[med-svn] r16 - in trunk/packages: . dialign dialign/branches
dialign/branches/upstream dialign/branches/upstream/current
dialign/branches/upstream/current/dialign2_dir
dialign/branches/upstream/current/license
dialign/branches/upstream/current/src
Charles Plessy
charles-guest at costa.debian.org
Tue Apr 18 12:55:44 UTC 2006
Author: charles-guest
Date: 2006-04-18 12:55:28 +0000 (Tue, 18 Apr 2006)
New Revision: 16
Added:
trunk/packages/dialign/
trunk/packages/dialign/branches/
trunk/packages/dialign/branches/upstream/
trunk/packages/dialign/branches/upstream/current/
trunk/packages/dialign/branches/upstream/current/INSTALLATION_GUIDE
trunk/packages/dialign/branches/upstream/current/USER_GUIDE
trunk/packages/dialign/branches/upstream/current/dialign2_dir/
trunk/packages/dialign/branches/upstream/current/dialign2_dir/BLOSUM
trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_dna
trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_prot
trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_trans
trunk/packages/dialign/branches/upstream/current/license/
trunk/packages/dialign/branches/upstream/current/license/LGPL.TXT
trunk/packages/dialign/branches/upstream/current/license/LICENSE.TXT
trunk/packages/dialign/branches/upstream/current/src/
trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.c
trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.h
trunk/packages/dialign/branches/upstream/current/src/anchor.c
trunk/packages/dialign/branches/upstream/current/src/define.h
trunk/packages/dialign/branches/upstream/current/src/dialign.c
trunk/packages/dialign/branches/upstream/current/src/dialign.h
trunk/packages/dialign/branches/upstream/current/src/frag_chain.c
trunk/packages/dialign/branches/upstream/current/src/functions.c
trunk/packages/dialign/branches/upstream/current/src/input.c
trunk/packages/dialign/branches/upstream/current/src/makefile
trunk/packages/dialign/branches/upstream/current/src/output.c
trunk/packages/dialign/branches/upstream/current/src/para.c
trunk/packages/dialign/branches/upstream/current/src/pratique.c
trunk/packages/dialign/branches/upstream/current/src/pratique.h
trunk/packages/dialign/branches/upstream/current/src/regex.c
trunk/packages/dialign/branches/upstream/current/src/wgt.c
trunk/packages/dialign/tags/
Log:
[svn-inject] Installing original source of dialign
Added: trunk/packages/dialign/branches/upstream/current/INSTALLATION_GUIDE
===================================================================
--- trunk/packages/dialign/branches/upstream/current/INSTALLATION_GUIDE 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/INSTALLATION_GUIDE 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,52 @@
+
+
+ installation guide for
+
+ DIALIGN2
+ ========
+
+ program code written by
+
+ Burkhard Morgenstern and Said Abdeddaim
+
+ e-mail contact: bmorgen at gwdg.de
+
+
+(1) cd to the directory `src' that contains the dialign source code
+
+(2) type `make' to compile the program. This should create an executable
+ binary file called `dialign2-2'.
+
+(3) you may remove all object files (type `rm *.o')
+
+(4) to run DIALIGN2, you must create an environment variable
+ `DIALIGN2_DIR' pointing to the directory `dialign2_dir'
+
+ (type `setenv DIALIGN2_DIR /your_path/dialign2_dir/' where
+ `your_path' is the directory where you de-tarred the file with the
+ sources)
+
+ The program needs the files
+
+ tp400_dna
+ tp400_prot
+ tp400_trans
+ BLOSUM
+
+ that are contained in the directory `dialign2_dir'. You may move
+ these files to any other directory and set DIALIGN2_DIR accordingly.
+
+
+
+Please note that, unlike in the first version of DIALIGN, it is NOT
+POSSIBLE to replace the BLOSUM matrix by other similarity matrices !!
+
+DIALIGN comes with a detailed user guide. For additional information, please
+consult the DIALIGN home page at
+
+ http://bibiserv.techfak.uni-bielefeld.de/dialign/
+
+----------------------------------------------------------------------------
+BM, Goettingen, February 2003
+
+
Added: trunk/packages/dialign/branches/upstream/current/USER_GUIDE
===================================================================
--- trunk/packages/dialign/branches/upstream/current/USER_GUIDE 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/USER_GUIDE 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,537 @@
+
+
+ DIALIGN 2.2.2
+
+ User Guide
+
+ Program code written by
+
+ Burkhard Morgenstern, Said Abdeddaim
+
+at University of Bielefeld (FSPM and International Graduate School in
+Bioinformatics and Genome Research), GSF (ISG, IBB, MIPS/IBI),
+North Carolina State University, Universite de Rouen, MPI fuer
+Biochemie (Martinsried), University of Goettingen, Institute of
+Microbiology and Genetics.
+
+
+E-mail contact: bmorgen at gwdg.de
+
+
+ Reference:
+
+ B. Morgenstern (1999).
+ DIALIGN 2: improvement of the segment-to-segment approach to
+ multiple sequence alignment.
+ Bioinformatics 15, 211 - 218.
+
+Public research assisted by DIALIGN should cite this article. For more
+information, updated references etc. please visit the DIALIGN home page at
+
+ http://dialign.gobics.de/
+
+
+Program usage:
+
+ dialign2-2 [ options ] <seq_file>
+
+
+<seq_file> is the name of the input sequence file; this must be a multiple
+FASTA file (all sequences in one file), a description of the format is
+given below. The following options are available (a more detailed description
+of these options is given below):
+
+ -afc Creates additional output file "*.afc" containing data of
+ all fragments considered for alignment
+ WARNING: this file can be HUGE !
+
+ -afc_v like "-afc" but verbose: fragments are explicitly printed
+ WARNING: this file can be EVEN BIGGER !
+
+ -anc Anchored alignment. Requires a file <seq_file>.anc
+ containing anchor points.
+
+ -cs if segments are translated, not only the `Watson strand'
+ but also the `Crick strand' is looked at.
+
+ -cw additional output file in CLUSTAL W format.
+
+ -ds `dna alignment speed up' - non-translated nucleic acid
+ fragments are taken into account only if they start with
+ at least two matches. Speeds up DNA alignment at the expense
+ of sensitivity.
+
+ -fa additional output file in FASTA format.
+
+ -ff Creates file *.frg containing information about all
+ fragments that are part of the respective optimal pairwise
+ alignmnets plus information about consistency in the multiple
+ alignment
+
+ -fn <out_file> output files are named <out_file>.<extension> .
+
+
+ -fop Creates file *.fop containing coordinates of all fragments
+ that are part of the respective pairwise alignments.
+
+ -fsm Creates file *.fsm containing coordinates of all fragments
+ that are part of the final alignment
+
+ -iw overlap weights switched off (by default, overlap weights are
+ used if up to 35 sequences are aligned). This option
+ speeds up the alignment but may lead to reduced alignment
+ quality.
+
+ -lgs `long genomic sequences' - combines the following options:
+ -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff,
+ -fop, -ff, -cs, -ds, -pst
+
+ -lgs_t Like "-lgs" but with all segment pairs assessed at the
+ peptide level (rather than 'mixed alignments' as with the
+ "-lgs" option). Therefore faster than -lgs but not very
+ sensitive for non-coding regions.
+
+ -lmax <x> maximum fragment length = x (default: x = 40 or x = 120
+ for `translated' fragments). Shorter x speeds up the program
+ but may affect alignment quality.
+
+ -lo (Long Output) Additional file *.log with information abut
+ fragments selected for pairwise alignment and about
+ consistency in multi-alignment proceedure
+
+ -ma `mixed alignments' consisting of P-fragments and N-fragments
+ if nucleic acid sequences are aligned.
+
+ -mask residues not belonging to selected fragments are replaced
+ by `*' characters in output alignment (rather than being
+ printed in lower-case characters)
+
+ -mat Creates file *mat with substitution counts derived from the
+ fragments that have been selected for alignment
+
+ -mat_thr <t> Like "-mat" but only fragments with weight score > t
+ are considered
+
+ -max_link "maximum linkage" clustering used to construct sequence tree
+ (instead of UPGMA).
+
+ -min_link "minimum linkage" clustering used.
+
+ -mot "motif" option.
+
+ -msf separate output file in MSF format.
+
+ -n input sequences are nucleic acid sequences. No translation
+ of fragments.
+
+ -nt input sequences are nucleic acid sequences and `nucleic acid
+ segments' are translated to `peptide segments'.
+
+ -nta `no textual alignment' - textual alignment suppressed. This
+ option makes sense if other output files are of intrest --
+ e.g. the fragment files created with -ff, -fop, -fsm or -lo
+
+ -o fast version, resulting alignments may be slightly different.
+
+ -ow overlap weights enforced (By default, overlap weights are
+ used only if up to 35 sequences are aligned since calculating
+ overlap weights is time consuming). Warning: overlap weights
+ generally improve alignment quality but the running time
+ increases in the order O(n^4) with the number of sequences.
+ This is why, by default, overlap weights are used only for
+ sequence sets with < 35 sequences.
+
+ -pst "print status". Creates and updates a file *.sta with
+ information about the current status of the program run.
+ This option is recommended if large data sets are aligned
+ since it allows the user to estimate the remaining running
+ time.
+
+ -smin <x> minimum similarity value for first residue pair (or codon
+ pair) in fragments. Speeds up protein alignment or alignment
+ of translated DNA fragments at the expense of sensitivity.
+
+ -stars <x> maximum number of `*' characters indicating degree of
+ local similarity among sequences. By default, no stars
+ are used but numbers between 0 and 9, instead.
+
+ -stdo Results written to standard output.
