////////////////////////////////////////////////////////////////////
510902
public Vector<Object> toValuesVector() {
		final Vector<Object> values = new Vector<Object>();
		for (final JKTableColumnValue value : this.columnsValues) {
			values.add(value);
		}
		return values;
	}
469208
public static void main(String[] args) throws Exception{
        String google = "http://google.com";
        String yahoo = "http://yahoo.com";

        XMLDocument xml = new XMLDocument(new StreamResult(System.out), false, 4, null);

        xml.startDocument();{
            xml.addProcessingInstruction("san", "test='1.2'");
            xml.declarePrefix("google", google);
            xml.declarePrefix("yahoo", yahoo);
            xml.declarePrefix("http://msn.com");

            xml.startElement(google, "hello");{
                xml.addAttribute("name", "value");
                xml.addElement("xyz", "helloworld");
                xml.addElement(google, "hai", "test");
                xml.addXML(new InputSource("xml/xsds/note.xsd"), true);
                xml.addComment("this is comment");
                xml.addCDATA("this is sample cdata");
            }
        }
        xml.endDocument();
    }
468714
function(config, defaults) {
        var key, subdefaults, subconfig;
        for (key in defaults) {
            subdefaults = defaults[key];
            subconfig = config[key];
             if ($.isPlainObject(subdefaults)) {
                 if (!$.isPlainObject(subconfig)) {
                     subconfig = config[key] = {};
                 }
                 defaultsUpdater(subconfig, subdefaults);
                 // } else if (subconfig === undefined) {
                 //     config[key] = null;
                 // }
             } else {
                 if (subconfig === undefined) {
                     config[key] = subdefaults;
                 }
             }
        }
    }
5942
@Override
	public String onColumnName(String columnName) {
		if (onlyBindParameter)
			return null;

		if (currentSchema != null) {
			Set<SQLProperty> props = currentSchema.getPropertyBySimpleName(columnName);
			AssertKripton.assertTrueOrUnknownPropertyInJQLException(props != null && props.size() > 0, currentMethod, columnName);
			return props.iterator().next().columnName;
		} else {
			return null;
		}
	}
771132
@Override
    public void handleSelection(final CmsResourceTypeBean selectedType) {

        CmsObject cms = A_CmsUI.getCmsObject();
        m_selectedType = selectedType;
        try {

            CmsNewResourceBuilder builder = new CmsNewResourceBuilder(cms);
            builder.addCallback(new I_Callback() {

                public void onError(Exception e) {

                    m_dialogContext.error(e);
                }

                public void onResourceCreated(CmsNewResourceBuilder builderParam) {

                    finish(Lists.newArrayList(builderParam.getCreatedResource().getStructureId()));
                }
            });

            m_selectedType = selectedType;

            Boolean useDefaultLocation = m_defaultLocationCheckbox.getValue();
            if (useDefaultLocation.booleanValue() && (m_selectedType.getCreatePath() != null)) {
                try {
                    CmsADEConfigData configData = OpenCms.getADEManager().lookupConfiguration(
                        cms,
                        m_folderResource.getRootPath());

                    CmsResourceTypeConfig typeConfig = configData.getResourceType(m_selectedType.getType());
                    if (typeConfig != null) {
                        typeConfig.configureCreateNewElement(cms, m_folderResource.getRootPath(), builder);
                    }
                } catch (Exception e) {
                    m_dialogContext.error(e);
                }

            } else {
                boolean explorerNameGenerationMode = false;
                String sitePath = cms.getRequestContext().removeSiteRoot(m_folderResource.getRootPath());
                String namePattern = m_selectedType.getNamePattern();
                if (CmsStringUtil.isEmptyOrWhitespaceOnly(namePattern)) {
                    namePattern = OpenCms.getWorkplaceManager().getDefaultNamePattern(m_selectedType.getType());
                    explorerNameGenerationMode = true;
                }
                String fileName = CmsStringUtil.joinPaths(sitePath, namePattern);
                builder.setPatternPath(fileName);
                builder.setType(m_selectedType.getType());
                builder.setExplorerNameGeneration(explorerNameGenerationMode);

            }
            CmsPropertyDialogExtension ext = new CmsPropertyDialogExtension(A_CmsUI.get(), null);
            CmsAppWorkplaceUi.get().disableGlobalShortcuts();
            ext.editPropertiesForNewResource(builder);
            finish(new ArrayList<CmsUUID>());

