/**
* This function is used to re-run the analyser, and re-create the rows corresponding the its
* results.
*/
private void refreshReviewTable() {
reviewPanel.removeAll();
rows.clear();
GridBagLayout gbl = new GridBagLayout();
reviewPanel.setLayout(gbl);
GridBagConstraints gbc = new GridBagConstraints();
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.gridy = 0;
try {
Map<String, Long> sums =
analyser.processLogFile(config.getLogFilename(), fromDate.getDate(), toDate.getDate());
for (Entry<String, Long> entry : sums.entrySet()) {
String project = entry.getKey();
double hours = 1.0 * entry.getValue() / (1000 * 3600);
addRow(gbl, gbc, project, hours);
}
for (String project : main.getProjectsTree().getTopLevelProjects())
if (!rows.containsKey(project)) addRow(gbl, gbc, project, 0);
gbc.insets = new Insets(10, 0, 0, 0);
addLeftLabel(gbl, gbc, "TOTAL");
gbc.gridx = 1;
gbc.weightx = 1;
totalLabel.setBorder(BorderFactory.createEmptyBorder(0, 0, 0, 3));
gbl.setConstraints(totalLabel, gbc);
reviewPanel.add(totalLabel);
gbc.weightx = 0;
addRightLabel(gbl, gbc);
} catch (IOException e) {
e.printStackTrace();
}
recomputeTotal();
pack();
}
@Override
public void setValueAt(Object value, int rowIndex, int columnIndex) {
if ((columnIndex == 0) && (value instanceof Boolean)) {
Entry e = data.get(rowIndex);
e.enabled = (Boolean) value;
fireTableCellUpdated(rowIndex, columnIndex);
}
}
private void getParents(List<Entry> list) {
for (Entry entry : parents) {
if (entry.install && !list.contains(entry)) {
list.add(entry);
entry.getParents(list);
}
}
}
private String generateOverviewText() throws InsufficientDataException {
StringBuilder sb = new StringBuilder();
final String team = config.getTeam();
double total = checkTotal();
final String nl = System.getProperty("line.separator");
for (Entry<String, Row> entry : rows.entrySet()) {
double hours = Double.parseDouble(entry.getValue().hoursTF.getText());
double fraction = hours / total;
if (fraction < 0.004) continue;
String line = team + ", " + decimalFormat.format(fraction) + ", " + entry.getKey();
sb.append(line + nl);
}
return sb.toString();
}
// {{{ setSelectAll() method
public void setSelectAll(boolean b) {
if (isDownloadingList()) return;
int length = getRowCount();
for (int i = 0; i < length; i++) {
if (b) setValueAt(Boolean.TRUE, i, 0);
else {
Entry entry = (Entry) filteredEntries.get(i);
entry.parents = new LinkedList<Entry>();
entry.install = false;
}
}
fireTableChanged(new TableModelEvent(this));
} // }}}
// {{{ setValueAt() method
@Override
public void setValueAt(Object aValue, int row, int column) {
if (column != 0) return;
Object obj = filteredEntries.get(row);
if (obj instanceof String) return;
Entry entry = (Entry) obj;
boolean before = entry.install;
entry.install = Boolean.TRUE.equals(aValue);
if (before == entry.install) return;
if (!entry.install) deselectParents(entry);
List<PluginList.Dependency> deps = entry.plugin.getCompatibleBranch().deps;
for (int i = 0; i < deps.size(); i++) {
PluginList.Dependency dep = deps.get(i);
if ("plugin".equals(dep.what)) {
boolean found = false;
for (int j = 0; j < filteredEntries.size(); j++) {
Entry temp = (Entry) filteredEntries.get(j);
if (temp.plugin == dep.plugin) {
found = true;
if (entry.install) {
temp.parents.add(entry);
setValueAt(Boolean.TRUE, j, 0);
} else temp.parents.remove(entry);
break;
}
}
if (!found) {
// the dependency was not found in the filtered list so we search in
// global list.
for (int a = 0; a < entries.size(); a++) {
Entry temp = (Entry) entries.get(a);
if (temp.plugin == dep.plugin) {
if (entry.install) {
temp.parents.add(entry);
temp.install = true;
} else temp.parents.remove(entry);
break;
}
}
}
}
}
updateFilteredEntries();
} // }}}
// {{{ deselectParents() method
private void deselectParents(Entry entry) {
Entry[] parents = entry.getParents();
if (parents.length == 0) return;
String[] args = {entry.name};
int result = GUIUtilities.listConfirm(window, "plugin-manager.dependency", args, parents);
if (result != JOptionPane.OK_OPTION) {
entry.install = true;
return;
}
for (int i = 0; i < parents.length; i++) parents[i].install = false;
fireTableRowsUpdated(0, getRowCount() - 1);
} // }}}
/**
* Include row if each matcher succeeds in at least one column. In other words all the
* conditions are combined with "and"
*
* @param value
* @return
*/
@Override
public boolean include(Entry value) {
for (Pair<String, Matcher> entry : matchers) {
String column = entry.getFirst();
Matcher matcher = entry.getSecond();
// Search for a match in at least one column. The first column is the checkbox.
