/** 選択されている行をコピーする。 */
public void copyRow() {
StringBuilder sb = new StringBuilder();
int numRows = view.getTable().getSelectedRowCount();
int[] rowsSelected = view.getTable().getSelectedRows();
int numColumns = view.getTable().getColumnCount();
for (int i = 0; i < numRows; i++) {
if (tableModel.getObject(rowsSelected[i]) != null) {
StringBuilder s = new StringBuilder();
for (int col = 0; col < numColumns; col++) {
Object o = view.getTable().getValueAt(rowsSelected[i], col);
if (o != null) {
s.append(o.toString());
}
s.append(",");
}
if (s.length() > 0) {
s.setLength(s.length() - 1);
}
sb.append(s.toString()).append("\n");
}
}
if (sb.length() > 0) {
StringSelection stsel = new StringSelection(sb.toString());
Toolkit.getDefaultToolkit().getSystemClipboard().setContents(stsel, stsel);
}
}
private String toBlockedSequence(String sequence) {
char[] chars = sequence.toCharArray();
StringBuilder sb = new StringBuilder();
boolean modStart = false;
int count = 0;
for (char c : chars) {
String singleLetter = String.valueOf(c);
if (singleLetter.equals(ComplexProtein.START_MODIFICATION_DECORATOR)) {
modStart = true;
} else if (singleLetter.equals(ComplexProtein.END_MODIFICATION_DECORATOR)) {
modStart = false;
count++;
} else {
if (!modStart) {
count++;
}
}
sb.append(singleLetter);
if (count == AMINO_ACID_COUNT_PER_BLOCK) {
sb.append(" ");
count = 0;
}
}
return sb.toString();
}
private String escapePrintfChars(String str) {
if (str == null) return "";
StringBuilder sb = new StringBuilder();
for (int ci = 0; ci < str.length(); ci++) {
char ch = str.charAt(ci);
if (ch == '%') {
sb.append('%');
}
sb.append(ch);
}
return sb.toString();
}
/**
* Return a copy of the string with all reserved regexp chars escaped by backslash.
*
* @param str the string to add escapes to
* @return String return a string with escapes or "" if str is null
*/
private String escapeReservedChars(String str) {
if (str == null) return "";
StringBuilder sb = new StringBuilder();
for (int ci = 0; ci < str.length(); ci++) {
char ch = str.charAt(ci);
if (RESERVED_STRING.indexOf(ch) >= 0) {
sb.append('\\');
}
sb.append(ch);
}
return escapePrintfChars(sb.toString());
}
String getEnabledCiphers() {
StringBuilder sb = new StringBuilder();
for (Entry e : data) {
if (e.enabled) {
sb.append(e.cipher);
sb.append(',');
}
}
if (sb.length() == 0) {
return sb.toString();
} else {
return sb.substring(0, sb.length() - 1);
}
}
/**
* Creates a String representation of the given object.
*
* @param certificate to print
* @return the String representation
*/
private String toString(Object certificate) {
final StringBuilder sb = new StringBuilder();
sb.append("<html><body>\n");
if (certificate instanceof X509Certificate) {
renderX509(sb, (X509Certificate) certificate);
} else {
sb.append("<pre>\n");
sb.append(certificate.toString());
sb.append("</pre>\n");
}
sb.append("</body></html>");
return sb.toString();
}
public void showItem() {
if (!this.editorPanel.getViewer().isLanguageFunctionAvailable()) {
return;
}
this.highlight =
this.editorPanel
.getEditor()
.addHighlight(this.position, this.position + this.word.length(), null, true);
final FindSynonymsActionHandler _this = this;
QTextEditor editor = this.editorPanel.getEditor();
Rectangle r = null;
try {
r = editor.modelToView(this.position);
} catch (Exception e) {
// BadLocationException!
