/////////////////////////////////////////////////////////////////////
506502
private static com.enioka.jqm.api.Queue getQueue(Queue queue)
    {
        com.enioka.jqm.api.Queue q = new com.enioka.jqm.api.Queue();

        q.setDescription(queue.getDescription());
        q.setId(queue.getId());
        q.setName(queue.getName());

        return q;
    }
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;
    }
281171
private void initSelectBoxes() {

        m_atDay.getOpener().setStyleName(
            org.opencms.acacia.client.css.I_CmsWidgetsLayoutBundle.INSTANCE.widgetCss().selectBoxSelected());
        m_atDay.getSelectorPopup().addStyleName(I_CmsLayoutBundle.INSTANCE.globalWidgetCss().selectBoxPopup());
        m_atDay.addOption(WeekDay.SUNDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_SUNDAY_0));
        m_atDay.addOption(WeekDay.MONDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_MONDAY_0));
        m_atDay.addOption(WeekDay.TUESDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_TUESDAY_0));
        m_atDay.addOption(WeekDay.WEDNESDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_WEDNESDAY_0));
        m_atDay.addOption(WeekDay.THURSDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_THURSDAY_0));
        m_atDay.addOption(WeekDay.FRIDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_FRIDAY_0));
        m_atDay.addOption(WeekDay.SATURDAY.toString(), Messages.get().key(Messages.GUI_SERIALDATE_DAY_SATURDAY_0));
        m_atDay.setWidth("100px");
    }
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();
      }
    }
  }
1276100
@Override
  protected void reserveInternal(int newCapacity) {
    if (isArray() || type instanceof MapType) {
      int[] newLengths = new int[newCapacity];
      int[] newOffsets = new int[newCapacity];
      if (this.arrayLengths != null) {
        System.arraycopy(this.arrayLengths, 0, newLengths, 0, capacity);
        System.arraycopy(this.arrayOffsets, 0, newOffsets, 0, capacity);
      }
      arrayLengths = newLengths;
      arrayOffsets = newOffsets;
    } else if (type instanceof BooleanType) {
      if (byteData == null || byteData.length < newCapacity) {
        byte[] newData = new byte[newCapacity];
        if (byteData != null) System.arraycopy(byteData, 0, newData, 0, capacity);
        byteData = newData;
      }
    } else if (type instanceof ByteType) {
      if (byteData == null || byteData.length < newCapacity) {
        byte[] newData = new byte[newCapacity];
        if (byteData != null) System.arraycopy(byteData, 0, newData, 0, capacity);
        byteData = newData;
      }
    } else if (type instanceof ShortType) {
      if (shortData == null || shortData.length < newCapacity) {
        short[] newData = new short[newCapacity];
        if (shortData != null) System.arraycopy(shortData, 0, newData, 0, capacity);
        shortData = newData;
      }
    } else if (type instanceof IntegerType || type instanceof DateType ||
      DecimalType.is32BitDecimalType(type)) {
      if (intData == null || intData.length < newCapacity) {
        int[] newData = new int[newCapacity];
        if (intData != null) System.arraycopy(intData, 0, newData, 0, capacity);
        intData = newData;
      }
    } else if (type instanceof LongType || type instanceof TimestampType ||
        DecimalType.is64BitDecimalType(type)) {
      if (longData == null || longData.length < newCapacity) {
        long[] newData = new long[newCapacity];
        if (longData != null) System.arraycopy(longData, 0, newData, 0, capacity);
        longData = newData;
      }
    } else if (type instanceof FloatType) {
      if (floatData == null || floatData.length < newCapacity) {
        float[] newData = new float[newCapacity];
        if (floatData != null) System.arraycopy(floatData, 0, newData, 0, capacity);
        floatData = newData;
      }
    } else if (type instanceof DoubleType) {
      if (doubleData == null || doubleData.length < newCapacity) {
        double[] newData = new double[newCapacity];
        if (doubleData != null) System.arraycopy(doubleData, 0, newData, 0, capacity);
        doubleData = newData;
      }
    } else if (childColumns != null) {
      // Nothing to store.
    } else {
      throw new RuntimeException("Unhandled " + type);
    }

    byte[] newNulls = new byte[newCapacity];
    if (nulls != null) System.arraycopy(nulls, 0, newNulls, 0, capacity);
    nulls = newNulls;

    capacity = newCapacity;
  }
1318787
private void checkIndices(int row, int col) {
        if (row < 0 || row >= rows)
            throw new ArrayIndexOutOfBoundsException("row: " + row);
        else if (col < 0 || col >= cols)
            throw new ArrayIndexOutOfBoundsException("column: " + col);
    }
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);
        }

