Author: mcreech
Date: 2011-05-25 10:28:50 -0700 (Wed, 25 May 2011)
New Revision: 25527
Modified:
csplugins/trunk/agilent/creech/HyperEdge/src/main/java/cytoscape/hyperedge/impl/utils/HEUtils.java
Log:
v2.63
Modified:
csplugins/trunk/agilent/creech/HyperEdge/src/main/java/cytoscape/hyperedge/impl/utils/HEUtils.java
===================================================================
---
csplugins/trunk/agilent/creech/HyperEdge/src/main/java/cytoscape/hyperedge/impl/utils/HEUtils.java
2011-05-25 16:54:41 UTC (rev 25526)
+++
csplugins/trunk/agilent/creech/HyperEdge/src/main/java/cytoscape/hyperedge/impl/utils/HEUtils.java
2011-05-25 17:28:50 UTC (rev 25527)
@@ -1,4 +1,3 @@
-
/*
Copyright (c) 2008, The Cytoscape Consortium (www.cytoscape.org)
@@ -33,7 +32,6 @@
along with this library; if not, write to the Free Software Foundation,
Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.
*/
-
/*
*
* Revisions:
@@ -66,7 +64,6 @@
*/
package cytoscape.hyperedge.impl.utils;
-
import giny.model.GraphObject;
import java.io.File;
@@ -90,7 +87,6 @@
import cytoscape.hyperedge.impl.HyperEdgeImpl;
import cytoscape.logger.CyLogger;
-
/**
* Utility operations used throughout HyperEdge.
* @author Michael L. Creech
@@ -98,35 +94,35 @@
*/
public final class HEUtils {
private static final String ATTRIBUTE_TRUE = "true";
- private static boolean doLogging = true;
- private static CyLogger logger = CyLogger.getLogger("HyperEdge");
+ private static boolean doLogging = true;
+ private static CyLogger logger =
CyLogger.getLogger("HyperEdge");
static {
- logger.setDebug (doLogging);
+ logger.setDebug(doLogging);
}
-
// used for making generateUUID() thread-safe and reducing the span of
// what is locked:
- private static Boolean lockObjForUUID = new Boolean(true);
- private static String localHostCache = cacheLocalHostInfo();
-
+ private static Boolean lockObjForUUID = new Boolean(true);
+ private static String localHostCache = cacheLocalHostInfo();
// The number of calls to the UUID routine:
- private static long uuidCallNum;
+ private static long uuidCallNum;
// Don't want people to manipulate the utility class constructor.
- private HEUtils() {}
-
+ private HEUtils() {
+ }
+
/**
* Convenience method for throwing an IllegalArgumentException given
* a message.
* @param msg the String message associated with the exception.
* @throws IllegalArgumentException
*/
- public static void throwIllegalArgumentException(final String msg){
+ public static void throwIllegalArgumentException(final String msg) {
final IllegalArgumentException ex = new IllegalArgumentException(msg);
ex.fillInStackTrace();
-
// ex.printStackTrace();
- logger.error (msg,ex);
+ // MLC 05/25/11:
+ // Don't log exceptions since they may be caught by higher-level
routines:
+ // logger.error(msg, ex);
throw ex;
}
@@ -139,16 +135,16 @@
public static void throwIllegalStateException(final String msg) {
final IllegalStateException ex = new IllegalStateException(msg);
ex.fillInStackTrace();
-
// ex.printStackTrace();
- logger.error (msg,ex);
+ // MLC 05/25/11:
+ // Don't log exceptions since they may be caught by higher-level
routines:
+ // logger.error (msg,ex);
throw ex;
}
// static public Iterator createEmptyUnmodifiableListIterator() {
// return (Collections.unmodifiableList(new
ArrayList(0))).iterator();
// }
-
/**
* Output a message to a CyLogger for HyperEdges.
* Commonly used for debugging. Will not log when
@@ -158,10 +154,10 @@
* @see HEUtils#setLogging
*/
public static void log(final String msg) {
- // if (doLogging) {
- // System.out.println(msg);
- // }
- logger.info(msg);
+ // if (doLogging) {
+ // System.out.println(msg);
+ // }
+ logger.info(msg);
}
/**
@@ -172,7 +168,7 @@
*/
public static void errorLog(final String msg) {
// System.err.println(msg);
- logger.warn (msg);
+ logger.warn(msg);
}
/**
@@ -189,7 +185,7 @@
public static boolean setLogging(final boolean doLog) {
final boolean retVal = doLogging;
doLogging = doLog;
- logger.setDebug (doLogging);
+ logger.setDebug(doLogging);
return retVal;
}
@@ -203,19 +199,15 @@
// (!obj.isState (LifeState.CREATION_IN_PROGRESS)) &&
// (!obj.isState (LifeState.DELETION_IN_PROGRESS)))
if (obj.isState(LifeState.DELETED)) {
- final String msg = "Attempting operation on object
" +
- obj.getIdentifier() + " in state " +
- obj.getState() +
- " when we expected the object to be in
state " +
- LifeState.NORMAL + ", " +
- LifeState.CREATION_IN_PROGRESS +
- ", or " +
- LifeState.DELETION_IN_PROGRESS + ".";
+ final String msg = "Attempting operation on object " +
obj.getIdentifier()
+ + " in state " + obj.getState()
+ + " when we expected the object to be in state " +
LifeState.NORMAL + ", "
+ + LifeState.CREATION_IN_PROGRESS + ", or " +
LifeState.DELETION_IN_PROGRESS
+ + ".";
final IllegalStateException ex = new IllegalStateException(msg);
ex.fillInStackTrace();
-
// ex.printStackTrace();
- logger.error (msg,ex);
+ logger.error(msg, ex);
throw ex;
}
}
@@ -245,27 +237,22 @@
* @return the String representing the UUID.
