File: tool_doc.h

package info (click to toggle)
seqan2 2.4.0%2Bdfsg-11~bpo9%2B1
  • links: PTS, VCS
  • area: main
  • in suites: stretch-backports
  • size: 223,500 kB
  • sloc: cpp: 256,886; ansic: 91,672; python: 8,339; sh: 995; xml: 570; makefile: 251; awk: 51
file content (1637 lines) | stat: -rw-r--r-- 53,496 bytes parent folder | download | duplicates (4)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
1001
1002
1003
1004
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
1017
1018
1019
1020
1021
1022
1023
1024
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
1136
1137
1138
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
1169
1170
1171
1172
1173
1174
1175
1176
1177
1178
1179
1180
1181
1182
1183
1184
1185
1186
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
1260
1261
1262
1263
1264
1265
1266
1267
1268
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
1286
1287
1288
1289
1290
1291
1292
1293
1294
1295
1296
1297
1298
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
1323
1324
1325
1326
1327
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
1348
1349
1350
1351
1352
1353
1354
1355
1356
1357
1358
1359
1360
1361
1362
1363
1364
1365
1366
1367
1368
1369
1370
1371
1372
1373
1374
1375
1376
1377
1378
1379
1380
1381
1382
1383
1384
1385
1386
1387
1388
1389
1390
1391
1392
1393
1394
1395
1396
1397
1398
1399
1400
1401
1402
1403
1404
1405
1406
1407
1408
1409
1410
1411
1412
1413
1414
1415
1416
1417
1418
1419
1420
1421
1422
1423
1424
1425
1426
1427
1428
1429
1430
1431
1432
1433
1434
1435
1436
1437
1438
1439
1440
1441
1442
1443
1444
1445
1446
1447
1448
1449
1450
1451
1452
1453
1454
1455
1456
1457
1458
1459
1460
1461
1462
1463
1464
1465
1466
1467
1468
1469
1470
1471
1472
1473
1474
1475
1476
1477
1478
1479
1480
1481
1482
1483
1484
1485
1486
1487
1488
1489
1490
1491
1492
1493
1494
1495
1496
1497
1498
1499
1500
1501
1502
1503
1504
1505
1506
1507
1508
1509
1510
1511
1512
1513
1514
1515
1516
1517
1518
1519
1520
1521
1522
1523
1524
1525
1526
1527
1528
1529
1530
1531
1532
1533
1534
1535
1536
1537
1538
1539
1540
1541
1542
1543
1544
1545
1546
1547
1548
1549
1550
1551
1552
1553
1554
1555
1556
1557
1558
1559
1560
1561
1562
1563
1564
1565
1566
1567
1568
1569
1570
1571
1572
1573
1574
1575
1576
1577
1578
1579
1580
1581
1582
1583
1584
1585
1586
1587
1588
1589
1590
1591
1592
1593
1594
1595
1596
1597
1598
1599
1600
1601
1602
1603
1604
1605
1606
1607
1608
1609
1610
1611
1612
1613
1614
1615
1616
1617
1618
1619
1620
1621
1622
1623
1624
1625
1626
1627
1628
1629
1630
1631
1632
1633
1634
1635
1636
1637
// ==========================================================================
//                 SeqAn - The Library for Sequence Analysis
// ==========================================================================
// Copyright (c) 2006-2018, Knut Reinert, FU Berlin
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are met:
//
//     * Redistributions of source code must retain the above copyright
//       notice, this list of conditions and the following disclaimer.
//     * Redistributions in binary form must reproduce the above copyright
//       notice, this list of conditions and the following disclaimer in the
//       documentation and/or other materials provided with the distribution.
//     * Neither the name of Knut Reinert or the FU Berlin nor the names of
//       its contributors may be used to endorse or promote products derived
//       from this software without specific prior written permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL KNUT REINERT OR THE FU BERLIN BE LIABLE
// FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
// DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
// CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
// LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
// OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
// DAMAGE.
//
// ==========================================================================
// Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
// ==========================================================================

#ifndef SEQAN_INCLUDE_ARG_PARSE_TOOL_DOC_H_
#define SEQAN_INCLUDE_ARG_PARSE_TOOL_DOC_H_

#include <iterator>

#include <seqan/misc/terminal.h>
#include <seqan/arg_parse/xml_support.h>
#include <seqan/version.h>

namespace seqan {

// ==========================================================================
// Forwards
// ==========================================================================

class ToolDoc;
inline void clearEntries(ToolDoc & doc);
inline void append(ToolDoc & a, ToolDoc const & b);

// ==========================================================================
// Tags, Classes, Enums
// ==========================================================================

// --------------------------------------------------------------------------
// Class ToolDocEntry_
// --------------------------------------------------------------------------

// Base class for entries in the ToolDoc class.

class ToolDocEntry_
{
public:
    enum EntryType
    {
        SUBSECTION, SECTION, LINE, LIST_ITEM
    };

    virtual ~ToolDocEntry_() {}

    virtual EntryType getType() const = 0;
};

// --------------------------------------------------------------------------
// Class ToolDocSection_
// --------------------------------------------------------------------------

// A section in the ToolDoc class.

class ToolDocSection_ :
    public ToolDocEntry_
{
public:
    CharString _title;

    ToolDocSection_(ToolDocSection_ const & sec) :
        ToolDocEntry_(sec), _title(sec._title)
    {}

    ToolDocSection_(CharString const & title) :
        _title(title)
    {}

    virtual EntryType getType() const
    {
        return SECTION;
    }

};

// --------------------------------------------------------------------------
// Class ToolDocSubSection_
// --------------------------------------------------------------------------

// A subsection.

class ToolDocSubSection_ :
    public ToolDocSection_
{
public:
    ToolDocSubSection_(ToolDocSubSection_ const & sec) :
        ToolDocSection_(sec)
    {}

