Example usage for org.apache.commons.collections.list GrowthList decorate

List of usage examples for org.apache.commons.collections.list GrowthList decorate

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Introduction

In this page you can find the example usage for org.apache.commons.collections.list GrowthList decorate.

Prototype

public static List decorate(List list)

Source Link

Document

Factory method to create a growth list.

Usage

From source file:edu.scripps.fl.hibernate.DoubleListStringType.java

public List<Double> newList(int initialCapacity) {
    return (List<Double>) GrowthList.decorate(new ArrayList<Double>(initialCapacity));
}

From source file:edu.scripps.fl.hibernate.BooleanListStringType.java

public List<Boolean> newList(int initialCapacity) {
    return (List<Boolean>) GrowthList.decorate(new ArrayList<Boolean>(initialCapacity));
}

From source file:edu.scripps.fl.hibernate.StringListStringType.java

public List<String> newList(int initialCapacity) {
    return (List<String>) GrowthList.decorate(new ArrayList<String>(initialCapacity));
}

From source file:edu.scripps.fl.pubchem.PubChemXMLParserFactory.java

protected void populateAssayResultsFromXML(PCAssay assay, Node assayDescriptionNode) throws Exception {
    List<PCAssayResult> results = null;
    List<Node> assayResultNodes = assayDescriptionNode
            .selectNodes("../../../PC-AssaySubmit_data/PC-AssayResults");
    if (assayResultNodes.size() == 0)
        return;/*from   w  w  w  . ja  va  2  s .  co m*/
    else
        results = new ArrayList<PCAssayResult>(assayResultNodes.size());

    List<PCAssayColumn> testedCols = assay.getTestedColumns();
    PCAssayColumn activeColumn = assay.getActiveColumn();

    for (Node resultNode : assayResultNodes) {
        PCAssayResult result = new PCAssayResult();

        String val = resultNode.selectSingleNode("PC-AssayResults_sid").valueOf("text()");
        result.setSID(Long.parseLong(val));

        val = resultNode.selectSingleNode("PC-AssayResults_outcome").valueOf("@value");
        val = val.substring(0, 1).toUpperCase() + val.substring(1);
        result.setOutcome(val);

        val = resultNode.selectSingleNode("PC-AssayResults_rank").valueOf("text()");
        result.setRankScore(Integer.parseInt(val));

        List<Node> assayDataNodes = resultNode.selectNodes("PC-AssayResults_data/PC-AssayData");

        List<String> all = GrowthList.decorate(new ArrayList(assay.getColumns().size() - 2));
        result.setAllValues(all);
        for (Node node : assayDataNodes) {
            val = node.valueOf("PC-AssayData_tid/text()");
            int index = Integer.parseInt(val) - 1;
            val = node.selectSingleNode(".//*[starts-with(name(),'PC-AssayData_value_')]").getText();
            all.set(index, val);
        }

        // if a dose response assay with a marked activeConcentration
        if ("confirmatory".equals(assay.getActivityOutcomeMethod()) && activeColumn != null) {
            String actConc = all.get(activeColumn.getTID() - 1);
            if (null != actConc && !"".equals(actConc)) {
                result.setPrimaryValue(Double.valueOf(actConc));
                result.setPrimaryColumn(activeColumn);

                PCAssayColumn qualCol = assay.getQualifierColumn();
                if (qualCol != null) {
                    String qual = all.get(qualCol.getTID() - 1);
                    if (!"".equals(qual))
                        result.setQualifier(qual);
                }
            }

        } else if ("screening".equals(assay.getActivityOutcomeMethod()) && testedCols.size() > 0) {
            PCAssayColumn testedCol = testedCols.get(0);
            String value = all.get(testedCol.getTID() - 1);
            result.setPrimaryColumn(testedCol);
            if (null != value && !"".equals(value))
                if ("float".equals(testedCol.getType()) || "int".equals(testedCol.getType()))
                    result.setPrimaryValue(Double.parseDouble(value));
                else
                    result.setPrimaryValueAsString(value);
        }

        // put all testedConcentration columns into an ordered array. Interested in numbers here only.
        result.getTestedValues().clear();
        for (int ii = 0; ii < testedCols.size(); ii++) {
            PCAssayColumn testedCol = testedCols.get(ii);
            String value = all.get(testedCol.getTID() - 1);
            if (null != value && !"".equals(value)) {
                try {
                    Double dbl = Double.parseDouble(value);
                    result.getTestedValues().set(ii, dbl);
                } catch (NumberFormatException ex) {
                    // if not a number then don't worry about it.
                }
            }
        }
        assay.getResults().add(result);
    }