Environment.logError("Location: " + this.position + " is not valid", e);
UIUtils.showErrorMessage(this.editorPanel, "Unable to display synonyms.");
return;
}
int y = r.y;
// Show a panel of all the items.
final QPopup p = this.popup;
p.setOpaque(false);
Synonyms syns = null;
try {
syns = this.projectViewer.getSynonymProvider().getSynonyms(this.word);
} catch (Exception e) {
UIUtils.showErrorMessage(this.editorPanel, "Unable to display synonyms.");
Environment.logError("Unable to lookup synonyms for: " + word, e);
return;
}
if ((syns.words.size() == 0) && (this.word.toLowerCase().endsWith("ed"))) {
// Trim off the ed and try again.
try {
syns = this.projectViewer.getSynonyms(this.word.substring(0, this.word.length() - 2));
} catch (Exception e) {
UIUtils.showErrorMessage(this.editorPanel, "Unable to display synonyms.");
Environment.logError("Unable to lookup synonyms for: " + word, e);
return;
}
}
if ((syns.words.size() == 0) && (this.word.toLowerCase().endsWith("s"))) {
// Trim off the ed and try again.
try {
syns = this.projectViewer.getSynonyms(this.word.substring(0, this.word.length() - 1));
} catch (Exception e) {
UIUtils.showErrorMessage(this.editorPanel, "Unable to display synonyms.");
Environment.logError("Unable to lookup synonyms for: " + word, e);
return;
}
}
StringBuilder sb = new StringBuilder();
if (syns.words.size() > 0) {
sb.append("6px");
for (int i = 0; i < syns.words.size(); i++) {
if (sb.length() > 0) {
sb.append(", ");
}
sb.append("p, 3px, [p,90px], 5px");
}
/*
if (syns.words.size () > 0)
{
sb.append (",5px");
}
*/
} else {
sb.append("6px, p, 6px");
}
FormLayout summOnly = new FormLayout("3px, fill:380px:grow, 3px", sb.toString());
PanelBuilder pb = new PanelBuilder(summOnly);
CellConstraints cc = new CellConstraints();
int ind = 2;
Map<String, String> names = new HashMap();
names.put(Synonyms.ADJECTIVE + "", "Adjectives");
names.put(Synonyms.NOUN + "", "Nouns");
names.put(Synonyms.VERB + "", "Verbs");
names.put(Synonyms.ADVERB + "", "Adverbs");
names.put(Synonyms.OTHER + "", "Other");
if (syns.words.size() == 0) {
JLabel l = new JLabel("No synonyms found.");
l.setFont(l.getFont().deriveFont(Font.ITALIC));
pb.add(l, cc.xy(2, 2));
}
// Determine what type of word we are looking for.
for (Synonyms.Part i : syns.words) {
JLabel l = new JLabel(names.get(i.type + ""));
l.setFont(l.getFont().deriveFont(Font.ITALIC));
l.setFont(l.getFont().deriveFont((float) UIUtils.getEditorFontSize(10)));
l.setBorder(
new CompoundBorder(
new MatteBorder(0, 0, 1, 0, Environment.getBorderColor()),
new EmptyBorder(0, 0, 3, 0)));
pb.add(l, cc.xy(2, ind));
ind += 2;
HTMLEditorKit kit = new HTMLEditorKit();
HTMLDocument doc = (HTMLDocument) kit.createDefaultDocument();
JTextPane t = new JTextPane(doc);
t.setEditorKit(kit);
t.setEditable(false);
t.setOpaque(false);
StringBuilder buf =
new StringBuilder(
"<style>a { text-decoration: none; } a:hover { text-decoration: underline; }</style><span style='color: #000000; font-size: "
+ ((int) UIUtils.getEditorFontSize(10) /*t.getFont ().getSize () + 2*/)
+ "pt; font-family: "
+ t.getFont().getFontName()
+ ";'>");
for (int x = 0; x < i.words.size(); x++) {
String w = (String) i.words.get(x);
buf.append("<a class='x' href='http://" + w + "'>" + w + "</a>");
if (x < (i.words.size() - 1)) {
buf.append(", ");
}
}
buf.append("</span>");
t.setText(buf.toString());
t.addHyperlinkListener(
new HyperlinkAdapter() {
public void hyperlinkUpdate(HyperlinkEvent ev) {
if (ev.getEventType() == HyperlinkEvent.EventType.ACTIVATED) {
QTextEditor ed = _this.editorPanel.getEditor();
ed.replaceText(
_this.position, _this.position + _this.word.length(), ev.getURL().getHost());
ed.removeHighlight(_this.highlight);
_this.popup.setVisible(false);
_this.projectViewer.fireProjectEvent(
ProjectEvent.SYNONYM, ProjectEvent.REPLACE, ev.getURL().getHost());
}
}
});
// Annoying that we have to do this but it prevents the text from being too small.
