|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectbaobab.bio.permutation.PermutationBPGraphFormatter
public class PermutationBPGraphFormatter
The PermutationBPGraphFormatter class gives a text representation of a breakpoint graph
Method Summary | |
---|---|
java.lang.String |
getCanonizedString()
Generates a one-line string representation of a permutation |
java.lang.String |
getHighlightedString(boolean isCanonized,
int start,
int end)
|
java.lang.String |
getHighlightedString(boolean isCanonized,
int start,
int middle,
int end)
|
java.lang.String |
getHighlightedString(int start,
int end)
Generates a two-lines string representation of a permutation |
java.lang.String |
getHighlightedString(int start,
int middle,
int end)
Generates a two-lines string representation of a permutation |
java.lang.String |
getIndexedCycledString()
Generates a four-lines string representation of a permutation (... represents an adjacency) |
java.lang.String |
getIndexedCycledString(boolean isCanonized)
|
java.lang.String |
getIndexedHighlightedCycledString(boolean isCanonized,
int start,
int end)
|
java.lang.String |
getIndexedHighlightedCycledString(boolean isCanonized,
int start,
int middle,
int end)
|
java.lang.String |
getIndexedHighlightedCycledString(int start,
int end)
Generates a five-lines string representation of a permutation (... represents an adjacency) |
java.lang.String |
getIndexedHighlightedCycledString(int start,
int middle,
int end)
Generates a five-lines string representation of a permutation (... represents an adjacency) |
java.lang.String |
getIndexedHighlightedString(boolean isCanonized,
int start,
int end)
|
java.lang.String |
getIndexedHighlightedString(boolean isCanonized,
int start,
int middle,
int end)
|
java.lang.String |
getIndexedHighlightedString(int start,
int end)
Generates a three-lines string representation of a permutation |
java.lang.String |
getIndexedHighlightedString(int start,
int middle,
int end)
Generates a three-lines string representation of a permutation |
java.lang.String |
getIndexedString()
Generates a two-lines string representation of a permutation |
java.lang.String |
getIndexedString(boolean isCanonized)
|
PermutationBPGraph |
getPermutation()
|
java.lang.String |
getSimpleMappedString()
Generates a one-line string representation of a permutation with its (mapped) values |
java.lang.String |
getString()
Generates a one-line string representation of a permutation |
java.lang.String |
reversalToCanonizedString(int start,
int end)
|
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
---|
public PermutationBPGraph getPermutation()
public java.lang.String reversalToCanonizedString(int start, int end)
public java.lang.String getCanonizedString()
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, we have
:: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles
public java.lang.String getString()
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, we have
:: -4 -3 +12 -11 -8 +10 +9 +7 -6 -5 +2 -1 :: 5 cycles
public java.lang.String getIndexedString()
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, we have
01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index) :: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles
public java.lang.String getIndexedString(boolean isCanonized)
public java.lang.String getHighlightedString(int start, int end)
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, highlighting positions from 9 to 11 makes:
:: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles -------- (from [9] to [11]) 01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index, only as reference)
start
- the beggining of the block to be highlightedend
- the end of the block to be highlighted
public java.lang.String getHighlightedString(boolean isCanonized, int start, int end)
public java.lang.String getHighlightedString(int start, int middle, int end)
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, highlighting positions from 1 to 5, with middle at position 2 makes:
:: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles ---|------------ (from [1] to [2] to [5]) 01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index, only as reference)
start
- the beggining of the block to be highlightedmiddle
- the middle of the block to be highlightedend
- the end of the block to be highlighted
public java.lang.String getHighlightedString(boolean isCanonized, int start, int middle, int end)
public java.lang.String getIndexedHighlightedString(int start, int end)
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, highlighting positions from 9 to 11 makes:
01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index) :: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles -------- (from [9] to [11])
start
- the beggining of the block to be highlightedend
- the end of the block to be highlighted
public java.lang.String getIndexedHighlightedString(boolean isCanonized, int start, int end)
public java.lang.String getIndexedHighlightedCycledString(int start, int end)
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, highlighting positions from 9 to 11 makes:
01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index) 01> ... 01> <01 03> <02 <03 <02 02> ... 01> <01 <01 (the cycle numbers, with black edge directions) :13 ... :12 :03 :07 :09 :05 :06 :08 ... :01 :11 :04 (each cycle tour in an arbitrary direction) :: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles -------- (from [9] to [11])
start
- the beggining of the block to be highlightedend
- the end of the block to be highlighted
public java.lang.String getIndexedHighlightedCycledString(boolean isCanonized, int start, int end)
public java.lang.String getIndexedHighlightedString(int start, int middle, int end)
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, highlighting positions from 1 to 5, with middle at position 2 makes:
01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index) :: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles ---|------------ (from [1] to [2] to [5])
start
- the beggining of the block to be highlightedmiddle
- the middle of the block to be highlightedend
- the end of the block to be highlighted
public java.lang.String getIndexedHighlightedString(boolean isCanonized, int start, int middle, int end)
public java.lang.String getIndexedHighlightedCycledString(int start, int middle, int end)
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, highlighting positions from 1 to 5, with middle at position 2 makes:
01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (position index) 01> ... 01> <01 03> <02 <03 <02 02> ... 01> <01 <01 (the cycle numbers, with black edge directions) :13 ... :12 :03 :07 :09 :05 :06 :08 ... :01 :11 :04 (each cycle tour in an arbitrary direction) :: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles ---|------------ (from [1] to [2] to [5])
start
- the beggining of the block to be highlightedmiddle
- the middle of the block to be highlightedend
- the end of the block to be highlighted
public java.lang.String getIndexedHighlightedCycledString(boolean isCanonized, int start, int middle, int end)
public java.lang.String getIndexedCycledString()
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, we have
01. 02. 03. 04. 05. 06. 07. 08. 09. 10. 11. 12. 13. (index) 01> ... 01> <01 03> <02 <03 <02 02> ... 01> <01 <01 (the cycle numbers, with black edge directions) :13 ... :12 :03 :07 :09 :05 :06 :08 ... :01 :11 :04 (each cycle tour in an arbitrary direction) :: -04 -03 +12 -11 -08 +10 +09 +07 -06 -05 +02 -01 :: 5 cycles
public java.lang.String getIndexedCycledString(boolean isCanonized)
public java.lang.String getSimpleMappedString()
Example: for the permutation -4,-3,12,-11,-8,9,7,-6,-5,2,-1, we have
-4.-3.12.-11.-8.10.9.7.-6.-5.2.-1
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |