/usr/share/doc/libclustalo-doc/api/html/seq_8h.html is in libclustalo-doc 1.2.4-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
<meta http-equiv="X-UA-Compatible" content="IE=9"/>
<meta name="generator" content="Doxygen 1.8.12"/>
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<title>Clustal Omega: src/clustal/seq.h File Reference</title>
<link href="tabs.css" rel="stylesheet" type="text/css"/>
<script type="text/javascript" src="jquery.js"></script>
<script type="text/javascript" src="dynsections.js"></script>
<link href="doxygen.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="top"><!-- do not remove this div, it is closed by doxygen! -->
<div id="titlearea">
<table cellspacing="0" cellpadding="0">
<tbody>
<tr style="height: 56px;">
<td id="projectalign" style="padding-left: 0.5em;">
<div id="projectname">Clustal Omega
 <span id="projectnumber">1.2.4</span>
</div>
</td>
</tr>
</tbody>
</table>
</div>
<!-- end header part -->
<!-- Generated by Doxygen 1.8.12 -->
<script type="text/javascript" src="menudata.js"></script>
<script type="text/javascript" src="menu.js"></script>
<script type="text/javascript">
$(function() {
initMenu('',false,false,'search.php','Search');
});
</script>
<div id="main-nav"></div>
<div id="nav-path" class="navpath">
<ul>
<li class="navelem"><a class="el" href="dir_68267d1309a1af8e8297ef4c3efbcdba.html">src</a></li><li class="navelem"><a class="el" href="dir_078e8be2a200f8a2ce3af8fa572ccadf.html">clustal</a></li> </ul>
</div>
</div><!-- top -->
<div class="header">
<div class="summary">
<a href="#nested-classes">Data Structures</a> |
<a href="#define-members">Macros</a> |
<a href="#func-members">Functions</a> </div>
<div class="headertitle">
<div class="title">seq.h File Reference</div> </div>
</div><!--header-->
<div class="contents">
<div class="textblock"><code>#include "squid/squid.h"</code><br />
<code>#include "<a class="el" href="util_8h_source.html">util.h</a>"</code><br />
</div><div class="textblock"><div class="dynheader">
Include dependency graph for seq.h:</div>
<div class="dyncontent">
<div class="center"><img src="seq_8h__incl.png" border="0" usemap="#src_2clustal_2seq_8h" alt=""/></div>
<map name="src_2clustal_2seq_8h" id="src_2clustal_2seq_8h">
<area shape="rect" id="node3" href="util_8h.html" title="util.h" alt="" coords="205,80,258,107"/>
</map>
</div>
</div><div class="textblock"><div class="dynheader">
This graph shows which files directly or indirectly include this file:</div>
<div class="dyncontent">
<div class="center"><img src="seq_8h__dep__incl.png" border="0" usemap="#src_2clustal_2seq_8hdep" alt=""/></div>
<map name="src_2clustal_2seq_8hdep" id="src_2clustal_2seq_8hdep">
<area shape="rect" id="node2" href="hhalign__wrapper_8c.html" title="src/clustal/hhalign\l_wrapper.c" alt="" coords="5,244,141,285"/>
<area shape="rect" id="node3" href="symmatrix_8h.html" title="src/clustal/symmatrix.h" alt="" coords="524,80,695,107"/>
<area shape="rect" id="node4" href="tree_8h.html" title="src/clustal/tree.h" alt="" coords="60,162,188,189"/>
<area shape="rect" id="node7" href="clustal-omega_8h.html" title="src/clustal-omega.h" alt="" coords="563,251,711,278"/>
<area shape="rect" id="node11" href="ktuple__pair_8h.html" title="src/clustal/ktuple\l_pair.h" alt="" coords="1165,155,1294,196"/>
<area shape="rect" id="node12" href="pair__dist_8h.html" title="src/clustal/pair_dist.h" alt="" coords="933,162,1089,189"/>
<area shape="rect" id="node16" href="mbed_8h.html" title="src/clustal/mbed.h" alt="" coords="769,162,908,189"/>
<area shape="rect" id="node17" href="seq_8c.html" title="src/clustal/seq.c" alt="" coords="871,80,995,107"/>
<area shape="rect" id="node5" href="mbed_8c.html" title="src/clustal/mbed.c" alt="" coords="769,251,908,278"/>
<area shape="rect" id="node10" href="ktuple__pair_8c.html" title="src/clustal/ktuple\l_pair.c" alt="" coords="1062,244,1191,285"/>
<area shape="rect" id="node13" href="muscle__upgma_8c.html" title="src/clustal/muscle\l_upgma.c" alt="" coords="368,244,504,285"/>
<area shape="rect" id="node14" href="muscle__upgma_8h.html" title="src/clustal/muscle\l_upgma.h" alt="" coords="212,155,348,196"/>
<area shape="rect" id="node15" href="symmatrix_8c.html" title="src/clustal/symmatrix.c" alt="" coords="525,162,694,189"/>
<area shape="rect" id="node6" href="tree_8c.html" title="src/clustal/tree.c" alt="" coords="217,251,343,278"/>
