/**
ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
License:
ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
EXHIBIT A. CPAL version 1.0
The contents of this file are subject to the CPAL version 1.0 (the License);
you may not use this file except in compliance with the License. You may obtain a
copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
The License is based on the Mozilla Public License version 1.1 but Sections
14 and 15 have been added to cover use of software over a computer network and
provide for limited attribution for the Original Developer. In addition, Exhibit
A has been modified to be consistent with Exhibit B.
Software distributed under the License is distributed on an AS IS basis,
WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
the specific language governing rights and limitations under the License.
The Original Code is ISAcreator.
The Original Developer is the Initial Developer. The Initial Developer of the
Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com;
Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com;
http://www.isa-tools.org). All portions of the code written by the ISA Team are
Copyright (c) 2007-2011 ISA Team. All Rights Reserved.
EXHIBIT B. Attribution Information
Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team
Attribution Phrase: Developed by the ISA Team
Attribution URL: http://www.isa-tools.org
Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png
Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.
Sponsors:
The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu), the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone).
*/
package org.isatools.isacreator.gui.formelements;
import com.explodingpixels.macwidgets.IAppWidgetFactory;
import org.apache.commons.collections15.OrderedMap;
import org.apache.commons.collections15.map.ListOrderedMap;
import org.apache.log4j.Logger;
import org.isatools.isacreator.api.utils.SpreadsheetUtils;
import org.isatools.isacreator.autofiltercombo.AutoFilterCombo;
import org.isatools.isacreator.autofiltercombo.AutoFilterComboCellEditor;
import org.isatools.isacreator.calendar.DateCellEditor;
import org.isatools.isacreator.common.ExcelAdaptor;
import org.isatools.isacreator.common.UIHelper;
import org.isatools.isacreator.common.button.ButtonType;
import org.isatools.isacreator.common.button.FlatButton;
import org.isatools.isacreator.factorlevelentry.FactorLevelEntryCellEditor;
import org.isatools.isacreator.filechooser.FileSelectCellEditor;
import org.isatools.isacreator.gui.*;
import org.isatools.isacreator.io.UserProfileManager;
import org.isatools.isacreator.longtexteditor.TextCellEditor;
import org.isatools.isacreator.managers.ApplicationManager;
import org.isatools.isacreator.model.Contact;
import org.isatools.isacreator.ontologymanager.OntologyManager;
import org.isatools.isacreator.ontologymanager.OntologySourceRefObject;
import org.isatools.isacreator.ontologymanager.common.OntologyTerm;
import org.isatools.isacreator.ontologyselectiontool.OntologyCellEditor;
import org.isatools.isacreator.utils.StringProcessing;
import org.jdesktop.fuse.InjectedResource;
import org.jdesktop.fuse.ResourceInjector;
import javax.swing.*;
import javax.swing.border.EmptyBorder;
import javax.swing.border.TitledBorder;
import javax.swing.event.ListSelectionEvent;
import javax.swing.event.ListSelectionListener;
import javax.swing.table.*;
import java.awt.*;
import java.awt.event.*;
import java.beans.PropertyChangeEvent;
import java.beans.PropertyChangeListener;
import java.util.*;
import java.util.List;
/**
* SubForm
*
* @author Eamonn Maguire
* @date Jan 11, 2010
*/
public abstract class SubForm extends JPanel implements ListSelectionListener, FocusListener {
private static final Logger log = Logger.getLogger(SubForm.class.getName());
protected static SubFormLockedCellRenderer lockedTableHeaderRenderer = new SubFormLockedCellRenderer();
protected static SubFormHeaderRenderer scrollTableHeaderRenderer = new SubFormHeaderRenderer();
private static final int numFrozenColumns = 1;
// we create a static instance because the one component can be used across multiple SubForm elements in this way
protected static EmptyBorder em = new EmptyBorder(0, 0, 0, 0);
private static final SubFormCellRenderer DEFAULT_LOCKED_TABLE_RENDERER = new SubFormCellRenderer(UIHelper.VER_11_BOLD, UIHelper.DARK_GREEN_COLOR, new Color(141, 198, 63, 40), true);
private static final SubFormCellRenderer DEFAULT_SCROLL_TABLE_RENDERER = new SubFormCellRenderer(UIHelper.VER_11_PLAIN, UIHelper.DARK_GREEN_COLOR, null);
@InjectedResource
protected ImageIcon ontologyLookupHelp, textEditHelp, confirmRemoveColumn, addRecordIcon, addRecordIconOver,
removeIcon, removeIconOver, selectFromHistoryIcon, selectFromHistoryIconOver, searchIcon, searchIconOver;
protected String title;
protected DefaultTableModel defaultTableModel;
protected ExtendedJTable lockedTable;
protected ExtendedJTable scrollTable;
private JScrollPane frozenTable;
protected List<SubFormField> fields;
protected RowEditor rowEditor = new RowEditor();
protected FieldTypes fieldType;
protected DataEntryForm dataEntryForm;
protected DataEntryEnvironment dataEntryEnvironment;
private boolean createBorder = true;
protected Set<Integer> uneditableRecords = new HashSet<Integer>();
// this will house the translation between Comment aliases e.g. Publication Journal [c] to Comment[Publication Journal]
protected Map<String, String> aliasesToRealNames;
protected Map<String, String> realNamesToAliases;
protected int initialNoFields;
protected int width;
protected int height;
// we only ever create one textcelleditor.