    }
1037482
@Override
    public void executeListSingleActions() throws IOException, ServletException {

        String indexSource = getSelectedItem().getId();
        Map<String, String[]> params = new HashMap<String, String[]>();
        String action = getParamListAction();
        if (action.equals(CmsSearchIndexSourceControlList.LIST_ACTION_OVERVIEW_INDEXSOURCE)
            || action.equals(CmsSearchIndexSourceControlList.LIST_ACTION_OVERVIEW_INDEXSOURCE2)) {
            // forward to the index overview screen
            params.put(A_CmsEditIndexSourceDialog.PARAM_INDEXSOURCE, new String[] {indexSource});
            params.put(PARAM_ACTION, new String[] {DIALOG_INITIAL});
            params.put(PARAM_STYLE, new String[] {CmsToolDialog.STYLE_NEW});
            getToolManager().jspForwardTool(this, "/searchindex/indexsources/indexsource", params);
        }
    }
1234050
@SuppressWarnings("unchecked")
    // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
    private void initComponents() {
        java.awt.GridBagConstraints gridBagConstraints;

        lblMessage = new javax.swing.JLabel();
        barProgressActivity = new javax.swing.JProgressBar();
        cmdCancelOperation = new javax.swing.JButton();

        setLayout(new java.awt.GridBagLayout());

        lblMessage.setText("Executing Query");
        gridBagConstraints = new java.awt.GridBagConstraints();
        gridBagConstraints.gridx = 0;
        gridBagConstraints.gridy = 0;
        gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
        gridBagConstraints.anchor = java.awt.GridBagConstraints.NORTHWEST;
        gridBagConstraints.insets = new java.awt.Insets(10, 10, 10, 10);
        add(lblMessage, gridBagConstraints);

        barProgressActivity.setIndeterminate(true);
        barProgressActivity.setMinimumSize(new java.awt.Dimension(200, 15));
        barProgressActivity.setPreferredSize(new java.awt.Dimension(300, 18));
        gridBagConstraints = new java.awt.GridBagConstraints();
        gridBagConstraints.gridx = 0;
        gridBagConstraints.gridy = 1;
        gridBagConstraints.fill = java.awt.GridBagConstraints.BOTH;
        gridBagConstraints.insets = new java.awt.Insets(0, 10, 0, 10);
        add(barProgressActivity, gridBagConstraints);

        cmdCancelOperation.setText("Cancel Operation");
        cmdCancelOperation.setEnabled(false);
        cmdCancelOperation.addActionListener(new java.awt.event.ActionListener() {
            public void actionPerformed(java.awt.event.ActionEvent evt) {
            	cmdCancelOperationActionPerformed(evt);
            }
        });
        gridBagConstraints = new java.awt.GridBagConstraints();
        gridBagConstraints.gridx = 0;
        gridBagConstraints.gridy = 2;
        gridBagConstraints.insets = new java.awt.Insets(10, 0, 10, 0);
        add(cmdCancelOperation, gridBagConstraints);
    }
295230
public static List<UserCustomColumn> createRequiredColumns(
			int startingIndex, String idColumnName) {

		if (idColumnName == null) {
			idColumnName = COLUMN_ID;
		}

		List<UserCustomColumn> columns = new ArrayList<>();
		columns.add(createIdColumn(startingIndex++, idColumnName));
		columns.add(createDataColumn(startingIndex++));
		columns.add(createContentTypeColumn(startingIndex++));

		return columns;
	}
1288686
function(session) {
    this.session = session;
    this.doc = session.getDocument();