+
+ -ta standard textual alignment printed (overrides suppression
+ of textual alignments in special options, e.g. -lgs)
+
+ -thr <x> Threshold T = x.
+
+ -xfr "exclude fragments" - list of fragments can be specified
+ that are NOT considered for pairwise alignment
+
+
+General remark: If contradictory options are used, subsequent options
+override previous ones, e.g.:
+
+ dialign2-2 -nt -n <seq_file>
+
+runs the program with the "-n" option (no translation!), while
+
+ dialign2-2 -n -nt <seq_file>
+
+runs it with the "-nt" option (translation!).
+
+
+
+ Input File:
+
+Sequences to be aligned must be contained in a single file in FASTA
+format. Example:
+
+
+ >HTL2
+ LDTAPCLFSDGSPQKAAYVLWDQTILQQDITPLPSHETHSAQKGELLALICGLRAAKPWP
+ SLNIFLDSKY
+ >MMLV
+ GKKLNVYTDSRYAFATAHIHGEIYRRRGLLTSEGKEIKNKDEILALLKALFLPKRLSIIH
+ CPGHQKGHSAEARGNRMADQAARKAAITETPDTSTLL
+ >HEPB
+ RPGLCQVFADATPTGWGLVMGHQRMRGTFSAPLPIHTAELLAACFARSRSGANIIGTDNS
+ GRTSLYADSPSVPSHLPDRVH
+
+
+The first line for each sequence starts with ">" and contains the name of
+the sequence. Please make sure, that the first line in the input file is
+not empty and that the first character in the first line is not blank.
+
+Some details about avaliable options:
+
+ (1) Sequence Type:
+
+ The user can decide if nucleic acid or protein sequences are to be
+ aligned.
+
+ (2) Threshold T:
+
+ As described in our papers, the program DIALIGN constructs alignments
+ from gapfree pairs of similar segments of the sequences. Such segment
+ pairs are referred to as `(alignment) fragments' (previously, we called
+ them `diagonals').
+
+ Every possible fragment is given a so-called weight reflecting the
+ degree of similarity among the two segments involved. The overall
+ score of an alignment is then defined as the sum of weights of the
+ fragments it consists of and the program tries to find an alignment with
+ maximum score -- in other words: the program tries to find a consistent
+ collection of fragments with maximum sum of weights. This novel scoring
+ scheme for alignments is the basic difference between DIALIGN and other
+ global or local alignment methods. Note that DIALIGN does not employ any
+ kind of gap penalty.
+
+ It is possible to use a threshold T for the quality of the fragments.
+ In this case, a fragment is considered for alignment only if its
+ `weight' exceeds this threshold. Regions of lower similarity are ignored.
+
+ In the first version of the program (DIALIGN 1), this threshold was in
+ many situations absolutely necessary to obtain meaningful alignments.
+ By contrast, DIALIGN 2 should produce reasonable alignments without a
+ threshold, i.e. with T = 0. This is the most important difference between
+ DIALIGN 2 and the first version of the program. Nevertheless, it is still
+ possible to use a positive threshold T to filter out regions of lower
+ significance and to include only high scoring fragments into the
+ alignment.
+
+ (3) Different levels of sequence similarity:
+
+ If (possibly) coding nucleic acid sequences are to be aligned, DIALIGN
+ optionally translates the compared `nucleic acid segments' to `peptide
+ segments' according to the genetic code -- without presupposing any of
+ the three possible reading frames, so all combinations of reading frames
+ get checked for significant similarity. If this option is used, the
+ similarity among segments will be assessed on the `peptide level' rather
+ than on the `nucleotide level'.
+
+ We strongly recommend to use the `translation' option if nucleic acid
+ sequences are expected to contain protein coding regions, as it will
+ significantly increase the sensitivity of the alignment procedure in
+ such cases.
+
+ For the levels of sequence similarity, release 2.2 of DIALIGN has
+ two additional options:
+
+ (a) it can measure the similarity among segment pairs at both levels
+ of similarity (nucleotide-level and peptide-level similarity). The
+ score of a fragment is based on whatever similarity is stronger. As a
+ result, the program can now produce `mixed alignments' that contain
+ both types of fragments. Fragments with stronger similarity at the
+ `nucleotide level' referred to as N-fragments whereas fragments with
+ stronger similarity a the peptide level are called P-fragments.
+
+ (b) if the `translation' or `mixed alignment' option is used, it is
+ possible to consider the `reverse complements' of segments, too. In
+ this case, both the original segments and their reverse complements
+ are translated and both pairs of implied `peptide segments' are
+ compared. This option is useful if DNA sequences contain coding regions
+ not only on the `Watson strand' but also on the `Crick strand'.
+
+ (4) The score that DIALIGN assigns to a fragment is based on the
+ probability to find a fragment of the same respective length and number
+ of matches (or BLOSUM values, if the translation option is used) in
+ random sequences of the same length as the input sequences. If long
+ genomic sequences are aligned, an iterative procedure can be applied
+ where the program first looks for fragments with strong similarity.
+ In subsequent steps, regions between these fragments are realigned.
+ Here, the score of a fragment is based on random occurrence in these
+ regions between the previously aligned segment pairs.
+
+ (5) With the -ff (or -lgs) option, a file with all fragments contained
+ in the output alignment can be returned. This file contains additional
+ information about the identified fragments such as
+
+ - start coordinates in the respective sequences
+ - length
+ - fragment weight,
+ - iteration step (if the iterative option is used)
+ - whether the similarity among the segments is strongest at the
+ nucleotide level (N-frg) or at the peptide level (P-frg) if the
+ `mixed alignment' option is used
+ - whether the similarity is stronger on the `Watson strand' (" + " )
+ or on the `Crick strand' (" - " ) - if a fragment is translated
+ and the respective option is used
+
+ All this information can be used to further post-process the DIALIGN
+ output, for example by customized visualisation tools.
+
+ The file containing this information looks like this:
+
+
+ # program call: ./dialign2-2 -lgs seq_file
+
+ seq_len: 552 527
+ sequences: seq1 seq2
+
+ 1) seq: 1 2 beg: 161 351 len: 27 wgt: 7.60 it: 1 cons P-frg +
+ 2) seq: 1 2 beg: 300 507 len: 17 wgt: 4.40 it: 1 cons N-frg
+ 3) seq: 1 2 beg: 111 170 len: 12 wgt: 4.34 it: 1 cons N-frg
+
+
+ (6) Degree of local sequence similarity:
+
+ Numbers between 0 and 9 are printed below the alignment to indicate
+ the degree of local sequence similarity (in previous verions of the
+ program, "*" characters were used instead of numbers). These numbers
+ are normalized such that the region of highest similarity gets a
+ score of 9. With the -stars option, "*" characters can be used as
+ previously.
+
+ (7) `overlap weights':
+
+ This option improves the sensitivity of the program if multiple sequences
+ are aligned but it also increases the running time, especially if large
+ numbers of sequences are aligned. By default, `overlap weights' are used
+ if up to 35 sequences are aligned but switched off for larger data sets.
+ In the command-line version, `overlap weights' can be switched on or off
+ for data sets of any size, see below.
+
+ (8) `anchored alignment':
+
+ Forces the program to align user-specified anchor points to speed-up
+ the alignment procedure for long sequences. Anchor points are given in
+ a file <seq_file>.anc where <seq_file> is the name of the sequence file
+ (without extension .fa or .seq). Note that anchoring is possible for
+ pairwise as well as for multiple alignment. The format of the .anc file
+ is as follows (each line represents one anchor point):
+
+
+ 2 5 13724 7646 23 23.45345
+ 1 3 6596 517 5 12.34555
+ 3 5 33511 9438 34 27.45459
+
+ The first two columns are the sequences to be anchored, columns 3
+ and 4 contain the beginning positions of the anchored segments in
+ the specified sequences, and column 5 contains a score of the
+ anchor that specifies its priority compared to other anchoring
+ regions in case there is a conflict between inconsistent anchor
+ points (see below).
+
+ In the above example, three anchored segment pairs are specified.
+ Here, 13724 is the beginning position of the first anchor in sequence 2,
+ 7646 is the beginning position of the first anchor in sequence 5 and
+ 23 is the length of the first anchor. In other words, the program is
+ forced to align positions 13724 - 13746 in sequence 2 with positions
+ 7646 - 7668 in sequence 5. Similarly, a segment of sequence 1 starting
+ at position 6596 is anchored with a segment of sequence 3 starting
+ at position 517 etc.
+
+ The program can use only consistent sets of anchor points. This means,
+ that all anchored regions must fit into one single multiple alignment
+ (see our papers for our notion of "consistency"). The anchor points
+ in the specified file are sorted according to their scores (as given
+ in the last column of the anchor file) and then accepted one-by-one
+ -- provided they are consistent with the already accepted anchor points.
+
+ This is exactly the way, dialign includes fragments (segment pairs
+ or "diagonals") into a resulting multiple alignment, see the dialign
+ papers for more details.
+
+ Anchor points can be created by any suitable software program,
+ for example by CHAOS developed by Mike Brudno, Stanford:
+
+ http://www.stanford.edu/~brudno/chaos/
+
+
+ (9) `Motif' option:
+
+ A motif can be specified by a simple regular expression such as "TY[ILV]A".
+ Gaps are not allowed in motifs; all residues within brackets are allowed
+ at the respective position. For example, "TYIA", "TYLA" and "TYVA" would
+ match the above motif. Alignments where instances of the motif are aligned
+ to each other, are preferred. They receive a bonus which can be specified
+ by the user. There are two paramters to determine the bonus for matched
+ motifs: a first weighting factor (fct1) assigns a bonus for aligned
+ instances of the motif occurring at the same relative position in the
+ input sequences. The bonus decreases with the distance between the
+ matched motif in the sequences. A second parameter (fct2) controls how fast
+ the bonus decreases.
