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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2011-10-17 14:35:14 -04:00
parent 6b02354d84 3550798c4c
commit 589df6b7cf
3 changed files with 8 additions and 8 deletions
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2
public/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -380,7 +380,7 @@ class RodBindingArgumentTypeDescriptor extends ArgumentTypeDescriptor {
if ( tribbleType == null ) if ( tribbleType == null )
if ( ! file.canRead() | ! file.isFile() ) { if ( ! file.canRead() | ! file.isFile() ) {
throw new UserException.BadArgumentValue(name, "Couldn't read file to determine type: " + file); throw new UserException.CouldNotReadInputFile(file, "file does exist or couldn't be read");
} else { } else {
throw new UserException.CommandLineException( throw new UserException.CommandLineException(
String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " + String.format("No tribble type was provided on the command line and the type of the file could not be determined dynamically. " +

10
public/java/src/org/broadinstitute/sting/utils/SimpleTimer.java
View File

@ -46,7 +46,7 @@ public class SimpleTimer {
* @return the name associated with this timer * @return the name associated with this timer
*/ */
@Ensures("result != null") @Ensures("result != null")
public String getName() { public synchronized String getName() {
return name; return name;
} }
@ -82,14 +82,14 @@ public class SimpleTimer {
/** /**
* @return is this timer running? * @return is this timer running?
*/ */
public boolean isRunning() { public synchronized boolean isRunning() {
return running; return running;
} }
/** /**
* @return A convenience function to obtain the current time in milliseconds from this timer * @return A convenience function to obtain the current time in milliseconds from this timer
*/ */
public long currentTime() { public synchronized long currentTime() {
return System.currentTimeMillis(); return System.currentTimeMillis();
} }
@ -119,8 +119,4 @@ public class SimpleTimer {
public synchronized double getElapsedTime() { public synchronized double getElapsedTime() {
return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0; return (running ? (currentTime() - startTime + elapsed) : elapsed) / 1000.0;
} }
public void printElapsedTime(PrintStream out) {
out.printf("SimpleTimer %s: %.2f%n", name, getElapsedTime());
}
} }

4
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -111,6 +111,10 @@ public class UserException extends ReviewedStingException {
super(String.format("Couldn't read file because %s caused by %s", message, e.getMessage())); super(String.format("Couldn't read file because %s caused by %s", message, e.getMessage()));
} }
public CouldNotReadInputFile(File file) {
super(String.format("Couldn't read file %s", file.getAbsolutePath()));
}
public CouldNotReadInputFile(File file, String message) { public CouldNotReadInputFile(File file, String message) {
super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message)); super(String.format("Couldn't read file %s because %s", file.getAbsolutePath(), message));
} }