<area shape="rect" id="node8" href="pair__dist_8c.html" title="src/clustal/pair_dist.c" alt="" coords="933,333,1088,360"/>
<area shape="rect" id="node9" href="clustal-omega_8c.html" title="src/clustal-omega.c" alt="" coords="564,333,711,360"/>
</map>
</div>
</div>
<p><a href="seq_8h_source.html">Go to the source code of this file.</a></p>
<table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="nested-classes"></a>
Data Structures</h2></td></tr>
<tr class="memitem:"><td class="memItemLeft" align="right" valign="top">struct  </td><td class="memItemRight" valign="bottom"><a class="el" href="structmseq__t.html">mseq_t</a></td></tr>
<tr class="memdesc:"><td class="mdescLeft"> </td><td class="mdescRight">structure for storing multiple sequences <a href="structmseq__t.html#details">More...</a><br /></td></tr>
<tr class="separator:"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="define-members"></a>
Macros</h2></td></tr>
<tr class="memitem:a03dbc4840c83155125914ed849f74416"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a03dbc4840c83155125914ed849f74416">SEQTYPE_UNKNOWN</a>   kOtherSeq</td></tr>
<tr class="separator:a03dbc4840c83155125914ed849f74416"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5e07e6c291f096c3e6b6e8cda4efb37b"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a5e07e6c291f096c3e6b6e8cda4efb37b">SEQTYPE_DNA</a>   kDNA</td></tr>
<tr class="separator:a5e07e6c291f096c3e6b6e8cda4efb37b"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af455eb393971ad3ce026bda535abc82c"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#af455eb393971ad3ce026bda535abc82c">SEQTYPE_RNA</a>   kRNA</td></tr>
<tr class="separator:af455eb393971ad3ce026bda535abc82c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a193343bb1bec0dd172e9b24b9b13c077"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a193343bb1bec0dd172e9b24b9b13c077">SEQTYPE_PROTEIN</a>   kAmino</td></tr>
<tr class="separator:a193343bb1bec0dd172e9b24b9b13c077"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af396304082d44225e44933577c320e43"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#af396304082d44225e44933577c320e43">AMINOACID_ANY</a>   'X'</td></tr>
<tr class="separator:af396304082d44225e44933577c320e43"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:acf7121d916e81f2ee9ac83680434bb9a"><td class="memItemLeft" align="right" valign="top">#define </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#acf7121d916e81f2ee9ac83680434bb9a">NUCLEOTIDE_ANY</a>   'N'</td></tr>
<tr class="separator:acf7121d916e81f2ee9ac83680434bb9a"><td class="memSeparator" colspan="2"> </td></tr>
</table><table class="memberdecls">
<tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="func-members"></a>
Functions</h2></td></tr>
<tr class="memitem:a7fa5b7c740c8906424057c112b192088"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a7fa5b7c740c8906424057c112b192088">AliStat</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq, bool bSampling, bool bReportAll)</td></tr>
<tr class="memdesc:a7fa5b7c740c8906424057c112b192088"><td class="mdescLeft"> </td><td class="mdescRight">Stripped down version of squid's alistat. <a href="#a7fa5b7c740c8906424057c112b192088">More...</a><br /></td></tr>
<tr class="separator:a7fa5b7c740c8906424057c112b192088"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a27f31ca0bdcd5b52610651b7e0e52cd7"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a27f31ca0bdcd5b52610651b7e0e52cd7">AddSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **prMSeqDest_p, char *pcSeqName, char *pcSeqRes)</td></tr>
<tr class="memdesc:a27f31ca0bdcd5b52610651b7e0e52cd7"><td class="mdescLeft"> </td><td class="mdescRight">Creates a new sequence entry and appends it to an existing mseq structure. <a href="#a27f31ca0bdcd5b52610651b7e0e52cd7">More...</a><br /></td></tr>
<tr class="separator:a27f31ca0bdcd5b52610651b7e0e52cd7"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a593f05a8f9329d0409320fed313c720c"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a593f05a8f9329d0409320fed313c720c">SeqSwap</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *mseq, int i, int j)</td></tr>
<tr class="memdesc:a593f05a8f9329d0409320fed313c720c"><td class="mdescLeft"> </td><td class="mdescRight">Swap two sequences in an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> structure. <a href="#a593f05a8f9329d0409320fed313c720c">More...</a><br /></td></tr>