+
+ With the two user-defined parameters fct1 and fct2, the bonus for each
+ matched motif is calculated as follows: If a matched motif occurs at
+ positions i and j in two of the input sequences, |i-j| is the `offset'
+ of the motif. The bonus is then
+
+ fct1 * exp - ( |i-j|^2 / (fct2^2 * 10 ) )
+
+ I.e. a high value of fct2 means that even matches of the motif that are
+ far apart within the sequences reveive a high bonus.
+
+ With the motif-search option, the program call is:
+
+ ./dialign2-2 [para] -mot <regex> <fct1> <fct2> [para] <seq>
+
+ where
+ <regex> is a regular expression, e.g. "AT[CG]XT",
+ <fct1> is the first parameter
+ <fct2> is the second parameter
+ <seq> is the input sequence file and
+ [para] are (optional) additional program parameters
+
+
+Similarity Matrix:
+
+DIALIGN 2 uses the BLOSUM62 amino acid substitution matrix. In the current
+version, it is NOT possible to replace BLOSUM62 by other similarity matrices,
+since the probability values contained in the files n_prob and p_prob refer
+to the BLOSUM62 matrix.
+
+
+
+ Program Output:
+
+By default, DIALIGN creates a single file containing
+
+ - An alignment of the input sequences in DIALIGN format.
+ - The same alignment in FASTA format.
+ - A sequence tree in PHYLIP format. This tree is constructed by applying
+ the UPGMA clustering method to the DIALIGN similarity scores. It roughly
+ reflects the different degrees of similarity among sequences. For
+ detailed phylogenetic analysis, we recommend the usual methods for
+ phylogenetic reconstruction.
+
+
+This is the DIALIGN alignment format:
+
+
+
+SMb21199_AA- 1 mtemkdsila vrglkvdfyt pd-GTVE-AV KGIDLDVRSG ETLAVVGESG
+SMb21206_AA- 1 mpapatepgt apfVRLTGVT KRFGTARpAL DAVAGEIFGG RVTGLVGPDG
+SMb21592_AA- 1 mtlq------ ---IELNGVN KFYGSYH-AL KDIDLAIEEG TFVALVGPSG
+SMb21605_AA- 1 msg------- ---IKLTGVS KSFGAVK-VI HGVDIEIGQG EFAVFVGPSG
+
+ 0000000000 0000000000 0002222022 2222233356 6666666666
+
+
+SMb21199_AA- 49 SGKSQTMMGI MGLLakngtv tgsaryrgqe lvgLAPKALN KVRGS-KITM
+SMb21206_AA- 51 AGKTTLIRLM TGLMLPDAGT IE-------- ---VLGydtr rdpasiQAAI
+SMb21592_AA- 41 CGKSTLLRSL AGLEKISAGE MK-------- ---IAGARMN DVPPR-KRDV
+SMb21605_AA- 40 CGKSTLLRMI AGLEETTGGE IR-------- ---Idaedvt hkePS-KRGV
+
+ 6666666666 6664333333 3300000000 0003110000 0001102222
+
+
+SMb21199_AA- 98 IFQEPMTSLD PLYTIGRQIA EPIvhhRGGS FKEA---RRR VLELLELVGI
+SMb21206_AA- 90 GYMPQRFGLY EDLSVQENLD LYADL-RGLP KTER---SRT FGELLDFTDL
+SMb21592_AA- 79 AMVFQSYALY PHMTVEENLT YSLRI-RGVK KAEA---LKA AAEVATTTGL
+SMb21605_AA- 78 AMVFQSYALY PHLSVFDNMA FSLSI-ARRP KAEieqkVKA AAEIlrlsdy
+
+ 2222222222 2222222222 2222202222 2220000000 0000000000
+
+
+
+ Names of aligned sequences are shown on the left hand side of the
+ alignment.
+
+ Numbers on the left hand side of the alignment denote the position
+ of the first residue in a line within the respective sequence.
+
+ Capital letters denote aligned residues, i.e. residues involved in
+ at least one of the fragments the alignment consists of. Lower-case
+ letters denote residues not belonging to any of these selected
+ fragments. They are not considered to be aligned by DIALIGN. Thus,
+ if a lower-case letter is standing in the same column with other letters,
+ this is pure chance; these residues are not considered to be homologous.
+
+ Numbers below the alignment reflects the degree of local similarity
+ among sequences. More precisely: They represent the sum of `weights'
+ of fragments connecting residues at the respective position.
+
+ These numbers are normalized such that regions of maximum similarity
+ always get a score of 9 - no matter how strong this maximum simliarity
+ is.
+
+
+
+This is FASTA alignment format:
+
+
+>HTL2
+ldtapcLFSDGS------PQKAAYVLWDQTIL---QQDITPLPSHethSA
+QKGELLALICGLRAAKPWPSLNIFLDSKYLIKYLHslaigaflgtsah--
+-------QT---LQAALPPLLQGKTIYLHHVRSHT------NLPDPISTF
+NEYTDSLILApl--------------------------------------
+----------
+>MMLV
+pdadhtwYTDGSSLLQEGQRKAGAAVTTETeviwaKALDAG---T---SA
+QRAELIALTQALKMAEgkk-LNVYTDSRYAFATAHIHGEIYRRRGLLTSE
+GKEIKNKDE---ILALLKALFLPKRLSIIHCPGHQ------KGHSAEARG
+NRMADQAARKAAITETPDTStll---------------------------
+----------
+>HEPB
+rpglcQVFADAT------PTGWGLVMGHQRMR---GTFSAPLPIHt----
+--AELLAACFArsrsgan---IIGTDN-----------------------
+-------------SVVLSR--------------KYTSFPWLLGCAANWI-
+LRGTSFVYVPSALNPADDPSrgrlglsrpllrlpfrpttgrtslyadsps
+vpshlpdrvh
+
+
+
+This is PHYLIP tree format:
+
+
+((HTL2:0.111024,
+(MMLV:0.078471,
+ECOL:0.078471):0.032554):0.121218,
+HEPB:0.232242);
+
+
+
+Trees can be visualized using the treetool program that is part of
+Joe Felsenstein's PHYLIP software package:
+
+ http://evolution.genetics.washington.edu/phylip.html
+
+
+---------------------------------------------------------------------
+
+Last update by Burkhard Morgenstern, Goettingen, February 2005
+
+
+
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/dialign2_dir/BLOSUM
===================================================================
--- trunk/packages/dialign/branches/upstream/current/dialign2_dir/BLOSUM 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/dialign2_dir/BLOSUM 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,23 @@
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Added: trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_dna
===================================================================
--- trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_dna 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_dna 2006-04-18 12:55:28 UTC (rev 16)
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Added: trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_prot
===================================================================
--- trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_prot 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_prot 2006-04-18 12:55:28 UTC (rev 16)
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Added: trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_trans
===================================================================
--- trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_trans 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/dialign2_dir/tp400_trans 2006-04-18 12:55:28 UTC (rev 16)
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Added: trunk/packages/dialign/branches/upstream/current/license/LGPL.TXT
===================================================================
--- trunk/packages/dialign/branches/upstream/current/license/LGPL.TXT 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/license/LGPL.TXT 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,458 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 2.1, February 1999
+
+ Copyright (C) 1991, 1999 Free Software Foundation, Inc.
+ 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ Everyone is permitted to copy and distribute verbatim copies
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+
+[This is the first released version of the Lesser GPL. It also counts
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+ 14. If you wish to incorporate parts of the Library into other free
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+
+ END OF TERMS AND CONDITIONS
Added: trunk/packages/dialign/branches/upstream/current/license/LICENSE.TXT
===================================================================
--- trunk/packages/dialign/branches/upstream/current/license/LICENSE.TXT 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/license/LICENSE.TXT 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,21 @@
+
+ This library is free software; you can redistribute it and/or
+ modify it under the terms of the GNU Lesser General Public
+ License as published by the Free Software Foundation; either
+ version 2.1 of the License, or (at your option) any later version.
+
+ This library is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ Lesser General Public License for more details.
+
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+ Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+
+
+ Burkhard Morgenstern hereby disclaims all copyright interest in
+ DIALIGN, written by Burkhard Morgenstern and Said Abdeddaim.