    this.clearSelection();
    this.selectionLead = this.doc.createAnchor(0, 0);
    this.selectionAnchor = this.doc.createAnchor(0, 0);

    var _self = this;
    this.selectionLead.on("change", function(e) {
        _self._emit("changeCursor");
        if (!_self.$isEmpty)
            _self._emit("changeSelection");
        if (!_self.$preventUpdateDesiredColumnOnChange && e.old.column != e.value.column)
            _self.$updateDesiredColumn();
    });

    this.selectionAnchor.on("change", function() {
        if (!_self.$isEmpty)
            _self._emit("changeSelection");
    });
}
1183692
public static void main(String[] args) throws Exception {

		final List<String> arguments = new ArrayList<String>(args.length);

		final Settings settings = new Settings();
		final PartialCmdLineParser parser = new PartialCmdLineParser(settings);
		int position = 0;

		while (position < args.length) {
			final int consumed = parser.parseArgument(args, position);
			if (consumed == 0) {
				arguments.add(args[position++]);
			} else {
				position += consumed;
			}
		}

		if (!arguments.contains(JsonixPlugin.OPTION)) {
			arguments.add(JsonixPlugin.OPTION);
		}

		if (!arguments.contains("-extension")) {
			arguments.add("-extension");
		}

		// TODO
		arguments.add("-disableXmlSecurity");
		// TODO
		System.setProperty("javax.xml.accessExternalSchema", "all");
		// TODO
		System.setProperty("javax.xml.accessExternalDTD", "all");

		File targetDirectory = settings.getTargetDirectory();

		if (targetDirectory == null) {
			targetDirectory = new File(".");
		}

		if (!targetDirectory.exists()) {
			targetDirectory.mkdirs();
		}

		arguments.add("-d");
		arguments.add(targetDirectory.getAbsolutePath());

		final Options options = new Options();

		options.parseArguments(arguments.toArray(new String[arguments.size()]));

		new JsonixMain(settings, options).execute();
	}
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; ");
	}
1290284
public void logException(Level level) {
        if (!LOG.isLoggable(level)) {
            return;
        }
        final StringBuilder builder = new StringBuilder();
        builder.append("\n----------------------------------------------------");
        builder.append("\nMonitoringException");
        builder.append("\n----------------------------------------------------");
        builder.append("\nCode:    ").append(code);
        builder.append("\nMessage: ").append(message);
        builder.append("\n----------------------------------------------------");
        if (events != null) {
            for (Event event : events) {
                builder.append("\nEvent:");
                if (event.getMessageInfo() != null) {
                    builder.append("\nMessage id: ").append(event.getMessageInfo().getMessageId());
                    builder.append("\nFlow id:    ").append(event.getMessageInfo().getFlowId());
                    builder.append("\n----------------------------------------------------");
                } else {
                    builder.append("\nNo message id and no flow id");
                }
            }
        }
        builder.append("\n----------------------------------------------------\n");
        LOG.log(level, builder.toString(), this);
    }
182999
protected void assertArrayHasMinLengthAndAllElementsNotNull(final Object[] array, final Integer minLength) throws ArgumentCountException, ArgumentNullException  {

		if (array.length < minLength) {
			throw ArgumentCountException.tooFew(array.length, minLength);
		}

		for (final Object element : array) {

			if (element == null) {
				throw new ArgumentNullException();
			}
		}
	}
778212
@Override
    protected void configureFindbugsEngine() {
        if (not != null) {
            addArg("-not");
        }
        addBoolOption("-notAProblem", notAProblem);
        addBoolOption("-withSource", withSource);
        addOption("-exclude", exclude);
        addOption("-include", include);
        addOption("-annotation", annotation);
        addOption("-after", after);
        addOption("-before", before);
        addOption("-first", first);
        addOption("-last", last);
        addOption("-fixed", fixed);
        addOption("-present", present);
        addOption("-absent", absent);
        addBoolOption("-active", active);
        addBoolOption("-introducedByChange", introducedByChange);
        addBoolOption("-removedByChange", removedByChange);
        addBoolOption("-newCode", newCode);
        addBoolOption("-removedCode", removedCode);
        addOption("-priority", priority);
        addOption("-maxRank", maxRank);
        addOption("-class", clazz);
        addOption("-bugPattern", bugPattern);
        addOption("-category", category);
        addOption("-designation", designation);
        addBoolOption("-withMessages", withMessages);
        addBoolOption("-applySuppression", applySuppression);
        if (excludeBugs != null) {
            addArg("-excludeBugs");
            addArg(excludeBugs);
        }

