charite.christo.protein
Class Gaps2Columns

java.lang.Object
  charite.christo.protein.Gaps2Columns

public class Gaps2Columns
extends java.lang.Object

HELP When there are gaps occurring in all loaded sequences at the same position they are usually not displayed.
Consider the following case:

ASGATA  YTG
ATGATG  YTA
ASGGTAG FSG
       ^

This is a common gap which is not displayed. The view shows:

ASGATA YTG
ATGATG YTA
ASGGTAGFSG

When the sequence "ASGGTAGAFSG" was added to the multiple sequence alignment the gap would not be a common gap any more and would become visible. In the multiple sequence alignment panel is the following:

ASGATA  YTG
ATGATG  YTA
ASGGTAG FSG
ASGGTAGAFSG

This is the reason for the following phenomenon: When gaps are added to one sequence it might seem that gaps are erased in all other sequences instead.

Constructor Summary

Gaps2Columns()

Method Summary

static int[]	computeColumns(int[] wide2narrow, int[] gaps, int nRes, int[] oldCols)
int[]	computeWide2narrow(Protein[] pp) Calculates the horizontal position (column) of all residues in the alignment.
int	countColumns()
static int	eliminateCommonGaps(Protein[] pp, int fromCol, int toCol)
boolean	isWide()
int	modificationCount()
int[]	narrow2wideColumn()
void	setInvalid()
void	setProteinsV(java.util.List<Protein> v)
void	setWide(boolean b)
int[]	wide2narrowColumn()
int[]	wide2narrowColumn(Protein[] pp)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Gaps2Columns

public Gaps2Columns()

Method Detail

setProteinsV

public void setProteinsV(java.util.List<Protein> v)

setWide

public void setWide(boolean b)

countColumns

public int countColumns()

isWide

public boolean isWide()

modificationCount

public int modificationCount()

setInvalid

public void setInvalid()

computeWide2narrow

public int[] computeWide2narrow(Protein[] pp)

Calculates the horizontal position (column) of all residues in the alignment. from the number of gaps of each residue Used for the default modus where redundant gaps are suppressed.

wide2narrowColumn

public int[] wide2narrowColumn()

wide2narrowColumn

public int[] wide2narrowColumn(Protein[] pp)

narrow2wideColumn

public int[] narrow2wideColumn()

computeColumns

public static int[] computeColumns(int[] wide2narrow,
                                   int[] gaps,
                                   int nRes,
                                   int[] oldCols)

eliminateCommonGaps

public static int eliminateCommonGaps(Protein[] pp,
                                      int fromCol,
                                      int toCol)