+
+ Burkhard Morgenstern, January 2005
+
Added: trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,683 @@
+
+/************************************************************/
+/************************************************************/
+/** GABIOS-LIB 1.0 (1999) **/
+/** A library for Greedy Alignment of BIOlogical Sequences **/
+/** Developed by Said Abdeddaim **/
+/** Said.Abdeddaim at dir.univ-rouen.fr **/
+/************************************************************/
+/************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+
+#include "pratique.h"
+#include "alig_graph_closure.h"
+
+void alloc_closure(CLOSURE *clos);
+void free_closure(CLOSURE *clos);
+void realloc_closure(CLOSURE *clos);
+void computeClosure(CLOSURE *clos);
+int path(CLOSURE *clos, int x, int i, int y, int j);
+void moveAligSet(CLOSURE *clos, int n1, int n2);
+void read_closure(CLOSURE *clos, int nbreancr, int **ancrages);
+void init_closure(CLOSURE *clos, int nbreancr, int **ancrages);
+void init_seq(CLOSURE *clos, int nbreseq, int *longseq);
+void desinit_seq(CLOSURE *clos);
+
+int print_aligSets(CLOSURE *clos, int nseq, int i);
+
+char DEBUG=0;
+
+void computeClosure(CLOSURE *clos)
+{
+int **Succ, **Pred, *NSucc, *NPred, *npred;
+int nsucc, ni, nj, s, top, bottom, n0, p, n, i, k, pos_n;
+int x;
+
+Succ = (int **) callouer_mat(sizeof(int), clos->nbrAligSets+2, clos->seqNbr);
+Pred = (int **) callouer_mat(sizeof(int), clos->nbrAligSets+2, clos->seqNbr);
+NSucc = (int *) allouer((clos->nbrAligSets+2) * sizeof(int));
+NPred = (int *) allouer((clos->nbrAligSets+2) * sizeof(int));
+npred = (int *) allouer((clos->nbrAligSets+2) * sizeof(int));
+clos->topolog = (int *) allouer(sizeof(int));
+
+/* C A L C U L des Succ[n][x] et NPred[n] */
+
+for (n=1; n <= clos->nbrAligSets; n++) NPred[n] = 0;
+
+for (n=1; n <= clos->nbrAligSets; n++)
+ {
+ nsucc = 0;
+ for (x=0; x < clos->seqNbr; x++)
+ if (clos->aligSet[n].pos[x] > 0)
+ {
+ pos_n = clos->aligSet[n].pos[x];
+ for (i=pos_n+1; i <= clos->seq[x].longueur && clos->seq[x].aligSetNbr[i] == 0; i++)
+ clos->seq[x].predAligSetPos[i] = pos_n;
+ if (i <= clos->seq[x].longueur)
+ {
+ clos->seq[x].predAligSetPos[i] = pos_n;
+ if (clos->aligSet[clos->seq[x].aligSetNbr[i]].nbr > 0)
+ {
+ n0 = Succ[n][nsucc] = clos->seq[x].aligSetNbr[i];
+ clos->aligSet[n0].nbr = - clos->aligSet[n0].nbr;
+ nsucc++;
+ }
+ }
+ for (i=pos_n-1; i > 0 && clos->seq[x].aligSetNbr[i] == 0; i--)
+ clos->seq[x].succAligSetPos[i] = pos_n;
+ if (i > 0)
+ clos->seq[x].succAligSetPos[i] = pos_n;
+ }
+ for (p=0; p < nsucc; p++)
+ {
+ n0 = Succ[n][p];
+ Pred[n0][NPred[n0]] = n;
+ NPred[n0]++;
+
+ clos->aligSet[n0].nbr = - clos->aligSet[n0].nbr;
+ }
+ NSucc[n] = nsucc;
+ }
+
+/* C A L C U L de clos->topolog */
+
+clos->topolog = (int *) reallouer(clos->topolog, (clos->nbrAligSets+2) * sizeof(int));
+
+bottom = top = 0;
+
+for (n=1; n <= clos->nbrAligSets; n++)
+ {
+ npred[n] = NPred[n];
+ if (npred[n] == 0) { top++; clos->topolog[top] = n; }
+ }
+
+
+while( bottom != top)
+ {
+ bottom++;
+ ni = clos->topolog[bottom];
+ for (s=0; s < NSucc[ni]; s++)
+ {
+ nj = Succ[ni][s];
+ npred[nj]--;
+ if (npred[nj] == 0)
+ {
+ top++;
+ clos->topolog[top] = nj;
+ }
+ }
+ }
+
+
+for (x=0; x < clos->seqNbr; x++)
+ {
+ clos->predFrontier[0][x] = 0;
+ clos->succFrontier[clos->nbrAligSets+1][x] = clos->seq[x].longueur+1;
+ }
+
+
+for (k=1; k <= clos->nbrAligSets; k++)
+ {
+ n0 = clos->topolog[k];
+ for (x=0; x < clos->seqNbr; x++)
+ {
+ if (clos->aligSet[n0].pos[x] > 0)
+ clos->predFrontier[n0][x] = clos->aligSet[n0].pos[x];
+ else
+ for (p=0, clos->predFrontier[n0][x]=0; p < NPred[n0]; p++)
+ {
+ n = Pred[n0][p];
+ if (clos->predFrontier[n][x] > clos->predFrontier[n0][x])
+ clos->predFrontier[n0][x] = clos->predFrontier[n][x];
+ }
+ }
+ }
+
+
+for (k=clos->nbrAligSets; k > 0; k--)
+ {
+ n0 = clos->topolog[k];
+ for (x=0; x < clos->seqNbr; x++)
+ {
+ if (clos->aligSet[n0].pos[x] > 0)
+ clos->succFrontier[n0][x] = clos->aligSet[n0].pos[x];
+ else
+ for (p=0, clos->succFrontier[n0][x]=clos->seq[x].longueur+1;
+ p < NSucc[n0]; p++)
+ {
+ n = Succ[n0][p];
+ if (clos->succFrontier[n][x] < clos->succFrontier[n0][x])
+ clos->succFrontier[n0][x] = clos->succFrontier[n][x];
+ }
+ }
+ }
+
+liberer(npred); liberer(NPred); liberer(NSucc);
+liberer_mat((void **) Pred, clos->nbrAligSets+2);
+liberer_mat((void **) Succ, clos->nbrAligSets+2);
+liberer(clos->topolog);
+}
+
+void moveAligSet(CLOSURE *clos, int n1, int n2)
+{
+int x;
+int k;
+
+for (x=0; x < clos->seqNbr; x++)
+ {
+ k = clos->aligSet[n1].pos[x] = clos->aligSet[n2].pos[x];
+ if (k > 0) clos->seq[x].aligSetNbr[k] = n1;
+
+ clos->predFrontier[n1][x] = clos->predFrontier[n2][x];
+ clos->succFrontier[n1][x] = clos->succFrontier[n2][x];
+ }
+
+clos->aligSet[n1].nbr = clos->aligSet[n2].nbr;
+}
+
+void read_closure(CLOSURE *clos, int nbreancr, int **ancrages)
+{
+FILE *f;
+int x;
+int i, ind, k, n;
+int **Succ, **Pred, *NSucc, *NPred, *npred;
+
+for (n=0; n < nbreancr; n++)
+ {
+ clos->nbrAligSets++;
+ realloc_closure(clos);
+
+ clos->aligSet[clos->nbrAligSets].nbr = 0;
+ for (x=0; x < clos->seqNbr; x++)
+ {
+ ind = clos->aligSet[clos->nbrAligSets].pos[x] = ancrages[n][x];
+ if (ind > 0)
+ {
+ clos->aligSet[clos->nbrAligSets].nbr++;
+ clos->seq[x].aligSetNbr[ind] = clos->nbrAligSets;
+ }
+ }
+ }
+
+computeClosure(clos);
+}
+
+void init_closure(CLOSURE *clos, int nbreancr, int **ancrages)
+{
+int x;
+int i, *longsequ;
+
+longsequ = (int *) allouer(clos->seqNbr * sizeof(int));
+
+for (x=0; x < clos->seqNbr; x++)
+ {
+ longsequ[x] = clos->seq[x].longueur;
+ for (i=1; i <= clos->seq[x].longueur; i++)
+ clos->seq[x].aligSetNbr[i] = clos->seq[x].succAligSetPos[i]
+ = clos->seq[x].predAligSetPos[i] = 0;
+ }
+
+clos->nbrAligSets = 0;
+
+if (nbreancr > 0)
+ read_closure(clos, nbreancr, ancrages);
+
+for (x=0; x < clos->seqNbr; x++)
+ clos->seq[x].longueur = longsequ[x];
+
+liberer(longsequ);
+}
+
+
+void alloc_closure(CLOSURE *clos)
+{
+long nmax, na;
+int x;
+
+clos->predFrontier = (int **) callouer_mat(sizeof(int), clos->maxLong+2, clos->seqNbr+1); /* sera re'alloue' */
+clos->succFrontier = (int **) callouer_mat(sizeof(int), clos->maxLong+2, clos->seqNbr+1); /* sera re'alloue' */
+
+clos->aligSet = (positionSet *) allouer((clos->maxLong+2) * sizeof(positionSet)); /* sera re'alloue' */
+for (na=0; na <= clos->maxLong+1; na++)
+ {
+ clos->aligSet[na].pos = (int *) allouer(clos->seqNbr * sizeof(int));
+ }
+clos->oldNbrAligSets = clos->maxLong;
+
+for (x=0; x < clos->seqNbr; x++)
+ {
+ clos->seq[x].aligSetNbr = (int *) allouer((clos->seq[x].longueur+2)*sizeof(int));
+ clos->seq[x].predAligSetPos = (int *)
+ allouer((clos->seq[x].longueur+2)*sizeof(int));
+ clos->seq[x].succAligSetPos = (int *)
+ allouer((clos->seq[x].longueur+2)*sizeof(int));
+ }
+
+clos->gauche1 = (int *) allouer(clos->seqNbr * sizeof(int));
+clos->gauche2 = (int *) allouer(clos->seqNbr * sizeof(int));
+clos->droite1 = (int *) allouer(clos->seqNbr * sizeof(int));
+clos->droite2 = (int *) allouer(clos->seqNbr * sizeof(int));
+clos->pos_ = (int **) callouer_mat(sizeof(int), clos->seqNbr, clos->seqNbr);
+}
+
+void free_closure(CLOSURE *clos)
+{
+long nmax, na;
+int x;
+
+liberer(clos->gauche1); liberer(clos->gauche2); liberer(clos->droite1); liberer(clos->droite2);
+liberer_mat((void **) clos->pos_, clos->seqNbr);
+
+liberer_mat((void **) clos->succFrontier, clos->oldNbrAligSets+2);
