getCellEditorValue() {
Object obj = super.getCellEditorValue();
if (obj instanceof Profesor) {
return ((Profesor) obj);
}
return null;
}
@Override
public Component getTableCellEditorComponent(
JTable table, Object value, boolean isSelected, int row, int column) {
Component c = super.getTableCellEditorComponent(tabla, value, isSelected, row, column);
try {
int id = Num.getInt(value);
if (id > 0) {
Profesor p = Profesor.getProfesor(id);
((JComboBox) c).setSelectedItem(p);
} else {
((JComboBox) c).setSelectedIndex(0);
}
} catch (Exception ex) {
Logger.getLogger(PanelGrupos.class.getName()).log(Level.SEVERE, null, ex);
}
return c;
}
};
dceTutor.setClickCountToStart(2);
colTutor.setCellEditor(dceTutor);
}
/**
* Create a table for peptide quantitative data
*
* @param se search engine
* @return JTable peptide table
*/
public static JTable createQuantPeptideTable(DataAccessController controller, SearchEngine se) {
QuantPeptideTableModel tableModel = new QuantPeptideTableModel(se);
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable quantPeptideTable = new DefaultPrideTable(tableModel, columnModel);
quantPeptideTable.setAutoCreateColumnsFromModel(false);
// add table model change listener
tableModel.addTableModelListener(new BarChartColumnListener(quantPeptideTable));
// hide protein accession
TableColumnExt proteinAccColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PROTEIN_ACCESSION_COLUMN.getHeader());
proteinAccColumn.setVisible(false);
// hide mapped protein accession
String mappedProtAccHeader =
QuantPeptideTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader();
TableColumnExt mappedProtAccColumn =
(TableColumnExt) quantPeptideTable.getColumn(mappedProtAccHeader);
mappedProtAccColumn.setCellRenderer(new HyperLinkCellRenderer());
mappedProtAccColumn.setVisible(false);
// add hyper link click listener
quantPeptideTable.addMouseMotionListener(
new TableCellMouseMotionListener(quantPeptideTable, mappedProtAccHeader));
quantPeptideTable.addMouseListener(
new HyperLinkCellMouseClickListener(
quantPeptideTable, mappedProtAccHeader, new ProteinAccHyperLinkGenerator()));
// peptide sequence column renderer
TableColumnExt peptideColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PEPTIDE_PTM_COLUMN.getHeader());
peptideColumn.setCellRenderer(new PeptideSequenceCellRenderer());
// set peptide column width
peptideColumn.setPreferredWidth(150);
// hide protein name
TableColumnExt proteinNameColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PROTEIN_NAME.getHeader());
proteinNameColumn.setVisible(false);
// hide protein status
TableColumnExt proteinStatusColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PROTEIN_STATUS.getHeader());
proteinStatusColumn.setVisible(false);
// hide protein sequence coverage
TableColumnExt proteinSeqCoverageColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PROTEIN_SEQUENCE_COVERAGE.getHeader());
proteinSeqCoverageColumn.setVisible(false);
// peptide sequence present in protein sequence
TableColumnExt peptideFitColumn =
(TableColumnExt)
quantPeptideTable.getColumn(QuantPeptideTableModel.TableHeader.PEPTIDE_FIT.getHeader());
peptideFitColumn.setCellRenderer(new PeptideFitCellRenderer());
peptideFitColumn.setVisible(false);
// precursor charge column
TableColumnExt precursorChargeColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PRECURSOR_CHARGE_COLUMN.getHeader());
precursorChargeColumn.setVisible(false);
// delta mass column
TableColumnExt deltaMassColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.DELTA_MASS_COLUMN.getHeader());
deltaMassColumn.setVisible(false);
double minLimit =
Double.parseDouble(
Desktop.getInstance().getDesktopContext().getProperty("delta.mz.min.limit"));
double maxLimit =
Double.parseDouble(