        } catch (Exception e) {
            throw new RuntimeException(e);
        }

    }
1128089
public final void mELEMENTS() throws RecognitionException {
		try {
			int _type = ELEMENTS;
			int _channel = DEFAULT_TOKEN_CHANNEL;
			// hql.g:21:10: ( 'elements' )
			// hql.g:21:12: 'elements'
			{
			match("elements"); if (state.failed) return;

			}

			state.type = _type;
			state.channel = _channel;
		}
		finally {
			// do for sure before leaving
		}
	}
4310
private void createDayPanel() {

        CmsCheckBox box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_MONDAY_0));
        box.setInternalValue(WeekDay.MONDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
        box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_TUESDAY_0));
        box.setInternalValue(WeekDay.TUESDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
        box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_WEDNESDAY_0));
        box.setInternalValue(WeekDay.WEDNESDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
        box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_THURSDAY_0));
        box.setInternalValue(WeekDay.THURSDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
        box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_FRIDAY_0));
        box.setInternalValue(WeekDay.FRIDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
        box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_SATURDAY_0));
        box.setInternalValue(WeekDay.SATURDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
        box = new CmsCheckBox(Messages.get().key(Messages.GUI_SERIALDATE_DAY_SUNDAY_0));
        box.setInternalValue(WeekDay.SUNDAY.toString());
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        box.addValueChangeHandler(m_checkBoxValueChangeHandler);
        m_checkboxes.add(box);
        m_dayPanel.add(box);
    }
819036
void submit() {

        CmsObject cms = A_CmsUI.getCmsObject();
        try {
            List<CmsUUID> changedIds = Lists.newArrayList();
            CmsResourceDeleteMode mode = (CmsResourceDeleteMode)m_deleteSiblings.getValue();
            for (CmsResource resource : m_context.getResources()) {
                changedIds.add(resource.getStructureId());
                CmsLockActionRecord lockRecord = CmsLockUtil.ensureLock(cms, resource);
                try {
                    cms.deleteResource(cms.getSitePath(resource), mode);
                } finally {
                    if (lockRecord.getChange().equals(LockChange.locked)) {
                        if (!resource.getState().isNew()) {
                            try {
                                cms.unlockResource(resource);
                            } catch (CmsVfsResourceNotFoundException e) {
                                LOG.warn(e.getLocalizedMessage(), e);
                            } catch (CmsLockException e) {
                                LOG.warn(e.getLocalizedMessage(), e);
                            }
                        }
                    }
                }
            }
            m_context.finish(changedIds);
        } catch (Exception e) {
            m_context.error(e);
        }
    }
475123
@Override
    public final void onBrowserEvent(final Event event) {

        super.onBrowserEvent(event);
        switch (DOM.eventGetType(event)) {
            // Unhighlight and cancel keyboard events
            case Event.ONBLUR:
                m_keyTimer.cancel();
                if (m_slidingMouse) {
                    stopMouseSliding(event);

                } else if (m_slidingKeyboard) {
                    m_slidingKeyboard = false;

                }

                break;

            // Mousewheel events
            case Event.ONMOUSEWHEEL:
                int velocityY = event.getMouseWheelVelocityY() * m_stepSize;
                event.preventDefault();
                CmsDebugLog.getInstance().printLine("Whell velocity: " + velocityY);
                if (velocityY > 0) {
                    shiftDown(velocityY);
                } else {
                    shiftUp(-velocityY);
                }
                break;

            // Shift left or right on key press
            case Event.ONKEYDOWN:
                if (!m_slidingKeyboard) {
                    int multiplier = 1;
                    if (event.getCtrlKey() || event.getMetaKey()) {
                        multiplier = m_stepSize;
                    }

                    switch (event.getKeyCode()) {
                        case KeyCodes.KEY_HOME:
                            event.preventDefault();
                            setValue(Integer.valueOf(0));
                            break;
                        case KeyCodes.KEY_END:
                            event.preventDefault();
                            setValue(Integer.valueOf(getMaximumVerticalScrollPosition()));
                            break;
                        case KeyCodes.KEY_PAGEUP:
                            event.preventDefault();
                            m_slidingKeyboard = true;
                            shiftUp(m_pageSize);
                            m_keyTimer.schedule(INITIALDELAY, true, m_pageSize);
                            break;
                        case KeyCodes.KEY_PAGEDOWN:
                            event.preventDefault();
                            m_slidingKeyboard = true;

                            shiftDown(m_pageSize);
                            m_keyTimer.schedule(INITIALDELAY, false, m_pageSize);
                            break;
                        case KeyCodes.KEY_UP:
                            event.preventDefault();
                            m_slidingKeyboard = true;