}

From source file:bard.pubchem.xml.PubChemXMLParserFactory.java

protected void populateAssayResultsFromXML(PCAssay assay, Node assayDescriptionNode) {
    List<Node> assayResultNodes = assayDescriptionNode
            .selectNodes("../../../PC-AssaySubmit_data/PC-AssayResults");
    if (assayResultNodes.size() == 0)
        return;/*from  w  w w .  j av a2 s .  c o  m*/

    for (Node resultNode : assayResultNodes) {
        PCAssayResult result = new PCAssayResult();

        String val = resultNode.selectSingleNode("PC-AssayResults_sid").valueOf("text()");
        result.setSID(Long.parseLong(val));

        val = resultNode.selectSingleNode("PC-AssayResults_outcome").valueOf("@value");
        val = val.substring(0, 1).toUpperCase() + val.substring(1);
        result.setOutcome(val);

        val = resultNode.selectSingleNode("PC-AssayResults_rank").valueOf("text()");
        result.setRankScore(Integer.parseInt(val));

        List<Node> assayDataNodes = resultNode.selectNodes("PC-AssayResults_data/PC-AssayData");

        List<String> all = GrowthList.decorate(new ArrayList<String>(assay.getColumns().size() - 2));
        result.setAllValues(all);
        for (Node node : assayDataNodes) {
            val = node.valueOf("PC-AssayData_tid/text()");
            int index = Integer.parseInt(val) - 1;
            val = node.selectSingleNode(".//*[starts-with(name(),'PC-AssayData_value_')]").getText();
            all.set(index, val);
        }
        assay.getResults().add(result);
    }

}

From source file:org.agnitas.web.RecipientForm.java

public RecipientForm() {
    updateButton = new ImageButton();
    deleteButton = new ImageButton();
    targetAddButton = new ImageButton();

    targetRemoveList = (List<ImageButton>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<ImageButton>(), imageButtonFactory));
    columnAndTypeList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    chainOperatorList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    parenthesisOpenedList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    primaryOperatorList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    primaryValueList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    parenthesisClosedList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    dateFormatList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    secondaryOperatorList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    secondaryValueList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    validTargetOperatorsList = (List<TargetOperator[]>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<TargetOperator[]>(), nullFactory));
    columnNameList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    columnTypeList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    advancedSearchVisible = false;/*from ww  w.j  av a  2  s. c  o m*/
    selectedFields = DEFAULT_FIELDS;
    selectedFieldsOld = DEFAULT_FIELDS;
}

From source file:org.agnitas.web.TargetForm.java

public TargetForm() {
    columnAndTypeList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    chainOperatorList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    parenthesisOpenedList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    primaryOperatorList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    primaryValueList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    parenthesisClosedList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    dateFormatList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    secondaryOperatorList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
    secondaryValueList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    validTargetOperatorsList = (List<TargetOperator[]>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<TargetOperator[]>(), nullFactory));
    columnNameList = (List<String>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<String>(), emptyStringFactory));
    columnTypeList = (List<Integer>) GrowthList
            .decorate(LazyList.decorate(new ArrayList<Integer>(), zeroIntegerFactory));
}

From source file:org.diffkit.diff.sns.DKPoiSheet.java

@SuppressWarnings("unchecked")
private List<Type> discoverColumnTypes(List<Row> rows_) {
    if (CollectionUtils.isEmpty(rows_))
        return null;
    List<Type> columnTypes = GrowthList
            .decorate(LazyList.decorate(new ArrayList<Type>(), FactoryUtils.nullFactory()));
    int start = this.hasHeader() ? 1 : 0;
    for (int i = start; i < rows_.size(); i++) {
        Row aRow = rows_.get(i);/*from   w ww.j  av a2s . c  o  m*/
        int width = aRow.getLastCellNum();
        for (int j = 0; j < width; j++) {
            Cell cell = aRow.getCell(j);
            if (cell == null)
                continue;
            if (_isDebugEnabled) {
                _log.debug(String.format("cell->%s formatString->%s format->%s", cell.getColumnIndex(),
                        cell.getCellStyle().getDataFormatString(), cell.getCellStyle().getDataFormat()));
            }
            Type cellType = mapColumnType(cell);
            Type columnType = columnTypes.get(j);
            if (_isDebugEnabled)
                _log.debug("cellType->{} columnType->{}", cellType, columnType);
            if (columnType == null)
                columnTypes.set(j, cellType);
            else if (columnType != cellType)
                columnTypes.set(j, Type.MIXED);
        }
    }
    return columnTypes;
}

From source file:uk.co.certait.htmlexporter.ss.CellRangeRow.java

@SuppressWarnings("unchecked")
protected CellRangeRow(int index) {
    this.index = index;
    cells = GrowthList.decorate(new ArrayList<TableCellReference>());
}