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java.lang.Objectjava.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JPanel
org.biojava.bio.structure.gui.JMatrixPanel
public class JMatrixPanel
a JPanel that can display a difference of distance matrix and paths that have been taken for the alignment
Note: This panel displays the transpose of its underlying matrix.
Thus its width will be the same as Matrix.getRowDimension()
and its
height the same as Matrix.getColumnDimension()
. This stems from the
unfortunate ordering of Matrix.get(int, int)
parameters as (row, col),
which is opposite from the normal (x,y) order used when displaying graphics.
Nested Class Summary |
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Nested classes/interfaces inherited from class javax.swing.JPanel |
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JPanel.AccessibleJPanel |
Nested classes/interfaces inherited from class javax.swing.JComponent |
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JComponent.AccessibleJComponent |
Nested classes/interfaces inherited from class java.awt.Container |
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Container.AccessibleAWTContainer |
Nested classes/interfaces inherited from class java.awt.Component |
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Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy |
Field Summary |
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Fields inherited from class javax.swing.JComponent |
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accessibleContext, listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW |
Fields inherited from class java.awt.Component |
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BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT |
Fields inherited from interface java.awt.image.ImageObserver |
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ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH |
Constructor Summary | |
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JMatrixPanel()
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Method Summary | |
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void |
drawBoxes(Graphics g)
draw high scoring fragments that are used for the initial alignment seed selection |
void |
drawDistances(Graphics g1)
For each element in matrix, draw it as a colored square or pixel. |
void |
drawPairs(Graphics g)
draw alternative alignments |
AlternativeAlignment[] |
getAlternativeAligs()
|
ContinuousColorMapper |
getCellColor()
|
FragmentPair[] |
getFragmentPairs()
|
Matrix |
getMatrix()
|
float |
getSaturation()
Deprecated. |
float |
getScale()
|
float |
getScalevalue()
Deprecated. |
int |
getSelectedAlignmentPos()
|
void |
paintComponent(Graphics g)
|
void |
setAlternativeAligs(AlternativeAlignment[] aligs)
|
void |
setCellColor(ContinuousColorMapper cellColor)
|
void |
setFragmentPairs(FragmentPair[] fragmentPairs)
|
void |
setMatrix(Matrix matrix)
sets the distance matrix to be displayed |
void |
setPreferredSize()
|
void |
setSaturation(float saturation)
Deprecated. |
void |
setScale(float scale)
|
void |
setScalevalue(float scalevalue)
Deprecated. |
void |
setSelectedAlignmentPos(int selectedAlignmentPos)
|
Methods inherited from class javax.swing.JPanel |
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getAccessibleContext, getUI, getUIClassID, paramString, setUI, updateUI |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
Constructor Detail |
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public JMatrixPanel()
Method Detail |
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public int getSelectedAlignmentPos()
public void setSelectedAlignmentPos(int selectedAlignmentPos)
public AlternativeAlignment[] getAlternativeAligs()
public void setAlternativeAligs(AlternativeAlignment[] aligs)
public FragmentPair[] getFragmentPairs()
public void setFragmentPairs(FragmentPair[] fragmentPairs)
public float getScale()
public void setPreferredSize()
public void setScale(float scale)
public Matrix getMatrix()
public void setMatrix(Matrix matrix)
matrix
- public void paintComponent(Graphics g)
paintComponent
in class JComponent
public void drawPairs(Graphics g)
g
- public void drawBoxes(Graphics g)
g
- public void drawDistances(Graphics g1)
g1
- @Deprecated public float getSaturation()
@Deprecated public void setSaturation(float saturation)
@Deprecated public float getScalevalue()
@Deprecated public void setScalevalue(float scalevalue)
public ContinuousColorMapper getCellColor()
public void setCellColor(ContinuousColorMapper cellColor)
cellColor
- the color mapping of the JMatrixPanel to set
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