protected void updateLDS(int original_index, int new_index) {
TableColumn tc = this.getColumn(new_index);
int model_index = tc.getModelIndex();
DataColumn dc = lds.getDataColumn(model_index);
dc.setIncludePosition(new_index);
if (Math.abs(original_index - new_index) == 1) {
// two adjacent columns were swapped, so set include value for neighbor
TableColumn tc2 = this.getColumn(original_index);
int model_index2 = tc2.getModelIndex();
DataColumn dc2 = lds.getDataColumn(model_index2);
dc2.setIncludePosition(original_index);
// swap names for dc and dc2, as well as table column header values and identifiers
String name = dc.getName();
int type = dc.getType();
dc.setName(dc2.getName());
dc.setType(dc2.getType());
dc2.setName(name);
dc2.setType(type);
tc2.setHeaderValue(dc2.getName());
tc2.setIdentifier(dc2.getName());
tc.setHeaderValue(dc.getName());
tc.setIdentifier(dc.getName());
} else {
syncIncludes();
}
}
private void initEmptyTable() {
_table.setModel(new DefaultTableModel());
_colName = new TableColumn();
_colName.setHeaderValue("Name");
_colName.setIdentifier("Name");
_table.addColumn(_colName);
_colValue = new TableColumn();
_colValue.setHeaderValue("Value");
_colValue.setIdentifier("Value");
_table.addColumn(_colValue);
}
/**
* Set the state from the last saved in the PreferencesExt.
*
* @param store ok if null or empty
*/
public void restoreState(PreferencesExt store) {
if (store == null) return;
int ncols = table.getColumnCount();
// stored column order
int[] modelIndex = (int[]) store.getBean("ColumnOrder", null);
if ((modelIndex != null) && (modelIndex.length == ncols)) { // what about invisible ??
// make invisible any not stored
boolean[] visible = new boolean[ncols];
for (int i = 0; i < modelIndex.length; i++)
if (modelIndex[i] < ncols) visible[modelIndex[i]] = true;
// modify popup menu
for (int i = 0; i < ncols; i++)
if (!visible[i]) {
// System.out.println( colName[i]+" hide "+i);
acts[i].hideColumn();
acts[i].putValue(BAMutil.STATE, new Boolean(false));
}
// now set the header order
TableColumnModel tcm = table.getColumnModel();
int n = Math.min(modelIndex.length, table.getColumnCount());
for (int i = 0; i < n; i++) {
TableColumn tc = tcm.getColumn(i);
tc.setModelIndex(modelIndex[i]);
String name = model.getColumnName(modelIndex[i]);
tc.setHeaderValue(name);
tc.setIdentifier(name);
if (useThreads && (modelIndex[i] == threadCol)) {
threadHeaderRenderer = new ThreadHeaderRenderer(threadCol);
tc.setHeaderRenderer(threadHeaderRenderer);
} else tc.setHeaderRenderer(new SortedHeaderRenderer(name, modelIndex[i]));
}
}
// set the column widths
Object colWidths = store.getBean("ColumnWidths", null);
if (colWidths == null) return;
int[] size = (int[]) colWidths;
if (size != null) setColumnWidths(size);
if (debug) {
System.out.println(" read widths = ");
for (int i = 0; i < size.length; i++) System.out.print(" " + size[i]);
System.out.println();
}
boolean isThreadsOn = store.getBoolean("isThreadsOn", false);
if (useThreads) {
model.setThreadsOn(isThreadsOn);
threadHeaderRenderer.setOn(isThreadsOn);
}
int colNo = store.getInt("SortOnCol", 0);
boolean reverse = store.getBoolean("SortReverse", false);
model.setSortCol(colNo);
model.setReverse(reverse);
setSortCol(colNo, reverse);
model.sort();
table.fireDataChanged();
}
public void createColumns() {
// clear column groups
ColumnGroup groups[] = header.getColumnGroups();
if (groups != null) {
for (ColumnGroup group : groups) {
header.removeColumnGroup(group);
}
}
// clear the column model
while (getColumnCount() > 0) {
TableColumn col = getColumn(0);
removeColumn(col);
}
// create the "average" group
ColumnGroup averageGroup = new ColumnGroup("Average");
header.addColumnGroup(averageGroup);
JTextField editorField = new JTextField();
editorField.setFont(editFont);
DefaultCellEditor defaultEditor = new DefaultCellEditor(editorField);
ColumnSettingParameter<CommonColumnType> csPar =
parameters.getParameter(PeakListTableParameters.commonColumns);
CommonColumnType visibleCommonColumns[] = csPar.getValue();
// This is a workaround for a bug - we need to always show the ID, m/z
// and RT columns, otherwise manual editing of peak identities does not
// work.