    ToolDocSubSection_(CharString const & title) :
        ToolDocSection_(title)
    {}

    virtual EntryType getType() const
    {
        return SUBSECTION;
    }

};

// --------------------------------------------------------------------------
// Class ToolDocLine__
// --------------------------------------------------------------------------

// A Line/Paragraph in ToolDoc documents.

class ToolDocLine_ :
    public ToolDocEntry_
{
public:
    CharString _text;
    // Evaluates to true if it is a paragraph and separated by .sp, false if it is a line, separated by .br.
    bool _isPar;

    ToolDocLine_(ToolDocLine_ const & line) :
        ToolDocEntry_(line), _text(line._text), _isPar(line._isPar)
    {}

    ToolDocLine_(CharString const & text, bool isParagraph) :
        _text(text), _isPar(isParagraph)
    {}

    virtual EntryType getType() const
    {
        return LINE;
    }

    bool isParagraph() const
    {
        return _isPar;
    }

};

// --------------------------------------------------------------------------
// Class ToolDocListItem_
// --------------------------------------------------------------------------

// A list item in ToolDoc documents.

class ToolDocListItem_ :
    public ToolDocEntry_
{
public:
    CharString _term;
    CharString _description;

    ToolDocListItem_(ToolDocListItem_ const & item) :
        ToolDocEntry_(item), _term(item._term), _description(item._description)
    {}

    ToolDocListItem_(CharString const & term, CharString const & description) :
        _term(term), _description(description)
    {}

    virtual EntryType getType() const
    {
        return LIST_ITEM;
    }

};

// --------------------------------------------------------------------------
// Class ToolDocPrinter_
// --------------------------------------------------------------------------

// Abstrace base class for ToolDoc printers.

class ToolDocPrinter_
{
public:
    virtual void print(std::ostream & stream, ToolDoc const & doc) = 0;
};

// --------------------------------------------------------------------------
// Class ManToolDocPrinter_
// --------------------------------------------------------------------------

// Print ToolDoc instance in man format.

class ManToolDocPrinter_ :
    public ToolDocPrinter_
{
public:
    virtual void print(std::ostream & stream, ToolDoc const & doc);
};

// --------------------------------------------------------------------------
// Class HtmlToolDocPrinter_
// --------------------------------------------------------------------------

// Print ToolDoc instance in HTML format.

class HtmlToolDocPrinter_ :
    public ToolDocPrinter_
{
public:
    void _maybeCloseList(std::ostream & stream, bool & isListOpen)
    {
        if (!isListOpen)
            return;

        stream << "</dl>\n";
        isListOpen = false;
    }

    void _maybeCloseParagraph(std::ostream & stream, bool & isParOpen)
    {
        if (!isParOpen)
            return;

        stream << "</p>\n";
        isParOpen = false;
    }

    // Converts formatting with \fI, \fB, and \fP to HTML.
    template <typename TSequence>
    TSequence _toHtml(TSequence const & input) const
    {
        TSequence buffer = xmlEscape(input);
        TSequence result;
        String<TSequence> openTags;

        typedef typename Iterator<TSequence const, Standard>::Type TIterator;
        TIterator endIt = end(input, Standard());
        for (TIterator it = begin(input, Standard()); it != endIt; goNext(it))
        {
            if (*it == '\\')
            {
                // Handle escape sequence, we interpret only "\-", "\fI", and "\fB".
                goNext(it);
                SEQAN_ASSERT_NOT(it == endIt);
                if (*it == '-')
                {
                    appendValue(result, *it);
                }
                else if (*it == 'f')
                {
                    goNext(it);
                    SEQAN_ASSERT_NOT(it == endIt);
                    if (*it == 'I')
                    {
                        appendValue(openTags, "em");
                        append(result, "<em>");
                    }
                    else if (*it == 'B')
                    {
                        appendValue(openTags, "strong");
                        append(result, "<strong>");
                    }
                    else if (*it == 'P')
                    {
                        SEQAN_ASSERT_NOT(empty(openTags));
                        append(result, "</");
                        append(result, back(openTags));
                        append(result, ">");
                        eraseBack(openTags);
                    }
                    else
                    {
                        append(result, "\\f");
                        appendValue(result, *it);
                    }
                }
                else
                {
                    appendValue(result, '\\');
                    appendValue(result, *it);
                }
            }
            else
            {
                appendValue(result, *it);
            }
        }

        return result;
    }

    virtual void print(std::ostream & stream, ToolDoc const & doc);
};

// --------------------------------------------------------------------------
// Class TextToolDocPrinter_
// --------------------------------------------------------------------------

// Print ToolDoc objects in Text format, suitable for console output.

class TextToolDocPrinter_ :
    public ToolDocPrinter_
{
public:
    // Stores the relevant parameters of the documentation on the screen.
    struct Layout_
    {
        unsigned screenWidth;
        unsigned defaultScreenWidth;
        unsigned maximalScreenWidth;
        unsigned minimalScreenWidth;
        unsigned leftPadding;
        unsigned centerPadding;
        unsigned rightPadding;
        unsigned leftColumnWidth;
        unsigned rightColumnWidth;
        unsigned rightColumnTab;

        Layout_() :
            screenWidth(0), defaultScreenWidth(80), maximalScreenWidth(120), minimalScreenWidth(40),
            leftPadding(4), centerPadding(2), rightPadding(2), leftColumnWidth(4), rightColumnWidth(0)
        {
            // Guess terminal screen width and set into layout.
            unsigned cols = 0, rows = 0;
            bool success = getTerminalSize(cols, rows);
            screenWidth = (success && cols > 0) ? cols : defaultScreenWidth;
            screenWidth = std::max(screenWidth, minimalScreenWidth);
            screenWidth = std::min(screenWidth, maximalScreenWidth);
            screenWidth -= rightPadding;

            rightColumnWidth = screenWidth - leftPadding - leftColumnWidth - centerPadding - rightPadding;
            rightColumnTab = leftPadding + leftColumnWidth + centerPadding;

