Class MultipleAlignmentCoordManager


  • public class MultipleAlignmentCoordManager
    extends java.lang.Object
    Generalization of the Coodinate Manager to include an arbitrary number of sequences (lines) for MultipleAlignment visualization.
    Author:
    Aleix Lafita
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int getAligSeq​(java.awt.Point point)
      Returns the index of the structure, for a given point in the Panel.
      java.awt.Point getEndLegendPosition​(int lineNr, int structure)  
      java.awt.Point getLegendPosition​(int lineNr, int structure)
      Provide the coordinates for where to draw the legend for line X given the structure index.
      java.awt.Point getPanelPos​(int structure, int pos)
      Get the X position on the Panel of a particular sequence position.
      int getPreferredHeight()
      Y coordinate size
      int getPreferredWidth()
      X coordinate size
      int getSeqPos​(int aligSeq, java.awt.Point p)
      Convert from an X position in the JPanel to the position in the sequence alignment.
      int getSummaryPos()  
      • 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.
        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 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:
        Constant Field Values
      • DEFAULT_LINE_SEPARATION

        public static final int DEFAULT_LINE_SEPARATION
        Separation between sequences in the 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

      • MultipleAlignmentCoordManager

        public MultipleAlignmentCoordManager​(int size,
                                             int length)
        Constructor.
        Parameters:
        size - number of structures/sequences aligned (rows).
        length - number of aligned residues (columns)
    • 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 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 java.awt.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​(java.awt.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 java.awt.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 java.awt.Point getEndLegendPosition​(int lineNr,
                                                   int structure)