t.setSize(new Dimension(380, Short.MAX_VALUE));
JScrollPane sp = new JScrollPane(t);
t.setCaretPosition(0);
sp.setOpaque(false);
sp.getVerticalScrollBar().setValue(0);
/*
sp.setPreferredSize (t.getPreferredSize ());
sp.setMaximumSize (new Dimension (380,
75));
*/
sp.getViewport().setOpaque(false);
sp.setOpaque(false);
sp.setBorder(null);
sp.getViewport().setBackground(Color.WHITE);
sp.setAlignmentX(Component.LEFT_ALIGNMENT);
pb.add(sp, cc.xy(2, ind));
ind += 2;
}
JPanel pan = pb.getPanel();
pan.setOpaque(true);
pan.setBackground(Color.WHITE);
this.popup.setContent(pan);
// r.y -= this.editorPanel.getScrollPane ().getVerticalScrollBar ().getValue ();
Point po = SwingUtilities.convertPoint(editor, r.x, r.y, this.editorPanel);
r.x = po.x;
r.y = po.y;
// Subtract the insets of the editorPanel.
Insets ins = this.editorPanel.getInsets();
r.x -= ins.left;
r.y -= ins.top;
this.editorPanel.showPopupAt(this.popup, r, "above", true);
}
protected String consume(BufferedReader br) throws Exception {
StringBuilder ret = new StringBuilder();
int ch;
while ((ch = br.read()) != -1) ret.appendCodePoint(ch);
return ret.toString();
}
private <T extends Enum<T>> String getPropertyValue(T algo) {
StringBuilder strb = new StringBuilder();
for (T it : active.algos(algo)) {
strb.append(it.name());
strb.append(';');
}
return strb.toString();
}
public static String getLines(String s) {
StringBuilder sb = new StringBuilder();
int index = 0;
for (int i = 1; index != -1; i++) {
sb.append(i + "\n");
index = s.indexOf("\n", index + 1);
}
return sb.toString();
}
/**
* Converts the byte array to hex string.
*
* @param raw the data.
* @return the hex string.
*/
private String getHex(byte[] raw) {
if (raw == null) return null;
StringBuilder hex = new StringBuilder(2 * raw.length);
Formatter f = new Formatter(hex);
try {
for (byte b : raw) f.format("%02x", b);
} finally {
f.close();
}
return hex.toString();
}
public String toString() {
final StringBuilder sb = new StringBuilder();
sb.append((int) _dim.getWidth());
sb.append(' ');
sb.append((int) _dim.getHeight());
sb.append(' ');
sb.append(_loc.x);
sb.append(' ');
sb.append(_loc.y);
sb.append(' ');
sb.append(_currentStrategyIndex);
return sb.toString();
}
public static String inputStreamReaderToString(InputStreamReader in) throws Exception {
StringBuilder sb = new StringBuilder();
char[] buf = new char[1025];
while (in.ready()) {
sb.append((new String(buf, 0, in.read(buf, 0, 1024))).replaceAll("\r\n", "\n"));
}
in.close();
String tmp = sb.toString();
while (tmp.contains("\r\n")) {
tmp = tmp.replaceAll("\r\n", "\n");
}
return tmp;
}
public String cutToLine(String str, int lineChars) {
String eol = "\n";
str = str.replace("\n", "%{EOL}");
StringBuilder builder = new StringBuilder();
int pointer = 0;
for (char c : str.toCharArray()) {
if ((++pointer % lineChars) == 0) {
builder.append(eol);
}
builder.append(c);
}
return builder.toString();
}
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();