protected static TextCellEditor longTextEditor = new TextCellEditor();
protected JLabel removeRecord;
protected JPanel options;
private boolean showRemoveOption = true;
private ExcelAdaptor excelAdaptor;
public SubForm(String title, FieldTypes fieldType, List<SubFormField> fields, DataEntryEnvironment dataEntryEnvironment) {
this(title, fieldType, fields, dataEntryEnvironment, true);
}
public SubForm(String title, FieldTypes fieldType, List<SubFormField> fields, DataEntryEnvironment dataEntryEnvironment, boolean createBorder) {
this.title = title;
this.fieldType = fieldType;
this.fields = fields;
this.dataEntryEnvironment = dataEntryEnvironment;
this.createBorder = createBorder;
}
public SubForm(String title, FieldTypes fieldType,
List<SubFormField> fields, int initialNoFields, int width,
int height, DataEntryForm dataEntryForm) {
this(title, fieldType, fields, initialNoFields, width, height, dataEntryForm, true);
}
public SubForm(String title, FieldTypes fieldType,
List<SubFormField> fields, int initialNoFields, int width,
int height, DataEntryForm dataEntryForm, boolean createBorder) {
this.title = title;
this.fieldType = fieldType;
this.fields = fields;
this.initialNoFields = initialNoFields;
this.width = width;
this.height = height;
this.dataEntryForm = dataEntryForm;
this.createBorder = createBorder;
generateAliases();
if (dataEntryForm instanceof DataEntryEnvironment) {
this.dataEntryEnvironment = (DataEntryEnvironment) dataEntryForm;
} else if (dataEntryForm != null) {
this.dataEntryEnvironment = dataEntryForm.getDataEntryEnvironment();
} else {
dataEntryEnvironment = null;
}
}
public void createGUI() {
ResourceInjector.get("gui-package.style").inject(true, new Object[]{this});
initialisePanel();
setupTableModel(initialNoFields);
add(setupOptionsPanel(), BorderLayout.NORTH);
add(getFrozenTable(defaultTableModel, width, height), BorderLayout.CENTER);
reformPreviousContent();
}
public FieldTypes getFieldType() {
return fieldType;
}
public String getTitle() {
return title;
}
private void generateAliases() {
if (aliasesToRealNames == null) {
aliasesToRealNames = new HashMap<String, String>();
realNamesToAliases = new HashMap<String, String>();
}
for (SubFormField field : fields) {
String fieldName = field.getFieldName();
if (fieldName.toLowerCase().startsWith("comment")) {
String alias = StringProcessing.extractQualifierFromField(fieldName) + " [c]";
aliasesToRealNames.put(alias, fieldName);
realNamesToAliases.put(fieldName, alias);
}
}
}
protected void initialisePanel() {
this.setLayout(new BorderLayout());
this.setBackground(UIHelper.BG_COLOR);
if (createBorder) {
setBorder(new TitledBorder(
UIHelper.GREEN_ROUNDED_BORDER, title,
TitledBorder.DEFAULT_JUSTIFICATION,
TitledBorder.CENTER,
UIHelper.VER_12_BOLD, UIHelper.DARK_GREEN_COLOR));
} else {
setBorder(new EmptyBorder(2, 2, 2, 2));
}
}
public JScrollPane getFrozenTable(DefaultTableModel model, int width,
int height) {
// number of initial records equal to the number of columns in the model - the first column which contains field names!