Desktop.getInstance().getDesktopContext().getProperty("delta.mz.max.limit"));
DeltaMZRenderer renderer = new DeltaMZRenderer(minLimit, maxLimit);
deltaMassColumn.setCellRenderer(renderer);
// precursor m/z column
TableColumnExt precursorMzColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PRECURSOR_MZ_COLUMN.getHeader());
precursorMzColumn.setVisible(false);
// number of ptms column
TableColumnExt ptmsColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PEPTIDE_PTM_NUMBER_COLUMN.getHeader());
ptmsColumn.setVisible(false);
ImageIcon icon =
GUIUtilities.loadImageIcon(
Desktop.getInstance().getDesktopContext().getProperty("open.ptm.small.icon"));
ptmsColumn.setCellRenderer(new OpenPTMRenderer(icon));
// hide modified peptide sequence
TableColumnExt peptideSeqColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PEPTIDE_PTM_MASS_COLUMN.getHeader());
peptideSeqColumn.setVisible(false);
// hide ptm summary
TableColumnExt ptmSummaryColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PEPTIDE_PTM_SUMMARY.getHeader());
ptmSummaryColumn.setVisible(false);
// hide number of fragment ions
TableColumnExt fragIonsColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.NUMBER_OF_FRAGMENT_IONS_COLUMN.getHeader());
fragIonsColumn.setVisible(false);
// hide peptide sequence length
TableColumnExt seqLengthColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.PEPTIDE_SEQUENCE_LENGTH_COLUMN.getHeader());
seqLengthColumn.setVisible(false);
// hide sequence start
TableColumnExt sequenceStartColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.SEQUENCE_START_COLUMN.getHeader());
sequenceStartColumn.setVisible(false);
// hide sequence end
TableColumnExt sequenceEndColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.SEQUENCE_END_COLUMN.getHeader());
sequenceEndColumn.setVisible(false);
// hide pi point column
TableColumnExt piColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.THEORITICAL_ISOELECTRIC_POINT_COLUMN
.getHeader());
piColumn.setVisible(false);
// hide spectrum id
TableColumnExt spectrumIdColumn =
(TableColumnExt)
quantPeptideTable.getColumn(QuantPeptideTableModel.TableHeader.SPECTRUM_ID.getHeader());
spectrumIdColumn.setVisible(false);
// hide protein id column
TableColumnExt proteinIdColumn =
(TableColumnExt)
quantPeptideTable.getColumn(
QuantPeptideTableModel.TableHeader.IDENTIFICATION_ID.getHeader());
proteinIdColumn.setVisible(false);
// hide peptide id column
TableColumnExt peptideIdColumn =
(TableColumnExt)
quantPeptideTable.getColumn(QuantPeptideTableModel.TableHeader.PEPTIDE_ID.getHeader());
peptideIdColumn.setVisible(false);
// add hyper link click listener
String protAccColumnHeader =
QuantPeptideTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader();
quantPeptideTable.addMouseMotionListener(
new TableCellMouseMotionListener(quantPeptideTable, protAccColumnHeader));
quantPeptideTable.addMouseListener(
new HyperLinkCellMouseClickListener(
quantPeptideTable, protAccColumnHeader, new ProteinAccHyperLinkGenerator()));
// additional column
String additionalColHeader = ProteinTableModel.TableHeader.ADDITIONAL.getHeader();
TableColumnExt additionalCol =
(TableColumnExt) quantPeptideTable.getColumn(additionalColHeader);
Icon detailIcon =
GUIUtilities.loadIcon(
Desktop.getInstance().getDesktopContext().getProperty("view.detail.small.icon"));
additionalCol.setCellRenderer(new IconRenderer(detailIcon));
additionalCol.setMaxWidth(50);
additionalCol.setVisible(false);
// add mouse motion listener
quantPeptideTable.addMouseMotionListener(
new TableCellMouseMotionListener(quantPeptideTable, additionalColHeader));
quantPeptideTable.addMouseListener(
new ShowParamsMouseListener(controller, quantPeptideTable, additionalColHeader));
return quantPeptideTable;
}
/**
* Build a table to display identification related details.
