
***************************************************
* This NEXUS file is designed to test the NCL by  *
* presenting it with several different variants   *
* of the CHARACTERS block.  After each variant,   *
* a special 'showall' comment directs the nexus   *
* reader to spit out the contents of all blocks   *
* currently stored.  The file reference.txt holds *
* the output expected (use the DOS command fc or  *
* the UNIX command diff to compare your output to * 
* reference.txt to see if your implementation is  * 
* working correctly.                              *
***************************************************

Reading "TAXA" block...
Finished with "TAXA" block.

*************
* Standard  *
*************

Reading "CHARACTERS" block...
Finished with "CHARACTERS" block.

********** Contents of the TAXA block **********

TAXA block contains 6 taxa
	1	P. fimbriata
	2	P. robusta
	3	P. americana
	4	P. myriophylla
	5	P. polygama
	6	P. macrophylla

********** Contents of the CHARACTERS block **********

CHARACTERS block contains 6 taxa and 45 characters
  Data type is "DNA"
  Ignoring case
  Data matrix entries are expected to be single symbols
  Taxon labels are expected on left side of matrix
  Matrix neither transposed nor interleaved
  Missing data symbol is '?'
  No match character specified
  Gap character specified is '-'
  Valid symbols are: ACGT
  Equate macros in effect:
    B = {CGT}
    D = {AGT}
    H = {ACT}
    K = {GT}
    M = {AC}
    N = {ACGT}
    R = {AG}
    S = {CG}
    V = {ACG}
    W = {AT}
    X = {ACGT}
    Y = {CT}
  No characters were eliminated
  The following characters have been excluded:
    (no characters excluded)
  The following taxa have been deleted:
    (no taxa deleted)
  Data matrix:
    P. fimbriata       ACCTCGGCTTAACGAACCTCGGCTTAACGAACCTCGGCTTAACGA
    P. robusta         ACCTCGGCTTAACCAACCTCGGCTTAACGAACCTCGGCTTAACGA
    P. americana       ACGTCGCTTTCA---ACGTCGCTTTCACCAACGTCGCTTTCACCA
    P. myriophylla     ACGTCGCTTTCA---ACGTCGCTTTCACCAACGTC?CTTTCACCA
    P. polygama        ACGTCGCTCTCACCAACGTCGCTTTCACCAACGTC?CTTTCACCA
    P. macrophylla     ACGTCGCTCTCACCAACGTCGCTTTCACCAACGTCGCTTTCACCA

**********
* Tokens *
**********

Reading "CHARACTERS" block...
Finished with "CHARACTERS" block.

********** Contents of the TAXA block **********

TAXA block contains 6 taxa
	1	P. fimbriata
	2	P. robusta
	3	P. americana
	4	P. myriophylla
	5	P. polygama
	6	P. macrophylla

********** Contents of the CHARACTERS block **********

CHARACTERS block contains 6 taxa and 3 characters
  Data type is "standard"
  Ignoring case
  Multicharacter tokens allowed in data matrix
  Taxon labels are expected on left side of matrix
  Character and character state labels:
	1	leaf margins
		entire
		fimbriate
	2	flower color
		white to cream
		crimson
	3	breeding system
		hermaphroditic
		gynomonoecious
		gynodioecious
		dioecious
  Matrix neither transposed nor interleaved
  Missing data symbol is '?'
  No match character specified
  No gap character specified
  Valid symbols are: 01
  No equate macros have been defined
  No characters were eliminated
  The following characters have been excluded:
    (no characters excluded)
  The following taxa have been deleted:
    (no taxa deleted)
  Data matrix:
    P. fimbriata         fimbriate  crimson  gynomonoecious
    P. robusta           fimbriate  crimson  gynomonoecious
    P. americana         entire  white to cream  hermaphroditic
    P. myriophylla       entire  white to cream  hermaphroditic
    P. polygama          entire  white to cream  dioecious
    P. macrophylla       entire  crimson  gynodioecious

***********
* Symbols *
***********

Reading "CHARACTERS" block...
Finished with "CHARACTERS" block.

