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 static final int DEFAULT_Y_STEP

  size of space between rows

  See Also:

  Constant Field Values

• 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 of line 1 and 2 in 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

• 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,
                       java.awt.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 java.awt.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​(java.awt.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 java.awt.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 java.awt.Point getEndLegendPosition​(int lineNr,
                                             int chainNr)