*
* @param controller data access controller
* @return JTable identification table
*/
public static JTable createIdentificationTable(DataAccessController controller) {
ProteinTableModel identTableModel = new ProteinTableModel();
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable table = new DefaultPrideTable(identTableModel, columnModel);
TableColumnExt proteinIdColumn =
(TableColumnExt)
table.getColumn(ProteinTableModel.TableHeader.IDENTIFICATION_ID.getHeader());
proteinIdColumn.setVisible(false);
TableColumnExt proteinNameColumn =
(TableColumnExt) table.getColumn(ProteinTableModel.TableHeader.PROTEIN_NAME.getHeader());
// set protein name width
proteinNameColumn.setPreferredWidth(200);
// hide the protein name column
proteinNameColumn.setVisible(false);
// protein status column
TableColumnExt proteinStatusColumn =
(TableColumnExt) table.getColumn(ProteinTableModel.TableHeader.PROTEIN_STATUS.getHeader());
proteinStatusColumn.setVisible(false);
// sequence coverage column
TableColumnExt seqCoverageColumn =
(TableColumnExt)
table.getColumn(ProteinTableModel.TableHeader.PROTEIN_SEQUENCE_COVERAGE.getHeader());
seqCoverageColumn.setCellRenderer(new SequenceCoverageRenderer());
seqCoverageColumn.setVisible(false);
// isoelectric point column
TableColumnExt isoelectricColumn =
(TableColumnExt)
table.getColumn(
ProteinTableModel.TableHeader.THEORITICAL_ISOELECTRIC_POINT_COLUMN.getHeader());
isoelectricColumn.setVisible(false);
// add hyper link click listener
String protAccColumnHeader =
ProteinTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader();
table.addMouseMotionListener(new TableCellMouseMotionListener(table, protAccColumnHeader));
table.addMouseListener(
new HyperLinkCellMouseClickListener(
table, protAccColumnHeader, new ProteinAccHyperLinkGenerator()));
// ptm accession hyperlink
TableColumn protAcc =
table.getColumn(ProteinTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader());
protAcc.setCellRenderer(new HyperLinkCellRenderer());
// additional column
String additionalColHeader = ProteinTableModel.TableHeader.ADDITIONAL.getHeader();
TableColumnExt additionalCol = (TableColumnExt) table.getColumn(additionalColHeader);
Icon icon =
GUIUtilities.loadIcon(
Desktop.getInstance().getDesktopContext().getProperty("view.detail.small.icon"));
additionalCol.setCellRenderer(new IconRenderer(icon));
additionalCol.setMaxWidth(50);
// add mouse motion listener
table.addMouseMotionListener(new TableCellMouseMotionListener(table, additionalColHeader));
table.addMouseListener(new ShowParamsMouseListener(controller, table, additionalColHeader));
return table;
}
/**
* Create a table for quantitative protein data with a given table model
*
* @param tableModel quant protein table model
* @return JTable quant protein table
*/
public static JTable createQuantProteinTable(
DataAccessController controller, TableModel tableModel) {
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable quantProteinTable = new DefaultPrideTable(tableModel, columnModel);
quantProteinTable.setAutoCreateColumnsFromModel(false);
// add table model change listener
tableModel.addTableModelListener(new BarChartColumnListener(quantProteinTable));
// in case the compare doesn't exist
List<TableColumn> columns = columnModel.getColumns(true);
for (TableColumn column : columns) {
if (column.getHeaderValue().equals(QuantProteinTableModel.TableHeader.COMPARE.getHeader())) {