ArrayList<CommonColumnType> commonColumnsList =
new ArrayList<>(Arrays.asList(visibleCommonColumns));
commonColumnsList.remove(CommonColumnType.ROWID);
commonColumnsList.remove(CommonColumnType.AVERAGEMZ);
commonColumnsList.remove(CommonColumnType.AVERAGERT);
commonColumnsList.add(0, CommonColumnType.ROWID);
commonColumnsList.add(1, CommonColumnType.AVERAGEMZ);
commonColumnsList.add(2, CommonColumnType.AVERAGERT);
visibleCommonColumns = commonColumnsList.toArray(visibleCommonColumns);
ColumnSettingParameter<DataFileColumnType> dfPar =
parameters.getParameter(PeakListTableParameters.dataFileColumns);
DataFileColumnType visibleDataFileColumns[] = dfPar.getValue();
for (int i = 0; i < visibleCommonColumns.length; i++) {
CommonColumnType commonColumn = visibleCommonColumns[i];
int modelIndex = Arrays.asList(CommonColumnType.values()).indexOf(commonColumn);
TableColumn newColumn = new TableColumn(modelIndex);
newColumn.setHeaderValue(commonColumn.getColumnName());
newColumn.setIdentifier(commonColumn);
switch (commonColumn) {
case AVERAGEMZ:
newColumn.setCellRenderer(mzRenderer);
break;
case AVERAGERT:
newColumn.setCellRenderer(rtRenderer);
break;
case IDENTITY:
newColumn.setCellRenderer(identityRenderer);
break;
case COMMENT:
newColumn.setCellRenderer(defaultRendererLeft);
newColumn.setCellEditor(defaultEditor);
break;
case PEAKSHAPE:
newColumn.setCellRenderer(peakShapeRenderer);
break;
default:
newColumn.setCellRenderer(defaultRenderer);
}
this.addColumn(newColumn);
newColumn.setPreferredWidth(csPar.getColumnWidth(modelIndex));
if ((commonColumn == CommonColumnType.AVERAGEMZ)
|| (commonColumn == CommonColumnType.AVERAGERT)) {
averageGroup.add(newColumn);
}
}
for (int i = 0; i < peakList.getNumberOfRawDataFiles(); i++) {
RawDataFile dataFile = peakList.getRawDataFile(i);
ColumnGroup fileGroup = new ColumnGroup(dataFile.getName());
header.addColumnGroup(fileGroup);
for (int j = 0; j < visibleDataFileColumns.length; j++) {
DataFileColumnType dataFileColumn = visibleDataFileColumns[j];
int dataFileColumnIndex =
Arrays.asList(DataFileColumnType.values()).indexOf(dataFileColumn);
int modelIndex =
CommonColumnType.values().length
+ (i * DataFileColumnType.values().length)
+ dataFileColumnIndex;
TableColumn newColumn = new TableColumn(modelIndex);
newColumn.setHeaderValue(dataFileColumn.getColumnName());
newColumn.setIdentifier(dataFileColumn);
switch (dataFileColumn) {
case MZ:
newColumn.setCellRenderer(mzRenderer);
break;
case PEAKSHAPE:
newColumn.setCellRenderer(peakShapeRenderer);
break;
case STATUS:
newColumn.setCellRenderer(peakStatusRenderer);
break;
case RT:
newColumn.setCellRenderer(rtRenderer);
break;
case RT_START:
newColumn.setCellRenderer(rtRenderer);
break;
case RT_END:
newColumn.setCellRenderer(rtRenderer);
break;
case DURATION:
newColumn.setCellRenderer(rtRenderer);
break;
case HEIGHT:
newColumn.setCellRenderer(intensityRenderer);
break;
case AREA:
newColumn.setCellRenderer(intensityRenderer);
break;
default:
newColumn.setCellRenderer(defaultRenderer);
break;
}
this.addColumn(newColumn);
newColumn.setPreferredWidth(dfPar.getColumnWidth(dataFileColumnIndex));
fileGroup.add(newColumn);
}
}
}