                            shiftUp(multiplier);
                            m_keyTimer.schedule(INITIALDELAY, true, multiplier);
                            break;
                        case KeyCodes.KEY_DOWN:
                            event.preventDefault();
                            m_slidingKeyboard = true;

                            shiftDown(multiplier);
                            m_keyTimer.schedule(INITIALDELAY, false, multiplier);
                            break;

                        default:
                    }
                }
                break;
            // Stop shifting on key up
            case Event.ONKEYUP:
                m_keyTimer.cancel();
                if (m_slidingKeyboard) {
                    m_slidingKeyboard = false;
                }
                break;

            // Mouse Events
            case Event.ONMOUSEDOWN:
                if (sliderClicked(event)) {
                    startMouseSliding(event);
                    event.preventDefault();
                }
                break;
            case Event.ONMOUSEUP:
                stopMouseSliding(event);
                break;
            case Event.ONMOUSEMOVE:
                slideKnob(event);
                break;
            default:
        }

    }
795193
@Override
	public void actionPerformed(ActionEvent event) {

		Object mysource = event.getSource();

		if ( ! (mysource instanceof JComboBox )) {
			super.actionPerformed(event);
			return;
		}

		@SuppressWarnings("unchecked")
		JComboBox<String> source = (JComboBox<String>) event.getSource();
		String value = source.getSelectedItem().toString();
		evalString("save selection; ");

		String selectLigand = "select ligand;wireframe 0.16;spacefill 0.5; color cpk ;";

		if ( value.equals("Cartoon")){
			String script = "hide null; select all;  spacefill off; wireframe off; backbone off;" +
					" cartoon on; " +
					" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
					" select *.FE; spacefill 0.7; color cpk ; " +
					" select *.CU; spacefill 0.7; color cpk ; " +
					" select *.ZN; spacefill 0.7; color cpk ; " +
					" select all; ";
			this.executeCmd(script);
		} else if (value.equals("Backbone")){
			String script = "hide null; select all; spacefill off; wireframe off; backbone 0.4;" +
					" cartoon off; " +
					" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
					" select *.FE; spacefill 0.7; color cpk ; " +
					" select *.CU; spacefill 0.7; color cpk ; " +
					" select *.ZN; spacefill 0.7; color cpk ; " +
					" select all; ";
			this.executeCmd(script);
		} else if (value.equals("CPK")){
			String script = "hide null; select all; spacefill off; wireframe off; backbone off;" +
					" cartoon off; cpk on;" +
					" select ligand; wireframe 0.16;spacefill 0.5; color cpk; " +
					" select *.FE; spacefill 0.7; color cpk ; " +
					" select *.CU; spacefill 0.7; color cpk ; " +
					" select *.ZN; spacefill 0.7; color cpk ; " +
					" select all; ";
			this.executeCmd(script);

		} else if (value.equals("Ligands")){
			this.executeCmd("restrict ligand; cartoon off; wireframe on;  display selected;");
		} else if (value.equals("Ligands and Pocket")){
			this.executeCmd(" select within (6.0,ligand); cartoon off; wireframe on; backbone off; display selected; ");
		} else if ( value.equals("Ball and Stick")){
			String script = "hide null; restrict not water;  wireframe 0.2; spacefill 25%;" +
					" cartoon off; backbone off; " +
					" select ligand; wireframe 0.16; spacefill 0.5; color cpk; " +
					" select *.FE; spacefill 0.7; color cpk ; " +
					" select *.CU; spacefill 0.7; color cpk ; " +
					" select *.ZN; spacefill 0.7; color cpk ; " +
					" select all; ";
			this.executeCmd(script);
		} else if ( value.equals("By Chain")){
			jmolColorByChain();
			String script = "hide null; select all;set defaultColors Jmol; color_by_chain(\"cartoon\"); color_by_chain(\"\"); " + selectLigand + "; select all; ";
			this.executeCmd(script);
		} else if ( value.equals("Rainbow")) {
			this.executeCmd("hide null; select all; set defaultColors Jmol; color group; color cartoon group; " + selectLigand + "; select all; " );
		} else if ( value.equals("Secondary Structure")){
			this.executeCmd("hide null; select all; set defaultColors Jmol; color structure; color cartoon structure;" + selectLigand + "; select all; " );