            // std::cerr << "screen width\t" << screenWidth << std::endl;
        }

    };

    Layout_ _layout;

    virtual void print(std::ostream & stream, ToolDoc const & doc);

    void _printSection(std::ostream & stream, ToolDocSection_ const & section)
    {
        std::ostream_iterator<char> out(stream);
        stream << '\n' << _toText("\\fB");
        std::transform(begin(section._title), end(section._title), out, static_cast < int(*)(int) > (toupper));
        stream << _toText("\\fP") << '\n';
    }

    void _printSubSection(std::ostream & stream, ToolDocSection_ const & section)
    {
        std::ostream_iterator<char> out(stream);
        stream << '\n' << _toText("\\fB");
        std::fill_n(out, _layout.leftPadding / 2, ' ');
        stream << section._title << _toText("\\fP") << '\n';
    }

    void _printLine(std::ostream & stream, ToolDocLine_ const & line)
    {
        std::ostream_iterator<char> out(stream);
        std::fill_n(out, _layout.leftPadding, ' ');

        _printText(stream, line._text, _layout.leftPadding);
    }

    CharString _toText(CharString const & str) const
    {
        CharString result;

        typedef Iterator<CharString const, Rooted>::Type TIterator;
        for (TIterator it = begin(str, Rooted()); !atEnd(it); goNext(it))
        {
            if (*it == '\\')
            {
                // Handle escape sequence, we interpret only "\-", "\fI", and "\fB".
                goNext(it);
                SEQAN_ASSERT_NOT(atEnd(it));
                if (*it == '-')
                {
                    appendValue(result, *it);
                }
                else if (*it == 'f')
                {
                    goNext(it);
                    SEQAN_ASSERT_NOT(atEnd(it));
                    if (*it == 'I')
                    {
                        if (isTerminal())
                            append(result, "\033[4m");
                    }
                    else if (*it == 'B')
                    {
                        if (isTerminal())
                            append(result, "\033[1m");
                    }
                    else if (*it == 'P')
                    {
                        if (isTerminal())
                            append(result, "\033[0m");
                    }
                    else
                    {
                        append(result, "\\f");
                        appendValue(result, *it);
                    }
                }
                else
                {
                    appendValue(result, '\\');
                    appendValue(result, *it);
                }
            }
            else
            {
                appendValue(result, *it);
            }
        }

        return result;
    }

    void _printListItem(std::ostream & stream, ToolDocListItem_ const & listItem)
    {
        std::ostream_iterator<char> out(stream);

        // Print term.
        std::fill_n(out, _layout.leftPadding, ' ');
        stream << _toText(listItem._term);
        unsigned pos = _layout.leftPadding + length(listItem._term);

        if (empty(listItem._description))
        {
            stream << '\n';
            return;
        }

        if (pos + _layout.centerPadding > _layout.rightColumnTab)
        {
            stream << '\n';
            pos = 0;
        }
        std::fill_n(out, _layout.rightColumnTab - pos, ' ');

        _printText(stream, listItem._description, _layout.rightColumnTab);
    }

    // Returns width of text if printed, i.e. "\-" has length 1, "\fI", "\fB", "\fP" have length 0.
    unsigned _textWidth(CharString const & text)
    {
        unsigned result = 0;

        for (unsigned i = 0; i < length(text); ++i)
        {
            if (text[i] != '\\')
            {
                result += 1;
                continue;
            }

            if (i + 1 == length(text))
            {
                result += 1;  // Will print "\\".
                continue;
            }

            if (text[i + 1] == '\\' || text[i + 1] == '-')
            {
                i += 1;
                result += 1;
                continue;  // Will print '\\' or '-'.
            }

            if (i + 2 == length(text))
            {
                i += 1;
                result += 2;  // Will print two chars.
                continue;
            }

            if (text[i + 1] == 'f')
            {
                if (text[i + 2] == 'B' || text[i + 2] == 'I' || text[i + 2] == 'P')
                    i += 2;  // Skip f and {B, I, P}.
                else
                    result += 1;
            }
        }

        return result;
    }

    // Print text, must be at tab already.
    void _printText(std::ostream & stream, CharString const & text, unsigned tab)
    {
        unsigned pos = tab;
        std::ostream_iterator<char> out(stream);

        // Tokenize the text.
        std::istringstream iss(toCString(text));
        std::vector<std::string> tokens;
        std::copy(std::istream_iterator<std::string>(iss), std::istream_iterator<std::string>(),
                  std::back_inserter<std::vector<std::string> >(tokens));

        // Print the text.
        SEQAN_ASSERT_LEQ(pos, tab);
        std::fill_n(out, tab - pos, ' ');  // go to tab

        pos = tab;
        typedef std::vector<std::string>::const_iterator TConstIter;
        for (TConstIter it = tokens.begin(); it != tokens.end(); ++it)
        {
            if (it == tokens.begin())
            {
                stream << _toText(*it);
                pos += _textWidth(*it);
                if (pos > _layout.screenWidth)
                {
                    stream << '\n';
                    std::fill_n(out, tab, ' ');
                    pos = tab;
                }
            }
            else
            {
                if (pos + 1 + _textWidth(*it) > _layout.screenWidth)
                {
                    // Would go over screen with next, print current word on next line.
                    stream << '\n';
                    fill_n(out, tab, ' ');
                    stream << _toText(*it);
                    pos = tab + _textWidth(*it);
                }
                else
                {
                    stream << ' ';
                    stream << _toText(*it);
                    pos += _textWidth(*it) + 1;
                }
            }
        }
        if (!empty(tokens))
            stream << '\n';
    }

};

// --------------------------------------------------------------------------
// Class ToolDoc
// --------------------------------------------------------------------------