frozenTable = new JScrollPane();
IAppWidgetFactory.makeIAppScrollPane(frozenTable);
lockedTable = new ExtendedJTable(model, rowEditor);
lockedTable.getTableHeader().setReorderingAllowed(false);
setTableProperties(lockedTable, true);
scrollTable = new ExtendedJTable(model, rowEditor);
setTableProperties(scrollTable, false);
scrollTable.getSelectionModel()
.setSelectionMode(ListSelectionModel.MULTIPLE_INTERVAL_SELECTION);
scrollTable.getTableHeader().setResizingAllowed(true);
try {
lockedTable.setDefaultRenderer(Class.forName("java.lang.Object"),
DEFAULT_LOCKED_TABLE_RENDERER);
scrollTable.setDefaultRenderer(Class.forName("java.lang.Object"),
DEFAULT_SCROLL_TABLE_RENDERER);
} catch (ClassNotFoundException e) {
// ignore
}
scrollTable.putClientProperty("terminateEditOnFocusLost", Boolean.TRUE);
scrollTable.getSelectionModel().addListSelectionListener(this);
scrollTable.getColumnModel().getSelectionModel().addListSelectionListener(this);
scrollTable.addFocusListener(this);
scrollTable.setBackground(UIHelper.BG_COLOR);
UIHelper.renderComponent(scrollTable.getTableHeader(), UIHelper.VER_12_PLAIN, UIHelper.BG_COLOR, new Color(141, 198, 63, 40));
excelAdaptor = new ExcelAdaptor(scrollTable, false);
frozenTable.setViewportView(scrollTable);
frozenTable.setBorder(em);
setupTableTabBehaviour();
JTableHeader lockedHeader = lockedTable.getTableHeader();
setHeaderProperties(lockedTable, lockedTableHeaderRenderer);
lockedHeader.setReorderingAllowed(false);
frozenTable.setCorner(JScrollPane.UPPER_LEFT_CORNER, lockedHeader);
setHeaderProperties(scrollTable, scrollTableHeaderRenderer);
JViewport viewport = new JViewport();
viewport.setBackground(UIHelper.BG_COLOR);
viewport.setView(lockedTable);
frozenTable.setRowHeader(viewport);
updateTables();
frozenTable.setPreferredSize(new Dimension(width, height));
frozenTable.getViewport().setBackground(UIHelper.BG_COLOR);
frozenTable.getHorizontalScrollBar().setBackground(UIHelper.BG_COLOR);
return frozenTable;
}
public JScrollPane getFrozenTable() {
return frozenTable;
}
public ExtendedJTable getScrollTable() {
return scrollTable;
}
public void updateTables() {
TableColumnModel scrollColumnModel = scrollTable.getColumnModel();
if (scrollColumnModel.getColumnCount() > 0) {
for (int i = 0; i < numFrozenColumns; i++) {
scrollColumnModel.removeColumn(scrollColumnModel.getColumn(0));
}
TableColumnModel lockedColumnModel = lockedTable.getColumnModel();
while (lockedTable.getColumnCount() > numFrozenColumns) {
lockedColumnModel.removeColumn(lockedColumnModel.getColumn(
numFrozenColumns));
}
for (int i = 0; i < scrollTable.getColumnCount(); i++) {
scrollColumnModel.getColumn(i).setPreferredWidth(100);
}
lockedTable.getColumnModel().getColumn(0).setPreferredWidth(250);
lockedTable.setPreferredScrollableViewportSize(lockedTable.getPreferredSize());
setHeaderProperties(scrollTable, scrollTableHeaderRenderer);
setHeaderProperties(lockedTable, lockedTableHeaderRenderer);
}
}
/**
* Returns subform as an 2D array of Strings
*
* @return String[][] containing representation of data
*/
public String[][] getDataAsArray() {
java.util.List<String[]> data = new ArrayList<String[]>();
String[] val = new String[defaultTableModel.getRowCount()];
