AlignmentContentArea

java.lang.Object
- info.bioinfweb.tic.TICComponent
- - info.bioinfweb.libralign.alignmentarea.content.AlignmentContentArea

```
public class AlignmentContentArea
extends TICComponent
```
Toolkit independent component displaying the contents (not the labels) of a single alignment and its attached data areas.
This component is used a child component of AlignmentArea and in contrast to AlignmentArea does not contain a scroll container, but acts as the scrolled component. Application developers will not need to create instances of this class directly but should use AlignmentArea.

Since:

0.3.0

Author:

Ben Stöver

See Also:

AlignmentArea, AlignmentLabelArea

Field Summary
- Fields inherited from class info.bioinfweb.tic.TICComponent
  DISPATCHER_MAP, repaintRequested

Constructor Summary

Constructors
Constructor and Description

AlignmentContentArea(AlignmentArea owner)
Creates a new instance of this class.

Constructors
Constructor and Description
`AlignmentContentArea(AlignmentArea owner)` Creates a new instance of this class.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`columnByPaintX(double x)` Returns the column containing the specified x coordinate.
`java.util.Map<javax.swing.KeyStroke,javax.swing.Action>`	`getActionMap()`
`AlignmentSubArea`	`getAreaByPaintY(double y)` Returns the child component containing the specified y-coordinate.
`AlignmentSubAreaInfo`	`getAreaInfoByPaintY(double y)` Returns the child component containing the specified y-coordinate and its top most y-coordinate in an instance of `AlignmentSubAreaInfo`.
`java.awt.geom.Rectangle2D`	`getCursorRectangle()` Returns the rectangle in the paint coordinate system of scrolled area displaying the sequences, that contains all cells currently occupied by the alignment cursor.
`AlignmentArea`	`getOwner()`
`SequenceArea`	`getSequenceAreaByID(java.lang.String sequenceID)` Returns the `SequenceArea` inside this area that displays the sequence with the specified ID.
`SequenceArea`	`getSequenceAreaByRow(int row)` Returns the `SequenceArea` inside this area that displays the sequence in the specified row.
`protected SequenceAreaMap`	`getSequenceAreaMap()`
`java.awt.Dimension`	`getSize()`
`protected java.lang.String`	`getSwingComponentClassName(java.lang.Object... parameters)`
`protected java.lang.String`	`getSWTComponentClassName(java.lang.Object... parameters)`
`ToolkitSpecificAlignmentContentArea`	`getToolkitComponent()`
`void`	`paint(TICPaintEvent event)` Paints the contents (sequences and data areas) of an alignment, if this instance is set to use direct painting.
`double`	`paintXByColumn(int column)` Returns the left most x-coordinate of the area the specified column is painted in relative to the component on which the sequences are painted.
`double`	`paintYByRow(int row)` Returns the top most y-coordinate of the area the specified row is painted in relative to the component on which the sequences are painted.
`int`	`rowByPaintY(double y)` Returns the row index of the sequence displayed at the specified y coordinate considering the current order of sequences.
`AlignmentSubAreaIterator`	`subAreaIterator()`
`void`	`updateSubelements()`

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

- Constructor Detail
  - AlignmentContentArea
```
public AlignmentContentArea(AlignmentArea owner)
```
    Creates a new instance of this class.
    If code is part of a MultipleAlignmentsContainer the shared edit settings of this container will automatically be used by the returned instance.
    
    Parameters:
    
    owner - the alignment area component that will be containing the return instance
- Method Detail
  - getOwner
```
public AlignmentArea getOwner()
```
  - subAreaIterator
```
public AlignmentSubAreaIterator subAreaIterator()
```
  - getSequenceAreaMap
```
protected SequenceAreaMap getSequenceAreaMap()
```
  - getSequenceAreaByID
```
public SequenceArea getSequenceAreaByID(java.lang.String sequenceID)
```
    Returns the SequenceArea inside this area that displays the sequence with the specified ID.
    
    Parameters:
    
    sequenceID - the ID of the sequence displayed in the returned area
    
    Returns:
    
    the sequence area or null if no sequence with the specified ID is displayed in this area
  - getSequenceAreaByRow
```
public SequenceArea getSequenceAreaByRow(int row)
```
    Returns the SequenceArea inside this area that displays the sequence in the specified row.
    