boolean found = false; // Pessimistic
int nColumns = table.getColumnCount();
for (int index = 1; index < nColumns; index++) {
// Include column headings in search. This is to prevent premature filtering when
// entering a
// specific column condition (e.g. cataType=ChipSeq)
matcher.reset(table.getColumnName(index).toLowerCase());
if (matcher.find()) {
found = true;
break;
}
boolean wildcard = column.equals("*");
if (wildcard || column.equalsIgnoreCase(table.getColumnName(index))) {
matcher.reset(value.getStringValue(index));
if (matcher.find()) {
found = true;
break;
}
}
}
if (!found) return false;
}
return true; // If we get here we matched them all
}
/** Make an EntryEdit component from the given Entry. */
public static EntryEdit makeEntryEdit(final Entry entry) {
final Bases bases = entry.getBases();
final EntryGroup entry_group = new SimpleEntryGroup(bases);
entry_group.add(entry);
final EntryEdit entry_edit = new EntryEdit(entry_group);
return entry_edit;
}
/** Code completion. */
private void complete() {
if (selected()) return;
// find first character
final int caret = editor.pos(), startPos = editor.completionStart();
final String prefix = string(substring(editor.text(), startPos, caret));
if (prefix.isEmpty()) return;
// find insertion candidates
final TreeMap<String, String> tmp = new TreeMap<>();
for (final Entry<String, String> entry : REPLACE.entrySet()) {
final String key = entry.getKey();
if (key.startsWith(prefix)) tmp.put(key, entry.getValue());
}
if (tmp.size() == 1) {
// insert single candidate
complete(tmp.values().iterator().next(), startPos);
} else if (!tmp.isEmpty()) {
// show popup menu
final JPopupMenu pm = new JPopupMenu();
final ActionListener al =
new ActionListener() {
@Override
public void actionPerformed(final ActionEvent ae) {
complete(ae.getActionCommand().replaceAll("^.*?\\] ", ""), startPos);
}
};
for (final Entry<String, String> entry : tmp.entrySet()) {
final JMenuItem mi = new JMenuItem("[" + entry.getKey() + "] " + entry.getValue());
pm.add(mi);
mi.addActionListener(al);
}
pm.addSeparator();
final JMenuItem mi = new JMenuItem(Text.INPUT + Text.COLS + prefix);
mi.setEnabled(false);
pm.add(mi);
final int[] cursor = rend.cursor();
pm.show(this, cursor[0], cursor[1]);
// highlight first entry
final MenuElement[] me = {pm, (JMenuItem) pm.getComponent(0)};
MenuSelectionManager.defaultManager().setSelectedPath(me);
}
}
/** Read the entries given in the uk.ac.sanger.artemis.ini file. */
private void readDefaultEntries() {
final EntryInformation artemis_entry_information = Options.getArtemisEntryInformation();
final String default_sequence_file_name = Options.getOptions().getDefaultSequenceFileName();
final String default_feature_file_name = Options.getOptions().getDefaultFeatureFileName();
if (default_sequence_file_name != null) {
final String default_sequence_file_name_embl = default_sequence_file_name + "_embl";
uk.ac.sanger.artemis.io.Entry new_embl_entry = null;
// try opening the default sequence file with "_embl" added to the name
// if that fails try the plain sequence file name
final Document entry_document = DocumentFactory.makeDocument(default_sequence_file_name_embl);
final InputStreamProgressListener progress_listener = getInputStreamProgressListener();
entry_document.addInputStreamProgressListener(progress_listener);
if (entry_document.readable()) {
new_embl_entry =
EntryFileDialog.getEntryFromFile(
this, entry_document, artemis_entry_information, false);
}
if (new_embl_entry == null
|| new_embl_entry.getSequence() == null
|| new_embl_entry.getSequence().length() == 0) {
final File entry_file = new File(default_sequence_file_name);
if (entry_file.exists()) {
new_embl_entry =
EntryFileDialog.getEntryFromFile(
this, entry_document, artemis_entry_information, false);
} else {
// read failed
System.err.println(
"file does not exist: " + default_sequence_file_name + "(given in options files)");
return;
}
}
if (new_embl_entry == null
|| new_embl_entry.getSequence() == null
|| new_embl_entry.getSequence().length() == 0) {
// read failed
System.err.println(
"failed to read " + default_sequence_file_name + "(given in options files)");
return;
}
getStatusLabel().setText("");
try {
final Entry entry = new Entry(new_embl_entry);
final EntryEdit new_entry_edit = makeEntryEdit(entry);
new_entry_edit.setVisible(true);
if (default_feature_file_name != null) {
final Document feature_document = DocumentFactory.makeDocument(default_feature_file_name);
final uk.ac.sanger.artemis.io.Entry new_embl_table_entry =
EntryFileDialog.getEntryFromFile(
this, feature_document, artemis_entry_information, false);
if (new_embl_table_entry == null) // open failed
return;
final EntryGroup entry_group = new_entry_edit.getEntryGroup();
final Entry new_table_entry = new Entry(entry.getBases(), new_embl_table_entry);
entry_group.add(new_table_entry);
}
} catch (OutOfRangeException e) {
new MessageDialog(
this,
"read failed: one of the features in "
+ default_feature_file_name
+ " has an out of range location: "
+ e.getMessage());
} catch (NoSequenceException e) {
new MessageDialog(
this, "read failed: " + new_embl_entry.getName() + " contains no sequence");
}
}
}