Examples with CyTable org.cytoscape.model.CyTable used on opensource projects

Example 41 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class TableBrowserToolBar method getAttributeArray.

private String[] getAttributeArray() {
    final CyTable attrs = browserTableModel.getDataTable();
    final Collection<CyColumn> columns = attrs.getColumns();
    final String[] attributeArray = new String[columns.size() - 1];
    int index = 0;
    for (final CyColumn column : columns) {
        if (!column.isPrimaryKey())
            attributeArray[index++] = column.getName();
    }
    Arrays.sort(attributeArray);
    return attributeArray;
}

Example 42 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class TableBrowserToolBar method createNewAttribute.

private void createNewAttribute(final String type, boolean isShared) {
    try {
        final String[] existingAttrs = getAttributeArray();
        String newAttribName = null;
        do {
            newAttribName = JOptionPane.showInputDialog(this, "Column Name: ", "Create New " + type + " Column", JOptionPane.QUESTION_MESSAGE);
            if (newAttribName == null)
                return;
            newAttribName = newAttribName.trim();
            if (newAttribName.isEmpty()) {
                JOptionPane.showMessageDialog(null, "Column name must not be blank.", "Error", JOptionPane.ERROR_MESSAGE);
                newAttribName = null;
            } else if (Arrays.binarySearch(existingAttrs, newAttribName) >= 0) {
                JOptionPane.showMessageDialog(null, "Column " + newAttribName + " already exists.", "Error", JOptionPane.ERROR_MESSAGE);
                newAttribName = null;
            }
        } while (newAttribName == null);
        final CyTable attrs;
        if (isShared) {
            final CyNetwork network = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetwork();
            if (network instanceof CySubNetwork) {
                final CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
                CyTable sharedTable = null;
                if (this.objType == CyNode.class)
                    sharedTable = rootNetwork.getSharedNodeTable();
                else if (this.objType == CyEdge.class)
                    sharedTable = rootNetwork.getSharedEdgeTable();
                else if (this.objType == CyNetwork.class)
                    sharedTable = rootNetwork.getSharedNetworkTable();
                else
                    throw new IllegalStateException("Object type is not valid.  This should not happen.");
                attrs = sharedTable;
            } else {
                throw new IllegalArgumentException("This is not a CySubNetwork and there is no shared table.");
            }
        } else {
            attrs = browserTableModel.getDataTable();
        }
        if (type.equals("String"))
            attrs.createColumn(newAttribName, String.class, false);
        else if (type.equals("Floating Point"))
            attrs.createColumn(newAttribName, Double.class, false);
        else if (type.equals("Integer"))
            attrs.createColumn(newAttribName, Integer.class, false);
        else if (type.equals("Long Integer"))
            attrs.createColumn(newAttribName, Long.class, false);
        else if (type.equals("Boolean"))
            attrs.createColumn(newAttribName, Boolean.class, false);
        else if (type.equals("String List"))
            attrs.createListColumn(newAttribName, String.class, false);
        else if (type.equals("Floating Point List"))
            attrs.createListColumn(newAttribName, Double.class, false);
        else if (type.equals("Integer List"))
            attrs.createListColumn(newAttribName, Integer.class, false);
        else if (type.equals("Long Integer List"))
            attrs.createListColumn(newAttribName, Long.class, false);
        else if (type.equals("Boolean List"))
            attrs.createListColumn(newAttribName, Boolean.class, false);
        else
            throw new IllegalArgumentException("unknown column type \"" + type + "\".");
    } catch (IllegalArgumentException e) {
        JOptionPane.showMessageDialog(null, e.getMessage(), "Error", JOptionPane.ERROR_MESSAGE);
    }
}

Example 43 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class NetworkLineParser method mapAttribute.

/**
 * Based on the attribute types, map the entry to Node or Edge tables.
 */
@SuppressWarnings({ "unchecked", "rawtypes" })
private <T extends CyIdentifiable> void mapAttribute(final T element, final String entry, final int index) {
    if (entry == null || entry.length() == 0)
        return;
    final AttributeDataType type = mapping.getDataTypes()[index];
    if (type.isList()) {
        final CyTable table = network.getRow(element).getTable();
        if (table.getColumn(mapping.getAttributeNames()[index]) == null)
            table.createListColumn(mapping.getAttributeNames()[index], type.getListType(), false);
        final String[] delimiters = mapping.getListDelimiters();
        String delimiter = delimiters != null && delimiters.length > index ? delimiters[index] : AbstractMappingParameters.DEF_LIST_DELIMITER;
        if (delimiter == null || delimiter.isEmpty())
            delimiter = AbstractMappingParameters.DEF_LIST_DELIMITER;
        Object value = parse(entry, type, delimiter);
        if (value instanceof List) {
            // In case of list, do not overwrite the attribute. Get the existing list, and add it to the list.
            List<Object> curList = network.getRow(element).get(mapping.getAttributeNames()[index], List.class);
            if (curList == null)
                curList = new ArrayList<>();
            curList.addAll((List) value);
            value = curList;
        }
        network.getRow(element).set(mapping.getAttributeNames()[index], value);
    } else {
        createColumn(element, mapping.getAttributeNames()[index], type.getType());
        final Object value = parse(entry, type, null);
        network.getRow(element).set(mapping.getAttributeNames()[index], value);
    }
}

Example 44 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class OBOReader method mapHeader.

private void mapHeader() {
    final CyTable networkTable = this.ontologyDAG.getDefaultNetworkTable();
    for (String tag : header.keySet()) {
        if (networkTable.getColumn(tag) == null)
            networkTable.createColumn(tag, String.class, false);
        networkTable.getRow(ontologyDAG.getSUID()).set(tag, header.get(tag));
    }
    if (networkTable.getColumn(DAG_ATTR) == null)
        networkTable.createColumn(DAG_ATTR, Boolean.class, true);
    networkTable.getRow(ontologyDAG.getSUID()).set(DAG_ATTR, true);
    ontologyDAG.getRow(ontologyDAG).set(CyNetwork.NAME, dagName);
}

Example 45 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class LoadTableReaderTask method loadAnnotation.

private void loadAnnotation(TaskMonitor tm) {
    tm.setProgress(0.0);
    TextTableReader reader = this.reader;
    AttributeMappingParameters readerAMP = (AttributeMappingParameters) reader.getMappingParameter();
    String primaryKey = readerAMP.getAttributeNames()[readerAMP.getKeyIndex()];
    tm.setProgress(0.1);
    final CyTableFactory tableFactory = serviceRegistrar.getService(CyTableFactory.class);
    final CyTable table = tableFactory.createTable("AttrTable " + inputName.substring(inputName.lastIndexOf('/') + 1) + " " + Integer.toString(numImports++), primaryKey, String.class, true, true);
    cyTables = new CyTable[] { table };
    tm.setProgress(0.3);
    try {
        this.reader.readTable(table);
    } catch (IOException e) {
        e.printStackTrace();
    }
    tm.setProgress(1.0);
}