java.lang.Object
- org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager

```
public class MultipleAlignmentCoordManager
extends Object
```
Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.

Author:

Aleix Lafita

Field Summary

Fields
Modifier and Type	Field	Description
`static int`	`DEFAULT_CHAR_SIZE`	Size per character
`static int`	`DEFAULT_LINE_LENGTH`	Number of chars per line
`static int`	`DEFAULT_LINE_SEPARATION`	Separation between sequences in the alignment
`static int`	`DEFAULT_RIGHT_SPACER`	Space on the right side between sequence and legend.
`static int`	`DEFAULT_X_SPACE`	Left boundary
`static int`	`DEFAULT_Y_SPACE`	Top boundary
`int`	`DEFAULT_Y_STEP`	Size of space between rows.
`static int`	`SUMMARY_POS`	Position at which the alignment summary is printed

Constructor Summary

Constructors
Constructor Description

MultipleAlignmentCoordManager(int size, int length)
Constructor.

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 size
`int`	`getPreferredWidth()`	X coordinate size
`int`	`getSeqPos(int aligSeq, Point p)`	Convert from an X position in the JPanel to the position in the sequence alignment.
`int`	`getSummaryPos()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - DEFAULT_RIGHT_SPACER
```
public static final int DEFAULT_RIGHT_SPACER
```
    Space on the right side between sequence and legend.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_LINE_LENGTH
```
public static final int DEFAULT_LINE_LENGTH
```
    Number of chars per line
    
    See Also:
    
    Constant Field Values
  - DEFAULT_Y_STEP
```
public final int DEFAULT_Y_STEP
```
    Size of space between rows. Depends on the number of structures aligned.
  - DEFAULT_CHAR_SIZE
```
public static final int DEFAULT_CHAR_SIZE
```
    Size per character
    
    See Also:
    
    Constant Field Values
  - DEFAULT_LINE_SEPARATION
```
public static final int DEFAULT_LINE_SEPARATION
```
    Separation between sequences in the alignment
    
    See Also:
    
    Constant Field Values
  - DEFAULT_X_SPACE
```
public static final int DEFAULT_X_SPACE
```
    Left boundary
    
    See Also:
    
    Constant Field Values
  - DEFAULT_Y_SPACE
```
public static final int DEFAULT_Y_SPACE
```
    Top boundary
    
    See Also:
    
    Constant Field Values
  - SUMMARY_POS
```
public static final int SUMMARY_POS
```
    Position at which the alignment summary is printed
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - MultipleAlignmentCoordManager
```
public MultipleAlignmentCoordManager(int size,
                                     int length)
```
    Constructor.
    
    Parameters:
    
    size - number of structures/sequences aligned (rows).
    
    length - number of aligned residues (columns)
- Method Detail
  - getSummaryPos
```
public int getSummaryPos()
```
  - getPreferredWidth
```
public int getPreferredWidth()
```
    X coordinate size
    
    Returns:
    
    the preferred width
  - getPreferredHeight
```
public int getPreferredHeight()
```
    Y coordinate size
    
    Returns:
    
    the preferred height
  - 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 number
    
    p - point on panel
    
    Returns:
    
    the sequence position for a point on the Panel
  - 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
  - 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
  - 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 Panel
    
    structure - the structure index
    
    Returns:
    
    get the point where to draw the legend
  - getEndLegendPosition
```
public Point getEndLegendPosition(int lineNr,
                                  int structure)
```

Class MultipleAlignmentCoordManager

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_RIGHT_SPACER

DEFAULT_LINE_LENGTH

DEFAULT_Y_STEP

DEFAULT_CHAR_SIZE

DEFAULT_LINE_SEPARATION

DEFAULT_X_SPACE

DEFAULT_Y_SPACE

SUMMARY_POS

Constructor Detail

MultipleAlignmentCoordManager

Method Detail

getSummaryPos

getPreferredWidth

getPreferredHeight

getSeqPos

getPanelPos

getAligSeq

getLegendPosition

getEndLegendPosition