Package org.biojava.nbio.structure.align.gui.aligpanel

Class AFPChainCoordManager

java.lang.Object
org.biojava.nbio.structure.align.gui.aligpanel.AFPChainCoordManager
public class AFPChainCoordManager extends Object

  • Field Details

    • DEFAULT_RIGHT_SPACER

      public static final int DEFAULT_RIGHT_SPACER
      Space on the right side between sequence and legend.
      See Also:

    • DEFAULT_LINE_LENGTH

      public static final int DEFAULT_LINE_LENGTH
      number of chars per line
      See Also:

    • DEFAULT_Y_STEP

      public static final int DEFAULT_Y_STEP
      size of space between rows
      See Also:

    • DEFAULT_CHAR_SIZE

      public static final int DEFAULT_CHAR_SIZE
      size per character
      See Also:

    • DEFAULT_LINE_SEPARATION

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

    • DEFAULT_X_SPACE

      public static final int DEFAULT_X_SPACE
      left boundary
      See Also:

    • DEFAULT_Y_SPACE

      public static final int DEFAULT_Y_SPACE
      top boundary
      See Also:

    • SUMMARY_POS

      public static final int SUMMARY_POS
      Position at which the alignment summary is printed
      See Also:

  • Constructor Details

    • AFPChainCoordManager

      public AFPChainCoordManager()

  • Method Details

    • 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)