Class AFPChainCoordManager


  • public class AFPChainCoordManager
    extends java.lang.Object
    • 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
      • 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)