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java.lang.Objectuk.ac.vamsas.objects.utils.Mapping
Constructor Summary | |
Mapping(int[] local,
int[] mapped,
int i,
int j)
create a new mapping from (in Jalview) param to was the destination sequence being mapped |
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Mapping(MapList map)
The seuqence that map maps the associated seuqence to (if any). |
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Mapping(Mapping map2)
create a duplicate (and independent) mapping object with the same reference to any SequenceI being mapped to. |
Method Summary | |
boolean |
equals(Mapping other)
Equals that compares both the to references and MapList mappings. |
MapList |
getMap()
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int |
getMappedPosition(int pos)
get mapped position in the associated reference frame for position pos in the associated sequence. |
int |
getMappedWidth()
width of unit in mapped reference frame |
int[] |
getMappedWord(int pos)
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int |
getPosition(int mpos)
get the 'initial' position in the associated sequence for a position in the mapped reference frame |
int |
getWidth()
width of mapped unit in associated sequence |
int[] |
getWord(int mpos)
gets boundary in direction of mapping |
Mapping |
intersectVisContigs(int[] viscontigs)
return a new mapping object with a maplist modifed to only map the visible regions defined by viscontigs. |
int[] |
locateFeature(int begin,
int end)
locates the region of feature f in the associated (local) sequence's reference frame |
int[] |
locateMappedRange(int from,
int to)
return a series of mapped contigs mapped from a range on the associated sequence |
int[] |
locateRange(int from,
int to)
return a series of contigs on the associated sequence corresponding to the from,to interval on the mapped reference frame |
static void |
main(java.lang.String[] args)
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void |
setMap(MapList map)
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Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public Mapping(MapList map)
public Mapping(int[] local, int[] mapped, int i, int j)
local
- int[] {start,end,start,end} series on associated sequencemapped
- int[] {start,end,...} ranges on the reference frame being mapped
toi
- step size on associated sequencej
- step size on mapped framepublic Mapping(Mapping map2)
map2
- Method Detail |
public MapList getMap()
public void setMap(MapList map)
map
- the map to setpublic boolean equals(Mapping other)
other
-
public int getPosition(int mpos)
mpos
-
public int[] getWord(int mpos)
public int getWidth()
public int getMappedWidth()
public int getMappedPosition(int pos)
pos
-
public int[] getMappedWord(int pos)
public int[] locateFeature(int begin, int end)
public int[] locateRange(int from, int to)
from
- to
-
public int[] locateMappedRange(int from, int to)
from
- to
-
public Mapping intersectVisContigs(int[] viscontigs)
viscontigs
-
public static void main(java.lang.String[] args)
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