/**
* 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 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;
}
/**
* 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;
}