org.biojava.bio.structure.align.gui.aligpanel
Class AFPChainCoordManager

java.lang.Object
  extended by org.biojava.bio.structure.align.gui.aligpanel.AFPChainCoordManager

public class AFPChainCoordManager
extends Object


Field Summary
static int DEFAULT_CHAR_SIZE
          size per character
static int DEFAULT_LINE_LENGTH
          number of chars per line
static int DEFAULT_LINE_SEPARATION
          separation of line 1 and 2 in 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
static int DEFAULT_Y_STEP
          size of space between rows
static int SUMMARY_POS
          Position at which the alignment summary is printed
 
Constructor Summary
AFPChainCoordManager()
           
 
Method Summary
 int getAligSeq(Point point)
          returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.
 Point getEndLegendPosition(int lineNr, int chainNr)
           
 Point getLegendPosition(int lineNr, int chainNr)
          provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2
 Point getPanelPos(int aligSeq, int i)
          get the position of the sequence position on the Panel
 int getPreferredHeight()
          Y coordinate size
 int getPreferredWidth()
          X coordinate size
 int getSeqPos(int aligSeq, Point p)
          Convert from a X position in the JPanel to alignment position
 int getSummaryPos()
           
 void setAFPChain(AFPChain afpChain)
           
 
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.

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Constant Field Values

DEFAULT_LINE_LENGTH

public static final int DEFAULT_LINE_LENGTH
number of chars per line

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Constant Field Values

DEFAULT_Y_STEP

public static final int DEFAULT_Y_STEP
size of space between rows

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Constant Field Values

DEFAULT_CHAR_SIZE

public static final int DEFAULT_CHAR_SIZE
size per character

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Constant Field Values

DEFAULT_LINE_SEPARATION

public static final int DEFAULT_LINE_SEPARATION
separation of line 1 and 2 in alignment

See Also:
Constant Field Values

DEFAULT_X_SPACE

public static final int DEFAULT_X_SPACE
left boundary

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Constant Field Values

DEFAULT_Y_SPACE

public static final int DEFAULT_Y_SPACE
top boundary

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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

AFPChainCoordManager

public AFPChainCoordManager()
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 a X position in the JPanel to alignment position

Parameters:
aligSeq - sequence 0 or 1
p - point on panel
Returns:
the sequence position for a point on the Panel

getPanelPos

public Point getPanelPos(int aligSeq,
                         int i)
get the position of the sequence position on the Panel

Parameters:
aligSeq - 0 or 1 for which of the two sequences to ask for.
i - sequence position
Returns:
the point on a panel for a sequence position

setAFPChain

public void setAFPChain(AFPChain afpChain)

getAligSeq

public int getAligSeq(Point point)
returns the AligSeq (0 or 1) for a point returns -1 if not over an alig seq.

Parameters:
point -
Returns:
which of the two sequences a point on the panel corresponds to

getLegendPosition

public Point getLegendPosition(int lineNr,
                               int chainNr)
provide the coordinates for where to draw the legend for line X and if it is chain 1 or 2

Parameters:
lineNr - which line is this for
chainNr - is it chain 0 or 1
Returns:
get the point where to draw the legend

getEndLegendPosition

public Point getEndLegendPosition(int lineNr,
                                  int chainNr)