/*!
 * @class ToolDoc
 * @implements AssignableConcept
 * @headerfile <seqan/arg_parse.>
 * @brief Container for string documentation on a command line tool.
 *
 * @signature class ToolDoc;
 *
 * @section Remarks
 *
 * This class is generally not used directly by the user but through @link ArgumentParser @endlink. It allows one to store
 * and represent all information related to a command line tool that would normally go into a man page. It can be
 * printed to STL streams in different formats, currently plain text, HTML and man pages are supported.
 *
 * You can also use basic formatting in text. This formatting is tailored to the usage on the command line. Use
 * <tt>\fB</tt> to start bold font, <tt>\fI</tt> to start italic font and <tt>\fP</tt> to use the previous font (of
 * course, use correct escaping of the backslash in C strings, so use <tt>"\\fB"</tt>, <tt>"\\fI"</tt>, and
 * <tt>"\\fP"</tt> in your code.
 *
 * @section Examples
 *
 * The following shows a brief example of how to use @link ToolDoc @endlink.
 *
 * @code{.cpp}
 * ToolDoc doc;
 * setName(doc, "RazerS");
 * setShortDescription(doc, "Read mapping with controllable sensitivity.");
 * setDate(doc, "04 March 2012");
 * setVersion(doc, "1.0");
 * setCategory(doc, "Read Mapping");
 * setManTitle(doc, "SeqAn Apps Reference Manual");
 *
 * addSection(doc, "Synopsis");
 * addText(doc, "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fIREADS\\fP", false);
 * addText(doc,
 *         "\\fBrazers\\fP [\\fIOPTIONS\\fP] \\fIREFERENCE\\fP \\fILEFT_READS\\fP "
 *         "\\fIRIGHT_READS\\fP", false);
 *
 * addSection(doc, "Description");
 * addText(doc,
 *         "RazerS is a read mapper with controllable, sensitivity.  This "
 *         "means that you can find all read matches in the reference sequence "
 *         "and optionally, you can trade lower sensitivity for better "
 *         "performance.");
 * addText(doc,
 *         "What's special about RazerS is that you can control the sensitivity.");
 *
 * addSection(doc, "Options");
 * addSubSection(doc, "Main Options");
 * addListItem(doc, "\\fB-id\\fP, \\fB--indels\\fP",
 *             "Enable mapping with indels enabled.");
 * addListItem(doc, "\\fB-i\\fP, \\fB--identity\\fP \\fIIDENTITY\\fP",
 *             "Set minimal identity of matches to find.");
 *
 * print(std::cout, doc, "text");
 * @endcode
 *
 * @see ToolDoc#addText
 * @see ToolDoc#addListItem
 * @see ArgumentParser
 */

/*!
 * @fn ToolDoc::ToolDoc
 * @brief Constructor
 *
 * @signature ToolDoc::ToolDoc()
 */

class ToolDoc
{
public:
    CharString _name;
    CharString _shortDescription;
    CharString _url;
    CharString _date;
    CharString _version;
    CharString _shortCopyright;
    CharString _longCopyright;
    CharString _citation;
    CharString _manTitle;
    CharString _category;
    unsigned _manSection;

    String<ToolDocEntry_ *> _entries;

    enum Format {FORMAT_HTML, FORMAT_MAN, FORMAT_TXT};

    ToolDoc() :
        _manSection(1) {}

    ToolDoc(ToolDoc const & toolDoc) :
        _name(toolDoc._name), _shortDescription(toolDoc._shortDescription), _url(toolDoc._url),
        _date(toolDoc._date), _version(toolDoc._version), _shortCopyright(toolDoc._shortCopyright),
        _longCopyright(toolDoc._longCopyright), _citation(toolDoc._citation), _manTitle(toolDoc._manTitle),
        _category(toolDoc._category), _manSection(1)
    {
        append(*this, toolDoc);
    }

    ~ToolDoc()
    {
        clearEntries(*this);
    }

    void print(std::ostream & stream, Format format) const
    {
        switch (format)
        {
        case FORMAT_HTML:
        {
            HtmlToolDocPrinter_ p;
            p.print(stream, *this);
        }
        break;

        case FORMAT_MAN:
        {
            ManToolDocPrinter_ p;
            p.print(stream, *this);
        }
        break;

        case FORMAT_TXT:
        {
            TextToolDocPrinter_ p;
            p.print(stream, *this);
        }
        break;
        }
    }

    void print(std::ostream & stream, CharString const & format) const
    {
        if (format == "html")
            print(stream, FORMAT_HTML);
        else if (format == "man")
            print(stream, FORMAT_MAN);
        else
            print(stream, FORMAT_TXT);
    }

};

// ==========================================================================
// Metafunctions
// ==========================================================================

// ==========================================================================
// Functions
// ==========================================================================

// --------------------------------------------------------------------------
// Function append()                                                  ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#append
 * @headerfile <seqan/arg_parse.h>
 * @brief Append two @link ToolDoc @endlink objects.
 *
 * @signature void append(a, b);
 *
 * @param[in,out] a This object is updated
 * @param[in]     b This object is appended to <tt>b</tt>.
 */

inline void append(ToolDoc & a, ToolDoc const & b)
{
    for (unsigned i = 0; i < length(b._entries); ++i)
    {
        // TODO(holtgrew): This is quite ugly and can be made better with shared_ptr<> in C++11.
        switch (b._entries[i]->getType())
        {
        case ToolDocEntry_::SUBSECTION:
            appendValue(a._entries, new ToolDocSubSection_(*static_cast<ToolDocSubSection_ *>(b._entries[i])));
            break;

        case ToolDocEntry_::SECTION:
            appendValue(a._entries, new ToolDocSection_(*static_cast<ToolDocSection_ *>(b._entries[i])));
            break;

        case ToolDocEntry_::LINE:
            appendValue(a._entries, new ToolDocLine_(*static_cast<ToolDocLine_ *>(b._entries[i])));
            break;

        case ToolDocEntry_::LIST_ITEM:
            appendValue(a._entries, new ToolDocListItem_(*static_cast<ToolDocListItem_ *>(b._entries[i])));
            break;
        }
    }
}

