| Modifier and Type | Field and Description |
|---|---|
| private final @NotNull BasedSequence | |
| private final @NotNull BasedSequence | |
| private final @NotNull HashMap | |
| private @Nullable BasedSequence | |
| private final BasedSegmentBuilder |
| Access | Constructor and Description |
|---|---|
| private | SequenceBuilder(@NotNull BasedSequence
base sequence for which to create a builder base, @Nullable SegmentOptimizer optimizer for based segment builder, or default optimizer)CharRecoveryOptimizerConstruct a base sequence builder for given base sequence with default options. |
| private | SequenceBuilder(@NotNull BasedSequence base, @Nullable SegmentOptimizer optimizer, @NotNull HashMap<BasedSequence, Boolean> equivalentBases)
|
| private | SequenceBuilder(@NotNull BasedSequence
base sequence for which to create a builder base, int builder options options, @Nullable SegmentOptimizer optimizer for based segment builder, or default optimizer, @NotNull HashMap<BasedSequence, Boolean> equivalentBases)CharRecoveryOptimizerConstruct a base sequence builder for given base sequence with specific options. |
| Modifier and Type | Method and Description |
|---|---|
| public @NotNull SequenceBuilder | |
| public @NotNull SequenceBuilder | |
| public @NotNull SequenceBuilder | |
| public @NotNull SequenceBuilder | append(@Nullable CharSequence
The character sequence from which a subsequence will be
appended. If chars, int csq is null, then characters
will be appended as if csq contained the four
characters "null".The index of the first character in the subsequence startIndex, int The index of the character following the last character in the
subsequence endIndex)Implements java. Appends a subsequence of the specified character sequence to this
|
| public @NotNull SequenceBuilder | append(char
The character to append c)Implements com. Appends the specified character to this |
| public @NotNull SequenceBuilder | append(char c, int count)
Implements com.
|
| public @NotNull SequenceBuilder | |
| public @NotNull SequenceBuilder | |
| public char | |
| public static @NotNull SequenceBuilder | |
| public static @NotNull SequenceBuilder | |
| public static @NotNull SequenceBuilder | |
| public static @NotNull SequenceBuilder | |
| public @NotNull BasedSequence | |
| public @NotNull SequenceBuilder | |
| public @Nullable Range | |
| public @NotNull BasedSegmentBuilder | |
| public @Nullable BasedSequence | getSingleBasedSequence()
Implements com. Note returns non-null value if the underlying |
| pack-priv boolean | |
| public int | |
| public @NotNull BasedSequence | |
| public @NotNull BasedSequence | Returns: builder with offsets mapped to altSequencebased sequence which is character identical to this builder's baseSeq altSequence)Construct sequence from this builder using another based sequence which is character identical to this builder's baseSeq |
| public @NotNull BasedSequence | Returns: builder with offsets mapped to altSequencebased sequence which is character identical to this builder's baseSeq altSequence, @Nullable CharPredicate character set of characters to trim trimStart, @Nullable CharPredicate chars which should be treated as equivalent for verification purposes (Space, Tab, EOL, usually) ignoreCharDiff)Construct sequence from this builder using another based sequence which is character identical to this builder's baseSeq |
| public @NotNull BasedSequence | Returns: builder with offsets mapped to altSequencebased sequence which is character identical to this builder's baseSeq altSequence, @Nullable CharPredicate character set of characters to trim trimStart, @Nullable CharPredicate chars which should be treated as equivalent for verification purposes (Space, Tab, EOL, usually) ignoreCharDiff)Construct sequence from this builder using another based sequence which is character identical to this builder's baseSeq by length |
| public @NotNull String | |
| public @NotNull String | |
| public @NotNull String | |
| public @NotNull String |
| altBase | back to summary |
|---|---|
| private final @NotNull BasedSequence altBase
| |
| baseSeq | back to summary |
|---|---|
| private final @NotNull BasedSequence baseSeq
| |
| equivalentBases | back to summary |
|---|---|
| private final @NotNull HashMap<BasedSequence, Boolean> equivalentBases
| |
| resultSeq | back to summary |
|---|---|
| private @Nullable BasedSequence resultSeq
| |
| segments | back to summary |
|---|---|
| private final BasedSegmentBuilder segments | |
| SequenceBuilder | back to summary |
|---|---|
| private SequenceBuilder(@NotNull BasedSequence base, @Nullable SegmentOptimizer optimizer) Construct a base sequence builder for given base sequence with default options. Note the builder is always constructed for the base sequence of the base.
