/htsjdk

annotating deprecated methods with @Deprecated #698

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merged 2 commits into from Sep 14, 2016

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@lbergelson @coveralls @droazen @magicDGS
@lbergelson
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lbergelson commented Sep 6, 2016

Description

Some methods are documented as being /** @deprecated */ but are missing a @Deprecated tag
This causes tools to not correctly identify them as being deprecated.

also updating documentation of deprecated methods to point to the replacement method with a valid {@link}

Checklist

  • Code compiles correctly
  • New tests covering changes and new functionality
  • All tests passing
  • Extended the README / documentation, if necessary
  • Is not backward compatible (breaks binary or source compatibility)
@lbergelson lbergelson annotating deprecated methods with @Deprecated 
some methods that were documented as deprecated were not also annotated with @Deprecated
annotating them as deprecated allows tools to warn when these methods are accidentally used

also updating documentation of deprecated methods to point to the replacement method with a valid {@link}

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coverage/coveralls — First build on lb_annotate_deprecated_method at 68.927%
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8ec6a65
@coveralls

coveralls commented Sep 6, 2016

Coverage Status

Coverage remained the same at 68.921% when pulling 8ec6a65 on lb_annotate_deprecated_method into c3d5a88 on master.

@magicDGS magicDGS and 1 other commented on an outdated diff Sep 7, 2016

View full outdated diff
...ain/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
@@ -52,6 +52,7 @@ public String getAttribute(final String key) {
* @param value attribute value
* @deprecated Use the version that takes a String value instead
@magicDGS

magicDGS Sep 7, 2016

Contributor

Could this have a {@link}?

@lbergelson

lbergelson Sep 14, 2016

Contributor

done

@magicDGS magicDGS and 1 other commented on an outdated diff Sep 7, 2016

View full outdated diff
src/main/java/htsjdk/samtools/SamFileHeaderMerger.java
@@ -122,8 +122,9 @@ public int compare(final AbstractSAMHeaderRecord o1, final AbstractSAMHeaderReco
*
* @param readers sam file readers to combine
* @param sortOrder sort order new header should have
- * @deprecated replaced by SamFileHeaderMerger(Collection<SAMFileHeader>, SAMFileHeader.SortOrder, boolean)
+ * @deprecated replaced by{@link #SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)}
@magicDGS

magicDGS Sep 7, 2016

Contributor

Missing space after by

@lbergelson

lbergelson Sep 14, 2016

Contributor

done

droazen self-assigned this Sep 13, 2016

@droazen
Contributor

droazen commented Sep 13, 2016

👍 merge when ready @lbergelson

@droazen droazen assigned lbergelson and unassigned droazen Sep 13, 2016

@lbergelson lbergelson responding to comments

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3 successful checks
continuous-integration/travis-ci/pr — The Travis CI build passed
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continuous-integration/travis-ci/push — The Travis CI build passed
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coverage/coveralls — Coverage decreased (-0.006%) to 68.921%
Details
c23f1e9
@lbergelson

lbergelson reviewed Sep 14, 2016
View changes

responded to comments, thank you @magicDGS

src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java
@@ -52,6 +52,7 @@ public String getAttribute(final String key) {
* @param value attribute value
* @deprecated Use the version that takes a String value instead
@lbergelson

lbergelson Sep 14, 2016

Contributor

done

src/main/java/htsjdk/samtools/SamFileHeaderMerger.java
@@ -122,8 +122,9 @@ public int compare(final AbstractSAMHeaderRecord o1, final AbstractSAMHeaderReco
*
* @param readers sam file readers to combine
* @param sortOrder sort order new header should have
- * @deprecated replaced by SamFileHeaderMerger(Collection<SAMFileHeader>, SAMFileHeader.SortOrder, boolean)
+ * @deprecated replaced by{@link #SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)}
@lbergelson

lbergelson Sep 14, 2016

Contributor

done

@coveralls

coveralls commented Sep 14, 2016

Coverage Status

Coverage increased (+0.06%) to 68.984% when pulling c23f1e9 on lb_annotate_deprecated_method into c3d5a88 on master.

@lbergelson lbergelson merged commit 255e41a into master Sep 14, 2016
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continuous-integration/travis-ci/pr The Travis CI build passed
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continuous-integration/travis-ci/push The Travis CI build passed
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coverage/coveralls Coverage decreased (-0.006%) to 68.921%
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lbergelson deleted the lb_annotate_deprecated_method branch Sep 14, 2016

magicDGS referenced this pull request Sep 21, 2016

Merged

Clean some deprecated classes/methods usages in htsjdk #707

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