// --------------------------------------------------------------------------
// Function setName()                                                 ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setName
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool name.
 *
 * @signature void setName(toolDoc, name);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the name for.
 * @param[in]     name    The name of the tool (@link CharString @endlink).
 */

inline void setName(ToolDoc & doc, CharString const & name)
{
    doc._name = name;
}

// --------------------------------------------------------------------------
// Function getName()                                                 ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getName
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool name.
 *
 * @signature CharString getName(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the name for.
 *
 * @return CharString Resulting name (@link CharString @endlink).
 */

inline CharString const & getName(ToolDoc const & doc)
{
    return doc._name;
}

// --------------------------------------------------------------------------
// Function setCategory()                                             ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setCategory
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool name.
 *
 * @signature void setName(toolDoc, name);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the name for.
 * @param[in]     name    The name of the tool (@link CharString @endlink).
 */

inline void setCategory(ToolDoc & doc, CharString const & category)
{
    doc._category = category;
}

// --------------------------------------------------------------------------
// Function getCategory()                                             ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getCategory
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool category.
 *
 * @signature CharString getCategory(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the category for.
 *
 * @return CharString Resulting category (@link CharString @endlink).
 */

inline CharString const & getCategory(ToolDoc const & doc)
{
    return doc._category;
}

// --------------------------------------------------------------------------
// Function setShortDescription()                                     ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setShortDescription
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool short description.
 *
 * @signature void setShortDescription(toolDoc, text);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the short description for.
 * @param[in]     text    The short description of the tool (@link CharString @endlink).
 */

inline void setShortDescription(ToolDoc & doc, CharString const & shortDescription)
{
    doc._shortDescription = shortDescription;
}

// --------------------------------------------------------------------------
// Function getShortDescription()                                     ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getShortDescription
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool short description.
 *
 * @signature CharString getShortDescription(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the short description for.
 *
 * @return CharString Resulting short description (@link CharString @endlink).
 */

inline CharString const & getShortDescription(ToolDoc const & doc)
{
    return doc._shortDescription;
}

// --------------------------------------------------------------------------
// Function setUrl()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setUrl
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the url string to the app repository or website.
 *
 * @signature void setUrl(toolDoc, str);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the version string for.
 * @param[in]     str     The url string of the tool (@link CharString @endlink).
 */

inline void setUrl(ToolDoc & doc, CharString url)
{
    std::swap(doc._url, url);
}

// --------------------------------------------------------------------------
// Function getUrl()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getUrl
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the url string to the app repository or website.
 *
 * @signature CharString getUrl(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the version string.
 *
 * @return CharString Resulting url string (@link CharString @endlink).
 */

inline CharString const & getUrl(ToolDoc const & doc)
{
    return doc._url;
}

// --------------------------------------------------------------------------
// Function setDate()                                                 ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setDate
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the date string.
 *
 * @signature void setName(toolDoc, str);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the date string for.
 * @param[in]     str     The date string of the tool (@link CharString @endlink).
 */

inline void setDate(ToolDoc & doc, CharString const & date)
{
    doc._date = date;
}

// --------------------------------------------------------------------------
// Function getDate()                                                 ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getDate
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the date.
 *
 * @signature CharString getDate(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the date from.
 *
 * @return CharString Resulting date string (@link CharString @endlink).
 */

inline CharString const & getDate(ToolDoc const & doc)
{
    return doc._date;
}

// --------------------------------------------------------------------------
// Function setVersion()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setVersion
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool version string.
 *
 * @signature void setVersion(toolDoc, str);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the version string for.
 * @param[in]     str     The version string of the tool (@link CharString @endlink).
 */

inline void setVersion(ToolDoc & doc, CharString const & version)
{
    doc._version = version;
}

// --------------------------------------------------------------------------
// Function getVersion()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getVersion
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool version string.
 *
 * @signature CharString getVersion(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the version string.
 *
 * @return CharString Resulting version string (@link CharString @endlink).
 */

inline CharString const & getVersion(ToolDoc const & doc)
{
    return doc._version;
}

// --------------------------------------------------------------------------
// Function setShortCopyright()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setShortCopyright
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool short copyright string.
 *
 * @signature void setShortCopyright(toolDoc, str);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the short copyright string for.
 * @param[in]     str     The short copyright string of the tool (@link CharString @endlink).
 */

inline void setShortCopyright(ToolDoc & doc, CharString const & shortCopyright)
{
    doc._shortCopyright = shortCopyright;
}

// --------------------------------------------------------------------------
// Function getShortCopyright()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getShortCopyright
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool short copyright string.
 *
 * @signature CharString getShortCopyright(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the short copyright string.
 *
 * @return CharString Resulting short copyright string (@link CharString @endlink).
 */

inline CharString const & getShortCopyright(ToolDoc const & doc)
{
    return doc._shortCopyright;
}

// --------------------------------------------------------------------------
// Function setLongCopyright()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setLongCopyright
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool long copyright string.
 *
 * @signature void setLongCopyright(toolDoc, str);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the long copyright string for.
 * @param[in]     str     The long copyright string of the tool (@link CharString @endlink).
 */

inline void setLongCopyright(ToolDoc & doc, CharString const & longCopyright)
{
    doc._longCopyright = longCopyright;
}

// --------------------------------------------------------------------------
// Function getLongCopyright()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getLongCopyright
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool long copyright string.
 *
 * @signature CharString getLongCopyright(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the long copyright string.
 *
 * @return CharString Resulting long copyright string (@link CharString @endlink).
 */

inline CharString const & getLongCopyright(ToolDoc const & doc)
{
    return doc._longCopyright;
}

