                            ROCPLOT documentation



CONTENTS

   1.0 SUMMARY
   2.0 INPUTS & OUTPUTS
   3.0 INPUT FILE FORMAT
   4.0 OUTPUT FILE FORMAT
   5.0 DATA FILES
   6.0 USAGE
   7.0 KNOWN BUGS & WARNINGS
   8.0 NOTES
   9.0 DESCRIPTION
   10.0 ALGORITHM
   11.0 RELATED APPLICATIONS
   12.0 DIAGNOSTIC ERROR MESSAGES
   13.0 AUTHORS
   14.0 REFERENCES

1.0 SUMMARY

   Provides interpretation and graphical display of the performance of
   discriminating elements (e.g. profiles for protein families). rocplot
   reads file(s) of hits from discriminator-database search(es), performs
   ROC analysis on the hits, and writes graphs illustrating the diagnostic
   performance of the discriminating elements. Performs ROC analysis on
   hits files

2.0 INPUTS & OUTPUTS

   ROCPLOT reads a directory of one or more hits files and writes a text,
   summary file containing ROC value(s), which are a convenient numerical
   measure of the sensitivity and specificity of a predictive method.
   GNUPLOT files for the following graphs are also written.
   (i) ROC plots displaying graphically the method sensitivity and
   specificity.
   (ii) Classification plots, which are a useful aid in interpreting ROC
   plots and ROC values.
   (iii) In some modes (see below) a bar chart of the distribution of ROC
   values is generated.

  2.1 ROCPLOT modes

   ROCPLOT runs in one of two basic modes:
   (i) "Single hits file"
   (ii) "Multiple hits file".

  2.1.1 Single hits file mode

   ROC analysis is performed on the single hits file. A ROC plot
   containing one ROC curve and a single ROC value and classification plot
   are generated.

  2.1.2 Multiple hits files mode

   The same ROC number must be given in the hits files and each file must
   contain at least this number of non-TRUE hits (see Section 3.1): an
   error is generated and the program terminates otherwise. In "multiple
   hits file mode" there are two sub-modes:
   (i) "Do not combine data"
   (ii) "Combine data".

  2.1.3 Do not combine data mode

   ROC analysis is performed separately for each hits file. Multiple ROC
   curves are given on the same ROC plot. A ROC value and classification
   plot are generated for each hits file. A bar chart giving the
   distribution of ROCn values is also generated. The mean and standard
   deviation of ROCn values are written to the summary file.

  2.1.4 Combine data mode

   The hits are combined and ROC analysis is performed on the whole (see
   Section 9.6). A ROC plot containing one ROC curve and a single ROC
   value and classification plot are generated.
   In "combine data" mode there are a further two sub-modes:
   (i) "Single gold standard"
   (ii) "Multiple gold standard".
   These determine how the ROC number and value are calculated.

  2.1.5 Single gold standard mode

   There is a single gold standard (list of known true hits) for the
   different searches. The same number of known true hits must be
   specified in the hits files: an error is generated and the program
   terminates otherwise. The accession number (or other code) and start
   and end point of each hit must also be given (see Section 3.1).

  2.1.6 Multiple gold standard mode

   There is a gold standard for each different search.
   The output in the different modes is summarised (Figure 1).
   Figure 1 Summary of ROCPLOT output

                      ____________________________________________________
                      | SINGLE HITS FILE  |      MULTIPLE HITS FILES     |
                      |                   |                |             |
                      |                   | Do not combine |   Combine   |
                      |                   | data           |   data      |
 _____________________|___________________|________________|_____________|
                      |                   |                |             |
 ROC curves / value   | Single            | Multiple (1)   | Single      |
 Bar chart            | -                 | Yes            | -           |
 Classification plot  | Single            | Multiple       | Single      |
 Summary file         | Yes               | Yes            | Yes         |
 _____________________|___________________|________________|_____________|

   (1) Multiple ROC curves are given on a single ROC plot.