<tr class="separator:a593f05a8f9329d0409320fed313c720c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a0533ef67eccd9c952b43d53072e9a1f1"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a0533ef67eccd9c952b43d53072e9a1f1">DealignMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *mseq)</td></tr>
<tr class="memdesc:a0533ef67eccd9c952b43d53072e9a1f1"><td class="mdescLeft"> </td><td class="mdescRight">Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE. <a href="#a0533ef67eccd9c952b43d53072e9a1f1">More...</a><br /></td></tr>
<tr class="separator:a0533ef67eccd9c952b43d53072e9a1f1"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a30c7f4d7600fec2eaa564df74cac731a"><td class="memItemLeft" align="right" valign="top">const char * </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a30c7f4d7600fec2eaa564df74cac731a">SeqTypeToStr</a> (int seqtype)</td></tr>
<tr class="memdesc:a30c7f4d7600fec2eaa564df74cac731a"><td class="mdescLeft"> </td><td class="mdescRight">convert int-encoded iSeqType to string <a href="#a30c7f4d7600fec2eaa564df74cac731a">More...</a><br /></td></tr>
<tr class="separator:a30c7f4d7600fec2eaa564df74cac731a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a853633b9627f9048adf1e5000a6a0916"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a853633b9627f9048adf1e5000a6a0916">ReadSequences</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq_p, char *pcSeqFile, int iSeqType, int iSeqFmt, bool bIsProfile, bool bDealignInputSeqs, int iMaxNumSeq, int iMaxSeqLen, char *pcHMMBatch)</td></tr>
<tr class="memdesc:a853633b9627f9048adf1e5000a6a0916"><td class="mdescLeft"> </td><td class="mdescRight">reads sequences from file <a href="#a853633b9627f9048adf1e5000a6a0916">More...</a><br /></td></tr>
<tr class="separator:a853633b9627f9048adf1e5000a6a0916"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:af60f55dd9f9840f54bf5057d3ab90d42"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#af60f55dd9f9840f54bf5057d3ab90d42">NewMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **mseq)</td></tr>
<tr class="memdesc:af60f55dd9f9840f54bf5057d3ab90d42"><td class="mdescLeft"> </td><td class="mdescRight">allocate and initialise new <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> <a href="#af60f55dd9f9840f54bf5057d3ab90d42">More...</a><br /></td></tr>
<tr class="separator:af60f55dd9f9840f54bf5057d3ab90d42"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:abb8e94cbbfa6f0b8e527f7107c09ae65"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#abb8e94cbbfa6f0b8e527f7107c09ae65">FreeMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **mseq)</td></tr>
<tr class="memdesc:abb8e94cbbfa6f0b8e527f7107c09ae65"><td class="mdescLeft"> </td><td class="mdescRight">Frees an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> and it's members and zeros all members. <a href="#abb8e94cbbfa6f0b8e527f7107c09ae65">More...</a><br /></td></tr>
<tr class="separator:abb8e94cbbfa6f0b8e527f7107c09ae65"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b124a1118f2276d2a2978227efd0ab4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a6b124a1118f2276d2a2978227efd0ab4">CopyMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **prMSeqDest_p, <a class="el" href="structmseq__t.html">mseq_t</a> *prMSeqSrc)</td></tr>
<tr class="memdesc:a6b124a1118f2276d2a2978227efd0ab4"><td class="mdescLeft"> </td><td class="mdescRight">copies an mseq structure <a href="#a6b124a1118f2276d2a2978227efd0ab4">More...</a><br /></td></tr>
<tr class="separator:a6b124a1118f2276d2a2978227efd0ab4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a6b1d0d3e408720aa012f66f34f740262"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a6b1d0d3e408720aa012f66f34f740262">LogSqInfo</a> (SQINFO *sqinfo)</td></tr>
<tr class="memdesc:a6b1d0d3e408720aa012f66f34f740262"><td class="mdescLeft"> </td><td class="mdescRight">debug output of sqinfo struct <a href="#a6b1d0d3e408720aa012f66f34f740262">More...</a><br /></td></tr>
<tr class="separator:a6b1d0d3e408720aa012f66f34f740262"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a720cb218cff78249b898f4c56a9fee6c"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a720cb218cff78249b898f4c56a9fee6c">FindSeqName</a> (char *seqname, <a class="el" href="structmseq__t.html">mseq_t</a> *mseq)</td></tr>