for (int col = 1; col < defaultTableModel.getColumnCount(); col++) {
for (int row = 0; row < defaultTableModel.getRowCount(); row++) {
if (defaultTableModel.getValueAt(row, col) != null) {
val[row] = defaultTableModel.getValueAt(row, col).toString();
}
}
data.add(val);
val = new String[defaultTableModel.getRowCount()];
}
String[][] finalData = new String[data.size()][defaultTableModel.getRowCount()];
int dataSize = data.size();
for (int i = 0; i < dataSize; i++) {
finalData[i] = data.get(i);
}
return finalData;
}
protected Object[][] getRowData() {
Object[][] rowData = new Object[fields.size()][1];
for (int i = 0; i < fields.size(); i++) {
String fieldName = fields.get(i).getFieldName();
if (realNamesToAliases.containsKey(fieldName)) {
fieldName = realNamesToAliases.get(fieldName);
}
rowData[i][0] = fieldName;
if (fields.get(i).getDataType() == SubFormField.LONG_STRING) {
rowEditor.addCellEditorForRow(i, longTextEditor);
}
if (fields.get(i).getDataType() == SubFormField.DATE) {
rowEditor.addCellEditorForRow(i, new DateCellEditor());
}
if (fields.get(i).getDataType() == SubFormField.SINGLE_ONTOLOGY_SELECT) {
rowEditor.addCellEditorForRow(i,
new OntologyCellEditor(false, false, fields.get(i).getRecommendedOntologyType()));
}
if (fields.get(i).getDataType() == SubFormField.MULTIPLE_ONTOLOGY_SELECT) {
rowEditor.addCellEditorForRow(i,
new OntologyCellEditor(true, false, fields.get(i).getRecommendedOntologyType()));
}
if (fields.get(i).getDataType() == SubFormField.COMBOLIST) {
rowEditor.addCellEditorForRow(i,
new AutoFilterComboCellEditor(new AutoFilterCombo(
fields.get(i).getListValues(), false)));
}
if (fields.get(i).getDataType() == SubFormField.FILE) {
rowEditor.addCellEditorForRow(i, new FileSelectCellEditor());
}
if (fields.get(i).getDataType() == SubFormField.FACTOR_LEVEL_UNITS) {
rowEditor.addCellEditorForRow(i, new FactorLevelEntryCellEditor());
}
}
return rowData;
}
private int calculateNoRows() {
int noOntologyRows = 0;
for (int i = 0; i < scrollTable.getRowCount(); i++) {
if (scrollTable.getCellEditor(i, 0) instanceof OntologyCellEditor || defaultTableModel.getValueAt(i, 0).toString().contains("Assay Measurement Type") || defaultTableModel.getValueAt(i, 0).toString().contains("Assay Technology Type")) {
noOntologyRows++;
}
}
return scrollTable.getRowCount() + (noOntologyRows * 2);
}
public void toggleShowRemoveOption() {
showRemoveOption = !showRemoveOption;
}
protected void setupTableModel(int initialFieldNo) {
defaultTableModel = new DefaultTableModel(getRowData(), getColumnNames(initialFieldNo)) {
public Object getValueAt(int row, int col) {
if (col == 0) {
String fieldName = fields.get(row).toString();
if (realNamesToAliases.containsKey(fieldName)) {
fieldName = realNamesToAliases.get(fieldName);
}
return fieldName;
}
return super.getValueAt(row, col);
}
public boolean isCellEditable(int row, int col) {
return (col != 0) && !uneditableRecords.contains(col);
}
@Override
public void setValueAt(Object o, int i, int i2) {
super.setValueAt(o, i, i2);
ApplicationManager.setModified(true);
}
};
}
private Object[] getColumnNames(int initialFields) {
// add 1 to account for first column, which is nt used for data entry.