3.0 INPUT FILE FORMAT

  3.1 Hits files

   A hits file contains a list of classified hits that are rank-ordered on
   the basis of score. The first line must have '>' in the first character
   position and a space (' ') in the second, then two token - integer
   pairs delimited by ';'. The integer following 'RELATED' is the total
   number of known true hits ('relatives') and is the maximum number of
   TRUE tokens (see below) that could ever appear in the hits file. The
   integer following 'ROC' is the ROC value that will be calculated. This
   integer also determines the limit of the x-axes of the ROC and
   classification plots (see Sections 9.2 & 9.4).
   The file then contains a number of lines corresponding to a list of
   classified hits. The hits *must* be rank-ordered on the basis of score,
   p-value, E-value etc, with the highest scoring / most significant hit
   given in the highest rank (1); i.e. on the second line of the file.
   Other hits should then be given in order of decreasing score /
   significance.
   The first string in a hit line is the classification and must be one of
   the following: 'TRUE', 'CROSS', 'UNCERTAIN', 'UNKNOWN' or 'FALSE'. If
   ROCPLOT is run in "Multiple hits files" - "Combine data" - "Single gold
   standard" modes, each hit line must contain a second string followed by
   2 integers. These are required so that ROCPLOT can identify unique hits
   in the lists of hits (see Section 10.4). For hits to sequences, the
   string is the accession number (or other database code) and the
   integers are the start and end point of the hit relative to the full
   length sequence. For some applications the start and end point data are
   not required to define unique hits: in these cases the start and end
   values for all hits should be set to 0 and 1 respectively.

4.0 OUTPUT FILE FORMAT

  4.0 OUTPUT FILE FORMAT

  4.1 Summary file

   The summary file is shown in Figure 3. The first section is comments
   including the modes ROCPLOT was run in. The file may then contain a
   section where the file name, number of known true hits and ROCn value
   are given for each hits file. In cases where data from multiple hits
   files were combined a single ROCn value will be given instead of this
   section. The mean and SD of the ROCn values are given if calculated.

  4.2 GNUPLOT files

   ROCPLOT generates various gnuplot driver and data files depending upon
   mode. For example, the user specifies the base name of the rocplot,
   classification, bar chart and summary files to be "_rocplot",
   "_classplot", "_barchart" and "_summary" respectively. If ROCPLOT is
   run in "Multiple hits files" - "Combine data" - "Single gold standard"
   mode the following files are generated.

_classplot_dat0   Data file for classification plot
_classplot_dat1   Data file for classification plot
_classplot_dat2   Data file for classification plot
_classplot_dat3   Data file for classification plot
_classplot_dat4   Data file for classification plot
_classplot        Driver file for classification plot
_rocplot_dat0     Data file for roc plot.
_rocplot          Driver file for roc plot.
_summary          Summary file.

   If ROCPLOT is run in "Multiple hits files" - "Combine data" - "Single
   gold standard" mode the following files are generated.

_classplot0_dat0  Data file for first classification plot
_classplot0_dat1  ""
_classplot0_dat2  ""
_classplot0_dat3  ""
_classplot0_dat4  ""
_classplot0       Driver file for first classification plot
_classplot1_dat0  Data file for second classification plot
_classplot1_dat1  ""
_classplot1_dat3  ""
_classplot1_dat4  ""
_classplot1       Driver file for second classification plot
_rocplot_dat0     Data file for roc plot.
_rocplot_dat1     ""
_rocplot          Driver file for roc plot.
_summary          Summary file.

   Note that there is no _classplot1_dat2 indicating that the second hits
   file did not contain any hits for one of the data series (see Section
   9.4).
   If ROCPLOT is run in "Multiple hits files" - "Do not combine data" the
   following files are generated.

_barchart_dat      Data file for bar chart.
_barchart          Driver file for bar chart.

   The plots are visualised by using GNUPLOT, for example by typing load
   '_classplot1' from the GNUPLOT command line.

  Output files for usage example

  File: _rocplot

# GNUPLOT driver file for roc plot
set title "ROC plots for data1.hits & data2.hits (combined - "
set xlabel "1 - SPEC"
set ylabel "SENS"
set nokey
set noautoscale
set xrange [0:1]
set yrange [0:1]
set key top outside title "Data Series" box 3
set data style points
set pointsize 0.45
plot "_rocplot_dat0" smooth bezier title "Combined dataset (0.185)"