<tr class="separator:a720cb218cff78249b898f4c56a9fee6c"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:ad84a0cdc0c49df96ef9ef97a053f841e"><td class="memItemLeft" align="right" valign="top">int </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#ad84a0cdc0c49df96ef9ef97a053f841e">WriteAlignment</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *mseq, const char *aln_outfile, int msafile_format, int iWrap, bool bResno)</td></tr>
<tr class="memdesc:ad84a0cdc0c49df96ef9ef97a053f841e"><td class="mdescLeft"> </td><td class="mdescRight">Write alignment to file. <a href="#ad84a0cdc0c49df96ef9ef97a053f841e">More...</a><br /></td></tr>
<tr class="separator:ad84a0cdc0c49df96ef9ef97a053f841e"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a8a10a512577076df441dc133f7eb13d4"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a8a10a512577076df441dc133f7eb13d4">DealignSeq</a> (char *seq)</td></tr>
<tr class="memdesc:a8a10a512577076df441dc133f7eb13d4"><td class="mdescLeft"> </td><td class="mdescRight">Removes all gap-characters from a sequence. <a href="#a8a10a512577076df441dc133f7eb13d4">More...</a><br /></td></tr>
<tr class="separator:a8a10a512577076df441dc133f7eb13d4"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a38db9b206246a53873459ff7f1eace06"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a38db9b206246a53873459ff7f1eace06">ShuffleMSeq</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq)</td></tr>
<tr class="memdesc:a38db9b206246a53873459ff7f1eace06"><td class="mdescLeft"> </td><td class="mdescRight">Shuffle mseq order. <a href="#a38db9b206246a53873459ff7f1eace06">More...</a><br /></td></tr>
<tr class="separator:a38db9b206246a53873459ff7f1eace06"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a3f29666b8ab80ed563d96fdbfd681e9f"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a3f29666b8ab80ed563d96fdbfd681e9f">SortMSeqByLength</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq, const char cOrder)</td></tr>
<tr class="memdesc:a3f29666b8ab80ed563d96fdbfd681e9f"><td class="mdescLeft"> </td><td class="mdescRight">Sort sequences by length. <a href="#a3f29666b8ab80ed563d96fdbfd681e9f">More...</a><br /></td></tr>
<tr class="separator:a3f29666b8ab80ed563d96fdbfd681e9f"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:aa7c161c1402bdeb514c97a1ba287819a"><td class="memItemLeft" align="right" valign="top">void </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#aa7c161c1402bdeb514c97a1ba287819a">JoinMSeqs</a> (<a class="el" href="structmseq__t.html">mseq_t</a> **prMSeqDest_p, <a class="el" href="structmseq__t.html">mseq_t</a> *prMSeqToAdd)</td></tr>
<tr class="memdesc:aa7c161c1402bdeb514c97a1ba287819a"><td class="mdescLeft"> </td><td class="mdescRight">Appends an mseq structure to an already existing one. filename will be left untouched. <a href="#aa7c161c1402bdeb514c97a1ba287819a">More...</a><br /></td></tr>
<tr class="separator:aa7c161c1402bdeb514c97a1ba287819a"><td class="memSeparator" colspan="2"> </td></tr>
<tr class="memitem:a5ffded23e75f2ba58bcfdb024e8d1b92"><td class="memItemLeft" align="right" valign="top">bool </td><td class="memItemRight" valign="bottom"><a class="el" href="seq_8h.html#a5ffded23e75f2ba58bcfdb024e8d1b92">SeqsAreAligned</a> (<a class="el" href="structmseq__t.html">mseq_t</a> *prMSeq, bool bIsProfile, bool bDealignInputSeqs)</td></tr>
<tr class="memdesc:a5ffded23e75f2ba58bcfdb024e8d1b92"><td class="mdescLeft"> </td><td class="mdescRight">Checks if sequences in given mseq structure are aligned. By definition this is only true, if sequences are of the same length and at least one gap was found. <a href="#a5ffded23e75f2ba58bcfdb024e8d1b92">More...</a><br /></td></tr>
<tr class="separator:a5ffded23e75f2ba58bcfdb024e8d1b92"><td class="memSeparator" colspan="2"> </td></tr>
</table>
<h2 class="groupheader">Macro Definition Documentation</h2>