}
public void nick_name(String msg) {
try {
String name = msg.substring(13);
this.setName(name);
Vector v = father.onlineList;
boolean isRepeatedName = false;
int size = v.size();
for (int i = 0; i < size; i++) {
ServerAgentThread tempSat = (ServerAgentThread) v.get(i);
if (tempSat.getName().equals(name)) {
isRepeatedName = true;
break;
}
}
if (isRepeatedName == true) {
dout.writeUTF("<#NAME_REPEATED#>");
din.close();
dout.close();
sc.close();
flag = false;
} else {
v.add(this);
father.refreshList();
String nickListMsg = "";
StringBuilder nickListMsgSb = new StringBuilder();
size = v.size();
for (int i = 0; i < size; i++) {
ServerAgentThread tempSat = (ServerAgentThread) v.get(i);
nickListMsgSb.append("!");
nickListMsgSb.append(tempSat.getName());
}
nickListMsgSb.append("<#NICK_LIST#>");
nickListMsg = nickListMsgSb.toString();
Vector tempv = father.onlineList;
size = tempv.size();
for (int i = 0; i < size; i++) {
ServerAgentThread tempSat = (ServerAgentThread) tempv.get(i);
tempSat.dout.writeUTF(nickListMsg);
if (tempSat != this) {
tempSat.dout.writeUTF("<#MSG#>" + this.getName() + "is now online....");
}
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
private String addWhiteSpace(Document doc, int offset) throws BadLocationException {
StringBuilder whiteSpace = new StringBuilder("\n");
Element rootElement = doc.getDefaultRootElement();
int line = rootElement.getElementIndex(offset);
int i = rootElement.getElement(line).getStartOffset();
while (true) {
String temp = doc.getText(i, 1);
if (temp.equals(" ") || temp.equals("\t")) {
whiteSpace.append(temp);
i++;
} else break;
}
return whiteSpace.toString();
}
/**
* Calculates the hash of the certificate known as the "thumbprint" and returns it as a string
* representation.
*
* @param cert The certificate to hash.
* @param algorithm The hash algorithm to use.
* @return The SHA-1 hash of the certificate.
* @throws CertificateException
*/
private static String getThumbprint(X509Certificate cert, String algorithm)
throws CertificateException {
MessageDigest digest;
try {
digest = MessageDigest.getInstance(algorithm);
} catch (NoSuchAlgorithmException e) {
throw new CertificateException(e);
}
byte[] encodedCert = cert.getEncoded();
StringBuilder sb = new StringBuilder(encodedCert.length * 2);
Formatter f = new Formatter(sb);
try {
for (byte b : digest.digest(encodedCert)) f.format("%02x", b);
} finally {
f.close();
}
return sb.toString();
}
void assertSorted(String expected) {
Iterator<String> keys = mySortedParent.keySet().iterator();
StringBuilder result = new StringBuilder();
while (keys.hasNext()) {
String each = keys.next();
result.append(each);
int count = mySortedParent.get(each);
if (count > 1) {
result.append(" (").append(count).append(")");
}
if (keys.hasNext()) {
result.append("\n");
}
}
Assert.assertEquals(expected, result.toString());
mySortedParent.clear();
}
/**
* Sets the subject in the label.