		} else if ( value.equals("By Element")){
			this.executeCmd("hide null; select all; set defaultColors Jmol; color cpk; color cartoon cpk; " + selectLigand + "; select all; ");
		} else if ( value.equals("By Amino Acid")){
			this.executeCmd("hide null; select all; set defaultColors Jmol; color amino; color cartoon amino; " + selectLigand + "; select all; " );
		} else if ( value.equals("Hydrophobicity") ){
			this.executeCmd("hide null; set defaultColors Jmol; select hydrophobic; color red; color cartoon red; select not hydrophobic ; color blue ; color cartoon blue; "+ selectLigand+"; select all; ");
		} else if ( value.equals("Suggest Domains")){
			colorByPDP();
		} else if ( value.equals("Show SCOP Domains")){
			colorBySCOP();
		}
		evalString("restore selection; ");
	}
1246928
public static void main(String[] args){

		PDBFileReader pdbr = new PDBFileReader();
		pdbr.setPath("/tmp/");


		//String pdb1 = "1crl";
		//String pdb2 = "1ede";

		String pdb1 = "1buz";
		String pdb2 = "1ali";

		//String pdb1 = "5pti";
		//String pdb2 = "5pti";

		// NO NEED TO DO CHANGE ANYTHING BELOW HERE...

		StructurePairAligner sc = new StructurePairAligner();
		StrucAligParameters params = new StrucAligParameters();
		params.setMaxIter(1);
		sc.setParams(params);

		// step1 : read molecules
		try {
			Structure s1 = pdbr.getStructureById(pdb1);
			Structure s2 = pdbr.getStructureById(pdb2);

			System.out.println("aligning " + pdb1 + " vs. " + pdb2);
			System.out.println(s1);
			System.out.println();
			System.out.println(s2);
			// step 2 : do the calculations
			sc.align(s1,s2);


			ScaleableMatrixPanel smp = new ScaleableMatrixPanel();
			JFrame frame = new JFrame();
			frame.addWindowListener(new WindowAdapter(){
				@Override
				public void windowClosing(WindowEvent e){
					JFrame f = (JFrame) e.getSource();
					f.setVisible(false);
					f.dispose();
				}



			});

			smp.setMatrix(sc.getDistMat());
			smp.setFragmentPairs(sc.getFragmentPairs());
			smp.setAlternativeAligs(sc.getAlignments());

			for (int i = 0; i < sc.getAlignments().length; i++) {
				AlternativeAlignment aa =sc.getAlignments()[i];
				System.out.println(aa);

			}

			frame.getContentPane().add(smp);

			frame.pack();
			frame.setVisible(true);

		} catch (Exception e) {
			e.printStackTrace();
		}

	}
901123
@NonNull
    Collection<TObj> getColumnItems(int column) {
        Collection<TObj> result = new LinkedList<>();
        for (int count = mData.size(), i = 0; i < count; i++) {
            int key = mData.keyAt(i);
            TObj columnObj = mData.get(key).get(column);
            if (columnObj != null) {
                result.add(columnObj);
            }

        }
        return result;
    }
150608
@Override
    public void changed(Database.ChangeEvent event) {
        synchronized (changesLock) {
            if (isTimeout)
                return;

            lastChangesTimestamp = System.currentTimeMillis();

            // Stop timeout timer:
            stopTimeout();

            // In race condition, new doc or update doc is fired before starting to observe the
            // DatabaseChangeEvent, it allows to skip few document changes with /_changes REST API.
            // Make sure all document changes are tread by /_changes REST API.
            if (!filled) {
                filled = true;
                RevisionList changes = db.changesSince(changesSince, changesOptions,
                        changesFilter, changesFilterParams);
                if (changes.size() > 0) {
                    sendLongpollChanges(changes, changesSince);
                    return;
                }
            }

            List<RevisionInternal> revs = new ArrayList<RevisionInternal>();
            List<DocumentChange> changes = event.getChanges();
            for (DocumentChange change : changes) {
                RevisionInternal rev = change.getAddedRevision();
                if (rev == null)
                    continue;
                String winningRevID = change.getWinningRevisionID();
                if (!this.changesIncludesConflicts) {
                    if (winningRevID == null)
                        continue; // // this change doesn't affect the winning rev ID, no need to send it
                    else if (!winningRevID.equals(rev.getRevID())) {
                        // This rev made a _different_ rev current, so substitute that one.
                        // We need to emit the current sequence # in the feed, so put it in the rev.
                        // This isn't correct internally (this is an old rev so it has an older sequence)
                        // but consumers of the _changes feed don't care about the internal state.
                        RevisionInternal mRev = db.getDocument(rev.getDocID(), winningRevID, changesIncludesDocs);
                        mRev.setSequence(rev.getSequence());
                        rev = mRev;
                    }
                }

                if (!event.getSource().runFilter(changesFilter, changesFilterParams, rev))
                    continue;

                if (longpoll) {
                    revs.add(rev);
                } else {
                    Log.d(TAG, "Router: Sending continuous change chunk");
                    sendContinuousChange(rev);
                }