<a id="af396304082d44225e44933577c320e43"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af396304082d44225e44933577c320e43">§ </a></span>AMINOACID_ANY</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">#define AMINOACID_ANY   'X'</td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a id="acf7121d916e81f2ee9ac83680434bb9a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#acf7121d916e81f2ee9ac83680434bb9a">§ </a></span>NUCLEOTIDE_ANY</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">#define NUCLEOTIDE_ANY   'N'</td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a id="a5e07e6c291f096c3e6b6e8cda4efb37b"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5e07e6c291f096c3e6b6e8cda4efb37b">§ </a></span>SEQTYPE_DNA</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">#define SEQTYPE_DNA   kDNA</td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a id="a193343bb1bec0dd172e9b24b9b13c077"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a193343bb1bec0dd172e9b24b9b13c077">§ </a></span>SEQTYPE_PROTEIN</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">#define SEQTYPE_PROTEIN   kAmino</td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a id="af455eb393971ad3ce026bda535abc82c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af455eb393971ad3ce026bda535abc82c">§ </a></span>SEQTYPE_RNA</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">#define SEQTYPE_RNA   kRNA</td>
</tr>
</table>
</div><div class="memdoc">
</div>
</div>
<a id="a03dbc4840c83155125914ed849f74416"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a03dbc4840c83155125914ed849f74416">§ </a></span>SEQTYPE_UNKNOWN</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">#define SEQTYPE_UNKNOWN   kOtherSeq</td>
</tr>
</table>
</div><div class="memdoc">
<p>int-encoded sequence types. these are in sync with squid's seqtypes and only used for convenience here </p>
</div>
</div>
<h2 class="groupheader">Function Documentation</h2>
<a id="a27f31ca0bdcd5b52610651b7e0e52cd7"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a27f31ca0bdcd5b52610651b7e0e52cd7">§ </a></span>AddSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void AddSeq </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> ** </td>
<td class="paramname"><em>prMSeqDest_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>pcSeqName</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>pcSeqRes</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Creates a new sequence entry and appends it to an existing mseq structure. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeqDest_p</td><td>Already existing and initialised mseq structure </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">pcSeqName</td><td>sequence name of the sequence to add </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">pcSeqRes</td><td>the actual sequence (residues) to add</td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>Don't forget to update the align and type flag if necessary!</dd></dl>
<p>FIXME allow adding of more features </p>
</div>
</div>
<a id="a7fa5b7c740c8906424057c112b192088"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a7fa5b7c740c8906424057c112b192088">§ </a></span>AliStat()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void AliStat </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bSampling</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bReportAll</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Stripped down version of squid's alistat. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">prMSeq</td><td>The alignment to analyse </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">bSampling</td><td>For many sequences: samples from pool </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">bReportAll</td><td>Report identities for all sequence pairs</td></tr>
</table>
</dd>
</dl>
<p>Don't have to worry about sequence case because our version of PairwiseIdentity is case insensitive </p>
<p>mseq to squid msa</p>
<p>FIXME code overlap with WriteAlignment. Make it a function and take code there (contains more comments) as template</p>
</div>
</div>
<a id="a6b124a1118f2276d2a2978227efd0ab4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6b124a1118f2276d2a2978227efd0ab4">§ </a></span>CopyMSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void CopyMSeq </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> ** </td>
<td class="paramname"><em>prMSeqDest_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeqSrc</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>copies an mseq structure </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeqDest_p</td><td>Copy of mseq structure </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">prMSeqSrc</td><td>Source mseq structure to copy</td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>caller has to free copy by calling <a class="el" href="seq_8c.html#abb8e94cbbfa6f0b8e527f7107c09ae65" title="Frees an mseq_t and it's members and zeros all members. ">FreeMSeq()</a> </dd></dl>