// --------------------------------------------------------------------------
// Function setCitation()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setCitation
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the tool citation string.
 *
 * @signature void setCitation(toolDoc, str);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the citation string for.
 * @param[in]     str     The citation string of the tool (@link CharString @endlink).
 */

inline void setCitation(ToolDoc & doc, CharString const & citation)
{
    doc._citation = citation;
}

// --------------------------------------------------------------------------
// Function getCitation()                                              ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getCitation
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool citation string.
 *
 * @signature CharString getCitation(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the citation string.
 *
 * @return CharString Resulting citation string (@link CharString @endlink).
 */

inline CharString const & getCitation(ToolDoc const & doc)
{
    return doc._citation;
}


// --------------------------------------------------------------------------
// Function setManTitle()                                             ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#setManTitle
 * @headerfile <seqan/arg_parse.h>
 * @brief Set the man title.
 *
 * @signature void setTitle(toolDoc, title);
 *
 * @param[in,out] toolDoc The ToolDoc object to the set the title for.
 * @param[in]     title   The title of the tool (@link CharString @endlink).
 */

inline void setManTitle(ToolDoc & doc, CharString const & title)
{
    doc._manTitle = title;
}

// --------------------------------------------------------------------------
// Function getManTitle()                                             ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#getManTitle
 * @headerfile <seqan/arg_parse.h>
 * @brief Get the tool man page title of.
 *
 * @signature CharString getManTitle(toolDoc);
 *
 * @param[in] toolDoc The ToolDoc object to the get the man page title.
 *
 * @return CharString Resulting man page title (@link CharString @endlink).
 */

inline CharString const & getManTitle(ToolDoc & doc)
{
    return doc._manTitle;
}

// --------------------------------------------------------------------------
// Function addSection()ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#addSection
 * @headerfile <seqan/arg_parse.h>
 * @brief Add a section with the given title.
 *
 * @signature void addSection(toolDoc, title);
 *
 * @param[in,out] toolDoc The ToolDoc object to add a section for.
 * @param[in]     title   The section title (@link CharString @endlink).
 */

inline void addSection(ToolDoc & doc, CharString const & title)
{
    appendValue(doc._entries, new ToolDocSection_(title));
}

// --------------------------------------------------------------------------
// Function addSubSection()                                           ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#addSubSection
 * @headerfile <seqan/arg_parse.h>
 * @brief Add a subsection with the given title.
 *
 * @signature void addSubSection(toolDoc, title);
 *
 * @param[in,out] toolDoc The ToolDoc object to add a subsection for.
 * @param[in]     title   The subsection title (@link CharString @endlink).
 */

inline void addSubSection(ToolDoc & doc, CharString const & title)
{
    appendValue(doc._entries, new ToolDocSubSection_(title));
}

// --------------------------------------------------------------------------
// Function addText()                                                 ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#addText
 * @headerfile <seqan/arg_parse.h>
 * @brief Add a text line/paragraph to ToolDoc.
 *
 * @signature void addText(toolDoc, text[, isParagraph]);
 *
 * @param[in,out] toolDoc     The ToolDoc to add the text to.
 * @param[in]     text        The text to add (@link CharString @endlink).
 * @param[in]     isParagraph Whether to insert as paragraph or just a line (only one line break if not a paragraph).
 */

inline void addText(ToolDoc & doc, CharString const & text, bool isParagraph)
{
    appendValue(doc._entries, new ToolDocLine_(text, isParagraph));
}

inline void addText(ToolDoc & doc, CharString const & text)
{
    addText(doc, text, true);
}

// --------------------------------------------------------------------------
// Function addListItem()                                             ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#addListItem
 * @headerfile <seqan/arg_parse.h>
 * @brief Add a list item to a ToolDoc.
 *
 * @signature void addListItem(toolDoc, key, value);
 *
 * @param[in,out] toolDoc The ToolDoc object to add the list item to.
 * @param[in]     key     The key for the list (@link CharString @endlink).
 * @param[in]     value   The value for the list (@link CharString @endlink).
 */

inline void addListItem(ToolDoc & doc, CharString const & key, CharString const & value)
{
    appendValue(doc._entries, new ToolDocListItem_(key, value));
}

// --------------------------------------------------------------------------
// Function print()                                                   ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#print
 * @headerfile <seqan/arg_parse.h>
 * @brief Print ToolDoc object in a given format.
 *
 * @signature void print(stream, toolDoc, format);
 *
 * @param[in,out] stream  The <tt>std::ostream</tt> to write to.
 * @param[in]     toolDoc The ToolDoc to print.
 * @param[in]     format  The format, one of {"html", "man", "txt"}.
 */

inline void print(std::ostream & stream, ToolDoc const & doc, CharString const & format)
{
    doc.print(stream, format);
}

// --------------------------------------------------------------------------
// Function clearEntries()                                            ToolDoc
// --------------------------------------------------------------------------

/*!
 * @fn ToolDoc#clearEntries
 * @headerfile <seqan/arg_parse.h>
 * @brief Clear entries from ToolDoc.
 *
 * @signature void clearEntries(toolDoc);
 *
 * @param[in,out] toolDoc The ToolDoc object to clear entries from.
 */

inline void clearEntries(ToolDoc & doc)
{
    typedef Iterator<String<ToolDocEntry_ *>, Rooted>::Type TIter;
    for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it))
        delete *it;
    clear(doc._entries);
}

