Class MultipleAlignmentCoordManager
- java.lang.Object
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- org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
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public class MultipleAlignmentCoordManager extends Object
Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.- Author:
- Aleix Lafita
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_CHAR_SIZE
Size per characterstatic int
DEFAULT_LINE_LENGTH
Number of chars per linestatic int
DEFAULT_LINE_SEPARATION
Separation between sequences in the alignmentstatic int
DEFAULT_RIGHT_SPACER
Space on the right side between sequence and legend.static int
DEFAULT_X_SPACE
Left boundarystatic int
DEFAULT_Y_SPACE
Top boundaryint
DEFAULT_Y_STEP
Size of space between rows.static int
SUMMARY_POS
Position at which the alignment summary is printed
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Constructor Summary
Constructors Constructor Description MultipleAlignmentCoordManager(int size, int length)
Constructor.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description int
getAligSeq(Point point)
Returns the index of the structure, for a given point in the Panel.Point
getEndLegendPosition(int lineNr, int structure)
Point
getLegendPosition(int lineNr, int structure)
Provide the coordinates for where to draw the legend for line X given the structure index.Point
getPanelPos(int structure, int pos)
Get the X position on the Panel of a particular sequence position.int
getPreferredHeight()
Y coordinate sizeint
getPreferredWidth()
X coordinate sizeint
getSeqPos(int aligSeq, Point p)
Convert from an X position in the JPanel to the position in the sequence alignment.int
getSummaryPos()
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Field Detail
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DEFAULT_RIGHT_SPACER
public static final int DEFAULT_RIGHT_SPACER
Space on the right side between sequence and legend.- See Also:
- Constant Field Values
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DEFAULT_LINE_LENGTH
public static final int DEFAULT_LINE_LENGTH
Number of chars per line- See Also:
- Constant Field Values
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DEFAULT_Y_STEP
public final int DEFAULT_Y_STEP
Size of space between rows. Depends on the number of structures aligned.
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DEFAULT_CHAR_SIZE
public static final int DEFAULT_CHAR_SIZE
Size per character- See Also:
- Constant Field Values
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DEFAULT_LINE_SEPARATION
public static final int DEFAULT_LINE_SEPARATION
Separation between sequences in the alignment- See Also:
- Constant Field Values
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DEFAULT_X_SPACE
public static final int DEFAULT_X_SPACE
Left boundary- See Also:
- Constant Field Values
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DEFAULT_Y_SPACE
public static final int DEFAULT_Y_SPACE
Top boundary- See Also:
- Constant Field Values
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SUMMARY_POS
public static final int SUMMARY_POS
Position at which the alignment summary is printed- See Also:
- Constant Field Values
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Constructor Detail
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MultipleAlignmentCoordManager
public MultipleAlignmentCoordManager(int size, int length)
Constructor.- Parameters:
size
- number of structures/sequences aligned (rows).length
- number of aligned residues (columns)
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Method Detail
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getSummaryPos
public int getSummaryPos()
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getPreferredWidth
public int getPreferredWidth()
X coordinate size- Returns:
- the preferred width
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getPreferredHeight
public int getPreferredHeight()
Y coordinate size- Returns:
- the preferred height
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getSeqPos
public int getSeqPos(int aligSeq, Point p)
Convert from an X position in the JPanel to the position in the sequence alignment.- Parameters:
aligSeq
- sequence numberp
- point on panel- Returns:
- the sequence position for a point on the Panel
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getPanelPos
public Point getPanelPos(int structure, int pos)
Get the X position on the Panel of a particular sequence position.- Parameters:
structure
- index of the structure for the sequence position.pos
- sequence position, the aligned position index- Returns:
- the point on a panel for a sequence position
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getAligSeq
public int getAligSeq(Point point)
Returns the index of the structure, for a given point in the Panel. Returns -1 if not over a position in the sequence alignment.- Parameters:
point
- x and y coordinates in the panel- Returns:
- which structure a point on the panel corresponds to
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getLegendPosition
public Point getLegendPosition(int lineNr, int structure)
Provide the coordinates for where to draw the legend for line X given the structure index.- Parameters:
lineNr
- line of the Panelstructure
- the structure index- Returns:
- get the point where to draw the legend
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getEndLegendPosition
public Point getEndLegendPosition(int lineNr, int structure)
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