</div>
</div>
<a id="a0533ef67eccd9c952b43d53072e9a1f1"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a0533ef67eccd9c952b43d53072e9a1f1">§ </a></span>DealignMSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void DealignMSeq </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>mseq</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Dealigns all sequences in mseq structure, updates the sequence length info and sets aligned to FALSE. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">mseq</td><td>The mseq structure to dealign </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a8a10a512577076df441dc133f7eb13d4"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a8a10a512577076df441dc133f7eb13d4">§ </a></span>DealignSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void DealignSeq </td>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>seq</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Removes all gap-characters from a sequence. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">seq</td><td>Sequence to dealign</td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>seq will not be reallocated </dd></dl>
</div>
</div>
<a id="a720cb218cff78249b898f4c56a9fee6c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a720cb218cff78249b898f4c56a9fee6c">§ </a></span>FindSeqName()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int FindSeqName </td>
<td>(</td>
<td class="paramtype">char * </td>
<td class="paramname"><em>seqname</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>mseq</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">seqname</td><td>The sequence name to search for </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">mseq</td><td>The multiple sequence structure to search in</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>-1 on failure, sequence index of matching name otherwise</dd></dl>
<dl class="section warning"><dt>Warning</dt><dd>If sequence name happens to be used twice, only the first one will be reported back </dd></dl>
</div>
</div>
<a id="abb8e94cbbfa6f0b8e527f7107c09ae65"></a>
<h2 class="memtitle"><span class="permalink"><a href="#abb8e94cbbfa6f0b8e527f7107c09ae65">§ </a></span>FreeMSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void FreeMSeq </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> ** </td>
<td class="paramname"><em>mseq</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Frees an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> and it's members and zeros all members. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">mseq</td><td>mseq_to to free</td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>use in conjunction with <a class="el" href="seq_8c.html#a7dcd309007c753f509c6589475229c11" title="allocate and initialise new mseq_t ">NewMSeq()</a> </dd></dl>
<dl class="section see"><dt>See also</dt><dd>new_mseq </dd></dl>
</div>
</div>
<a id="aa7c161c1402bdeb514c97a1ba287819a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#aa7c161c1402bdeb514c97a1ba287819a">§ </a></span>JoinMSeqs()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void JoinMSeqs </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> ** </td>
<td class="paramname"><em>prMSeqDest_p</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeqToAdd</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Appends an mseq structure to an already existing one. filename will be left untouched. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">prMSeqDest_p</td><td>MSeq structure to which to append to </td></tr>
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeqToAdd</td><td>MSeq structure which is to append </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a6b1d0d3e408720aa012f66f34f740262"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a6b1d0d3e408720aa012f66f34f740262">§ </a></span>LogSqInfo()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void LogSqInfo </td>
<td>(</td>
<td class="paramtype">SQINFO * </td>
<td class="paramname"><em>sqinfo</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>debug output of sqinfo struct </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">sqinfo</td><td>Squid's SQINFO struct for a certain seqeuence</td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>useful for debugging only </dd></dl>
