- <p>
- <em>VIEW_SETREF</em> marks the first sequence in the alignment, or
- alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
- statement, as the <a href="../features/refsequence.html">reference
- sequence</a> for the alignment.
- </p>
- <p>
- <em>HIDE_INSERTIONS</em>This command hides all gapped positions in the
- current target sequence. Any columns already hidden will be
- re-displayed.<br />
- <br>The current target sequence is either the one specified by
- the most recent <em>SEQUENCE_REF</em> statement, the alignment's
- reference sequence, or the first sequence in the alignment.
- </p>
- <p>
- <em>VIEW_HIDECOLS</em> modifies the visibility of columns in the view.
- The statement is followed by a single argument consisting of a comma
- separated series of single integers or integer pairs (like <em>3-4</em>).
- These define columns (starting from the left-hand column 0) that
- should be marked as hidden in the alignment view.
- </p>
+ <p>
+ <em>VIEW_SETREF</em><br />Marks the first sequence in the alignment,
+ or alternately, the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, as the <a href="../calculations/referenceseq.html">reference
+ sequence</a> for the alignment.
+ </p>
+ <p>
+ <em>HIDE_INSERTIONS</em><br />This command hides all gapped
+ positions in the current target sequence. Any columns already hidden
+ will be re-displayed.<br /> <br>The current target sequence is
+ either the one specified by the most recent <em>SEQUENCE_REF</em>
+ statement, the alignment's reference sequence, or the first sequence
+ in the alignment.
+ </p>
+ <p>
+ <em>VIEW_HIDECOLS</em><br />Modifies the visibility of columns in
+ the view. The statement is followed by a single argument consisting
+ of a comma separated series of single integers or integer pairs
+ (like <em>3-4</em>). These define columns (starting from the
+ left-hand column 0) that should be marked as hidden in the alignment
+ view.
+ </p>