*
* @param word the new subject that jumps over the lazy dog
*/
public void setSubject(String word) {
StringBuilder text = new StringBuilder(prefix);
text.append(word);
text.append(suffix);
label.setText(text.toString());
}
public static String getNextName(String base) {
StringBuilder sb = new StringBuilder();
sb.append(base);
sb.append(nextEntryNumber++);
return sb.toString();
}
void insertButton_actionPerformed(ActionEvent e) {
Object selected = paramComboBox.getSelectedItem();
ConfigParamDescr descr;
String key;
int type = 0;
String format = "";
if (selected instanceof ConfigParamDescr) {
descr = (ConfigParamDescr) selected;
key = descr.getKey();
type = descr.getType();
switch (type) {
case ConfigParamDescr.TYPE_STRING:
case ConfigParamDescr.TYPE_URL:
case ConfigParamDescr.TYPE_BOOLEAN:
format = "%s";
break;
case ConfigParamDescr.TYPE_INT:
case ConfigParamDescr.TYPE_LONG:
case ConfigParamDescr.TYPE_POS_INT:
NumericPaddingDialog dialog = new NumericPaddingDialog();
Point pos = this.getLocationOnScreen();
dialog.setLocation(pos.x, pos.y);
dialog.pack();
dialog.setVisible(true);
StringBuilder fbuf = new StringBuilder("%");
int width = dialog.getPaddingSize();
boolean is_zero = dialog.useZero();
if (width > 0) {
fbuf.append(".");
if (is_zero) {
fbuf.append(0);
}
fbuf.append(width);
}
if (type == ConfigParamDescr.TYPE_LONG) {
fbuf.append("ld");
} else {
fbuf.append("d");
}
format = fbuf.toString();
break;
case ConfigParamDescr.TYPE_YEAR:
if (key.startsWith(DefinableArchivalUnit.PREFIX_AU_SHORT_YEAR)) {
format = "%02d";
} else {
format = "%d";
}
break;
case ConfigParamDescr.TYPE_RANGE:
case ConfigParamDescr.TYPE_NUM_RANGE:
case ConfigParamDescr.TYPE_SET:
format = "%s";
break;
}
if (selectedPane == 0) {
insertParameter(descr, format, editorPane.getSelectionStart());
} else if (selectedPane == 1) {
// add the combobox data value to the edit box
int pos = formatTextArea.getCaretPosition();
formatTextArea.insert(format, pos);
pos = parameterTextArea.getCaretPosition();
parameterTextArea.insert(", " + key, pos);
}
} else {
key = selected.toString();
format =
escapePrintfChars(
(String)
JOptionPane.showInputDialog(
this,
"Enter the string you wish to input",
"String Literal Input",
JOptionPane.OK_CANCEL_OPTION));
if (StringUtil.isNullString(format)) {
return;
}
if (selectedPane == 0) {
insertText(format, PLAIN_ATTR, editorPane.getSelectionStart());
} else if (selectedPane == 1) {
// add the combobox data value to the edit box
formatTextArea.insert(format, formatTextArea.getCaretPosition());
}
}
}
public void setNotation(String notation) {
if (null == notation || notation.length() == 0) {
notFiringOnChange = true;
sequenceTextArea.setText("");
connectionTableModel.setupEmptyData(CONNECTION_TABLE_ROW_COUNT);
annotationTableModel.setupEmptyData(ANNOTATION_TABLE_ROW_COUNT);
notFiringOnChange = false;
return;
}
notFiringOnChange = true;
try {
ComplexProtein cp = ComplexProtein.convert(notation);
List<String> sequences = cp.getSequences();
if (null != sequences && !sequences.isEmpty()) {
StringBuilder sb = new StringBuilder();
for (String seq : sequences) {
if (sb.length() > 0) {
sb.append(ComplexProtein.SEQUENCE_SEPARATOR_SYMBOL);
sb.append("\n");
}
sb.append(toBlockedSequence(seq));
sb.append("\n");
}
sequenceTextArea.setText(sb.toString());
List<PeptideConnection> conList = cp.getConnections();
if (null != conList && !conList.isEmpty()) {
if (conList.size() >= CONNECTION_TABLE_ROW_COUNT) {
connectionTableModel.setData(conList);
} else {
List<PeptideConnection> l = new ArrayList<PeptideConnection>();
l.addAll(conList);
for (int i = 0; i < CONNECTION_TABLE_ROW_COUNT - conList.size(); i++) {
l.add(new PeptideConnection());
}
connectionTableModel.setData(l);
}
} else {
connectionTableModel.setupEmptyData(CONNECTION_TABLE_ROW_COUNT);
