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Add a reset() method to ProgressLoggerInterface. #1184

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merged 2 commits into from
Oct 5, 2018
Merged

Add a reset() method to ProgressLoggerInterface. #1184

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907d354
Add a reset() method to ProgressLoggerInterface.
nh13 Oct 3, 2018
daa8150
ProgressLoggerInterface.reset has a default method
nh13 Oct 5, 2018
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22 changes: 16 additions & 6 deletions src/main/java/htsjdk/samtools/util/AbstractProgressLogger.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,13 @@ abstract public class AbstractProgressLogger implements ProgressLoggerInterface
private final int n;
private final String verb;
private final String noun;
private final long startTime = System.currentTimeMillis();
private long startTime;
private final NumberFormat fmt = new DecimalFormat("#,###");
private final NumberFormat timeFmt = new DecimalFormat("00");
private long processed = 0;
// Set to -1 until the first record is added
private long lastStartTime = -1;
private String lastChrom = null;
private int lastPos = 0;
private long processed;
private long lastStartTime;
private String lastChrom;
private int lastPos;

/**
* Construct an AbstractProgressLogger.
Expand All @@ -37,6 +36,7 @@ protected AbstractProgressLogger(final String noun, final String verb, final int
this.noun = noun;
this.verb = verb;
this.n = n;
reset();
}

/**
Expand Down Expand Up @@ -124,6 +124,16 @@ public boolean record(final SAMRecord... recs) {
/** Returns the number of seconds since progress tracking began. */
public long getElapsedSeconds() { return (System.currentTimeMillis() - this.startTime) / 1000; }

/** Resets the start time to now and the number of records to zero. */
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In general, you want the javadoc on the baseclass or interface, so it's inherited by all subclassers and so a user can see the javadoc when dealing with the interface type.

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Agreed, but I am going to pass on this change to be consistent with how ProgressLoggerInterface currently is written.

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I agree with @pshapiro4broad but lets handle that separately.

public void reset() {
startTime = System.currentTimeMillis();
processed = 0;
// Set to -1 until the first record is added
lastStartTime = -1;
lastChrom = null;
lastPos = 0;
}

/** Left pads a string until it is at least the given length. */
private String pad (String in, final int length) {
while (in.length() < length) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/java/htsjdk/samtools/util/ProgressLoggerInterface.java
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Original file line number Diff line number Diff line change
Expand Up @@ -34,5 +34,5 @@ public interface ProgressLoggerInterface {
boolean record(final String chrom, final int pos);
boolean record(final SAMRecord rec);
boolean record(final SAMRecord... recs);

void reset();
}