  File: _rocplot_dat0

# GNUPLOT data file for rocplot, series 0
0.000    0.007
0.000    0.014
0.000    0.021
0.000    0.029
0.200    0.029
0.167    0.036
0.143    0.043
0.250    0.043
0.222    0.050
0.200    0.057
0.182    0.064
0.250    0.064
0.231    0.071
0.214    0.079
0.200    0.086
0.250    0.086
0.235    0.093
0.222    0.100
0.263    0.100
0.250    0.107
0.238    0.114
0.273    0.114
0.261    0.121
0.292    0.121
0.280    0.129
0.308    0.129
0.296    0.136
0.286    0.143
0.276    0.150
0.300    0.150
0.290    0.157
0.281    0.164
0.273    0.171
0.294    0.171
0.286    0.179
0.278    0.186
0.297    0.186
0.316    0.186
0.333    0.186
0.350    0.186
0.366    0.186
0.381    0.186
0.395    0.186
0.409    0.186
0.400    0.193
0.391    0.200
0.404    0.200
0.417    0.200
0.429    0.200
0.440    0.200
0.451    0.200
0.462    0.200
0.472    0.200
0.481    0.200
0.473    0.207
0.464    0.214
0.474    0.214
0.483    0.214
0.492    0.214
0.500    0.214
0.508    0.214
0.516    0.214
0.524    0.214
0.531    0.214
0.538    0.214
0.545    0.214
0.552    0.214
0.559    0.214
0.565    0.214
0.571    0.214
0.577    0.214
0.583    0.214
0.589    0.214
0.595    0.214
0.600    0.214
0.605    0.214
0.610    0.214
0.615    0.214
0.620    0.214
0.625    0.214

  File: _classplot

# GNUPLOT driver file for classification plot
set title "Classification plot for data1.hits & data2.hits (c"
set xlabel "Number of hits detected"
set ylabel "Proportion of hits detected that are of a certain type"
set nokey
set key top outside title "Data Series" box 3
set data style points
set pointsize 0.45
plot "_classplot_dat0" smooth bezier title "True hits", "_classplot_dat1" smooth
 bezier title "Cross hits", "_classplot_dat2" smooth bezier title "Uncertain hit
s", "_classplot_dat3" smooth bezier title "Unknown hits", "_classplot_dat4" smoo
th bezier title "False hits"

  File: _classplot_dat0

# GNUPLOT data file for True hits, series 0
1.000    1.000
2.000    1.000
3.000    1.000
4.000    1.000
5.000    0.800
6.000    0.833
7.000    0.857
8.000    0.750
9.000    0.778
10.000    0.800
11.000    0.818
12.000    0.750
13.000    0.769
14.000    0.786
15.000    0.800
16.000    0.750
17.000    0.765
18.000    0.778
19.000    0.737
20.000    0.750
21.000    0.762
22.000    0.727
23.000    0.739
24.000    0.708
25.000    0.720
26.000    0.692
27.000    0.704
28.000    0.714
29.000    0.724
30.000    0.700
31.000    0.710
32.000    0.719
33.000    0.727
34.000    0.706
35.000    0.714
36.000    0.722
37.000    0.703
38.000    0.684
39.000    0.667
40.000    0.650
41.000    0.634
42.000    0.619
43.000    0.605
44.000    0.591
45.000    0.600
46.000    0.609
47.000    0.596
48.000    0.583
49.000    0.571
50.000    0.560
51.000    0.549
52.000    0.538
53.000    0.528
54.000    0.519
55.000    0.527
56.000    0.536
57.000    0.526
58.000    0.517
59.000    0.508
60.000    0.500
61.000    0.492
62.000    0.484
63.000    0.476
64.000    0.469
65.000    0.462
66.000    0.455
67.000    0.448
68.000    0.441
69.000    0.435
70.000    0.429
71.000    0.423
72.000    0.417
73.000    0.411
74.000    0.405
75.000    0.400
76.000    0.395
77.000    0.390
78.000    0.385
79.000    0.380
80.000    0.375

  File: _classplot_dat1

# GNUPLOT data file for Cross hits, series 1
1.000    0.000
2.000    0.000
3.000    0.000
4.000    0.000
5.000    0.200
6.000    0.167
7.000    0.143
8.000    0.250
9.000    0.222
10.000    0.200
11.000    0.182
12.000    0.250
13.000    0.231
14.000    0.214
15.000    0.200
16.000    0.250
17.000    0.235
18.000    0.222
19.000    0.263
20.000    0.250
21.000    0.238
22.000    0.273
23.000    0.261
24.000    0.250
25.000    0.240
26.000    0.231
27.000    0.222
28.000    0.214
29.000    0.207
30.000    0.233
31.000    0.226
32.000    0.219
33.000    0.212
34.000    0.235
35.000    0.229
36.000    0.222
37.000    0.216
38.000    0.211
39.000    0.205
40.000    0.200
41.000    0.195
42.000    0.190
43.000    0.186
44.000    0.182
45.000    0.178
46.000    0.174
47.000    0.170
48.000    0.167
49.000    0.163
50.000    0.160
51.000    0.157
52.000    0.154
53.000    0.151
54.000    0.148
55.000    0.145
56.000    0.143
57.000    0.140
58.000    0.138
59.000    0.136
60.000    0.133
61.000    0.131
62.000    0.129
63.000    0.127
64.000    0.125
65.000    0.123
66.000    0.121
67.000    0.119
68.000    0.118
69.000    0.116
70.000    0.114
71.000    0.113
72.000    0.111
73.000    0.110
74.000    0.108
75.000    0.107
76.000    0.105
77.000    0.104
78.000    0.103
79.000    0.101
80.000    0.100

