Package pl.poznan.put.structure.formats

Class Ct.ExtendedEntry

java.lang.Object
pl.poznan.put.structure.formats.Ct.ExtendedEntry
All Implemented Interfaces:
Comparable<Ct.ExtendedEntry>
Direct Known Subclasses:
ImmutableExtendedEntry
Enclosing class:
Ct
@Immutable public abstract static class Ct.ExtendedEntry extends Object implements Comparable<Ct.ExtendedEntry>
A single entry in the CT formatted structure.

  • Constructor Details

    • ExtendedEntry

      public ExtendedEntry()

  • Method Details

    • fromString

      public static Ct.ExtendedEntry fromString(String line)
      Creates an instance from a string in format: int string int int int int.
      Parameters:
      line - A line of text formatted as a CT content line.
      Returns:
      An instance of this class.

    • fromEntry

      public static Ct.ExtendedEntry fromEntry(BpSeq.Entry entry)
      Converts a BPSEQ entry into an instance of this class.
      Parameters:
      entry - A BPSEQ entry to convert.
      Returns:
      An instance of this class.

    • index

      @Parameter(order=1) public abstract int index()
      Returns:
      The value of `index` column.

    • seq

      @Parameter(order=2) public abstract char seq()
      Returns:
      The value of `seq` column.

    • before

      @Parameter(order=3) public abstract int before()
      Returns:
      The value of `before` column.

    • after

      @Parameter(order=4) public abstract int after()
      Returns:
      The value of `after` column.

    • pair

      @Parameter(order=5) public abstract int pair()
      Returns:
      The value of `pair` column.

    • original

      @Parameter(order=6) public abstract int original()
      Returns:
      The value of `original` column.

    • comment

      @Default public String comment()
      Returns:
      An optional comment.

    • isPaired

      public boolean isPaired()
      Returns:
      True if `pair` column is non-zero.

    • hasInvalidBeforeOrAfter

      public boolean hasInvalidBeforeOrAfter()
      Returns:
      True if `before` or `after` column are not correct.

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • compareTo

      public int compareTo(Ct.ExtendedEntry t)
      Specified by:
      compareTo in interface Comparable<Ct.ExtendedEntry>