</div>
</div>
<a id="af60f55dd9f9840f54bf5057d3ab90d42"></a>
<h2 class="memtitle"><span class="permalink"><a href="#af60f55dd9f9840f54bf5057d3ab90d42">§ </a></span>NewMSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void NewMSeq </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> ** </td>
<td class="paramname"><em>prMSeq</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>allocate and initialise new <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>newly allocated and initialised <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a></td></tr>
</table>
</dd>
</dl>
<dl class="section note"><dt>Note</dt><dd>caller has to free by calling <a class="el" href="seq_8c.html#abb8e94cbbfa6f0b8e527f7107c09ae65" title="Frees an mseq_t and it's members and zeros all members. ">FreeMSeq()</a></dd></dl>
<dl class="section see"><dt>See also</dt><dd><a class="el" href="seq_8c.html#abb8e94cbbfa6f0b8e527f7107c09ae65" title="Frees an mseq_t and it's members and zeros all members. ">FreeMSeq</a> </dd></dl>
</div>
</div>
<a id="a853633b9627f9048adf1e5000a6a0916"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a853633b9627f9048adf1e5000a6a0916">§ </a></span>ReadSequences()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int ReadSequences </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>seqfile</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>iSeqType</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>iSeqFmt</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bIsProfile</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bDealignInputSeqs</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>iMaxNumSeq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>iMaxSeqLen</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">char * </td>
<td class="paramname"><em>pcHMMBatch</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>reads sequences from file </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>Multiple sequence struct. Must be preallocated. FIXME: would make more sense to allocate it here. </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">seqfile</td><td>Sequence file name. If '-' sequence will be read from stdin. </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">iSeqType</td><td>int-encoded sequence type. Set to SEQTYPE_UNKNOWN for autodetect (guessed from first sequence) </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">iMaxNumSeq</td><td>Return an error, if more than iMaxNumSeq have been read </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">iMaxSeqLen</td><td>Return an error, if a seq longer than iMaxSeqLen has been read</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>0 on success, -1 on error</dd></dl>
<dl class="section note"><dt>Note</dt><dd><ul>
<li>Depends heavily on squid</li>
<li>Sequence file format will be guessed</li>
<li>If supported by squid, gzipped files can be read as well. </li>
</ul>
</dd></dl>
</div>
</div>
<a id="a5ffded23e75f2ba58bcfdb024e8d1b92"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a5ffded23e75f2ba58bcfdb024e8d1b92">§ </a></span>SeqsAreAligned()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">bool SeqsAreAligned </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bIsProfile</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bDealignInputSeqs</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Checks if sequences in given mseq structure are aligned. By definition this is only true, if sequences are of the same length and at least one gap was found. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">prMSeq</td><td>Sequences to check</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>TRUE if sequences are aligned, FALSE if not </dd></dl>
</div>
</div>
<a id="a593f05a8f9329d0409320fed313c720c"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a593f05a8f9329d0409320fed313c720c">§ </a></span>SeqSwap()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void SeqSwap </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>i</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>j</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Swap two sequences in an <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> structure. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>Multiple sequence struct </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">i</td><td>Index of first sequence </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">j</td><td>Index of seconds sequence </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a30c7f4d7600fec2eaa564df74cac731a"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a30c7f4d7600fec2eaa564df74cac731a">§ </a></span>SeqTypeToStr()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">const char* SeqTypeToStr </td>
