Author: scooter
Date: 2010-09-24 21:48:38 -0700 (Fri, 24 Sep 2010)
New Revision: 22059
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/de/layclust/taskmanaging/io/Console.java
Log:
Convert to Cytoscape logging for Console too.
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/de/layclust/taskmanaging/io/Console.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/de/layclust/taskmanaging/io/Console.java
2010-09-24 23:54:32 UTC (rev 22058)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/TransClust/de/layclust/taskmanaging/io/Console.java
2010-09-25 04:48:38 UTC (rev 22059)
@@ -11,9 +11,14 @@
import java.util.PropertyResourceBundle;
import java.util.logging.ConsoleHandler;
import java.util.logging.Handler;
-import java.util.logging.Level;
-import java.util.logging.Logger;
+// import java.util.logging.Level;
+// import java.util.logging.Logger;
+import cytoscape.logger.CyLogger;
+import cytoscape.logger.LogLevel;
+
+import clusterMaker.algorithms.TransClust.TransClustCluster;
+
import clusterMaker.algorithms.TransClust.de.costmatrixcreation.main.Config;
import
clusterMaker.algorithms.TransClust.de.layclust.geometric_clustering.GeometricClusteringConfig;
import
clusterMaker.algorithms.TransClust.de.layclust.geometric_clustering.GeometricClusteringFactory;
@@ -35,7 +40,8 @@
*/
public class Console {
- private static Logger log = Logger.getLogger(Console.class.getName());
+ // private static Logger log =
Logger.getLogger(Console.class.getName());
+ private static CyLogger log =
CyLogger.getLogger(TransClustCluster.class);
private String[] args = null;
@@ -43,7 +49,7 @@
ArgsParseException, IOException {
this.args = args;
- log.fine("Available processors in system: "
+ log.debug("Available processors in system: "
+ Runtime.getRuntime().availableProcessors());
parseArgsAndInitProgram();
@@ -68,21 +74,21 @@
initGivenParameters();
/* set logging */
- Logger logger = Logger.getLogger("");
- if (TaskConfig.setLogLevel){
- logger.setLevel(TaskConfig.logLevel);
- }
- Handler[] handler = logger.getHandlers();
- for (Handler h : handler) {
- if (TaskConfig.setLogLevel){
- h.setLevel(TaskConfig.logLevel);
- }
- if (h instanceof ConsoleHandler) {
- if (!TaskConfig.verbose) {
- h.setLevel(Level.WARNING);
- }
- }
- }
+ // Logger logger = Logger.getLogger("");
+ // if (TaskConfig.setLogLevel){
+ // logger.setLevel(TaskConfig.logLevel);
+ // }
+ // Handler[] handler = logger.getHandlers();
+ // for (Handler h : handler) {
+ // if (TaskConfig.setLogLevel){
+ // h.setLevel(TaskConfig.logLevel);
+ // }
+ // if (h instanceof ConsoleHandler) {
+ // if (!TaskConfig.verbose) {
+ // h.setLevel(Level.WARNING);
+ // }
+ // }
+ // }
if (TaskConfig.gui) {
/* start gui with previous set parameters */
@@ -184,7 +190,7 @@
TaskConfig.useConfigFile =
Boolean.parseBoolean(value);
} else if (key.equals("-log")) {
TaskConfig.setLogLevel = true;
- TaskConfig.logLevel =
Level.parse(value.toUpperCase());
+ // TaskConfig.logLevel =
Level.parse(value.toUpperCase());
} else if (key.equals("-verbose")) {
TaskConfig.verbose =
Boolean.parseBoolean(value);
} else if (key.equals("-info")) {
@@ -422,7 +428,7 @@
FileInputStream s = new
FileInputStream(configPath);
PropertyResourceBundle configrb = new
PropertyResourceBundle(s);
- log.fine("Using config file " + configPath);
+ log.debug("Using config file " + configPath);
TaskConfig.initFromConfigFile(configrb);
FORCEnDLayoutConfig.initFromConfigFile(configrb);
@@ -431,7 +437,7 @@
} catch (MissingResourceException ex) {
log
- .severe("WARNING: Resources are
missing in the given config file: "
+ .error("WARNING: Resources are
missing in the given config file: "
+
TaskConfig.DEFAULTCONFIG
+ ", key="
+ ex.getKey()
@@ -439,12 +445,12 @@
+
TaskConfig.DEFAULTCONFIG
+ ". Or these
parameters do not interest you, because they belong to an unused
implemtation.");
} catch (IOException ex) {
- log.severe("ERROR: Unable to read the given
config file: "
+ log.fatal("ERROR: Unable to read the given
config file: "
+ configPath);
System.exit(-1);
} catch (InvalidTypeException ex) {
log
- .severe("ERROR: You have
perhaps given an incorrect class name of an "
+ .fatal("ERROR: You have perhaps
given an incorrect class name of an "
+
"implemtation. Please note that this is case sensitive.");
System.exit(-1);
}
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