  File: _classplot_dat2

# GNUPLOT data file for Uncertain hits, series 2
1.000    0.000
2.000    0.000
3.000    0.000
4.000    0.000
5.000    0.000
6.000    0.000
7.000    0.000
8.000    0.000
9.000    0.000
10.000    0.000
11.000    0.000
12.000    0.000
13.000    0.000
14.000    0.000
15.000    0.000
16.000    0.000
17.000    0.000
18.000    0.000
19.000    0.000
20.000    0.000
21.000    0.000
22.000    0.000
23.000    0.000
24.000    0.000
25.000    0.000
26.000    0.038
27.000    0.037
28.000    0.036
29.000    0.034
30.000    0.033
31.000    0.032
32.000    0.031
33.000    0.030
34.000    0.029
35.000    0.029
36.000    0.028
37.000    0.054
38.000    0.053
39.000    0.051
40.000    0.050
41.000    0.049
42.000    0.048
43.000    0.047
44.000    0.045
45.000    0.044
46.000    0.043
47.000    0.064
48.000    0.062
49.000    0.061
50.000    0.060
51.000    0.059
52.000    0.058
53.000    0.057
54.000    0.056
55.000    0.055
56.000    0.054
57.000    0.070
58.000    0.069
59.000    0.068
60.000    0.067
61.000    0.066
62.000    0.065
63.000    0.063
64.000    0.062
65.000    0.062
66.000    0.061
67.000    0.060
68.000    0.059
69.000    0.058
70.000    0.057
71.000    0.056
72.000    0.056
73.000    0.055
74.000    0.054
75.000    0.053
76.000    0.053
77.000    0.052
78.000    0.051
79.000    0.051
80.000    0.050

  File: _classplot_dat3

# GNUPLOT data file for Unknown hits, series 3
1.000    0.000
2.000    0.000
3.000    0.000
4.000    0.000
5.000    0.000
6.000    0.000
7.000    0.000
8.000    0.000
9.000    0.000
10.000    0.000
11.000    0.000
12.000    0.000
13.000    0.000
14.000    0.000
15.000    0.000
16.000    0.000
17.000    0.000
18.000    0.000
19.000    0.000
20.000    0.000
21.000    0.000
22.000    0.000
23.000    0.000
24.000    0.000
25.000    0.000
26.000    0.000
27.000    0.000
28.000    0.000
29.000    0.000
30.000    0.000
31.000    0.000
32.000    0.000
33.000    0.000
34.000    0.000
35.000    0.000
36.000    0.000
37.000    0.000
38.000    0.026
39.000    0.026
40.000    0.025
41.000    0.049
42.000    0.048
43.000    0.047
44.000    0.068
45.000    0.067
46.000    0.065
47.000    0.064
48.000    0.083
49.000    0.082
50.000    0.080
51.000    0.098
52.000    0.096
53.000    0.094
54.000    0.111
55.000    0.109
56.000    0.107
57.000    0.105
58.000    0.121
59.000    0.119
60.000    0.117
61.000    0.131
62.000    0.129
63.000    0.127
64.000    0.125
65.000    0.123
66.000    0.121
67.000    0.119
68.000    0.118
69.000    0.116
70.000    0.114
71.000    0.113
72.000    0.111
73.000    0.110
74.000    0.108
75.000    0.107
76.000    0.105
77.000    0.104
78.000    0.103
79.000    0.101
80.000    0.100