+liberer_mat((void **) clos->predFrontier, clos->oldNbrAligSets+2);
+
+for (x=0; x < clos->seqNbr; x++)
+ {
+ liberer(clos->seq[x].aligSetNbr);
+ liberer(clos->seq[x].predAligSetPos);
+ liberer(clos->seq[x].succAligSetPos);
+ }
+
+for (na=0; na <= clos->oldNbrAligSets+1; na++)
+ {
+ liberer(clos->aligSet[na].pos);
+ }
+liberer(clos->aligSet);
+}
+
+void realloc_closure(CLOSURE *clos)
+{
+int na;
+
+if (clos->nbrAligSets > clos->oldNbrAligSets)
+ {
+ clos->predFrontier = (int **) recallouer_mat((void **) clos->predFrontier, sizeof(int),
+ clos->oldNbrAligSets+2, clos->nbrAligSets+2, clos->seqNbr+1);
+ clos->succFrontier = (int **) recallouer_mat((void **) clos->succFrontier, sizeof(int),
+ clos->oldNbrAligSets+2, clos->nbrAligSets+2, clos->seqNbr+1);
+ clos->aligSet = (positionSet *) reallouer(clos->aligSet, (clos->nbrAligSets+2) * sizeof(positionSet));
+ for (na=clos->oldNbrAligSets+2; na <= clos->nbrAligSets+1; na++)
+ {
+ clos->aligSet[na].pos = (int *) allouer(clos->seqNbr * sizeof(int));
+ }
+ clos->oldNbrAligSets = clos->nbrAligSets;
+ }
+}
+
+
+int print_aligSets(CLOSURE *clos, int nseq, int i)
+{
+char nouveau_, terminer;
+int n, ng, nd, nn, k;
+int x, y;
+
+n = ng = nd = clos->seq[nseq].aligSetNbr[i];
+
+if (ng == 0)
+ {
+ k = clos->seq[nseq].predAligSetPos[i];
+ if (k > 0) ng = clos->seq[nseq].aligSetNbr[k];
+ k = clos->seq[nseq].succAligSetPos[i];
+ if (k > 0) nd = clos->seq[nseq].aligSetNbr[k];
+ }
+
+printf("echelle %d: ", n);
+if (n != 0)
+ for (x=0; x < clos->seqNbr; x++)
+ printf("%d ", clos->aligSet[n].pos[x]);
+
+printf("\nfrontiere clos->gauche %d: ", ng);
+if (ng != 0)
+ for (x=0; x < clos->seqNbr; x++)
+ printf("%d ", clos->predFrontier[ng][x]);
+
+printf("\nfrontiere clos->droite %d: ", nd);
+if (nd != 0)
+ for (x=0; x < clos->seqNbr; x++)
+ printf("%d ", clos->succFrontier[nd][x]);
+
+printf("\n");
+
+}
+
+void init_seq(CLOSURE *clos, int nbreseq, int *longseq)
+{
+int x;
+
+clos->seqNbr = nbreseq;
+
+clos->seq = (sequence *) allouer(clos->seqNbr * sizeof(sequence));
+
+for (x=clos->maxLong=0; x < clos->seqNbr; x++)
+ {
+ clos->seq[x].longueur = longseq[x];
+ if (clos->maxLong < longseq[x])
+ clos->maxLong = longseq[x];
+ }
+}
+
+void desinit_seq(CLOSURE *clos)
+{
+int x;
+
+liberer(clos->seq);
+}
+
+/*********************************************************/
+/************** EXTERN FONCTIONS *************************/
+/*********************************************************/
+
+CLOSURE *newAligGraphClosure(int nbreseq, int *longseq,
+ int nbreancr, int **ancrages)
+{
+
+CLOSURE *clos = (CLOSURE *) allouer(sizeof(CLOSURE));
+
+init_seq(clos, nbreseq, longseq);
+
+alloc_closure(clos); /* utilise clos->maxLong */
+
+init_closure(clos, nbreancr, ancrages);
+
+return clos;
+}
+
+void freeAligGraphClosure(CLOSURE *clos)
+{
+free_closure(clos);
+
+desinit_seq(clos);
+
+liberer(clos);
+}
+
+int addAlignedPositions(CLOSURE *clos, int seq1, int i, int seq2, int j)
+{
+char nouveau_, terminer;
+int n, n1, n2, ng1, ng2, nd1, nd2, nn, k;
+int x, y;
+
+n1 = ng1 = nd1 = clos->seq[seq1].aligSetNbr[i]; n2 = ng2 = nd2 = clos->seq[seq2].aligSetNbr[j];
+
+if (n1 == 0 || n2 == 0 || n1 != n2)
+ {
+ if (ng1 == 0)
+ {
+ k = clos->seq[seq1].predAligSetPos[i];
+ if (k > 0) ng1 = clos->seq[seq1].aligSetNbr[k];
+ k = clos->seq[seq1].succAligSetPos[i];
+ if (k > 0) nd1 = clos->seq[seq1].aligSetNbr[k];
+ }
+ if (ng2 == 0)
+ {
+ k = clos->seq[seq2].predAligSetPos[j];
+ if (k > 0) ng2 = clos->seq[seq2].aligSetNbr[k];
+ k = clos->seq[seq2].succAligSetPos[j];
+ if (k > 0) nd2 = clos->seq[seq2].aligSetNbr[k];
+ }
+
+ if (ng1 == 0) for (x=0; x < clos->seqNbr; x++) clos->gauche1[x] = 0;
+ else for (x=0; x < clos->seqNbr; x++) clos->gauche1[x] = clos->predFrontier[ng1][x];
+ if (nd1 == 0) for (x=0; x < clos->seqNbr; x++) clos->droite1[x] = clos->seq[x].longueur + 1;
+ else for (x=0; x < clos->seqNbr; x++) clos->droite1[x] = clos->succFrontier[nd1][x];
+ if (ng2 == 0) for (x=0; x < clos->seqNbr; x++) clos->gauche2[x] = 0;
+ else for (x=0; x < clos->seqNbr; x++) clos->gauche2[x] = clos->predFrontier[ng2][x];
+ if (nd2 == 0) for (x=0; x < clos->seqNbr; x++) clos->droite2[x] = clos->seq[x].longueur + 1;
+ else for (x=0; x < clos->seqNbr; x++) clos->droite2[x] = clos->succFrontier[nd2][x];
+
+ clos->gauche1[seq1] = clos->droite1[seq1] = i;
+ clos->gauche2[seq2] = clos->droite2[seq2] = j;
+
+ nn = clos->nbrAligSets + 1;
+
+ for (x=0; x < clos->seqNbr; x++)
+ {
+ clos->aligSet[nn].pos[x] = 0;
+ if (n1 > 0 && clos->aligSet[n1].pos[x] > 0)
+ clos->aligSet[nn].pos[x] = clos->aligSet[n1].pos[x];
+ else { if (n2 > 0 && clos->aligSet[n2].pos[x] > 0)
+ clos->aligSet[nn].pos[x] = clos->aligSet[n2].pos[x];}
+
+ if (clos->aligSet[nn].pos[x] == 0)
+ {
+ clos->predFrontier[nn][x] = max(clos->gauche1[x], clos->gauche2[x]);
+ clos->succFrontier[nn][x] = min(clos->droite1[x], clos->droite2[x]);
+ }
+ else clos->predFrontier[nn][x] = clos->succFrontier[nn][x] = clos->aligSet[nn].pos[x];
+ }
+ clos->predFrontier[nn][seq1] = clos->succFrontier[nn][seq1] = clos->aligSet[nn].pos[seq1] = i;
+ clos->predFrontier[nn][seq2] = clos->succFrontier[nn][seq2] = clos->aligSet[nn].pos[seq2] = j;
+
+
+ for (x=clos->aligSet[nn].nbr=0; x < clos->seqNbr; x++)
+ if (clos->aligSet[nn].pos[x] > 0)
+ {
+ k = clos->aligSet[nn].pos[x];
+ clos->seq[x].aligSetNbr[k] = nn;
+ clos->aligSet[nn].nbr++;
+ }
+
+ for (x=0; x < clos->seqNbr; x++)
+ if (clos->droite1[x] != clos->droite2[x]) /* => la front. clos->gauche peut changer */
+ for (y=0; y < clos->seqNbr; y++)
+ {
+ clos->pos_[x][y] = 0;
+ k = clos->succFrontier[nn][x];
+ if (k == clos->aligSet[nn].pos[x])
+ k = clos->seq[x].succAligSetPos[k];
+ if (k <= clos->seq[x].longueur)
+ while (k > 0)
+ {
+ n = clos->seq[x].aligSetNbr[k];
+ if (clos->predFrontier[n][y] < clos->predFrontier[nn][y])
+ {
+ clos->pos_[x][y] = k;
+ k = clos->seq[x].succAligSetPos[k];
+ }
+ else k = 0;
+ }
+ }
+
+ for (x=0; x < clos->seqNbr; x++)
+ if (clos->droite1[x] != clos->droite2[x])
+ /* => la front. gauche peut changer */
+ for (y=0; y < clos->seqNbr; y++)
+ {
+ k = clos->succFrontier[nn][x];
+ if (k == clos->aligSet[nn].pos[x])
+ k = clos->seq[x].succAligSetPos[k];
+ if (clos->pos_[x][y] > 0)
+ while (k > 0 && k <= clos->pos_[x][y])
+ {
+ n = clos->seq[x].aligSetNbr[k];
+ clos->predFrontier[n][y] = clos->predFrontier[nn][y];
+ k = clos->seq[x].succAligSetPos[k];
+ }
+ }
+
+ for (x=0; x < clos->seqNbr; x++)
+ if (clos->gauche1[x] != clos->gauche2[x])
+ /* => la front. droite peut changer */
+ for (y=0; y < clos->seqNbr; y++)
+ {
+ clos->pos_[x][y] = 0;
+ k = clos->predFrontier[nn][x];
+ if (k > 0 && k == clos->aligSet[nn].pos[x])
+ k = clos->seq[x].predAligSetPos[k];
+ while (k > 0)
+ {
+ n = clos->seq[x].aligSetNbr[k];
+ if (clos->succFrontier[n][y] > clos->succFrontier[nn][y])
+ {
+ clos->pos_[x][y] = k;
+ k = clos->seq[x].predAligSetPos[k];
+ }
+ else k = 0;
+ }
+ }
+
+ for (x=0; x < clos->seqNbr; x++)
+ if (clos->gauche1[x] != clos->gauche2[x]) /* => la front. clos->droite peut changer */
+ for (y=0; y < clos->seqNbr; y++)
+ {
+ k = clos->predFrontier[nn][x];
+ if (k > 0 && k == clos->aligSet[nn].pos[x])
+ k = clos->seq[x].predAligSetPos[k];
+ if (clos->pos_[x][y] > 0)
+ while (k >= clos->pos_[x][y])
+ {
+ n = clos->seq[x].aligSetNbr[k];
+ clos->succFrontier[n][y] = clos->succFrontier[nn][y];
+ k = clos->seq[x].predAligSetPos[k];
+ }