<td>(</td>
<td class="paramtype">int </td>
<td class="paramname"><em>iSeqType</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>convert int-encoded iSeqType to string </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">iSeqType</td><td>int-encoded sequence type</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>character pointer describing the sequence type </dd></dl>
</div>
</div>
<a id="a38db9b206246a53873459ff7f1eace06"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a38db9b206246a53873459ff7f1eace06">§ </a></span>ShuffleMSeq()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void ShuffleMSeq </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>mseq</em></td><td>)</td>
<td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Shuffle mseq order. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">mseq</td><td>mseq structure to shuffle </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="a3f29666b8ab80ed563d96fdbfd681e9f"></a>
<h2 class="memtitle"><span class="permalink"><a href="#a3f29666b8ab80ed563d96fdbfd681e9f">§ </a></span>SortMSeqByLength()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">void SortMSeqByLength </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>prMSeq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char </td>
<td class="paramname"><em>cOrder</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Sort sequences by length. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[out]</td><td class="paramname">prMSeq</td><td>mseq to sort by length </td></tr>
<tr><td class="paramdir">[out]</td><td class="paramname">cOrder</td><td>Sorting order. 'd' for descending, 'a' for ascending. </td></tr>
</table>
</dd>
</dl>
</div>
</div>
<a id="ad84a0cdc0c49df96ef9ef97a053f841e"></a>
<h2 class="memtitle"><span class="permalink"><a href="#ad84a0cdc0c49df96ef9ef97a053f841e">§ </a></span>WriteAlignment()</h2>
<div class="memitem">
<div class="memproto">
<table class="memname">
<tr>
<td class="memname">int WriteAlignment </td>
<td>(</td>
<td class="paramtype"><a class="el" href="structmseq__t.html">mseq_t</a> * </td>
<td class="paramname"><em>mseq</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">const char * </td>
<td class="paramname"><em>pcAlnOutfile</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>outfmt</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">int </td>
<td class="paramname"><em>iWrap</em>, </td>
</tr>
<tr>
<td class="paramkey"></td>
<td></td>
<td class="paramtype">bool </td>
<td class="paramname"><em>bResno</em> </td>
</tr>
<tr>
<td></td>
<td>)</td>
<td></td><td></td>
</tr>
</table>
</div><div class="memdoc">
<p>Write alignment to file. </p>
<dl class="params"><dt>Parameters</dt><dd>
<table class="params">
<tr><td class="paramdir">[in]</td><td class="paramname">mseq</td><td>The <a class="el" href="structmseq__t.html" title="structure for storing multiple sequences ">mseq_t</a> struct containing the aligned sequences </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">pcAlnOutfile</td><td>The name of the output file </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">outfmt</td><td>The alignment output format (defined in squid.h) </td></tr>
<tr><td class="paramdir">[in]</td><td class="paramname">iWrap</td><td>length of line for Clustal/Fasta format</td></tr>
</table>
</dd>
</dl>
<dl class="section return"><dt>Returns</dt><dd>Non-zero on error</dd></dl>
<dl class="section note"><dt>Note</dt><dd>We create a temporary squid MSA struct in here because we never use it within clustal. We might be better of using the old clustal output routines instead. </dd></dl>
</div>
</div>
</div><!-- contents -->
<!-- start footer part -->
<hr class="footer"/><address class="footer"><small>
Generated by  <a href="http://www.doxygen.org/index.html">
<img class="footer" src="doxygen.png" alt="doxygen"/>
</a> 1.8.12
</small></address>
</body>
</html>
|