}
List<SequenceAnnotation> annList = cp.getAnnotations();
if (null != annList && !annList.isEmpty()) {
if (annList.size() >= ANNOTATION_TABLE_ROW_COUNT) {
annotationTableModel.setData(annList);
} else {
List<SequenceAnnotation> l = new ArrayList<SequenceAnnotation>();
l.addAll(annList);
for (int i = 0; i < ANNOTATION_TABLE_ROW_COUNT - annList.size(); i++) {
l.add(new SequenceAnnotation());
}
annotationTableModel.setData(l);
}
} else {
annotationTableModel.setupEmptyData(ANNOTATION_TABLE_ROW_COUNT);
}
} else {
sequenceTextArea.setText("");
connectionTableModel.setupEmptyData(CONNECTION_TABLE_ROW_COUNT);
annotationTableModel.setupEmptyData(ANNOTATION_TABLE_ROW_COUNT);
}
} catch (Exception ex) {
Logger.getLogger(ProteinEditor.class.getName()).log(Level.SEVERE, null, ex);
ExceptionHandler.handleException(ex);
}
notFiringOnChange = false;
}
/**
* 検索を実行する。
*
* @param text キーワード
*/
private void find(String text) {
Log.outputFuncLog(Log.LOG_LEVEL_0, Log.FUNCTIONLOG_KIND_INFORMATION, "患者検索", text);
// 全角スペースをkill
text = text.replaceAll(" ", " ");
PatientSearchSpec spec = new PatientSearchSpec();
if (isDate(text)) {
spec.setCode(PatientSearchSpec.DATE_SEARCH);
spec.setDigit(text);
} else if (StringTool.startsWithKatakana(text)) {
spec.setCode(PatientSearchSpec.KANA_SEARCH);
spec.setName(text);
} else if (StringTool.startsWithHiragana(text)) {
text = StringTool.hiraganaToKatakana(text);
spec.setCode(PatientSearchSpec.KANA_SEARCH);
spec.setName(text);
} else if (isNameAddress(text)) {
spec.setCode(PatientSearchSpec.NAME_SEARCH);
spec.setName(text);
} else {
if (Project.getBoolean("zero.paddings.id.search", false)) {
int len = text.length();
int paddings = Project.getInt("patient.id.length", 0) - len;
StringBuilder sb = new StringBuilder();
for (int i = 0; i < paddings; i++) {
sb.append("0");
}
sb.append(text);
text = sb.toString();
}
spec.setCode(PatientSearchSpec.DIGIT_SEARCH);
spec.setDigit(text);
}
final PatientSearchSpec searchSpec = spec;
SimpleWorker worker =
new SimpleWorker<Collection, Void>() {
@Override
protected Collection doInBackground() throws Exception {
PatientDelegater pdl = new PatientDelegater();
Collection result = pdl.getPatients(searchSpec);
return result;
}
@Override
protected void succeeded(Collection result) {
List<PatientModel> list = (List<PatientModel>) result;
if (list != null && list.size() > 0) {
// minagawa^ 仮保存カルテ取得対応
/*
boolean sorted = true;
for (int i=0; i < COLUMN_NAMES.length; i++) {
if (sorter.getSortingStatus(i)==0) {
sorted = false;
break;
}
}
if (!sorted) {
switch (sortItem) {
case 0:
Comparator c = new Comparator<PatientModel>() {
@Override
public int compare(PatientModel o1, PatientModel o2) {
return o1.getPatientId().compareTo(o2.getPatientId());
}
};
Collections.sort(list, c);
break;
case 1:
Comparator c2 = new Comparator<PatientModel>() {
@Override
public int compare(PatientModel p1, PatientModel p2) {
String kana1 = p1.getKanaName();
String kana2 = p2.getKanaName();
if (kana1 != null && kana2 != null) {
return p1.getKanaName().compareTo(p2.getKanaName());
} else if (kana1 != null && kana2 == null) {
return -1;
} else if (kana1 == null && kana2 != null) {
return 1;
} else {
return 0;
}
}
};
Collections.sort(list, c2);
break;
}
}
*/
sortList(list);
// minagawa$
tableModel.setDataProvider(list);
Log.outputFuncLog(
Log.LOG_LEVEL_0,
Log.FUNCTIONLOG_KIND_INFORMATION,
"患者数：",
String.valueOf(list.size()));
} else {
tableModel.clear();
Log.outputFuncLog(Log.LOG_LEVEL_0, Log.FUNCTIONLOG_KIND_INFORMATION, "患者数：", "0");
}
updateStatusLabel();
}
@Override
protected void failed(Throwable cause) {}
@Override
protected void startProgress() {
doStartProgress();
}
@Override
protected void stopProgress() {
doStopProgress();
}
};
worker.execute();
}