+ }
+
+ if (n1 == 0)
+ {
+ for (k=i-1; k > 0 && clos->seq[seq1].aligSetNbr[k] == 0; k--)
+ clos->seq[seq1].succAligSetPos[k] = i;
+ if (k > 0)
+ clos->seq[seq1].succAligSetPos[k] = i;
+ for (k=i+1; k <= clos->seq[seq1].longueur
+ && clos->seq[seq1].aligSetNbr[k] == 0; k++)
+ clos->seq[seq1].predAligSetPos[k] = i;
+ if (k <= clos->seq[seq1].longueur)
+ clos->seq[seq1].predAligSetPos[k] = i;
+ }
+
+ if (n2 == 0)
+ {
+ for (k=j-1; k > 0 && clos->seq[seq2].aligSetNbr[k] == 0; k--)
+ clos->seq[seq2].succAligSetPos[k] = j;
+ if (k > 0)
+ clos->seq[seq2].succAligSetPos[k] = j;
+ for (k=j+1; k <= clos->seq[seq2].longueur
+ && clos->seq[seq2].aligSetNbr[k] == 0; k++)
+ clos->seq[seq2].predAligSetPos[k] = j;
+ if (k <= clos->seq[seq2].longueur)
+ clos->seq[seq2].predAligSetPos[k] = j;
+ }
+
+
+ if (n1 > n2) { n = n1; n1 = n2; n2 = n; }
+
+ if (n2 == 0)
+ {
+ clos->nbrAligSets++;
+
+ realloc_closure(clos);
+ }
+ else {
+ if (n1 == 0)
+ {
+ moveAligSet(clos, n2, nn);
+ }
+ else
+ {
+ moveAligSet(clos, n1, nn);
+
+ if (n2 < clos->nbrAligSets) moveAligSet(clos, n2, clos->nbrAligSets);
+ clos->nbrAligSets--;
+
+ realloc_closure(clos);
+ }
+ }
+ }
+}
+
+int path(CLOSURE *clos, int x, int i, int y, int j)
+{
+int n2, k;
+
+if (x == y) return(i <= j);
+
+n2 = clos->seq[y].aligSetNbr[j];
+
+if (n2 == 0)
+ {
+ k = clos->seq[y].predAligSetPos[j];
+ if (k > 0) n2 = clos->seq[y].aligSetNbr[k];
+ }
+
+if (n2 == 0) return(false);
+else return(i <= clos->predFrontier[n2][x]);
+}
+
+int alignedPositions(CLOSURE *clos, int x, int i, int y, int j)
+{
+
+return (x == y && i == j) || (clos->seq[x].aligSetNbr[i] != 0 &&
+ clos->seq[x].aligSetNbr[i] == clos->seq[y].aligSetNbr[j]);
+}
+
+int alignablePositions(CLOSURE *clos, int x, int i, int y, int j)
+{
+
+if (path(clos, x, i, y, j))
+ return(path(clos, y, j, x, i));
+else
+ return(!path(clos, y, j, x, i));
+}
+
+int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
+{
+int k;
+
+for (k=0; k < l; i++, j++, k++)
+ addAlignedPositions(clos, x, i, y, j);
+
+}
+
+int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
+{
+int k;
+
+for (k=0; k < l && alignablePositions(clos, x, i, y, j); i++, j++, k++);
+
+return(k==l);
+}
+
+int alignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l)
+{
+int k;
+
+for (k=0; k < l && alignedPositions(clos, x, i, y, j); i++, j++, k++);
+
+return(k==l);
+}
+
+int predFrontier(CLOSURE *clos, int x, int i, int y) /* on suppose que x!=y */
+{
+int n, k;
+
+n = clos->seq[x].aligSetNbr[i];
+
+if (n == 0)
+ {
+ k = clos->seq[x].predAligSetPos[i];
+ if (k > 0) n = clos->seq[x].aligSetNbr[k];
+ }
+
+if (n > 0) return(clos->predFrontier[n][y]);
+else return(0);
+}
+
+int succFrontier(CLOSURE *clos, int x, int i, int y) /* on suppose que x!=y */
+{
+int n, k;
+
+n = clos->seq[x].aligSetNbr[i];
+
+if (n == 0)
+ {
+ k = clos->seq[x].succAligSetPos[i];
+ if (k > 0) n = clos->seq[x].aligSetNbr[k];
+ }
+
+if (n > 0) return(clos->succFrontier[n][y]);
+else return(clos->seq[y].longueur+1);
+}
Added: trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.h
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.h 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/alig_graph_closure.h 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,63 @@
+/************************************************************/
+/************************************************************/
+/** GABIOS-LIB 1.0 (1999) **/
+/** A library for Greedy Alignment of BIOlogical Sequences **/
+/** Developed by Said Abdeddaim **/
+/** Said.Abdeddaim at dir.univ-rouen.fr **/
+/************************************************************/
+/************************************************************/
+
+#ifndef _ALIG_GRAPH_CLOSURE_H
+#define _ALIG_GRAPH_CLOSURE_H
+
+
+typedef struct {
+ int *pos;
+ int nbr;
+ } positionSet;
+
+typedef struct {
+ int longueur;
+
+ int *aligSetNbr, *predAligSetPos, *succAligSetPos;
+ } sequence;
+
+typedef struct {
+ int seqNbr;
+ sequence *seq;
+ int maxLong;
+
+ positionSet *aligSet;
+ int nbrAligSets, oldNbrAligSets;
+
+ int **predFrontier, **succFrontier;
+
+ int *topolog;
+ int *gauche1, *gauche2, *droite1, *droite2, **pos_;
+
+ } CLOSURE;
+
+
+CLOSURE *newAligGraphClosure(int nbreseq, int *longseq,
+ int nbreancr, int **ancrages);
+
+void freeAligGraphClosure(CLOSURE *clos);
+
+int addAlignedPositions(CLOSURE *clos, int x, int i, int y, int j);
+
+int alignablePositions(CLOSURE *clos, int x, int i, int y, int j);
+
+int alignedPositions(CLOSURE *clos, int x, int i, int y, int j);
+
+int addAlignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
+
+int alignableSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
+
+int alignedSegments(CLOSURE *clos, int x, int i, int y, int j, int l);
+
+int predFrontier(CLOSURE *clos, int x, int i, int y);
+
+int succFrontier(CLOSURE *clos, int x, int i, int y);
+
+
+#endif /* _ALIG_GRAPH_CLOSURE_H */
Added: trunk/packages/dialign/branches/upstream/current/src/anchor.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/anchor.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/anchor.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,167 @@
+
+ /*******************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * anchor.c *
+ * *
+ \*******************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+
+extern int anc_num, *seqlen ;
+extern int seqnum;
+extern char *seq[MAX_SEQNUM];
+extern struct multi_frag *anchor_frg ;
+
+void anchor_check( int s1, int s2, int b1, int b2, int l , float scr ) {
+
+ if(
+ ( s1 < 1 ) ||
+ ( s1 > seqnum )
+ ) {
+ printf(" \n\n wrong sequence # %d in anchoring file\n\n", s1 );
+ printf(" data set consists only of %d sequences \n\n", seqnum );
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit( 1 ) ;
+ }
+ if(
+ ( s2 < 1 ) ||
+ ( s2 > seqnum )
+ ) {
+ printf(" \n\n wrong sequence # %d in anchoring file\n\n", s2 );
+ printf(" data set consists only of %d sequences \n\n", seqnum );
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit( 1 ) ;
+ }
+
+
+ if( s1 == s2 ) {
+ printf("\n strange data in anchoring file:\n");
+ printf(" sequence # %d anchored with itself.\n\n", s1 );
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit(1) ;
+ }
+
+
+
+/*
+ if(
+ ( b1 < 1 ) ||
+ ( b1 + l - 1 > seqlen[ s1 - 1 ] )
+ ) {
+ printf(" \n\n anchor # %d starts", anc_num + 1 ) ;
+ printf(" at position %d in sequence %d and has a length of %d.\n", b1, s1, l ) ;
+ printf(" This does not fit into sequence # %d " , s1 );
+ printf(" (sequence length = %d) \n\n", seqlen[ s1 - 1 ] ) ;
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit( 1 ) ;
+ }
+*/
+
+ if(
+ ( b1 < 1 ) ||
+ ( b1 + l - 1 > seqlen[ s1 - 1 ] )
+ ) {
+ printf(" \n\n WARNING:");
+ printf(" \n\n anchor # %d starts", anc_num + 1 ) ;
+ printf(" at position %d in sequence %d\n ", b1, s1 ) ;
+ printf(" and is %d residues in length.\n", l ) ;
+ printf(" However, sequence %d" , s1 );
+ printf(" is only %d residues in length \n\n", seqlen[ s1 - 1 ] ) ;
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit( 1 ) ;
+ }
+
+ if(
+ ( b2 < 1 ) ||
+ ( b2 + l - 1 > seqlen[ s2 - 1 ] )
+ ) {
+ printf(" \n\n WARNING:");
+ printf(" \n\n anchor # %d starts", anc_num + 1 ) ;
+ printf(" at position %d in sequence %d\n ", b2, s2 ) ;
+ printf(" and is %d residues in length.\n", l ) ;
+ printf(" However, sequence %d" , s2 );
+ printf(" is only %d residues in length \n\n", seqlen[ s2 - 1 ] ) ;