Object[] colNames = new Object[initialFields + 1];
colNames[0] = "Field Name";
for (int i = 1; i < colNames.length; i++) {
colNames[i] = fieldType;
}
return colNames;
}
protected void setupTableTabBehaviour() {
InputMap im = scrollTable.getInputMap(JTable.WHEN_ANCESTOR_OF_FOCUSED_COMPONENT);
KeyStroke tab = KeyStroke.getKeyStroke(KeyEvent.VK_TAB, 0);
// Override the default tab behaviour
// Tab to the next editable cell. When no editable cells goto next cell.
final Action previousTabAction = scrollTable.getActionMap()
.get(im.get(tab));
Action newTabAction = new AbstractAction() {
public void actionPerformed(ActionEvent e) {
int rowSel = scrollTable.getSelectedRow();
int colSel = scrollTable.getSelectedColumn();
if (rowSel == (scrollTable.getRowCount() - 1)) {
scrollTable.setRowSelectionInterval(0, 0);
if ((colSel + 1) == scrollTable.getColumnCount()) {
scrollTable.setColumnSelectionInterval(0, 0);
} else {
scrollTable.setColumnSelectionInterval(colSel + 1,
colSel + 1);
}
} else {
rowSel = rowSel + 1;
scrollTable.setRowSelectionInterval(rowSel, rowSel);
if (colSel > -1) {
scrollTable.setColumnSelectionInterval(colSel,
colSel);
}
}
scrollTable.scrollRectToVisible(scrollTable.getCellRect(
rowSel, colSel, true));
JTable table = (JTable) e.getSource();
int row = table.getSelectedRow();
int originalRow = row;
int column = table.getSelectedColumn();
int originalColumn = column;
while (!table.isCellEditable(row, column)) {
previousTabAction.actionPerformed(e);
row = table.getSelectedRow();
column = table.getSelectedColumn();
// Back to where we started, get out.
if ((row == originalRow) && (column == originalColumn)) {
break;
}
}
if (table.editCellAt(row, column)) {
table.getEditorComponent().requestFocusInWindow();
}
}
};
scrollTable.getActionMap().put(im.get(tab), newTabAction);
}
protected void setHeaderProperties(JTable table, TableCellRenderer renderer) {
Enumeration<TableColumn> columns = table.getColumnModel().getColumns();
while (columns.hasMoreElements()) {
columns.nextElement().setHeaderRenderer(renderer);
}
}
protected void setTableProperties(JTable table, boolean isFieldName) {
Font font = (!isFieldName) ? UIHelper.VER_12_PLAIN : UIHelper.VER_12_BOLD;
table.setFont(font);
table.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
table.setColumnSelectionAllowed(true);
table.setRowSelectionAllowed(true);
table.setGridColor(UIHelper.LIGHT_GREEN_COLOR);
table.setShowGrid(true);
}
public void valueChanged(ListSelectionEvent event) {
int columnSelected = scrollTable.getSelectedColumn();
int rowSelected = scrollTable.getSelectedRow();
if ((rowSelected != -1) && (columnSelected != -1)) {
removeRecord.setText((showRemoveOption ? "Remove " : "Selected ") + fieldType + " " + (columnSelected + 1));
if (!removeRecord.isVisible()) {
removeRecord.setVisible(true);
}
if (scrollTable.getValueAt(rowSelected, columnSelected) != null) {
String s = scrollTable.getValueAt(rowSelected, columnSelected)
.toString();
OntologyTerm ooForSelectedTerm = OntologyManager.getOntologyTerm(s);
if (ooForSelectedTerm != null) {
dataEntryForm.getDataEntryEnvironment().setStatusPaneInfo("<html>" +
"<b>ontology term information</b>" +
"<p><term name: >" + ooForSelectedTerm.getOntologyTermName() +
"</p>" + "<p><b>source ref: </b> " +
ooForSelectedTerm.getOntologySource() + "</p>" +
"<p><b>accession no: </b>" +
ooForSelectedTerm.getOntologyTermAccession() + "</p>" +
"</html>");
}
ApplicationManager.setCurrentlySelectedField(fields.get(rowSelected).getFieldName());
} else {
TableCellEditor tce = scrollTable.getCellEditor(rowSelected, columnSelected);
Icon icon = null;
if (tce instanceof OntologyCellEditor) {
// insert images to inform user of what to do in this situation :o)
icon = ontologyLookupHelp;
} else if (tce instanceof TextCellEditor) {
icon = textEditHelp;
}
if (dataEntryForm != null && dataEntryForm.getDataEntryEnvironment() != null) {
if (icon != null) {
dataEntryForm.getDataEntryEnvironment().setStatusPaneInfo(icon);
} else {
dataEntryForm.getDataEntryEnvironment().setStatusPaneInfo("");
}
}
}
} else {
removeRecord.setVisible(false);
}
}
public void focusGained(FocusEvent event) {
removeRecord.setVisible(true);
}
public void focusLost(FocusEvent event) {
removeRecord.setVisible(false);
}
public boolean addColumn() {
DefaultTableModel model = (DefaultTableModel) scrollTable.getModel();
TableColumn col = new TableColumn(scrollTable.getModel().getColumnCount());
col.setHeaderRenderer(scrollTableHeaderRenderer);
SpreadsheetUtils.stopCellEditingInTable(scrollTable);
return doAddColumn(model, col);
}
public abstract boolean doAddColumn(DefaultTableModel model, TableColumn col);
public abstract void reformPreviousContent();
private void removalConfirmation(final FieldTypes whatIsBeingRemoved) {
// delete reference to protocol in subform
// add one to take into account the model and the initial column which contains fields names.