********** Contents of the TAXA block **********

TAXA block contains 6 taxa
	1	P. fimbriata
	2	P. robusta
	3	P. americana
	4	P. myriophylla
	5	P. polygama
	6	P. macrophylla

********** Contents of the CHARACTERS block **********

CHARACTERS block contains 6 taxa and 3 characters
  Data type is "standard"
  Ignoring case
  Data matrix entries are expected to be single symbols
  Taxon labels are expected on left side of matrix
  Character and character state labels:
	1	leaf margins
		entire
		fimbriate
	2	flower color
		white to cream
		crimson
	3	breeding system
		hermaphroditic
		gynomonoecious
		gynodioecious
		dioecious
  Matrix neither transposed nor interleaved
  Missing data symbol is '?'
  No match character specified
  No gap character specified
  Valid symbols are: 0123
  No equate macros have been defined
  No characters were eliminated
  The following characters have been excluded:
    (no characters excluded)
  The following taxa have been deleted:
    (no taxa deleted)
  Data matrix:
    P. fimbriata       111
    P. robusta         111
    P. americana       000
    P. myriophylla     000
    P. polygama        003
    P. macrophylla     012

*****************************
* Interleaved, missing taxa *
*****************************

Reading "CHARACTERS" block...
Finished with "CHARACTERS" block.

********** Contents of the TAXA block **********

TAXA block contains 6 taxa
	1	P. fimbriata
	2	P. robusta
	3	P. americana
	4	P. myriophylla
	5	P. polygama
	6	P. macrophylla

********** Contents of the CHARACTERS block **********

CHARACTERS block contains 4 taxa and 15 characters
  Data type is "DNA"
  Ignoring case
  Data matrix entries are expected to be single symbols
  Taxon labels are expected on left side of matrix
  Matrix interleaved but not transposed
  Missing data symbol is '?'
  No match character specified
  No gap character specified
  Valid symbols are: ACGT
  Equate macros in effect:
    B = {CGT}
    D = {AGT}
    H = {ACT}
    K = {GT}
    M = {AC}
    N = {ACGT}
    R = {AG}
    S = {CG}
    V = {ACG}
    W = {AT}
    X = {ACGT}
    Y = {CT}
  No characters were eliminated
  The following characters have been excluded:
    (no characters excluded)
  The following taxa have been deleted:
    (no taxa deleted)
  Data matrix:
    P. fimbriata       ACCTCGGCTTAACGA
    P. robusta         ACCTCGGCTTAACCA
    P. americana       ACGTCGCTCTCACCA
    P. myriophylla     ACGTCGCTTTCACCA

****************
** transposed **
****************

Reading "CHARACTERS" block...
Finished with "CHARACTERS" block.

TAXA block contains 6 taxa
	1	P. fimbriata
	2	P. robusta
	3	P. americana
	4	P. myriophylla
	5	P. polygama
	6	P. macrophylla

CHARACTERS block contains 6 taxa and 15 characters
  Data type is "DNA"
  Ignoring case
  Data matrix entries are expected to be single symbols
  Character labels are expected on left side of matrix
  Character and character state labels:
	1	site 1
	2	site 2
	3	site 3
	4	site 4
	5	site 5
	6	site 6
	7	site 7
	8	site 8
	9	site 9
	10	site 10
	11	site 11
	12	site 12
	13	site 13
	14	site 14
	15	site 15
  Matrix transposed but not interleaved
  Missing data symbol is '?'
  No match character specified
  No gap character specified
  Valid symbols are: ACGT
  Equate macros in effect:
    B = {CGT}
    D = {AGT}
    H = {ACT}
    K = {GT}
    M = {AC}
    N = {ACGT}
    R = {AG}
    S = {CG}
    V = {ACG}
    W = {AT}
    X = {ACGT}
    Y = {CT}
  No characters were eliminated
  The following characters have been excluded:
    (no characters excluded)
  The following taxa have been deleted:
    (no taxa deleted)
  Data matrix:
    P. fimbriata       ACCTCGGCTTAACGA
    P. robusta         ACCTCGGCTTAACCA
    P. americana       ACGTCGCTCTCACCA
    P. myriophylla     ACGTCGCTTTCACCA
    P. polygama        ACCTCGCTTTCACGA
    P. macrophylla     ACCTCGCTTTCACGA

