| add(ChromSegment segment) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| chromosome (defined in gov::lbl::genome::common::features::ChromSegment) | gov::lbl::genome::common::features::ChromSegment | [package] |
| ChromSegment(String inChromosome, long inStart, long inEnd, int rEnd) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| ChromSegment(String inChromosome, long inStart, long inEnd) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| ChromSegment(String inChrom, String inStart, String inEnd) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| ChromSegment(String inChrom, String neg, String inStart, String inEnd) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| ChromSegment(String inName, String inChromosome, long inStart, long inEnd) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| cloneSegment() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| compareTo(Object obj) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| contains(ChromSegment segment) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| contains(ChromPosition position) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| contains(long coordinate) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| Contig(String chrom, long start, long end) | gov::lbl::genome::common::features::Contig | [inline] |
| Contig(String chrom, long start, long end, boolean dir, int align, int base, int ds, int ctgId, String name, String dsChrom, long dsStart, long dsEnd, boolean dsStrand) | gov::lbl::genome::common::features::Contig | [inline] |
| end (defined in gov::lbl::genome::common::features::ChromSegment) | gov::lbl::genome::common::features::ChromSegment | [package] |
| getAlign() | gov::lbl::genome::common::features::Contig | [inline] |
| getBase() (defined in gov::lbl::genome::common::features::Contig) | gov::lbl::genome::common::features::Contig | [inline] |
| getChromName() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getChromosome() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getChromosome(boolean alter) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getContigName() | gov::lbl::genome::common::features::Contig | [inline] |
| getContigNum() | gov::lbl::genome::common::features::Contig | [inline] |
| getDir() | gov::lbl::genome::common::features::Contig | [inline] |
| getDs() | gov::lbl::genome::common::features::Contig | [inline] |
| getDsChrom() | gov::lbl::genome::common::features::Contig | [inline] |
| getDsEnd() | gov::lbl::genome::common::features::Contig | [inline] |
| getDsStart() | gov::lbl::genome::common::features::Contig | [inline] |
| getDsStrand() | gov::lbl::genome::common::features::Contig | [inline] |
| getEnd() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getName() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getPos() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getRealEnd() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getStart() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| getStrand() | gov::lbl::genome::common::features::Contig | [inline] |
| hashCode() (defined in gov::lbl::genome::common::features::ChromSegment) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| intersect(ChromSegment segment) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| isRealChrom() | gov::lbl::genome::common::features::ChromSegment | [inline] |
| parsePos(String pos) | gov::lbl::genome::common::features::ChromSegment | [inline, static] |
| parseSpan(String span) | gov::lbl::genome::common::features::ChromSegment | [inline, static] |
| positionFormat(String pos) | gov::lbl::genome::common::features::ChromSegment | [inline, static] |
| realChrom (defined in gov::lbl::genome::common::features::ChromSegment) | gov::lbl::genome::common::features::ChromSegment | [package] |
| realEnd (defined in gov::lbl::genome::common::features::ChromSegment) | gov::lbl::genome::common::features::ChromSegment | [package] |
| setChromosome(int chromosome) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| setChromosome(String chromosome) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| setDsEnd(long dsEnd) | gov::lbl::genome::common::features::Contig | [inline] |
| setDsStart(long dsStart) | gov::lbl::genome::common::features::Contig | [inline] |
| setEnd(long end) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| setRealChrom(boolean realChrom) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| setStart(long start) | gov::lbl::genome::common::features::ChromSegment | [inline] |
| start (defined in gov::lbl::genome::common::features::ChromSegment) | gov::lbl::genome::common::features::ChromSegment | [package] |
| toString() | gov::lbl::genome::common::features::Contig | [inline] |
| toString(long offset) | gov::lbl::genome::common::features::Contig | [inline] |
| touches(ChromSegment segment) | gov::lbl::genome::common::features::ChromSegment | [inline] |