                timeoutLastSeqence = rev.getSequence();
            }

            if (longpoll && revs.size() > 0)
                sendLongpollChanges(revs, changesSince);
            else
                // Restart timeout timer for continuous feed request:
                startTimeout();
        }
    }
174709
function () {
/*Line 30 - 'AtomSortableColumn.js' */                if (!this._value)
/*Line 31 - 'AtomSortableColumn.js' */                    return;
/*Line 32 - 'AtomSortableColumn.js' */                if (this._value.indexOf(this._sortField) == -1) {
/*Line 33 - 'AtomSortableColumn.js' */                    AtomBinder.setValue(this, "direction", "");
/*Line 34 - 'AtomSortableColumn.js' */                    return;
/*Line 35 - 'AtomSortableColumn.js' */                }

/*Line 37 - 'AtomSortableColumn.js' */                if (this._value.lastIndexOf("desc") != this._value.length - 4) {
/*Line 38 - 'AtomSortableColumn.js' */                    AtomBinder.setValue(this, "direction", "asc");
/*Line 39 - 'AtomSortableColumn.js' */                } else {
/*Line 40 - 'AtomSortableColumn.js' */                    AtomBinder.setValue(this, "direction", "desc");
/*Line 41 - 'AtomSortableColumn.js' */                }
/*Line 42 - 'AtomSortableColumn.js' */            }
556524
@Override
    public int doEndTag() throws JspException {

        ServletRequest req = pageContext.getRequest();
        ServletResponse res = pageContext.getResponse();

        if (CmsFlexController.isCmsRequest(req)) {
            // this will always be true if the page is called through OpenCms
            CmsObject cms = CmsFlexController.getCmsObject(req);
            String target = null;

            // try to find out what to do
            if (m_target != null) {
                // option 1: target is set with "page" or "file" parameter
                target = m_target + getSuffix();
            } else if (m_property != null) {
                // option 2: target is set with "property" parameter
                try {
                    String prop = cms.readPropertyObject(cms.getRequestContext().getUri(), m_property, true).getValue();
                    if (prop != null) {
                        target = prop + getSuffix();
                    }
                } catch (RuntimeException e) {
                    // target must be null
                    target = null;
                } catch (Exception e) {
                    // target will be null
                    e = null;
                }
            } else if (m_attribute != null) {
                // option 3: target is set in "attribute" parameter
                try {
                    String attr = (String)req.getAttribute(m_attribute);
                    if (attr != null) {
                        target = attr + getSuffix();
                    }
                } catch (RuntimeException e) {
                    // target must be null
                    target = null;
                } catch (Exception e) {
                    // target will be null
                    e = null;
                }
            } else {
                // option 4: target might be set in body
                String body = null;
                if (getBodyContent() != null) {
                    body = getBodyContent().getString();
                    if (CmsStringUtil.isNotEmptyOrWhitespaceOnly(body)) {
                        // target IS set in body
                        target = body + getSuffix();
                    }
                    // else target is not set at all, default will be used
                }
            }

            // now perform the include action
            includeTagAction(
                pageContext,
                target,
                m_element,
                null,
                m_editable,
                m_cacheable,
                m_parameterMap,
                CmsRequestUtil.getAtrributeMap(req),
                req,
                res);

            release();
        }

        return EVAL_PAGE;
    }
156040
public static void main(String[] args) throws Exception {
		CWSTagger tag = new CWSTagger("./models/seg.m");	

		RLSeg rlseg = new RLSeg(tag,"./tmpdata/FNLPDATA/all.dict");

		tag.setDictionary(tempdict);

		System.out.println("\n处理文件：");
		String s4 = tag.tagFile("../example-data/data-tag.txt");
		System.out.println(s4);
		String[] toks = s4.split("\\s+");
		int newset = rlseg.update(toks);
		rlseg.close();

		tag.setDictionary(tempdict);

		System.out.println("\n处理文件：");
		String s = tag.tagFile("../example-data/data-tag.txt");
		System.out.println(s);


	}
323554
public void f(int i, Object... args) {
    setIndex(i);
    setArguments(args);
    if (args.length == 1 && args[0] instanceof JavaScriptObject) {
      if (JsUtils.isElement((JavaScriptObject) args[0])) {
        setElement((com.google.gwt.dom.client.Element) args[0]);
        f(getElement(), i);
      } else if (JsUtils.isEvent((JavaScriptObject) args[0])) {
        setEvent((Event) args[0]);
        f(getEvent());
      } else {
        f();
      }
    }
  }