final int selectedItem = scrollTable.getSelectedColumn() + 1;
// check to ensure the value isn't 0, if it is, nothing is selected in the table since -1 (value returned by model if
// no column is selected + 1 = 0!)
if ((selectedItem != 0) && (dataEntryForm != null)) {
String displayText;
if ((whatIsBeingRemoved == FieldTypes.FACTOR) ||
(whatIsBeingRemoved == FieldTypes.PROTOCOL)) {
displayText = "<html>" + "<b>Confirm deletion of " +
fieldType + "</b>" + "<p>Deleting this " + fieldType +
" will result in all " + fieldType +
"s of this type in subsequent assays</p>" +
"<p>being deleted too! Do you wish to continue?</p>" +
"</html>";
} else {
displayText = "<html>" + "<b>Confirm deletion of " +
fieldType + "</b>" + "<p>Deleting this " + fieldType +
" will result in its complete removal from this experiment annotation!</p>" +
"<p>Do you wish to continue?</p>" + "</html>";
}
JOptionPane optionPane = new JOptionPane(displayText,
JOptionPane.INFORMATION_MESSAGE, JOptionPane.YES_NO_OPTION);
optionPane.addPropertyChangeListener(new PropertyChangeListener() {
public void propertyChange(PropertyChangeEvent event) {
if (event.getPropertyName()
.equals(JOptionPane.VALUE_PROPERTY)) {
int lastOptionAnswer = Integer.valueOf(event.getNewValue()
.toString());
if (lastOptionAnswer == JOptionPane.YES_OPTION) {
removeItem(selectedItem);
ApplicationManager.getCurrentApplicationInstance().hideSheet();
} else {
// just hide the sheet and cancel further actions!
ApplicationManager.getCurrentApplicationInstance().hideSheet();
}
}
}
});
optionPane.setIcon(confirmRemoveColumn);
UIHelper.applyOptionPaneBackground(optionPane, UIHelper.BG_COLOR);
ApplicationManager.getCurrentApplicationInstance()
.showJDialogAsSheet(optionPane.createDialog(this,
"Confirm Delete"));
} else {
removeColumn(selectedItem);
}
}
public abstract void removeItem(int itemToRemove);
protected void removeColumn(int curColDelete) {
if ((curColDelete == -1) || (curColDelete == 0)) {
return;
}
if (defaultTableModel.getColumnCount() == 2
&& curColDelete == (defaultTableModel.getColumnCount() - 1)) {
clearColumn(curColDelete);
return;
} else {
clearColumn(curColDelete);
}
if (fieldType == FieldTypes.ASSAY && (dataEntryForm != null)
&& !uneditableRecords.contains(curColDelete)) {
clearColumn(curColDelete);
return;
}
DefaultTableModel model = (DefaultTableModel) scrollTable.getModel();
// get the column. because 1 was added on previously to take account of the first column, we need to remove
// it this time since the column indexes are now coming from the table.