  File: _classplot_dat4

# GNUPLOT data file for False hits, series 4
1.000    0.000
2.000    0.000
3.000    0.000
4.000    0.000
5.000    0.000
6.000    0.000
7.000    0.000
8.000    0.000
9.000    0.000
10.000    0.000
11.000    0.000
12.000    0.000
13.000    0.000
14.000    0.000
15.000    0.000
16.000    0.000
17.000    0.000
18.000    0.000
19.000    0.000
20.000    0.000
21.000    0.000
22.000    0.000
23.000    0.000
24.000    0.042
25.000    0.040
26.000    0.038
27.000    0.037
28.000    0.036
29.000    0.034
30.000    0.033
31.000    0.032
32.000    0.031
33.000    0.030
34.000    0.029
35.000    0.029
36.000    0.028
37.000    0.027
38.000    0.026
39.000    0.051
40.000    0.075
41.000    0.073
42.000    0.095
43.000    0.116
44.000    0.114
45.000    0.111
46.000    0.109
47.000    0.106
48.000    0.104
49.000    0.122
50.000    0.140
51.000    0.137
52.000    0.154
53.000    0.170
54.000    0.167
55.000    0.164
56.000    0.161
57.000    0.158
58.000    0.155
59.000    0.169
60.000    0.183
61.000    0.180
62.000    0.194
63.000    0.206
64.000    0.219
65.000    0.231
66.000    0.242
67.000    0.254
68.000    0.265
69.000    0.275
70.000    0.286
71.000    0.296
72.000    0.306
73.000    0.315
74.000    0.324
75.000    0.333
76.000    0.342
77.000    0.351
78.000    0.359
79.000    0.367
80.000    0.375

  File: _summary

rocplot summary file (15 Jan 2010)

mode      == 2 (Multiple input file mode)
multimode == 2 (Combine data: single ROC plot, single classification plot.)
datamode  == 1 (Single list of known true relatives.)

File           Known
data1.hits     140
data2.hits     140

ROC50     == 0.185 (combined)

  File: rocplot.log

MODE INFO
modei: 2
multimodei: 2
datamodei: 1



NUMBER OF INPUT FILES
numfiles: 2



NAMES ONLY OF INPUT FILES
hitsnames[0]: data1.hits
hitsnames[1]: data2.hits



ROC NUMBER
roc: 50



ROC VALUES
rocn[0]: 0.184714



COUNT OF HITS
hitcnt[0]: 80




5.0 DATA FILES

   ROCPLOT does not use a data file.

