| 532 |
|
|
| 533 |
|
/** |
| 534 |
|
* Gets list of consecutive non-gapped sub-sequences (by means of an interval set). |
| 535 |
< |
* Example (X-denote any valid atomic sequence component): |
| 535 |
> |
* Example (X denotes any valid aminoacid): |
| 536 |
|
* <p> |
| 537 |
|
* |
| 538 |
|
* The data:<br> |
| 552 |
|
* <code>tagSet1[0] = "s1";</code><br> |
| 553 |
|
* <code>tagSet2[0] = "s2";</code><br> |
| 554 |
|
* <code>tagSet2[1] = "s3";</code><br> |
| 555 |
< |
* <code>System.out.println(ali.getConsecutiveChunks("s2",tagSet1));</code><br> |
| 556 |
< |
* <code>System.out.println(ali.getConsecutiveChunks("s1",tagSet2));</code><br> |
| 555 |
> |
* <code>System.out.println(ali.getMatchingBlocks("s2",tagSet1));</code><br> |
| 556 |
> |
* <code>System.out.println(ali.getMatchingBlocks("s1",tagSet2));</code><br> |
| 557 |
|
* <p> |
| 558 |
|
* The output:<br> |
| 559 |
|
* <code>[0 6, 7 9]</code><br> |
| 560 |
|
* <code>[0 2, 3 5, 6 6, 7 7]</code><br> |
| 561 |
|
* |
| 562 |
< |
* @param tag tag of the sequence of which the chunk list is be determined |
| 562 |
> |
* @param tag tag of the sequence of which the chunk list is to be determined |
| 563 |
|
* @param projectionTags list of tags of sequences in the alignment whose |
| 564 |
|
* projection along with sequence named tag is to be used as projection |
| 565 |
|
* from the whole alignment. Note, that invoking this function with |
| 566 |
|
* {@link #getTags()} set to this parameter, considers the whole alignment |
| 567 |
|
* matrix. |
| 568 |
+ |
* @param begin |
| 569 |
+ |
* @param end |
| 570 |
+ |
* @param degOfConservation |
| 571 |
|
* |
| 572 |
< |
* @return edge set representing the sequence of non-gapped sequence chunks, |
| 572 |
> |
* @return interval set representing the sequence of non-gapped sequence chunks, |
| 573 |
|
* where for each edge in the set Edge.i denotes the starting position and |
| 574 |
|
* Edge.j the ending position of a chunk, i.e., for a separated atomic |
| 575 |
|
* sequence component (e.g., between two gaps) this notion yields i == j. |
| 638 |
|
* |
| 639 |
|
* @param tag |
| 640 |
|
* @param projectionTags |
| 641 |
< |
* @param positions |
| 641 |
> |
* @param positions alignment columns for which we want to get the 2 matching interval sets |
| 642 |
|
* @param degOfConservation |
| 643 |
|
* @return The indexing respects the sequence indexing for this class, i.e., index 1 corresponds to the first position in the sequence. |
| 644 |
|
* @throws IndexOutOfBoundsException |
