Examples with LongObjHash org.cytoscape.util.intr.LongObjHash used on opensource projects

Example 1 with LongObjHash

use of org.cytoscape.util.intr.LongObjHash in project cytoscape-impl by cytoscape.

the class RTree method empty.

/**
 * Empties this R-tree of all entries.  This method returns in constant
 * time (note however that garbage collection will take place in the
 * background).
 */
public final void empty() {
    m_root = new Node(m_maxBranches, true);
    m_entryMap = new LongObjHash();
    m_zOrderMap = new HashMap<Long, Double>();
    m_deletedEntries = 0;
    m_mapExpansionThreshold = LongObjHash.maxCapacity(m_entryMap.size());
}

Example 2 with LongObjHash

use of org.cytoscape.util.intr.LongObjHash in project cytoscape-impl by cytoscape.

the class RTree method insert.

/**
 * Inserts a new data entry into this tree; the entry's extents
 * are specified by the input parameters.  "Extents" is a short way
 * of saying "minimum bounding rectangle".  The minimum bounding rectangle
 * of an entry is axis-aligned, meaning that its sides are parallel to the
 * axes of the data space.
 * @param objKey a user-defined unique identifier used to refer to the entry
 *   being inserted in later operations; this identifier must be
 *   non-negative.
 * @param xMin the minimum X coordinate of the entry's extents rectangle.
 * @param yMin the minimum Y coordinate of the entry's extents rectangle.
 * @param xMax the maximum X coordinate of the entry's extents rectangle.
 * @param yMax the maximum Y coordinate of the entry's extents rectangle.
 * @exception IllegalStateException if objKey is already used for an
 *   existing entry in this R-tree.
 * @exception IllegalArgumentException if objKey is negative,
 *   if xMin is not less than or equal to xMax, or
 *   if yMin is not less than or equal to yMax.
 */
public final void insert(final long objKey, final float xMin, final float yMin, final float xMax, final float yMax, final double z) {
    if (objKey < 0)
        throw new IllegalArgumentException("objKey is negative");
    if (!(xMin <= xMax))
        throw new IllegalArgumentException("xMin <= xMax not true: xMin " + xMin + " xMax " + xMax);
    if (!(yMin <= yMax))
        throw new IllegalArgumentException("yMin <= yMax not true: yMin " + yMin + " yMax " + yMax);
    if (m_entryMap.get(objKey) != null) {
        if (m_entryMap.get(objKey) != m_deletedEntry)
            throw new IllegalStateException("objkey " + objKey + " is already in this tree");
        m_deletedEntries--;
    } else // Old entry is m_deletedEntry.
    // We only allow underlying hashtable expansions if the number of deleted
    // keys in the table is one quarter or less of the total number of keys.
    {
        if (m_entryMap.size() == m_mapExpansionThreshold) {
            if ((m_deletedEntries * 4) > m_entryMap.size()) {
                // Prune map.
                final LongObjHash newEntryMap = new LongObjHash();
                final LongEnumerator objKeys = m_entryMap.keys();
                final Iterator leafNodes = m_entryMap.values();
                while (objKeys.numRemaining() > 0) {
                    final Object leafNode = leafNodes.next();
                    if (leafNode == m_deletedEntry) {
                        objKeys.nextLong();
                        continue;
                    }
                    newEntryMap.put(objKeys.nextLong(), leafNode);
                }
                m_entryMap = newEntryMap;
                m_deletedEntries = 0;
            }
            m_mapExpansionThreshold = LongObjHash.maxCapacity(m_entryMap.size() + 1);
        }
    }
    final Node rootSplit = insert(m_root, objKey, xMin, yMin, xMax, yMax, m_maxBranches, m_minBranches, m_entryMap, m_MBR, m_objKeyBuff, m_childrenBuff, m_xMinBuff, m_yMinBuff, m_xMaxBuff, m_yMaxBuff, m_tempBuff1, m_tempBuff2);
    if (rootSplit != null) {
        final Node newRoot = new Node(m_maxBranches, false);
        newRoot.entryCount = 2;
        m_root.parent = newRoot;
        rootSplit.parent = newRoot;
        newRoot.data.children[0] = m_root;
        newRoot.data.children[1] = rootSplit;
        newRoot.xMins[0] = m_root.xMins[m_maxBranches - 1];
        newRoot.yMins[0] = m_root.yMins[m_maxBranches - 1];
        newRoot.xMaxs[0] = m_root.xMaxs[m_maxBranches - 1];
        newRoot.yMaxs[0] = m_root.yMaxs[m_maxBranches - 1];
        newRoot.xMins[1] = rootSplit.xMins[m_maxBranches - 1];
        newRoot.yMins[1] = rootSplit.yMins[m_maxBranches - 1];
        newRoot.xMaxs[1] = rootSplit.xMaxs[m_maxBranches - 1];
        newRoot.yMaxs[1] = rootSplit.yMaxs[m_maxBranches - 1];
        if (isLeafNode(m_root))
            newRoot.data.deepCount = m_root.entryCount + rootSplit.entryCount;
        else
            newRoot.data.deepCount = m_root.data.deepCount + rootSplit.data.deepCount;
        m_root = newRoot;
        m_MBR[0] = Math.min(m_root.xMins[0], m_root.xMins[1]);
        m_MBR[1] = Math.min(m_root.yMins[0], m_root.yMins[1]);
        m_MBR[2] = Math.max(m_root.xMaxs[0], m_root.xMaxs[1]);
        m_MBR[3] = Math.max(m_root.yMaxs[0], m_root.yMaxs[1]);
    }
    // OK, now that we've done all *that*, add z
    if (z != 0.0 || m_zOrderMap.get(objKey) != null) {
        if (z == 0.0)
            m_zOrderMap.remove(objKey);
        else
            m_zOrderMap.put(objKey, Double.valueOf(z));
    }
}

Example 3 with LongObjHash

use of org.cytoscape.util.intr.LongObjHash in project cytoscape-impl by cytoscape.

the class RTree method delete.