6.0 USAGE

  6.1 COMMAND LINE ARGUMENTS

Performs ROC analysis on hits files
Version: EMBOSS:6.2.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-hitsfilespath]     dirlist    [rocplot] This option specifies the
                                  directory of hits files (input). A 'hits
                                  file'contains a list of hits (e.g. from a
                                  prediction method) that are classified and
                                  rank-ordered on the basis of score, p-value,
                                  E-value etc. The files generated by using
                                  SIGSCAN and LIBSCAN will contain the results
                                  of a search of a discriminating element
                                  (e.g. hidden Markov model, profile or
                                  signature) against a sequence database. The
                                  ROCPLOT application is run on the files to
                                  perform Receiver Operator Characteristic
                                  (ROC) analysis on the hits.
   -mode               menu       [1] This option specifies the mode of
                                  ROCPLOT operation (main mode). In 'single
                                  input file mode', ROC analysis is performed
                                  on the individual hits file; a ROC plot
                                  containing a single ROC curve, and a single
                                  ROC value and classification plot are
                                  generated. In 'multiple input file mode'
                                  there are two sub-modes depending upon
                                  whether (1) ROC analysis is to performed
                                  separately for the individual input files or
                                  (2) the lists of hits in the hits files are
                                  combined and ROC analysis is performed on
                                  the whole (see the ACD option called
                                  'multimode' for more information). If the
                                  input file does not contain at least as many
                                  'FALSE' hits as are specified after the
                                  'ROC' token in the input file, then an error
                                  will be generated and rocplot will
                                  terminate. Where multiple input files are
                                  given as input, each must contain the same
                                  value after the 'ROC' token, or an error
                                  will be generated and rocplot will
                                  terminate. The hits in the hits files *must*
                                  have been rank-ordered on the basis of
                                  score, p-value, E-value etc, with the
                                  highest scoring / most significant hit being
                                  given in the highest rank (1); i.e. on the
                                  second line of the file. Other hits should
                                  then be given in order of decreasing score /
                                  significance. (Values: 1 (Single input file
                                  mode); 2 (Multiple input file mode))
*  -multimode          menu       [1] This option specifies the mode of
                                  ROCPLOT operation (multimode). In 'Do not
                                  combine data' mode, ROC analysis is
                                  performed separately for the individual
                                  input files. Multiple ROC curves will be
                                  given on the same ROC plot and a ROC value
                                  and a classification plot will be generated
                                  for each input file. A bar chart giving the
                                  distribution of ROCn values, and the mean
                                  and standard deviation of ROCn values are
                                  also generated. In 'Combine data' mode, the
                                  lists of hits in the hits files are combined
                                  and ROC analysis is performed on the whole.
                                  A single ROC curve will be given in the ROC
                                  plot and a single ROC value and
                                  classification plot will be generated. In
                                  this second mode there are two further
                                  sub-modes depending on whether there is (1)
                                  a single list of known true relatives for
                                  the different searches or (2) there is a
                                  different list of known true relatives for
                                  each different search (see the ACD option
                                  called 'datamode' for more information)
                                  (Values: 1 (Do not combine data (multiple
                                  ROC curves in single ROC plot - multiple
                                  classification plots)); 2 (Combine data
                                  (single ROC curve - single classification
                                  plot)))
*  -datamode           menu       [1] This option specifies the mode of
                                  ROCPLOT operation (datamode). This determine
                                  how the ROC number and value are calculated
                                  in cases where there are multiple input
                                  files (lists of hits) and the user has
                                  specified the data are to be combined. See
                                  rocplot.c for more information. (Values: 1
                                  (Single list of known true relatives); 2
                                  (Multiple lists of known true relatives))
*  -thresh             integer    [10] This option specifies the overlap
                                  threshold for hits. In cases where the lists
                                  of hits are to be combined and there is a
                                  single set of relatives, the accession
                                  number (or other database identifier code)
                                  of the hit, and the start and end point
                                  respectively of the hit relative to full
                                  length sequence must be provided in the
                                  lists of hits (see 'Input file format'
                                  below). rocplot ensures that only unique
                                  hits are counted when calculating SENS and
                                  SPEC; two hits are 'unique' if they have (i)
                                  different accesssion numbers or (ii) the
                                  same accession numbers but which do not
                                  overlap by any more than a user-defined
                                  number of residues. The overlap is
                                  determined from the start and end points of
                                  the hit. For example two hits both with the
                                  same accession numbers and with the start
                                  and end points of 1-100 and 91 - 190
                                  respectively are considered to be the same
                                  hit if the overlap threshold is 10 or less.
                                  (Any integer value)
  [-outdir]            outdir     [./] This option specifies the directory
                                  where output files are written.
  [-rocbasename]       string     [_rocplot] This option specifies the base
                                  name of ROC plot file(s) (output). A file of
                                  meta data that contains graphs that
                                  illustrate the diagnostic performance of the
                                  discriminator. rocplot generates Receiver
                                  Operating Characteristic (ROC) curves, that
                                  display graphically the sensitivity and
                                  specificity of discriminating elements, and
                                  accompanying ROC value(s), which are a
                                  convenient numerical measure of the
                                  sensitivity and specificity of a method.
                                  Classification plots, which are a valuable
                                  aid in interpreting the ROC plot and value,
                                  are also generated and, depending upon the
                                  mode rocplot is run in, a plot of the
                                  distribution of ROC values. (Any string)
   -outfile            outfile    [_summary] This option specifies the name of
                                  the summary file (output). A text file
                                  summarising the analysis.
*  -barbasename        string     [_barchart] This option specifies the base
                                  name of bar chart for ROC value distribution
                                  (output). A bar chart giving the
                                  distribution of ROCn values will be
                                  generated when multiple input files (lists
                                  of hits) are provided and the user has
                                  specified 'Do not combine data (multiple ROC
                                  curves). (Any string)
   -classbasename      string     [_classplot] This option specifies the base
                                  name of classification plot file(s)
                                  (output). Classification plots are a
                                  valuable aid in interpreting the ROC plot
                                  and value. A single plot will be generated
                                  where a single input file is provided or
                                  where multiple input files are provided and
                                  the user has specified 'Combine data (single
                                  ROC curve)' mode. Multiple plots will be
                                  generated where multiple input files are
                                  provided and the user has specified 'Do not
                                  combine data (multiple ROC curves)' mode.
                                  (Any string)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -norange            boolean    [N] This option specifies whether to
                                  disregard range data when identifying unique
                                  hits. If set, the range data specified in
                                  the hits files are disregarded, two hits are
                                  classed as unique if they have different
                                  accession numbers (no requirement for
                                  overlapping ranges).
   -logfile            outfile    [rocplot.log] Domainatrix log output file

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   "-logfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