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit( 1 ) ;
+ }
+
+
+}
+
+
+int multi_anc_read( char *file_name ) {
+
+ char anc_file_name[ NAME_LEN ] ;
+ FILE *fp;
+ struct multi_frag *current_frg ;
+ char line[ 10000 ] ;
+ int i, len, beg1, beg2, sv = 0, wrdl, hv, word_num ;
+ int seq1, seq2 ;
+ float wgt;
+
+ strcpy( anc_file_name , file_name );
+ strcat( anc_file_name , ".anc" );
+
+ if( (fp = fopen( anc_file_name, "r")) == NULL)
+ erreur("\n\n cannot find file with anchor points \n\n\n");
+
+ if( ( anchor_frg = ( struct multi_frag * ) calloc( 1 , sizeof( struct multi_frag ) ))
+ == NULL) {
+ printf(" problems with memory allocation for `anchor fragments' ! \n \n");
+ exit(1);
+ }
+
+ current_frg = anchor_frg ;
+
+
+ while( fgets( line , MLINE , fp ) != NULL ) {
+
+ if( word_count( line ) == 6 ) {
+ sscanf(line,"%d %d %d %d %d %f ", &seq1 , &seq2 , &beg1, &beg2 , &len , &wgt );
+
+ anchor_check( seq1 , seq2 , beg1, beg2 , len , wgt ) ;
+
+ seq1 = seq1 - 1 ;
+ seq2 = seq2 - 1 ;
+
+ current_frg->s[0] = seq1 ;
+ current_frg->s[1] = seq2 ;
+ current_frg->b[0] = beg1 ;
+ current_frg->b[1] = beg2 ;
+ current_frg->ext = len ;
+ current_frg->weight = wgt;
+
+
+ current_frg->next = (struct multi_frag *)
+ calloc( 1 , sizeof(struct multi_frag) );
+
+ current_frg = current_frg->next;
+ anc_num++;
+ }
+ else {
+ if( word_count( line ) != 0 ){
+ printf("\n\n Anchor file has wrong format. ");
+ printf("\n Each line must contain 6 numbers! \n");
+ printf("\n Anchor file contains line \n\n");
+ printf(" %s \n", line);
+ printf(" PROGRAM TERMINATED \n\n" ) ;
+ exit(1) ;
+ }
+ }
+ }
+} /* multi_anc_read */
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/define.h
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/define.h 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/define.h 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,25 @@
+#define INT16 short int
+#ifdef __alpha
+#define INT32 int
+#else
+#define INT32 long int
+#endif
+#define REAL32 float
+#define REAL64 double
+
+#ifndef TRUE
+#define TRUE 1
+#endif
+
+#ifndef FALSE
+#define FALSE 0
+#endif
+
+#ifndef MAC
+#define Malloc malloc
+#define Calloc calloc
+#define Realloc realloc
+#define Free free
+#endif
+
+#define STATUS 0x10000002
Added: trunk/packages/dialign/branches/upstream/current/src/dialign.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/dialign.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/dialign.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,1296 @@
+
+ /************************\
+ * *
+ * DIALIGN 2.2.1 *
+ * *
+ * dialign.c *
+ * *
+ * written by *
+ * *
+ * B. Morgenstern *
+ * *
+ \************************/
+
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include <time.h>
+#include "dialign.h"
+#include "define.h"
+#include "alig_graph_closure.h"
+
+
+
+FILE *fp_dia, *fp_dpa, *fp_frg , *fp_mot ;
+struct multi_frag *anchor_frg ;
+
+int col_score = 0;
+int char_num[ MAX_REGEX ] ;
+char *mot_char[ MAX_REGEX ] ;
+int regex_len , mot_len = 0 ;
+
+
+clock_t beg_pa , end_pa , beg_ali , end_ali , beg_ts , end_ts ;
+float time_diff_pa , time_diff_ali , perc_pa_time , time_diff_srt ;
+float total_pa_time = 0 ;
+
+
+float mot_factor , mot_offset_factor , max_mot_offset ;
+
+int wgt_type_plot = 0 , motifs = 0 ;
+int bubblesort = 0 , cd_gobics = 0 ;
+int nas = 0 , ref_seq = 0 , i_max ;
+int speed_optimized = 0 ;
+int online = 0 ;
+int time_stamps = 0 ;
+int break1 = 0 ;
+int break2 = 0 ;
+int wgt_print = 0 ;
+int wgt_print_x = 0 ;
+short max_itnum = MAX_ITNUM ;
+int quali_num = 1 ;
+int wgt_plot = 0 ;
+int self_comparison = 0;
+short exclude_frg = 0;
+int ***exclude_list ;
+int max_sim_score = -2000 ;
+int sf_mat = 0 ;
+char nuc1, nuc2, nuc3 ;
+short crick_strand = 0;
+int frg_count = 0;
+int dna_speed = 0;
+char pst_name[NAME_LEN];
+int cont_it = 1 , wgt_type = 0 ;
+int mask = 0, strict = 0 , textual_alignment = 1;
+char prn[ NAME_LEN ] ;
+int redundant, print_max_nd = 1;
+int lmax = MAX_DIA;
+char **arguments;
+int pr_av_nd = 0, pr_av_max_nd ;
+char input_line[ NAME_LEN ];
+char input_parameters[ NAME_LEN ];
+int print_status = 0 ;
+char clust_sim[NAME_LEN] ;
+float tot_weight = 0, av_len;
+int anchors = 0;
+int pa_only = 0;
+int dia_num = 0;
+int max_dia_num = 0;
+float av_dia_num = 0;
+float av_max_dia_num = 0;
+int afc_file = 0;
+int afc_filex = 0;
+int dia_pa_file = 0;
+int frag_file = 0;
+int argnum;
+int standard_out = 0;
+int plot_num = 4 ;
+int default_name = 1;
+int fasta_file = 0;
+int cw_file = 0;
+int msf_file = 0;
+char *upg_str;
+int dcount = 0;
+
+
+int **shift;
+int thr_sim_score = 4 ;
+char *seq[MAX_SEQNUM]; /* sequences */
+char *newseq[MAX_SEQNUM]; /* sequences */
+int sim_score[21][21]; /* similarity matrix */
+float av_sim_score_pep ;
+float av_sim_score_nuc ;
+float **glob_sim; /* overall similarity between any two sequences */
+float **wgt_prot ; /* `weight' of diagonals */
+float **wgt_dna ; /* `weight' of diagonals */
+float **wgt_trans ; /* `weight' of diagonals */
+float **min_weight; /* `weight' of diagonals */
+int min_dia = MIN_DIA ; /* minimum length of diagonals */
+int max_dia = MAX_DIA ; /* maximum length of diagonals */
+int iter_cond_prob = 0;
+int *seqlen; /* lengths of sequences */
+char *full_name[MAX_SEQNUM] ;
+float **pair_score;
+short **cont_it_p;
+float score;
+int maxlen; /* maximum length of sequences */
+int seqnum; /* number of sequences */
+int *num_dia_bf; /* num_dia_bf[ istep ] = number of diagonals from
+ all pairwise alignments BEFORE FILTER
+ PROCEDURE in iteration step `istep' */
+int *num_dia_af; /* num_dia_af[istep] = number of diagonals from
+ all pairwise alignments AFTER FILTER
+ PROCEDURE in iteration step `it' */
+int num_dia_anc; /* number of diagonals definde by anchored
+ regions */
+int num_all_it_dia = 0; /* total number of diagonals in multiple alignment
+ in all iteration steps */
+float weight_sum_bf; /* sum of weights of diagonals in multiple
+ alignment before filter procedure */
+float weight_sum_af; /* sum of weights of diagonals in multiple
+ alignment after fliter procedure*/
+float threshold = 0.0 ; /* threshold T */
+int num_dia_p; /* number of diagonals in pairwise alignment */
+int long_output = 0; /* if long_output = 1, a log-file is produced. */
+int frg_mult_file = 0 ;
+int frg_mult_file_v = 0 ;
+int overlap_weights = 1 ;
+int ow_force = 0 ;
+int anc_num = 0; /* number of anchored regions
+ (specified in file *.anc) */
+int par_count; /* number of parameters */
+float pairalignsum; /* sum of weights in pairwise alignment */
+int pairalignlen; /* sum of aligned residues in pairwise alignment */
+char amino_acid[22];
+int istep;
+struct multi_frag /* pointer to first diagonal in multiple alignment */
+ *this_it_dia; /* in current iteration step */
+struct multi_frag /* pointer to first diagonal in multiple alignment */
+ *all_it_dia; /* in all iteration step */
+struct multi_frag *end_dia;
+ /* pointer to last diagonal in multiple alignment */
+
+char par_dir[NAME_LEN];
+char *seq_name[MAX_SEQNUM];
+char mat_name[NAME_LEN]; /* name of file containing similarity matrix */
+char mat_name_p[NAME_LEN];
+char anc_name[NAME_LEN]; /* anchored regions */
+char seq_file[NAME_LEN];
+char input_name[NAME_LEN];
+char tmp_str[NAME_LEN];
+char output_name[NAME_LEN];
+char printname[NAME_LEN];
+char mot_regex[MAX_REGEX] ;
+
+char *par_file;