    Parameters:
    
    row - the row of the sequence displayed in the returned area
    
    Returns:
    
    the sequence area
    
    Throws:
    
    java.lang.IndexOutOfBoundsException - if the specified row is below 0 or greater or equal to number of sequences
  - getActionMap
```
public java.util.Map<javax.swing.KeyStroke,javax.swing.Action> getActionMap()
```
  - updateSubelements
```
public void updateSubelements()
```
  - getCursorRectangle
```
public java.awt.geom.Rectangle2D getCursorRectangle()
```
    Returns the rectangle in the paint coordinate system of scrolled area displaying the sequences, that contains all cells currently occupied by the alignment cursor.
    If the last row has associated data areas, the height of these areas is also included in the rectangle.
    
    Returns:
    
    a rectangle with paint coordinates
  - getSize
```
public java.awt.Dimension getSize()
```
    Overrides:
    
    getSize in class TICComponent
  - paint
```
public void paint(TICPaintEvent event)
```
    Paints the contents (sequences and data areas) of an alignment, if this instance is set to use direct painting. This method is not used, if the instance is set to use subcomponents for each sequence and data area.
    
    Overrides:
    
    paint in class TICComponent
    
    See Also:
    
    TICComponent.paint(info.bioinfweb.tic.TICPaintEvent)
  - getToolkitComponent
```
public ToolkitSpecificAlignmentContentArea getToolkitComponent()
```
    Overrides:
    
    getToolkitComponent in class TICComponent
  - getSwingComponentClassName
```
protected java.lang.String getSwingComponentClassName(java.lang.Object... parameters)
```
    Overrides:
    
    getSwingComponentClassName in class TICComponent
  - getSWTComponentClassName
```
protected java.lang.String getSWTComponentClassName(java.lang.Object... parameters)
```
    Overrides:
    
    getSWTComponentClassName in class TICComponent
  - columnByPaintX
```
public int columnByPaintX(double x)
```
    Returns the column containing the specified x coordinate. If the coordinate lies behind the last column, the number of columns + 1 is returned.
    
    Parameters:
    
    x - the paint coordinate
    
    Returns:
    
    the alignment column
  - paintXByColumn
```
public double paintXByColumn(int column)
```
    Returns the left most x-coordinate of the area the specified column is painted in relative to the component on which the sequences are painted. Use this method to convert between cell indices and paint coordinates. This method takes the current horizontal zoom factor into account.
    
    Parameters:
    
    column - the column painted at the returned x-position
    
    Returns:
    
    a value >= 0
  - getAreaByPaintY
```
public AlignmentSubArea getAreaByPaintY(double y)
```
    Returns the child component containing the specified y-coordinate.
    
    Parameters:
    
    y - the y-coordinate relative to this alignment content area
    
    Returns:
    
    the sequence or data area at the specified position or null if y is below 0 or higher than this instance
  - getAreaInfoByPaintY
```
public AlignmentSubAreaInfo getAreaInfoByPaintY(double y)
```
    Returns the child component containing the specified y-coordinate and its top most y-coordinate in an instance of AlignmentSubAreaInfo.
    
    Parameters:
    
    y - the y-coordinate relative to this alignment content area
    
    Returns:
    
    the info object or null if y is below 0 or higher than this instance
  - rowByPaintY
```
public int rowByPaintY(double y)
```
    Returns the row index of the sequence displayed at the specified y coordinate considering the current order of sequences. If a data area is displayed at the specified position, the row of the associated sequence is returned anyway.
    
    Parameters:
    
    y - the y coordinate relative to the alignment part area containing the sequence areas
    
    Returns:
    
    a valid sequence position.
  - paintYByRow
```
public double paintYByRow(int row)
```
    Returns the top most y-coordinate of the area the specified row is painted in relative to the component on which the sequences are painted. Use this method to convert between cell indices and paint coordinates.
    If an index lower than zero or greater than the highest index is specified the y-coordinate of the first or the last sequence is returned accordingly.
    
    Parameters:
    
    row - the row painted at the returned x-position
    
    Returns:
    
    a value >= 0

Class AlignmentContentArea

Field Summary

Fields inherited from class info.bioinfweb.tic.TICComponent

Constructor Summary

Method Summary

Methods inherited from class info.bioinfweb.tic.TICComponent

Methods inherited from class java.lang.Object

Constructor Detail

AlignmentContentArea

Method Detail

getOwner

subAreaIterator

getSequenceAreaMap

getSequenceAreaByID

getSequenceAreaByRow

getActionMap

updateSubelements

getCursorRectangle

getSize

paint

getToolkitComponent

getSwingComponentClassName

getSWTComponentClassName

columnByPaintX

paintXByColumn

getAreaByPaintY

getAreaInfoByPaintY

rowByPaintY

paintYByRow