TableColumn col = scrollTable.getColumnModel()
.getColumn(curColDelete - 1);
int columnModelIndex = col.getModelIndex();
Vector data = model.getDataVector();
Vector<String> colIds = new Vector<String>();
for (int i = 0; i < model.getColumnCount(); i++) {
colIds.addElement(model.getColumnName(i));
}
scrollTable.removeColumn(col);
colIds.removeElementAt(columnModelIndex);
// remove any data present in the column on deletion
for (Object aData : data) {
Vector row = (Vector) aData;
row.removeElementAt(columnModelIndex);
}
model.setDataVector(data, colIds);
// decrease each column index after deleted column by 1 so that indexes can be kept intact.
Enumeration columnEnumeration = scrollTable.getColumnModel().getColumns();
while (columnEnumeration.hasMoreElements()) {
TableColumn c = (TableColumn) columnEnumeration.nextElement();
if (c.getModelIndex() >= columnModelIndex) {
c.setModelIndex(c.getModelIndex() - 1);
}
}
if (fieldType == FieldTypes.ASSAY && uneditableRecords.contains(defaultTableModel.getColumnCount() - 1)) {
uneditableRecords.remove(defaultTableModel.getColumnCount() - 1);
}
// update the model
model.fireTableStructureChanged();
updateTables();
}
protected void checkForSourcePresence(String source) {
if (dataEntryForm != null && dataEntryForm.getDataEntryEnvironment() != null) {
Collection<OntologySourceRefObject> definedSources = dataEntryForm.getDataEntryEnvironment()
.getOntologySources();
boolean isPresent = false;
for (OntologySourceRefObject osro : definedSources) {
if (osro.getSourceName().equals(source)) {
isPresent = true;
}
}
// if it doesn't exist, then add the ontology information to the defined sources
if (!isPresent) {
OntologySourceRefObject osro = UserProfileManager.getCurrentUser().getOntologySource(source);
if (osro == null) {
osro = OntologyManager.getOntologySourceReferenceObjectByAbbreviation(source);
}
dataEntryForm.getDataEntryEnvironment().getOntologySources().add(osro);
}
}
}
private void clearColumn(int colindex) {
int noRows = defaultTableModel.getRowCount();
for (int i = 0; i < noRows; i++) {
defaultTableModel.setValueAt("", i, colindex);
}
}
public Map<String, String> getRecord(int recordNumber) {
OrderedMap<String, String> record = new ListOrderedMap<String, String>();
int index = 0;
for (SubFormField field : fields) {
Object value = defaultTableModel.getValueAt(index, recordNumber);
String fieldName = field.getFieldName();
if (aliasesToRealNames.containsKey(field.getFieldName())) {
fieldName = aliasesToRealNames.get(fieldName);
}
record.put(fieldName, value == null ? "" : value.toString());
index++;
}
return record;
}
public int getColumnIndexForValue(int fieldIndex, String value) {
for (int column = 1; column < defaultTableModel.getColumnCount(); column++) {
if (defaultTableModel.getValueAt(fieldIndex, column).toString().equals(value)) {
return column;
}
}
return -1;
}
private JPanel setupOptionsPanel() {
options = new JPanel();
options.setLayout(new BoxLayout(options, BoxLayout.LINE_AXIS));
options.setOpaque(false);
String addRecordString = fieldType == FieldTypes.ASSAY && dataEntryForm != null ? "create assay" : "add a new " + fieldType + " column";
final JLabel addRecord = new JLabel(addRecordString, addRecordIcon, JLabel.LEFT);
String toolTipText;
if (fieldType == FieldTypes.ASSAY) {
toolTipText = "<html><b>Create a new Assay</b>" +
" <p>Complete the details for the assay in the fields provided</p>" +
" <p>and click this button to add the assay to this study...</p>" +
"</html>";
} else {
toolTipText = "<html><b>Add a new " + fieldType + "</b>" +
" <p>Click here to add a new column to enter an additional " + fieldType + "</p>" +
"</html>";
}
addRecord.setToolTipText(toolTipText);
