diff --git a/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java b/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java index 4475e005c..6bf28ef29 100644 --- a/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java +++ b/src/main/java/htsjdk/samtools/AbstractBAMFileIndex.java @@ -387,8 +387,9 @@ protected BitSet regionToBins(final int startPos, final int endPos) { } /** - * @deprecated Invoke htsjdk.samtools.Chunk#optimizeChunkList(java.util.List, long) directly. + * @deprecated Invoke {@link Chunk#optimizeChunkList} directly. */ + @Deprecated protected List optimizeChunkList(final List chunks, final long minimumOffset) { return Chunk.optimizeChunkList(chunks, minimumOffset); } diff --git a/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java b/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java index 42d09db17..769a7a735 100644 --- a/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java +++ b/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java @@ -50,8 +50,9 @@ public String getAttribute(final String key) { * Otherwise, the value will be converted to a String with toString. * @param key attribute name * @param value attribute value - * @deprecated Use the version that takes a String value instead + * @deprecated Use {@link #setAttribute(String, String) instead */ + @Deprecated public void setAttribute(final String key, final Object value) { setAttribute(key, value == null? null: value.toString()); } diff --git a/src/main/java/htsjdk/samtools/MergingSamRecordIterator.java b/src/main/java/htsjdk/samtools/MergingSamRecordIterator.java index 6b790fe00..a294752de 100644 --- a/src/main/java/htsjdk/samtools/MergingSamRecordIterator.java +++ b/src/main/java/htsjdk/samtools/MergingSamRecordIterator.java @@ -50,8 +50,9 @@ * * @param headerMerger The merged header and contents of readers. * @param forcePresorted True to ensure that the iterator checks the headers of the readers for appropriate sort order. - * @deprecated replaced by (SamFileHeaderMerger, Collection, boolean) + * @deprecated replaced by {@link #MergingSamRecordIterator(SamFileHeaderMerger, Collection, boolean)} */ + @Deprecated public MergingSamRecordIterator(final SamFileHeaderMerger headerMerger, final boolean forcePresorted) { this(headerMerger, headerMerger.getReaders(), forcePresorted); } diff --git a/src/main/java/htsjdk/samtools/SAMRecord.java b/src/main/java/htsjdk/samtools/SAMRecord.java index eb76c2841..dcd1a230b 100644 --- a/src/main/java/htsjdk/samtools/SAMRecord.java +++ b/src/main/java/htsjdk/samtools/SAMRecord.java @@ -985,9 +985,10 @@ public void setProperPairFlag(final boolean flag) { /** * the query sequence itself is unmapped. This method name is misspelled. - * Use setReadUnmappedFlag instead. + * Use {@link #setReadUnmappedFlag} instead. * @deprecated */ + @Deprecated public void setReadUmappedFlag(final boolean flag) { setReadUnmappedFlag(flag); } @@ -1648,8 +1649,9 @@ public int getAttributesBinarySize() { * * @return String representation of this. * @deprecated This method is not guaranteed to return a valid SAM text representation of the SAMRecord. - * To get standard SAM text representation, use htsjdk.samtools.SAMRecord#getSAMString(). + * To get standard SAM text representation, {@link SAMRecord#getSAMString}. */ + @Deprecated public String format() { final StringBuilder buffer = new StringBuilder(); addField(buffer, getReadName(), null, null); diff --git a/src/main/java/htsjdk/samtools/SAMSequenceRecord.java b/src/main/java/htsjdk/samtools/SAMSequenceRecord.java index cbc2b7a2b..6bca979cc 100644 --- a/src/main/java/htsjdk/samtools/SAMSequenceRecord.java +++ b/src/main/java/htsjdk/samtools/SAMSequenceRecord.java @@ -82,9 +82,10 @@ private SAMSequenceRecord() { } /** - * @deprecated Use SAMSequenceRecord(final String name, final int sequenceLength) instead. + * @deprecated Use {@link #SAMSequenceRecord(String, int)} instead. * sequenceLength is required for the object to be considered valid. */ + @Deprecated public SAMSequenceRecord(final String name) { this(name, UNKNOWN_SEQUENCE_LENGTH); } diff --git a/src/main/java/htsjdk/samtools/SAMUtils.java