/**
 * Deletes the specified data entry from this tree.
 * @param objKey a user-defined identifier that was potentially used in a
 *   previous insertion.
 * @return true if and only if objKey existed in this R-tree prior to this
 *   method invocation.
 */
public final boolean delete(final long objKey) {
    if (objKey < 0)
        return false;
    // Todo: Rename 'n' to 'leafNode'.
    final Node n;
    {
        final Object o = m_entryMap.get(objKey);
        if ((o == null) || (o == m_deletedEntry))
            return false;
        n = (Node) o;
    }
    // Delete record from leaf node.
    final int delInx;
    for (int i = 0; ; i++) if (n.objKeys[i] == objKey) {
        delInx = i;
        break;
    }
    n.entryCount--;
    if (delInx != n.entryCount) {
        // Plug the hole at index delInx.
        n.objKeys[delInx] = n.objKeys[n.entryCount];
        n.xMins[delInx] = n.xMins[n.entryCount];
        n.yMins[delInx] = n.yMins[n.entryCount];
        n.xMaxs[delInx] = n.xMaxs[n.entryCount];
        n.yMaxs[delInx] = n.yMaxs[n.entryCount];
    }
    // Fix up the tree from leaf to root.
    int currentDepth = condenseTree(n, 1, m_nodeStack, m_minBranches, m_MBR) - m_nodeStack.size() + 1;
    while (m_nodeStack.size() > 0) {
        final Node eliminatedNode = (Node) m_nodeStack.pop();
        for (int i = 0; i < eliminatedNode.entryCount; i++) {
            final Node rootSplit;
            if (isLeafNode(eliminatedNode)) {
                rootSplit = insert(m_root, eliminatedNode.objKeys[i], eliminatedNode.xMins[i], eliminatedNode.yMins[i], eliminatedNode.xMaxs[i], eliminatedNode.yMaxs[i], m_maxBranches, m_minBranches, m_entryMap, m_MBR, m_objKeyBuff, m_childrenBuff, m_xMinBuff, m_yMinBuff, m_xMaxBuff, m_yMaxBuff, m_tempBuff1, m_tempBuff2);
            } else {
                rootSplit = insert(m_root, currentDepth, eliminatedNode.data.children[i], eliminatedNode.xMins[i], eliminatedNode.yMins[i], eliminatedNode.xMaxs[i], eliminatedNode.yMaxs[i], m_maxBranches, m_minBranches, m_MBR, m_childrenBuff, m_xMinBuff, m_yMinBuff, m_xMaxBuff, m_yMaxBuff, m_tempBuff1, m_tempBuff2);
                eliminatedNode.data.children[i] = null;
            /* Facilitate gc. */
            }
            if (rootSplit != null) {
                final Node newRoot = new Node(m_maxBranches, false);
                newRoot.entryCount = 2;
                m_root.parent = newRoot;
                rootSplit.parent = newRoot;
                newRoot.data.children[0] = m_root;
                newRoot.data.children[1] = rootSplit;
                newRoot.xMins[0] = m_root.xMins[m_maxBranches - 1];
                newRoot.yMins[0] = m_root.yMins[m_maxBranches - 1];
                newRoot.xMaxs[0] = m_root.xMaxs[m_maxBranches - 1];
                newRoot.yMaxs[0] = m_root.yMaxs[m_maxBranches - 1];
                newRoot.xMins[1] = rootSplit.xMins[m_maxBranches - 1];
                newRoot.yMins[1] = rootSplit.yMins[m_maxBranches - 1];
                newRoot.xMaxs[1] = rootSplit.xMaxs[m_maxBranches - 1];
                newRoot.yMaxs[1] = rootSplit.yMaxs[m_maxBranches - 1];
                newRoot.data.deepCount = m_root.data.deepCount + rootSplit.data.deepCount;
                m_root = newRoot;
                m_MBR[0] = Math.min(m_root.xMins[0], m_root.xMins[1]);
                m_MBR[1] = Math.min(m_root.yMins[0], m_root.yMins[1]);
                m_MBR[2] = Math.max(m_root.xMaxs[0], m_root.xMaxs[1]);
                m_MBR[3] = Math.max(m_root.yMaxs[0], m_root.yMaxs[1]);
                currentDepth++;
            }
        }
        currentDepth++;
    }
    // If the root node has only one child, make the child the new root.
    if ((!isLeafNode(m_root)) && (m_root.entryCount == 1)) {
        final Node newRoot = m_root.data.children[0];
        newRoot.parent = null;
        m_root = newRoot;
    }
    // Finally, delete the objKey from m_entryMap.
    // If m_entryMap contains too many deleted entries, prune.
    m_entryMap.put(objKey, m_deletedEntry);
    if (((++m_deletedEntries * 2) > m_entryMap.size()) && (m_deletedEntries > 5)) {
        final LongObjHash newEntryMap = new LongObjHash();
        final LongEnumerator objKeys = m_entryMap.keys();
        final Iterator leafNodes = m_entryMap.values();
        while (objKeys.numRemaining() > 0) {
            final Object leafNode = leafNodes.next();
            if (leafNode == m_deletedEntry) {
                objKeys.nextLong();
                continue;
            }
            newEntryMap.put(objKeys.nextLong(), leafNode);
        }
        m_entryMap = newEntryMap;
        m_deletedEntries = 0;
        m_mapExpansionThreshold = LongObjHash.maxCapacity(m_entryMap.size());
    }
    return true;
}