column.setMaxWidth(25);
}
}
// hide mapped protein accession
String mappedProtAccHeader =
QuantProteinTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader();
TableColumnExt mappedProtAccColumn =
(TableColumnExt) quantProteinTable.getColumn(mappedProtAccHeader);
mappedProtAccColumn.setCellRenderer(new HyperLinkCellRenderer());
// add hyper link click listener
quantProteinTable.addMouseMotionListener(
new TableCellMouseMotionListener(quantProteinTable, mappedProtAccHeader));
quantProteinTable.addMouseListener(
new HyperLinkCellMouseClickListener(
quantProteinTable, mappedProtAccHeader, new ProteinAccHyperLinkGenerator()));
TableColumnExt proteinIdColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.IDENTIFICATION_ID.getHeader());
proteinIdColumn.setVisible(false);
// hide the protein name column
TableColumnExt proteinNameColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.PROTEIN_NAME.getHeader());
proteinNameColumn.setVisible(false);
// protein status column
TableColumnExt proteinStatusColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.PROTEIN_STATUS.getHeader());
proteinStatusColumn.setVisible(false);
// sequence coverage column
TableColumnExt seqCoverageColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.PROTEIN_SEQUENCE_COVERAGE.getHeader());
seqCoverageColumn.setCellRenderer(new SequenceCoverageRenderer());
seqCoverageColumn.setVisible(false);
// isoelectric point column
TableColumnExt isoelectricColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.THEORITICAL_ISOELECTRIC_POINT_COLUMN
.getHeader());
isoelectricColumn.setVisible(false);
// score
TableColumnExt proteinScoreColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.IDENTIFICATION_SCORE_COLUMN.getHeader());
proteinScoreColumn.setVisible(false);
// threshold
TableColumnExt proteinThresholdColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.IDENTIFICATION_THRESHOLD_COLUMN.getHeader());
proteinThresholdColumn.setVisible(false);
// number of peptides
TableColumnExt numOfPeptideColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.NUMBER_OF_PEPTIDES.getHeader());
numOfPeptideColumn.setVisible(false);
// number of unique peptides
TableColumnExt numOfUniquePeptideColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.NUMBER_OF_UNIQUE_PEPTIDES.getHeader());
numOfUniquePeptideColumn.setVisible(false);
// number of ptms
TableColumnExt numOfPtmColumn =
(TableColumnExt)
quantProteinTable.getColumn(
QuantProteinTableModel.TableHeader.NUMBER_OF_PTMS.getHeader());
numOfPtmColumn.setVisible(false);
// additional column
String additionalColHeader = ProteinTableModel.TableHeader.ADDITIONAL.getHeader();
TableColumnExt additionalCol =
(TableColumnExt) quantProteinTable.getColumn(additionalColHeader);
Icon icon =
GUIUtilities.loadIcon(
Desktop.getInstance().getDesktopContext().getProperty("view.detail.small.icon"));
additionalCol.setCellRenderer(new IconRenderer(icon));
additionalCol.setMaxWidth(50);
additionalCol.setVisible(false);
// add mouse motion listener
quantProteinTable.addMouseMotionListener(
new TableCellMouseMotionListener(quantProteinTable, additionalColHeader));
quantProteinTable.addMouseListener(
new ShowParamsMouseListener(controller, quantProteinTable, additionalColHeader));
return quantProteinTable;
}
/**
* Build a table to display peptide related details.