// --------------------------------------------------------------------------
// Function HtmlDocPrinter_::print()
// --------------------------------------------------------------------------

inline
void HtmlToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
{
    // Print HTML boilerplate header.
    stream << "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.01//EN\" "
           << "http://www.w3.org/TR/html4/strict.dtd\">\n"
           << "<html lang=\"en\">\n"
           << "<head>\n"
           << "<meta http-equiv=\"content-type\" content=\"text/html; charset=utf-8\">\n"
           << "<title>" << xmlEscape(doc._name) << " &mdash; " << xmlEscape(doc._shortDescription) << "</title>\n"
           << "</head>\n"
           << "<body>\n";

    stream << "<h1>" << _toHtml(doc._name) << "</h1>\n"
           << "<div>" << _toHtml(doc._shortDescription) << "</div>\n";

    typedef Iterator<String<ToolDocEntry_ *> const, Rooted>::Type TIter;
    bool isDl = false;
    bool isP = false;
    for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it))
    {
        SEQAN_ASSERT_NOT_MSG(isDl && isP, "Current <dl> and <p> are mutually exclusive.");
        ToolDocEntry_ * entry = *it;

        switch (entry->getType())
        {
        case ToolDocEntry_::SECTION:
        {
            _maybeCloseList(stream, isDl);
            _maybeCloseParagraph(stream, isP);
            ToolDocSection_ const * sec = static_cast<ToolDocSection_ const *>(entry);
            stream << "<h2>" << _toHtml(sec->_title) << "</h2>\n";
        }
        break;

        case ToolDocEntry_::SUBSECTION:
        {
            _maybeCloseList(stream, isDl);
            _maybeCloseParagraph(stream, isP);
            ToolDocSection_ const * sec = static_cast<ToolDocSection_ const *>(entry);
            stream << "<h3>" << _toHtml(sec->_title) << "</h3>\n";
        }
        break;

        case ToolDocEntry_::LINE:
        {
            ToolDocLine_ const * line = static_cast<ToolDocLine_ const *>(entry);
            _maybeCloseList(stream, isDl);
            if (!isP)
            {
                stream << "<p>\n";
                isP = true;
            }
            stream << _toHtml(line->_text) << "\n";
            if (line->isParagraph())
                _maybeCloseParagraph(stream, isP);
            else
                stream << "<br />\n";
        }
        break;

        case ToolDocEntry_::LIST_ITEM:
        {
            _maybeCloseParagraph(stream, isP);
            ToolDocListItem_ const * item = static_cast<ToolDocListItem_ const *>(entry);
            if (!isDl)
            {
                stream << "<dl>\n";
                isDl = true;
            }
            stream << "<dt>" << _toHtml(item->_term) << "</dt>\n"
                   << "<dd>" << _toHtml(item->_description) << "</dd>\n";
        }
        break;
        }
    }
    _maybeCloseList(stream, isDl);

    // Print version, date and url.
    stream << "<h2>Version</h2>\n"
           << "<strong>Last update:</strong> " << _toHtml(doc._date) << "<br>\n<strong>"
           << doc._name << " version:</strong> " << doc._version << "<br>\n"
           << "<strong>SeqAn version:</strong> " << SEQAN_VERSION_MAJOR << '.' <<  SEQAN_VERSION_MINOR << '.'
           << SEQAN_VERSION_PATCH;
    if (SEQAN_VERSION_PRE_RELEASE != 0)
        stream << "-pre" << SEQAN_VERSION_PRE_RELEASE;
    if (!empty(doc._url))
    {
        stream << "<h2>Url</h2>\n"
               << doc._url << "<br>\n";
    }
    stream << "<br>\n";

    // Print legal stuff
    if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation)))
    {
        stream << "<h2>Legal</h2>\n<strong>";

        if (!empty(doc._shortCopyright))
            stream << doc._name << " Copyright: </strong>"
                   << doc._shortCopyright << "<br>\n<strong>";

        stream << "SeqAn Copyright:</strong> 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.<br>\n<strong>";

        if (!empty(doc._citation))
            stream << "In your academic works please cite:</strong> " << doc._citation << "<br>\n";
        else
            stream << "</strong>";

        if (!empty(doc._longCopyright))
            stream << "For full copyright and/or warranty information see <tt>--copyright</tt>.\n";
    }

    // Print HTML boilerplate footer.
    stream << "</body></html>";
}

// --------------------------------------------------------------------------
// Function TextDocPrinter_::print()
// --------------------------------------------------------------------------

inline
void TextToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
{
    std::ostream_iterator<char> out(stream);

    stream << doc._name;
    if (!empty(doc._shortDescription))
        stream << " - " << doc._shortDescription;
    stream << "\n";
    unsigned len = _textWidth(doc._name) + (empty(doc._shortDescription) ? 0 : 3) + _textWidth(doc._shortDescription);
    std::fill_n(out, len, '=');
    stream << '\n';

    typedef Iterator<String<ToolDocEntry_ *> const, Rooted>::Type TIter;
    bool prevWasParagraph = false;  // Stores whether to add a line break.
    for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it))
    {
        ToolDocEntry_ * entry = *it;

        switch (entry->getType())
        {
        case ToolDocEntry_::SECTION:
        {
            ToolDocSection_ const * sec = static_cast<ToolDocSection_ const *>(entry);
            _printSection(stream, *sec);
            prevWasParagraph = false;
        }
        break;

        case ToolDocEntry_::SUBSECTION:
        {
            ToolDocSection_ const * sec = static_cast<ToolDocSection_ const *>(entry);
            _printSubSection(stream, *sec);
            prevWasParagraph = false;
        }
        break;

        case ToolDocEntry_::LINE:
        {
            if (prevWasParagraph)
                stream << '\n';
            ToolDocLine_ const * line = static_cast<ToolDocLine_ const *>(entry);
            _printLine(stream, *line);
            prevWasParagraph = line->isParagraph();
        }
        break;

        case ToolDocEntry_::LIST_ITEM:
        {
            if (prevWasParagraph)
                stream << '\n';
            ToolDocListItem_ const * item = static_cast<ToolDocListItem_ const *>(entry);
            _printListItem(stream, *item);
            prevWasParagraph = false;
        }
        break;
        }
    }