        addArg(inputFile.getName());

        addArg(outputFile.getPath());
    }
94939
Table moveDefinition(Session session, int newType, ColumnSchema column,
                         Constraint constraint, Index index, int colIndex,
                         int adjust, OrderedHashSet dropConstraints,
                         OrderedHashSet dropIndexes) {

        boolean newPK = false;

        if (constraint != null
                && constraint.constType == Constraint.PRIMARY_KEY) {
            newPK = true;
        }

        Table tn = new Table(database, tableName, newType);

        if (tableType == TEMP_TABLE) {
            tn.persistenceScope = persistenceScope;
        }

        for (int i = 0; i < getColumnCount(); i++) {
            ColumnSchema col = (ColumnSchema) columnList.get(i);

            if (i == colIndex) {
                if (column != null) {
                    tn.addColumn(column);
                }

                if (adjust <= 0) {
                    continue;
                }
            }

            tn.addColumn(col);
        }

        if (getColumnCount() == colIndex) {
            tn.addColumn(column);
        }

        int[] pkCols = null;

        if (hasPrimaryKey()
                && !dropConstraints.contains(
                    getPrimaryConstraint().getName())) {
            pkCols = primaryKeyCols;
            pkCols = ArrayUtil.toAdjustedColumnArray(pkCols, colIndex, adjust);
        } else if (newPK) {
            pkCols = constraint.getMainColumns();
        }

        tn.createPrimaryKey(getIndex(0).getName(), pkCols, false);

        for (int i = 1; i < indexList.length; i++) {
            Index idx = indexList[i];

            if (dropIndexes.contains(idx.getName())) {
                continue;
            }

            int[] colarr = ArrayUtil.toAdjustedColumnArray(idx.getColumns(),
                colIndex, adjust);

            // A VoltDB extension to support indexed expressions and assume unique attribute
            Expression[] exprArr = idx.getExpressions();
            boolean assumeUnique = idx.isAssumeUnique();
            Expression predicate = idx.getPredicate();
            // End of VoltDB extension
            idx = tn.createIndexStructure(idx.getName(), colarr,
                                          idx.getColumnDesc(), null,
                                          idx.isUnique(), idx.isMigrating(), idx.isConstraint(),
                                          idx.isForward());

            // A VoltDB extension to support indexed expressions and assume unique attribute and partial indexes
            if (exprArr != null) {
                idx = idx.withExpressions(adjustExprs(exprArr, colIndex, adjust));
            }
            if (predicate != null) {
                idx = idx.withPredicate(adjustExpr(predicate, colIndex, adjust));
            }
            idx = idx.setAssumeUnique(assumeUnique);
            // End of VoltDB extension
            tn.addIndex(idx);
        }

        if (index != null) {
            tn.addIndex(index);
        }

        HsqlArrayList newList = new HsqlArrayList();

        if (newPK) {
            constraint.core.mainIndex     = tn.indexList[0];
            constraint.core.mainTable     = tn;
            constraint.core.mainTableName = tn.tableName;

            newList.add(constraint);
        }

        for (int i = 0; i < constraintList.length; i++) {
            Constraint c = constraintList[i];

            if (dropConstraints.contains(c.getName())) {
                continue;
            }

            c = c.duplicate();

            c.updateTable(session, this, tn, colIndex, adjust);
            newList.add(c);
        }

        if (!newPK && constraint != null) {
            constraint.updateTable(session, this, tn, -1, 0);
            newList.add(constraint);
        }

        tn.constraintList = new Constraint[newList.size()];

        newList.toArray(tn.constraintList);
        tn.updateConstraintLists();
        tn.setBestRowIdentifiers();

        tn.triggerList  = triggerList;
        tn.triggerLists = triggerLists;

        return tn;
    }