*/
public static String generateUUID(final String prefix) {
- final long time = System.currentTimeMillis();
+ final long time = System.currentTimeMillis();
final StringBuilder sb = new StringBuilder();
-
if (prefix != null) {
sb.append(prefix);
sb.append('-');
}
-
// lockObjForUUID is only used to reduce the scope of what
// is locked when we change uuidCallNum. This is instead of
// doing a 'synchronized (this)' statement:
synchronized (lockObjForUUID) {
sb.append(++uuidCallNum);
}
-
sb.append(':');
sb.append(time);
sb.append(':');
-
sb.append(localHostCache);
-
return sb.toString();
}
@@ -277,8 +264,7 @@
try {
return InetAddress.getLocalHost().getHostAddress();
} catch (UnknownHostException e) {
- return (System.getProperty("user.name") +
- System.getProperty("user.home"));
+ return (System.getProperty("user.name") +
System.getProperty("user.home"));
}
}
@@ -321,14 +307,11 @@
if (obj == null) {
return null;
}
-
String fullName = obj.getClass().getName();
- final int index = fullName.lastIndexOf('.');
-
+ final int index = fullName.lastIndexOf('.');
if (index >= 0) {
fullName = fullName.substring(index + 1);
}
-
return fullName;
}
@@ -344,10 +327,8 @@
if (toCopy == null) {
return null;
}
-
final List<Element> copy = new ArrayList<Element>(toCopy.size());
copy.addAll(toCopy);
-
return (copy);
}
@@ -360,7 +341,8 @@
* @return true if the two fields are null
* or have the same characters. Return false otherwise.
*/
- public static boolean stringEqual(final String field1, final String field2,
+ public static boolean stringEqual(final String field1,
+ final String field2,
final boolean caseSensitive) {
if (field1 != field2) {
if (field1 != null) {
@@ -374,7 +356,6 @@
return false;
}
}
-
return true;
}
@@ -393,17 +374,14 @@
*/
public static String getSuffix(final String str, final char matchChar) {
String suffix = null;
-
if (str != null) {
final int i = str.lastIndexOf(matchChar);
-
// It must be less than length() - 1 to have any characters to the
right
// of match_char:
if ((i >= 0) && (i < (str.length() - 1))) {
suffix = str.substring(i + 1);
}
}
-
return suffix;
}
@@ -417,9 +395,8 @@
*
*/
public static boolean ensurePathCreated(final String dirPath) {
- final File f = new File(dirPath);
+ final File f = new File(dirPath);
final boolean exists = f.isDirectory();
-
if (!exists) {
return f.mkdirs();
} else {
@@ -458,12 +435,10 @@
// // log ("removeNode: " + node.getIdentifier ());
// _root_graph.removeNode(node);
// }
-
// public static void removeEdge(CyEdge edge) {
// // log ("removeEdge: " + edge.getIdentifier ());
// _root_graph.removeEdge(edge);
// }
-
// // TODO To be replaced with call to CytoscapeRootGraph.getEdge() when
// // bug is fixed.
// public static CyEdge slowGetEdge (String uuid)
@@ -498,15 +473,13 @@
// }
// return null;
// }
-
/**
* @param edge the CyEdge for which to find the associated interaction
type.
* @return the interaction type of a given edge.
*/
-
public static String getEdgeInteractionType(final CyEdge edge) {
return
Cytoscape.getEdgeAttributes().getStringAttribute(edge.getIdentifier(),
- Semantics.INTERACTION);
+
Semantics.INTERACTION);
}
/**
@@ -516,15 +489,16 @@
* @param edgeIType the interaction type of the CyEdge.
* @return the CyEdge created.
*/
- public static CyEdge createHEEdge(final CyNode source, final CyNode target,
+ public static CyEdge createHEEdge(final CyNode source,
+ final CyNode target,
final String edgeIType) {
final CyEdge edge = createEdge(source, target, edgeIType);
Cytoscape.getEdgeAttributes().setAttribute(edge.getIdentifier(),
HyperEdgeImpl.HYPEREDGE_EDGE_TAG_NAME,
ATTRIBUTE_TRUE);
-
return edge;
}
+
/**
* Create a CyEdge that connects two given CyNodes.
* @param source the source of the CyEdge.