ie. for the based sequence returned by
| |
| SequenceBuilder | back to summary |
|---|---|
| private SequenceBuilder(@NotNull BasedSequence base, @Nullable SegmentOptimizer optimizer, @NotNull HashMap<BasedSequence, Boolean> equivalentBases) | |
| SequenceBuilder | back to summary |
|---|---|
| private SequenceBuilder(@NotNull BasedSequence base, int options, @Nullable SegmentOptimizer optimizer, @NotNull HashMap<BasedSequence, Boolean> equivalentBases) Construct a base sequence builder for given base sequence with specific options. Note the builder is always constructed for the base sequence of the base.
ie. for the based sequence returned by
| |
| addByLength | back to summary |
|---|---|
public @NotNull SequenceBuilder addByLength(int startOffset, int textLength)
| |
| addByOffsets | back to summary |
|---|---|
public @NotNull SequenceBuilder addByOffsets(int startOffset, int endOffset)
| |
| addRange | back to summary |
|---|---|
public @NotNull SequenceBuilder addRange(@NotNull Range range)
| |
| append | back to summary |
|---|---|
| public @NotNull SequenceBuilder append(@Nullable CharSequence chars, int startIndex, int endIndex) Implements java. Doc from java. Appends a subsequence of the specified character sequence to this
An invocation of this method of the form
out.append(csq.subSequence(start, end))
The contents of this
| |
| append | back to summary |
|---|---|
| public @NotNull SequenceBuilder append(char c) Implements com. Doc from java. Appends the specified character to this
| |
| append | back to summary |
|---|---|
| public @NotNull SequenceBuilder append(char c, int count) Implements com.
| |
| append | back to summary |
|---|---|
public @NotNull SequenceBuilder append(int startOffset, int endOffset)
| |
| append | back to summary |
|---|---|
public @NotNull SequenceBuilder append(@NotNull Range chars)
| |
| charAt | back to summary |
|---|---|
| public char charAt(int index) Implements com.
| |
| emptyBuilder | back to summary |
|---|---|
public static @NotNull SequenceBuilder emptyBuilder(@NotNull BasedSequence base)
| |
| emptyBuilder | back to summary |
|---|---|
public static @NotNull SequenceBuilder emptyBuilder(@NotNull BasedSequence base, @NotNull SegmentOptimizer optimizer)
| |
| emptyBuilder | back to summary |
|---|---|
public static @NotNull SequenceBuilder emptyBuilder(@NotNull BasedSequence base, int options)
| |
| emptyBuilder | back to summary |
|---|---|
public static @NotNull SequenceBuilder emptyBuilder(@NotNull BasedSequence base, int options, @NotNull SegmentOptimizer optimizer)
| |
| getBaseSequence | back to summary |
|---|---|
public @NotNull BasedSequence getBaseSequence()
| |
| getBuilder | back to summary |
|---|---|
| public @NotNull SequenceBuilder getBuilder() Implements com. | |
| getLastRangeOrNull | back to summary |
|---|---|
public @Nullable Range getLastRangeOrNull()
| |
| getSegmentBuilder | back to summary |
|---|---|
public @NotNull BasedSegmentBuilder getSegmentBuilder()
| |
| getSingleBasedSequence | back to summary |
|---|---|
| public @Nullable BasedSequence getSingleBasedSequence() Implements com. Doc from com. Note returns non-null value if the underlying
| |
| isCommonBaseSequence | back to summary |
|---|---|
| pack-priv boolean isCommonBaseSequence(@NotNull BasedSequence chars) | |
| length | back to summary |
|---|---|
| public int length() Implements com.
| |
| toSequence | back to summary |
|---|---|
| public @NotNull BasedSequence toSequence() Implements com. | |
| toSequence | back to summary |
|---|---|
| public @NotNull BasedSequence toSequence(@NotNull BasedSequence altSequence) Construct sequence from this builder using another based sequence which is character identical to this builder's baseSeq
| |
| toSequence | back to summary |
|---|---|
| public @NotNull BasedSequence toSequence(@NotNull BasedSequence altSequence, @Nullable CharPredicate trimStart, @Nullable CharPredicate ignoreCharDiff) Construct sequence from this builder using another based sequence which is character identical to this builder's baseSeq
| |
| toSequenceByIndex | back to summary |
|---|---|
| public @NotNull BasedSequence toSequenceByIndex(@NotNull BasedSequence altSequence, @Nullable CharPredicate trimStart, @Nullable CharPredicate ignoreCharDiff) Construct sequence from this builder using another based sequence which is character identical to this builder's baseSeq by length
| |
| toString | back to summary |
|---|---|
| public @NotNull String toString() Overrides java. Doc from java. Returns a string representation of the object.
Satisfying this method's contract implies a non- | |
| toStringNoAddedSpaces | back to summary |
|---|---|
public @NotNull String toStringNoAddedSpaces()
| |
| toStringWithRanges | back to summary |
|---|---|
public @NotNull String toStringWithRanges()
| |
| toStringWithRanges | back to summary |
|---|---|
public @NotNull String toStringWithRanges(boolean toVisibleWhiteSpace)
| |