Font fontToUse = fieldType == FieldTypes.ASSAY && dataEntryForm != null ? UIHelper.VER_12_BOLD : UIHelper.VER_12_PLAIN;
UIHelper.renderComponent(addRecord, fontToUse, UIHelper.DARK_GREEN_COLOR, false);
addRecord.addMouseListener(new MouseAdapter() {
public void mousePressed(MouseEvent event) {
addRecord.setIcon(addRecordIcon);
if (addColumn()) {
updateTables();
}
}
@Override
public void mouseEntered(MouseEvent mouseEvent) {
addRecord.setIcon(addRecordIconOver);
}
@Override
public void mouseExited(MouseEvent mouseEvent) {
addRecord.setIcon(addRecordIcon);
}
});
options.add(addRecord);
options.add(Box.createHorizontalStrut(10));
removeRecord = new JLabel("Remove " + fieldType + "...", removeIcon, JLabel.LEFT);
removeRecord.setVisible(false);
UIHelper.renderComponent(removeRecord, UIHelper.VER_12_PLAIN, UIHelper.DARK_GREEN_COLOR, false);
removeRecord.addMouseListener(new MouseAdapter() {
public void mousePressed(MouseEvent event) {
if (removeRecord.getIcon() != null) {
removeRecord.setIcon(removeIcon);
}
removalConfirmation(fieldType);
}
@Override
public void mouseExited(MouseEvent mouseEvent) {
if (removeRecord.getIcon() != null) {
removeRecord.setIcon(removeIcon);
}
}
@Override
public void mouseEntered(MouseEvent mouseEvent) {
if (removeRecord.getIcon() != null) {
removeRecord.setIcon(removeIconOver);
}
}
});
if (!showRemoveOption) {
removeRecord.setIcon(null);
removeRecord.setText("");
}
options.add(removeRecord);
options.add(Box.createHorizontalStrut(10));
createCustomOptions();
options.add(Box.createGlue());
return options;
}
public ExtendedJTable getLockedTable() {
return lockedTable;
}
public void changeTableRenderer(JTable table, TableCellRenderer renderer) {
try {
TableCellRenderer rendererToUse = renderer;
if (rendererToUse == null) {
if (table == scrollTable) {
rendererToUse = DEFAULT_SCROLL_TABLE_RENDERER;
} else {
rendererToUse = DEFAULT_LOCKED_TABLE_RENDERER;
}
}
table.setDefaultRenderer(Class.forName("java.lang.Object"), rendererToUse);
} catch (ClassNotFoundException e) {
log.error("Problem occurred when changing TableRenderer : " + e.getMessage());
}
}
public void resetModel(int newSize) {
defaultTableModel = new DefaultTableModel();
setupTableModel(newSize);
}
public void setDataEntryEnvironment(DataEntryEnvironment dataEntryEnvironment) {
this.dataEntryEnvironment = dataEntryEnvironment;
}
public void setDataEntryForm(DataEntryForm parent) {
this.dataEntryForm = parent;
}
public RowEditor getRowEditor() {
return rowEditor;
}
protected boolean isNullRecord(Map<String, String> record) {
boolean allNulls = true;
for (String key : record.keySet()) {
if (record.get(key) != null && !record.get(key).trim().equals("")) {
allNulls = false;
}
}
return allNulls;
}
public abstract void update();
public abstract void updateItems();
public abstract void reformItems();
/**
* Implementing this method allows for the creation of additional menu
* elements in the options panel of the subform.
*/
public abstract void createCustomOptions();
public void cleanupReferences() {
setDataEntryEnvironment(null);
for (int rowIndex = 0; rowIndex < scrollTable.getRowCount(); rowIndex++) {
if (getRowEditor().getCellEditor(rowIndex) instanceof RowEditor) {
OntologyCellEditor editor = (OntologyCellEditor) getRowEditor().getCellEditor(rowIndex);
editor.cleanupReferences();
}
}
scrollTable.getParent().removeAll();
scrollTable.setModel(new DefaultTableModel());
scrollTable = null;
lockedTable.getParent().removeAll();
lockedTable.setModel(new DefaultTableModel());
lockedTable = null;
options.removeAll();
removeRecord = null;
defaultTableModel = null;
excelAdaptor.setJTable(null);
excelAdaptor = null;
getRowEditor().removeAllCellEditors();
setDataEntryForm(null);
removeAll();
}
public List<SubFormField> getSubFormFields() {
return fields;
}
}