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

Class MultipleAlignmentCoordManager

java.lang.Object
org.biojava.nbio.structure.align.gui.aligpanel.MultipleAlignmentCoordManager
public class MultipleAlignmentCoordManager extends Object
Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.
Author:
Aleix Lafita

  • 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 final int DEFAULT_Y_STEP
      Size of space between rows. Depends on the number of structures aligned.

    • 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 between sequences in the 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

    • MultipleAlignmentCoordManager

      public MultipleAlignmentCoordManager(int size, int length)
      Constructor.
      Parameters:
      size - number of structures/sequences aligned (rows).
      length - number of aligned residues (columns)

  • 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 an X position in the JPanel to the position in the sequence alignment.
      Parameters:
      aligSeq - sequence number
      p - point on panel
      Returns:
      the sequence position for a point on the Panel

    • getPanelPos

      public Point getPanelPos(int structure, int pos)
      Get the X position on the Panel of a particular sequence position.
      Parameters:
      structure - index of the structure for the sequence position.
      pos - sequence position, the aligned position index
      Returns:
      the point on a panel for a sequence position

    • getAligSeq

      public int getAligSeq(Point point)
      Returns the index of the structure, for a given point in the Panel. Returns -1 if not over a position in the sequence alignment.
      Parameters:
      point - x and y coordinates in the panel
      Returns:
      which structure a point on the panel corresponds to

    • getLegendPosition

      public Point getLegendPosition(int lineNr, int structure)
      Provide the coordinates for where to draw the legend for line X given the structure index.
      Parameters:
      lineNr - line of the Panel
      structure - the structure index
      Returns:
      get the point where to draw the legend

    • getEndLegendPosition

      public Point getEndLegendPosition(int lineNr, int structure)