b/src/main/java/htsjdk/samtools/SAMUtils.java index c0432acc8..685cb025f 100644 --- a/src/main/java/htsjdk/samtools/SAMUtils.java +++ b/src/main/java/htsjdk/samtools/SAMUtils.java @@ -421,8 +421,9 @@ public static int fastqToPhred(final char ch) { * * @param beg 0-based start of read (inclusive) * @param end 0-based end of read (exclusive) - * @deprecated Use GenomicIndexUtil.regionToBin + * @deprecated Use {@link GenomicIndexUtil#regionToBin} */ + @Deprecated static int reg2bin(final int beg, final int end) { return GenomicIndexUtil.regionToBin(beg, end); } diff --git a/src/main/java/htsjdk/samtools/SamFileHeaderMerger.java b/src/main/java/htsjdk/samtools/SamFileHeaderMerger.java index b162cb2e6..b3f588caa 100644 --- a/src/main/java/htsjdk/samtools/SamFileHeaderMerger.java +++ b/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.SortOrder, boolean) + * @deprecated replaced by {@link #SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)} */ + @Deprecated public SamFileHeaderMerger(final Collection readers, final SAMFileHeader.SortOrder sortOrder) { this(readers, sortOrder, false); } @@ -135,8 +136,9 @@ public SamFileHeaderMerger(final Collection readers, final SAMFileHea * @param sortOrder sort order new header should have * @param mergeDictionaries If true, merge sequence dictionaries in new header. If false, require that * all input sequence dictionaries be identical. - * @deprecated replaced by SamFileHeaderMerger(Collection, SAMFileHeader.SortOrder, boolean) + * @deprecated replaced by {@link #SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)} */ + @Deprecated public SamFileHeaderMerger(final Collection readers, final SAMFileHeader.SortOrder sortOrder, final boolean mergeDictionaries) { this(sortOrder, getHeadersFromReaders(readers), mergeDictionaries); this.readers = readers; @@ -188,7 +190,7 @@ public SamFileHeaderMerger(final SAMFileHeader.SortOrder sortOrder, final Collec } } - // Utilility method to make use with old constructor + // Utility method to make use with old constructor private static List getHeadersFromReaders(final Collection readers) { final List headers = new ArrayList(readers.size()); for (final SamReader reader : readers) { @@ -585,7 +587,7 @@ private SAMSequenceDictionary mergeSequences(final SAMSequenceDictionary mergeIn // Since sequenceRecord already exists in resultingDict, don't need to add it. // Add in all the sequences prior to it that have been held in holder. resultingDict.addAll(loc, holder); - // Remember the index of sequenceRecord so can check for merge imcompatibility. + // Remember the index of sequenceRecord so can check for merge incompatibility. prevloc = loc + holder.size(); previouslyMerged = sequenceRecord; holder.clear(); @@ -622,12 +624,12 @@ private static int getIndexOfSequenceName(final List list, fi * @param masterDictionary the superset dictionary we've created. */ private void createSequenceMapping(final Collection headers, final SAMSequenceDictionary masterDictionary) { - final LinkedList resultingDictStr = new LinkedList(); + final LinkedList resultingDictStr = new LinkedList<>(); for (final SAMSequenceRecord r : masterDictionary.getSequences()) { resultingDictStr.add(r.getSequenceName()); } for (final SAMFileHeader header : headers) { - final Map seqMap = new HashMap(); + final Map seqMap = new HashMap<>(); final SAMSequenceDictionary dict = header.getSequenceDictionary(); for (final SAMSequenceRecord rec : dict.getSequences()) { seqMap.put(rec.getSequenceIndex(), resultingDictStr.indexOf(rec.getSequenceName())); @@ -640,8 +642,9 @@ private void createSequenceMapping(final Collection headers, fina /** * Returns the read group id that should be used for the input read and RG id. * - * @deprecated replaced by getReadGroupId(SAMFileHeader, String) + * @deprecated replaced by {@link #getReadGroupId(SAMFileHeader, String)} */ + @Deprecated public String getReadGroupId(final SamReader reader, final String originalReadGroupId) { return getReadGroupId(reader.getFileHeader(), originalReadGroupId); } @@ -655,8 +658,9 @@ public String getReadGroupId(final SAMFileHeader header, final String originalRe * @param reader one of the input files * @param originalProgramGroupId a program group ID from the above input file * @return new ID from the merged list of program groups in the output file - * @deprecated replaced by getProgramGroupId(SAMFileHeader, String) + * @deprecated replaced by {@link #getProgramGroupId(SAMFileHeader, String)} */ + @Deprecated public String getProgramGroupId(final SamReader reader, final String originalProgramGroupId) { return getProgramGroupId(reader.getFileHeader(), originalProgramGroupId); } @@ -693,8 +697,9 @@ public SAMFileHeader getMergedHeader() { /** * Returns the collection of readers that this header merger is working with. May return null. * - * @deprecated replaced by getHeaders() + * @deprecated replaced by {@link #getHeaders()} */ + @Deprecated public Collection getReaders() { return this.readers; } @@ -712,8 +717,9 @@ public SAMFileHeader getMergedHeader() { * @param reader the reader * @param oldReferenceSequenceIndex the old sequence (also called reference) index * @return the new index value - * @deprecated replaced by getMergedSequenceIndex(SAMFileHeader, Integer) + * @deprecated replaced by {@link #getMergedSequenceIndex(SAMFileHeader, Integer)} */ + @Deprecated public Integer getMergedSequenceIndex(final SamReader reader, final Integer oldReferenceSequenceIndex) { return this.getMergedSequenceIndex(reader.getFileHeader(), oldReferenceSequenceIndex); } @@ -745,7 +751,7 @@ public Integer getMergedSequenceIndex(final SAMFileHeader header, final Integer * Implementations of this interface are used by mergeHeaderRecords(..) to instantiate * specific subclasses of AbstractSAMHeaderRecord. */ - private static interface HeaderRecordFactory { + private interface HeaderRecordFactory { /** * Constructs a new instance of RecordType. @@ -753,7 +759,7 @@ public Integer getMergedSequenceIndex(final SAMFileHeader header, final Integer * @param id The id of the new record. * @param srcRecord Except for the id, the new record will be a copy of this source record. */ - public RecordType createRecord(final String id, RecordType srcRecord); + RecordType createRecord(final String id, RecordType srcRecord); } /** diff --git a/src/main/java/htsjdk/samtools/SamFileValidator.java b/src/main/java/htsjdk/samtools/SamFileValidator.java index 3a6deb028..fb559b0fb 100644 --- a/src/main/java/htsjdk/samtools/SamFileValidator.java +++ b/src/main/java/htsjdk/samtools/SamFileValidator.java @@ -588,8 +588,9 @@ public void setBisulfiteSequenced(boolean bisulfiteSequenced) { } /** - * @deprecated use setIndexValidationStringency instead + * @deprecated use {@link #setIndexValidationStringency} instead */ + @Deprecated public SamFileValidator setValidateIndex(final boolean validateIndex) { // The SAMFileReader must also have IndexCaching enabled to have the index validated, return this.setIndexValidationStringency(validateIndex ? IndexValidationStringency.EXHAUSTIVE : IndexValidationStringency.NONE); diff --git a/src/main/java/htsjdk/samtools/sra/SRAAccession.java b/src/main/java/htsjdk/samtools/sra/SRAAccession.java index 17180d771..9aeb10fe8 100644 --- a/src/main/java/htsjdk/samtools/sra/SRAAccession.java +++ b/src/main/java/htsjdk/samtools/sra/SRAAccession.java @@ -74,10 +74,11 @@ public static void setAppVersionString(String appVersionString) { } /** - * @deprecated * @return true if SRA successfully loaded native libraries and fully initialized, * false otherwise + * @deprecated use {@link #checkIfInitialized} instead */ + @Deprecated public static boolean isSupported() { return checkIfInitialized() == null; } diff --git a/src/main/java/htsjdk/samtools/util/TestUtil.java b/src/main/java/htsjdk/samtools/util/TestUtil.java index bbdf464d9..fd840d145 100644 --- a/src/main/java/htsjdk/samtools/util/TestUtil.java +++ b/src/main/java/htsjdk/samtools/util/TestUtil.java @@ -50,8 +50,9 @@ public static File getTempDirectory(final String prefix, final String suffix) { } /** - * @deprecated Use properly spelled method. + * @deprecated Use properly spelled method. {@link #getTempDirectory} */ + @Deprecated public static File getTempDirecory(final String prefix, final String suffix) { return getTempDirectory(prefix, suffix); }