*
* @param se search engine
* @param controller data access controller
* @return JTable peptide table
*/
public static JTable createPeptideTable(SearchEngine se, DataAccessController controller) {
PeptideTableModel peptideTableModel = new PeptideTableModel(se);
DefaultTableColumnModelExt columnModel = new DefaultTableColumnModelExt();
DefaultPrideTable table = new DefaultPrideTable(peptideTableModel, columnModel);
// peptide sequence column renderer
TableColumnExt peptideColumn =
(TableColumnExt)
table.getColumn(PeptideTableModel.TableHeader.PEPTIDE_PTM_COLUMN.getHeader());
peptideColumn.setCellRenderer(new PeptideSequenceCellRenderer());
// delta mass column
TableColumnExt deltaMassColumn =
(TableColumnExt)
table.getColumn(PeptideTableModel.TableHeader.DELTA_MASS_COLUMN.getHeader());
double minLimit =
Double.parseDouble(
Desktop.getInstance().getDesktopContext().getProperty("delta.mz.min.limit"));
double maxLimit =
Double.parseDouble(
Desktop.getInstance().getDesktopContext().getProperty("delta.mz.max.limit"));
DeltaMZRenderer renderer = new DeltaMZRenderer(minLimit, maxLimit);
deltaMassColumn.setCellRenderer(renderer);
// peptide sequence present in protein sequence
TableColumnExt peptideFitColumn =
(TableColumnExt) table.getColumn(PeptideTableModel.TableHeader.PEPTIDE_FIT.getHeader());
peptideFitColumn.setCellRenderer(new PeptideFitCellRenderer());
peptideFitColumn.setVisible(false);
// hide modified peptide sequence
TableColumnExt peptideSeqColumn =
(TableColumnExt)
table.getColumn(PeptideTableModel.TableHeader.PEPTIDE_PTM_MASS_COLUMN.getHeader());
peptideSeqColumn.setVisible(false);
// hide protein id column
TableColumnExt proteinIdColumn =
(TableColumnExt)
table.getColumn(PeptideTableModel.TableHeader.IDENTIFICATION_ID.getHeader());
proteinIdColumn.setVisible(false);
// hide peptide id column
TableColumnExt peptideIdColumn =
(TableColumnExt) table.getColumn(PeptideTableModel.TableHeader.PEPTIDE_ID.getHeader());
peptideIdColumn.setVisible(false);
// set protein name column width
TableColumnExt proteinNameColumn =
(TableColumnExt) table.getColumn(PeptideTableModel.TableHeader.PROTEIN_NAME.getHeader());
proteinNameColumn.setPreferredWidth(200);
// hide the protein name column
proteinNameColumn.setVisible(false);
// protein status column
TableColumnExt proteinStatusColumn =
(TableColumnExt) table.getColumn(PeptideTableModel.TableHeader.PROTEIN_STATUS.getHeader());
proteinStatusColumn.setVisible(false);
// sequence coverage column
TableColumnExt coverageColumn =
(TableColumnExt)
table.getColumn(PeptideTableModel.TableHeader.PROTEIN_SEQUENCE_COVERAGE.getHeader());
coverageColumn.setCellRenderer(new SequenceCoverageRenderer());
coverageColumn.setVisible(false);
// add hyper link click listener
String protAccColumnHeader =
PeptideTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader();
table.addMouseMotionListener(new TableCellMouseMotionListener(table, protAccColumnHeader));
table.addMouseListener(
new HyperLinkCellMouseClickListener(
table, protAccColumnHeader, new ProteinAccHyperLinkGenerator()));
// ptm accession hyperlink
TableColumnExt protAcc =
(TableColumnExt)
table.getColumn(
PeptideTableModel.TableHeader.MAPPED_PROTEIN_ACCESSION_COLUMN.getHeader());
protAcc.setCellRenderer(new HyperLinkCellRenderer());
// set peptide column width
peptideColumn.setPreferredWidth(200);
// hide spectrum id column
String spectrumIdHeader = PeptideTableModel.TableHeader.SPECTRUM_ID.getHeader();
TableColumnExt spectrumIdColumn = (TableColumnExt) table.getColumn(spectrumIdHeader);
spectrumIdColumn.setVisible(false);
// additional column
String additionalColHeader = PeptideTableModel.TableHeader.ADDITIONAL.getHeader();
TableColumnExt additionalCol = (TableColumnExt) table.getColumn(additionalColHeader);
Icon icon =
GUIUtilities.loadIcon(
Desktop.getInstance().getDesktopContext().getProperty("view.detail.small.icon"));
additionalCol.setCellRenderer(new IconRenderer(icon));
additionalCol.setMaxWidth(50);
// hide pI column
String pIHeader =
PeptideTableModel.TableHeader.THEORITICAL_ISOELECTRIC_POINT_COLUMN.getHeader();
TableColumnExt pICol = (TableColumnExt) table.getColumn(pIHeader);
pICol.setVisible(false);
// add mouse motion listener
table.addMouseMotionListener(new TableCellMouseMotionListener(table, additionalColHeader));
table.addMouseListener(new ShowParamsMouseListener(controller, table, additionalColHeader));
return table;
}
