Merge remote-tracking branch 'origin/develop' into bug/JAL-2665-2.10.3

[jalview.git] / src / jalview / datamodel / SequenceCursor.java

diff --git a/src/jalview/datamodel/SequenceCursor.java b/src/jalview/datamodel/SequenceCursor.java
new file mode 100644 (file)
index 0000000..b5929bf
--- /dev/null
+++ b/src/jalview/datamodel/SequenceCursor.java
@@ -0,0 +1,125 @@
+package jalview.datamodel;
+
+/**
+ * An immutable object representing one or more residue and corresponding
+ * alignment column positions for a sequence
+ */
+public class SequenceCursor
+{
+  /**
+   * the aligned sequence this cursor applies to
+   */
+  public final SequenceI sequence;
+
+  /**
+   * residue position in sequence (start...), 0 if undefined
+   */
+  public final int residuePosition;
+
+  /**
+   * column position (1...) corresponding to residuePosition, or 0 if undefined
+   */
+  public final int columnPosition;
+
+  /**
+   * column position (1...) of first residue in the sequence, or 0 if undefined
+   */
+  public final int firstColumnPosition;
+
+  /**
+   * column position (1...) of last residue in the sequence, or 0 if undefined
+   */
+  public final int lastColumnPosition;
+
+  /**
+   * a token which may be used to check whether this cursor is still valid for
+   * its sequence (allowing it to be ignored if the sequence has changed)
+   */
+  public final int token;
+
+  /**
+   * Constructor
+   * 
+   * @param seq
+   *          sequence this cursor applies to
+   * @param resPos
+   *          residue position in sequence (start..)
+   * @param column
+   *          column position in alignment (1..)
+   * @param tok
+   *          a token that may be validated by the sequence to check the cursor
+   *          is not stale
+   */
+  public SequenceCursor(SequenceI seq, int resPos, int column, int tok)
+  {
+    this(seq, resPos, column, 0, 0, tok);
+  }
+
+  /**
+   * Constructor
+   * 
+   * @param seq
+   *          sequence this cursor applies to
+   * @param resPos
+   *          residue position in sequence (start..)
+   * @param column
+   *          column position in alignment (1..)
+   * @param firstResCol
+   *          column position of the first residue in the sequence (1..), or 0
+   *          if not known
+   * @param lastResCol
+   *          column position of the last residue in the sequence (1..), or 0 if
+   *          not known
+   * @param tok
+   *          a token that may be validated by the sequence to check the cursor
+   *          is not stale
+   */
+  public SequenceCursor(SequenceI seq, int resPos, int column, int firstResCol,
+          int lastResCol, int tok)
+  {
+    sequence = seq;
+    residuePosition = resPos;
+    columnPosition = column;
+    firstColumnPosition = firstResCol;
+    lastColumnPosition = lastResCol;
+    token = tok;
+  }
+
+  @Override
+  public int hashCode()
+  {
+    int hash = 31 * residuePosition;
+    hash = 31 * hash + columnPosition;
+    hash = 31 * hash + token;
+    if (sequence != null)
+    {
+      hash += sequence.hashCode();
+    }
+    return hash;
+  }
+
+  /**
+   * Two cursors are equal if they refer to the same sequence object and have
+   * the same residue position, column position and token value
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (!(obj instanceof SequenceCursor))
+    {
+      return false;
+    }
+    SequenceCursor sc = (SequenceCursor) obj;
+    return sequence == sc.sequence && residuePosition == sc.residuePosition
+            && columnPosition == sc.columnPosition && token == sc.token;
+  }
+
+  @Override
+  public String toString()
+  {
+    String name = sequence == null ? "" : sequence.getName();
+    return String.format("%s:Pos%d:Col%d:startCol%d:endCol%d:tok%d", name,
+            residuePosition, columnPosition, firstColumnPosition,
+            lastColumnPosition, token);
+  }
+}