    // Print version, date and url.
    stream << "\n" << _toText("\\fB") << "VERSION" << _toText("\\fP") << "\n";
    std::fill_n(out, _layout.leftPadding, ' ');
    stream << _toText("\\fB") << "Last update: " << _toText("\\fP") << doc._date << "\n";
    std::fill_n(out, _layout.leftPadding, ' ');
    stream << _toText("\\fB") << doc._name << " version: " << _toText("\\fP") << doc._version << "\n";
    std::fill_n(out, _layout.leftPadding, ' ');
    stream << _toText("\\fB") << "SeqAn version: " << _toText("\\fP") << SEQAN_VERSION_MAJOR << '.'
           <<  SEQAN_VERSION_MINOR << '.' << SEQAN_VERSION_PATCH;
    if (SEQAN_VERSION_PRE_RELEASE != 0)
        stream << "-pre" << SEQAN_VERSION_PRE_RELEASE;
    if (!empty(doc._url))
    {
        stream <<  "\n" << _toText("\\fB") << "URL" << _toText("\\fP") << "\n";
        std::fill_n(out, _layout.leftPadding, ' ');
        stream << doc._url << "\n";
    }
    stream << "\n";

    // Print legal stuff
    if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation)))
    {
        stream << "\n" << _toText("\\fB") << "LEGAL" << _toText("\\fP") << "\n";

        if (!empty(doc._shortCopyright))
        {
            std::fill_n(out, _layout.leftPadding, ' ');
            stream << _toText("\\fB") << doc._name << " Copyright: "
                   << _toText("\\fP") << doc._shortCopyright << "\n";
        }
        std::fill_n(out, _layout.leftPadding, ' ');
        stream << _toText("\\fB") << "SeqAn Copyright: " << _toText("\\fP")
               << "2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n";
        if (!empty(doc._citation))
        {
            std::fill_n(out, _layout.leftPadding, ' ');
            stream << _toText("\\fB") << "In your academic works please cite: " << _toText("\\fP")
                   << doc._citation << "\n";
        }
        if (!empty(doc._longCopyright))
        {
            std::fill_n(out, _layout.leftPadding, ' ');
            stream << "For full copyright and/or warranty information see " << _toText("\\fB")
                   << "--copyright" << _toText("\\fP") << ".\n";
        }
    }
}

// --------------------------------------------------------------------------
// Function ManToolDocPrinter_::print()
// --------------------------------------------------------------------------

//brief: "." or "'" indicate man page macros that need to be escaped with "\\&"
template <typename TString>
void print_first_in_line(std::ostream & stream, TString const & str)
{
    if (length(str) > 0 &&
        (str[0] == '.' || str[0] == '\''))
        stream << "\\&";
    stream << str;
}

inline
void ManToolDocPrinter_::print(std::ostream & stream, ToolDoc const & doc)
{
    std::ostream_iterator<char> out(stream);

    // Print .TH line.
    stream << ".TH ";
    std::transform(begin(doc._name), end(doc._name), out, static_cast < int(*)(int) > (toupper));
    stream << " " << doc._manSection << " \"" << doc._date << "\" \"";
    std::transform(begin(doc._name), end(doc._name), out, static_cast < int(*)(int) > (tolower));
    stream << " " << doc._version << "\" \"" << doc._manTitle << "\"\n";

    // Print NAME section.
    stream << ".SH NAME\n"
           << doc._name << " \\- " << doc._shortDescription << std::endl;

    // Print text.
    typedef Iterator<String<ToolDocEntry_ *> const, Rooted>::Type TIter;
    bool isFirstInSection = true;
    for (TIter it = begin(doc._entries, Rooted()); !atEnd(it); goNext(it))
    {
        ToolDocEntry_ * entry = *it;
        switch (entry->getType())
        {
        case ToolDocEntry_::SUBSECTION:
        {
            ToolDocSubSection_ const * sec = static_cast<ToolDocSubSection_ const *>(entry);
            stream << ".SS " << sec->_title << "\n";
            isFirstInSection = true;
        }
        break;

        case ToolDocEntry_::SECTION:
        {
            ToolDocSection_ const * sec = static_cast<ToolDocSection_ const *>(entry);
            stream << ".SH ";
            std::transform(begin(sec->_title), end(sec->_title), out, static_cast < int(*)(int) > (toupper));
            stream << "\n";
            isFirstInSection = true;
        }
        break;

        case ToolDocEntry_::LINE:
        {
            ToolDocLine_ const * line = static_cast<ToolDocLine_ const *>(entry);
            if (!isFirstInSection && line->isParagraph())
                stream << ".sp\n";
            else if (!isFirstInSection && !line->isParagraph())
                stream << ".br\n";
            print_first_in_line(stream, line->_text);
            stream << "\n";
            isFirstInSection = false;
        }
        break;

        case ToolDocEntry_::LIST_ITEM:
        {
            ToolDocListItem_ const * item = static_cast<ToolDocListItem_ const *>(entry);
            stream << ".TP\n";
            print_first_in_line(stream, item->_term);
            stream << "\n";
            print_first_in_line(stream, item->_description);
            stream << "\n";
            isFirstInSection = false;
        }
        break;
        }
    }

    // Print legal stuff
    if ((!empty(doc._shortCopyright)) || (!empty(doc._longCopyright)) || (!empty(doc._citation)))
    {
        stream << ".SH LEGAL\n";

        if (!empty(doc._shortCopyright))
            stream << "\\fB" << doc._name << " Copyright:\\fR " << doc._shortCopyright << "\n.br\n";

        stream << "\\fBSeqAn Copyright:\\fR 2006-2015 Knut Reinert, FU-Berlin; released under the 3-clause BSDL.\n.br\n";

        if (!empty(doc._citation))
            stream << "\\fBIn your academic works please cite:\\fR " << doc._citation << "\n.br\n";

        if (!empty(doc._longCopyright))
            stream << "For full copyright and/or warranty information see \\fB--copyright\\fR.\n";
    }
}

}  // namespace seqan

#endif  // #ifndef SEQAN_INCLUDE_MISC_TOOL_DOC_H_