@@ -532,10 +506,8 @@
* @param edgeIType the interaction type of the CyEdge.
* @return the CyEdge created.
*/
- public static CyEdge createEdge(final CyNode source, final CyNode target,
- final String edgeIType) {
- return Cytoscape.getCyEdge(source, target, Semantics.INTERACTION,
- edgeIType, true, true);
+ public static CyEdge createEdge(final CyNode source, final CyNode target,
final String edgeIType) {
+ return Cytoscape.getCyEdge(source, target, Semantics.INTERACTION,
edgeIType, true, true);
}
/**
@@ -545,25 +517,22 @@
*/
public static CyNode createConnectorNode(final String uuid) {
final CyNode retNode = getNode(uuid);
-
// TODO Fix hack for removing canonical name on connectors:
// &&& HACK getNode() sets the CANONICAL_NAME to the node id,
// which we don't want for connector nodes:
final CyAttributes nodeAddrs = Cytoscape.getNodeAttributes();
- // MLC 06/21/07:
+ // MLC 06/21/07:
// nodeAddrs.deleteAttribute(uuid, HyperEdgeImpl.LABEL_ATTRIBUTE_NAME);
- // MLC 06/21/07:
- deleteAttribute (nodeAddrs, uuid, HyperEdgeImpl.LABEL_ATTRIBUTE_NAME);
+ // MLC 06/21/07:
+ deleteAttribute(nodeAddrs, uuid, HyperEdgeImpl.LABEL_ATTRIBUTE_NAME);
+ nodeAddrs
+ .setAttribute(uuid,
HyperEdgeImpl.IS_CONNECTOR_NODE_ATTRIBUTE_NAME, ATTRIBUTE_TRUE);
nodeAddrs.setAttribute(uuid,
- HyperEdgeImpl.IS_CONNECTOR_NODE_ATTRIBUTE_NAME,
- ATTRIBUTE_TRUE);
- nodeAddrs.setAttribute(uuid, HyperEdgeImpl.ENTITY_TYPE_ATTRIBUTE_NAME,
+ HyperEdgeImpl.ENTITY_TYPE_ATTRIBUTE_NAME,
HyperEdgeImpl.ENTITY_TYPE_CONNECTOR_NODE_VALUE);
-
return retNode;
}
-
// delete's the given attribute from the given identifier from the
// given CyAttributes. This is temporary method until
// CyAttributes.deleteAttribute() if fixed to not throw an
@@ -575,13 +544,14 @@
* @param attrName the name of the attribute value to remove.
* @return true iff the attribute value was removed.
*/
- public static boolean deleteAttribute (final CyAttributes attrs,
- final String uuid , final String attrName) {
- if (!attrs.hasAttribute (uuid, attrName)) {
- return false;
- }
- // it really has the attribute:
- return attrs.deleteAttribute (uuid, attrName);
+ public static boolean deleteAttribute(final CyAttributes attrs,
+ final String uuid,
+ final String attrName) {
+ if (!attrs.hasAttribute(uuid, attrName)) {
+ return false;
+ }
+ // it really has the attribute:
+ return attrs.deleteAttribute(uuid, attrName);
}
/**
@@ -640,11 +610,9 @@
*/
public static <E> Collection<E> createCollection(final Iterator<E> colIt) {
final Collection<E> retCol = new ArrayList<E>();
-
while (colIt.hasNext()) {
retCol.add(colIt.next());
}
-
return retCol;
}
@@ -657,36 +625,28 @@
*/
public static String toString(final Object obj) {
final StringBuilder sb = new StringBuilder();
-
if (obj instanceof GraphObject) {
String id = ((GraphObject) obj).getIdentifier();
-
if (id == null) {
id = obj.toString();
}
-
primToString(id, obj, sb);
} else if (obj instanceof CyNetwork) {
String id = ((CyNetwork) obj).getIdentifier();
-
if (id == null) {
id = obj.toString();
}
-
primToString(id, obj, sb);
} else if (obj instanceof HyperEdge) {
- final HyperEdge he = (HyperEdge) obj;
- String label = he.getName();
-
+ final HyperEdge he = (HyperEdge) obj;
+ String label = he.getName();
if (label == null) {
label = he.getIdentifier();
}
-
primToString(label, he, sb);
} else {
sb.append(obj);
}
-
return sb.toString();
}
@@ -697,7 +657,6 @@
sb.append(label);
sb.append(']');
}
-
/**
* Ignore attributes found in a given List. For example:
* <PRE>
@@ -712,16 +671,19 @@
*/
public static class AttributeIgnoreFilter implements AttributeFilter {
private List<String> attrNames;
+
/**
* @param attrNames the list of attributes to ignore.
*/
public AttributeIgnoreFilter(final List<String> attrNames) {
this.attrNames = attrNames;
}
+
/**
* {@inheritDoc}
*/
- public boolean includeAttribute(final CyAttributes attr, final String
objID,
+ public boolean includeAttribute(final CyAttributes attr,
+ final String objID,
final String attrName) {
return (!attrNames.contains(attrName));
}
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