+
+short **mot_pos ; /* positions of pre-defined motifs */
+
+int **amino; /* amino acid residues in protein sequences or
+ translated DNA sequences, respective */
+
+int **amino_c; /* amino acid residues on crick strand */
+
+CLOSURE *clos; /* closure data structure for GABIOS-LIB */
+
+int ***open_pos; /* open_pos[i][j][p] = 1, if the p-th residue of
+ sequence i is not yet directly (by one diagonal)
+ aligned with any residue of sequence j and
+ open_pos[i][j][r] = 0 otherwise. So, at the
+ beginning of the first iteration step, all values
+ are 1. In the subsequent iteration steps,
+ only those parts of the sequence are considered,
+ that are not yet aligned. */
+
+
+struct multi_frag *pair_dia; /* diagonals in pairwise alignemnt */
+
+
+double **tp400_prot ; /* propability distribution for sums of similarity
+ socores in diagonals occurring in comparison matrix
+ (by random experiments and approximation */
+
+double **tp400_dna ; /* propability distribution for sums of similarity
+ socores in diagonals occurring in comparison matrix
+ (by random experiments and approximation */
+
+double **tp400_trans ; /* propability distribution for sums of similarity
+ socores in diagonals occurring in comparison matrix
+ (by random experiments and approximation */
+
+
+char dia_pa_name[NAME_LEN];
+char frag_file_name[NAME_LEN];
+char mot_file_name[NAME_LEN];
+
+
+/********************************/
+/* prototypes */
+/********************************/
+
+ extern float mot_dist_factor ( int offset , float parameter ) ;
+ extern int word_count( char *seq ) ;
+ extern void subst_mat(char *file_name, int fragno , struct multi_frag *smp );
+ extern int seq_read( char *in_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn) ;
+ extern int anc_read( char *file_name ) ;
+ extern int multi_anc_read( char *file_name ) ;
+ extern void randomize( int r_numb , FILE *fp1 );
+ extern int mini2(int a, int b);
+ extern int maxi2(int a, int b);
+ extern int mini3(int a, int b, int c);
+ extern int num_test( char *cp );
+ extern void mini(int *a, int b);
+ extern void maxi(int *a, int b);
+ extern void filter( int *num, struct multi_frag *vector );
+ extern void throw_out( float *weight_sum );
+ extern void sel_test();
+ extern float frag_chain( int n1 , int n2 , FILE *fp , FILE *fp2, int *num );
+ extern void para_read( int num , char **arg );
+ extern void frag_sort( int number , struct multi_frag *dp , int olw );
+ extern void ow_frag_sort( int number , struct multi_frag *dp , int olw );
+ extern void bubble_sort( int number , struct multi_frag *dp );
+ extern void ow_bubble_sort( int number , struct multi_frag *dp );
+ extern void seq_shift();
+ extern int translate(char c1, char c2, char c3, int s , int i);
+ extern char invert( char c1 ) ;
+ extern int int_test(float f);
+ extern int match_test( struct multi_frag *dia, int mn);
+
+ extern void para_print(char *s_f, FILE *f);
+ extern void ali_arrange(int fragno , struct multi_frag *smp, FILE *fp, FILE *fp2, FILE *fp3 , FILE *fp4 , FILE *fp_csc );
+ extern void print_log( struct multi_frag *d , FILE *fp_l , FILE *fp_fs);
+ extern void print_fragments( struct multi_frag *d , FILE *fp_frg );
+ extern void tp400_read( int wgt_type , double **pr_ptr );
+ extern void ow_add(struct multi_frag *sm1 , struct multi_frag *sm2);
+ extern void av_tree_print();
+ extern void matrix_read( FILE *fp_mat ) ;
+ extern void mem_alloc( ) ;
+
+
+ /******************************/
+ /* main */
+ /******************************/
+
+
+
+main(int argc, char **argv)
+{
+ int k, anc1, dia_counter, tmpi1, tmpi2 ;
+
+ struct multi_frag *current_dia, *diagonal1, *diagonal2, *anc_dia;
+ /* pointers to diagonals in multiple alignment */
+
+ char str[NAME_LEN], dist_name[NAME_LEN];
+ char par_str[NAME_LEN];
+ char *char_ptr;
+ char prn2[NAME_LEN];
+ char logname[NAME_LEN];
+ char fsm_name[NAME_LEN];
+ char dia_name[NAME_LEN];
+ char csc_name[NAME_LEN];
+ char itname[NAME_LEN], itname2[NAME_LEN], itname3[NAME_LEN];
+ char itname4[NAME_LEN];
+ char dialign_dir[NAME_LEN];
+
+ int i, j, hv, sv, fv;
+
+
+ FILE *fp_ali, *fp2, *fp3, *fp4, *fp_log, *fp_fsm, *fp_st , *fp_csc ;
+ FILE *fp_matrix ; /* file containing similarity matrix */
+
+ strcpy(mat_name,MATNAME);
+ strcpy( clust_sim , "av" );
+
+ par_file = (char *) calloc((size_t) NAME_LEN , sizeof(char) );
+
+
+ if( time_stamps )
+ beg_ali = clock() ;
+
+ strcpy ( dialign_dir , "DIALIGN2_DIR" );
+
+ if ((par_file = getenv(dialign_dir)) == NULL)
+ {
+ printf("\n \n \n Please set the environmentvariable DIALIGN2_DIR \n");
+ printf(" as described in the README file \n");
+ exit(1);
+ }
+
+ argnum = argc;
+
+ strcpy( par_dir , par_file );
+
+if(argc == 1)
+ {
+ printf("\n usage: %s [ options ] <seq_file> \n\n", argv[0] );
+ printf(" <seq_file> contains input sequences in FASTA format.\n");
+ printf(" Per default, sequences are assumed to be protein sequences.\n" ) ;
+ printf(" For DNA alignment, please use one of these options: \n\n");
+ printf(" -n DNA sequences; similarity calculated at the nucleotide level \n\n");
+ printf(" -nt DNA sequences; similarity calculated at the peptide level\n");
+ printf(" (by translation using the genetic code) \n\n");
+ printf(" -lgs long genomic sequences: Both nucleotide and peptide\n");
+ printf(" similarities calculated \n\n");
+ printf(" Many more options are available, please consult the \n");
+ printf(" DIALIGN USER_GUIDE that should come with the DIALIGN package.\n");
+ printf(" For more information on DIALIGN, please visit the DIALIGN\n");
+ printf(" home page at BiBiServ (Bielefeld Bioinformatic Server): \n\n") ;
+ printf(" http://bibiserv.techfak.uni-bielefeld.de/dialign/ \n\n");
+ exit(1) ;
+ }
+
+ arguments = ( char ** ) calloc( argnum , sizeof ( char * ) );
+
+ for( i = 0 ; i < argnum ; i++ )
+ {
+ arguments[i] = ( char *) calloc( NAME_LEN , sizeof (char) );
+ strcpy( arguments[i] , argv[i] );
+ }
+
+
+
+ strcpy( input_name , argv[ argc - 1 ] );
+
+ threshold = 0.0 ;
+
+
+ para_read( argnum , arguments );
+
+ if( ( textual_alignment == 0 ) && ( col_score == 1 ) ) {
+ printf("\n\n Option -csc makes sense only if \"textual alignment\"");
+ printf(" is produced. \n");
+ printf(" This can be enforced with option -ta \n\n");
+ printf(" program terminated \n\n\n");
+ exit(1) ;
+ }
+
+
+ if( cd_gobics ) {
+ strcpy( input_line , "program parameters: " ) ;
+ for( i = 1 ; i < ( argnum -1 ) ; i++ ) {
+ strcat( input_line , argv[i] );
+ strcat( input_line , " " );
+ }
+ }
+ else {
+ strcpy( input_line , "program call: " ) ;
+ for( i = 0 ; i < argnum ; i++ ) {
+ strcat( input_line , argv[i] );
+ strcat( input_line , " " );
+ }
+ }
+
+
+ if ( wgt_type > 0 )
+ strict = 1 ;
+
+ strcpy( seq_file , input_name );
+
+ if(
+ ( ! strcmp( input_name + strlen( input_name ) - 4 , ".seq" ) )
+ || ( ! strcmp( input_name + strlen( input_name ) - 3 , ".fa" ) )
+ || ( ! strcmp( input_name + strlen( input_name ) - 6 , ".fasta" ) )
+ )
+ if( ( char_ptr = strrchr(input_name,'.') ) != NULL)
+ *char_ptr = '\0';
+
+
+ strcpy( anc_name , input_name );
+ strcat( anc_name , ".anc" );
+
+ seqnum = seq_read( seq_file , seq , seq_name , full_name ) ;
+
+ if ( motifs )
+ regex_parse( mot_regex ) ;
+
+
+ if( ( seqnum == 2 ) && ( iter_cond_prob == 0 ) )
+ max_itnum = 1 ;
+
+
+ if( ( ow_force == 0 ) && ( seqnum > OVERLAP_THRESHOLD ) )
+ overlap_weights = 0;
+ if( seqnum == 2 )
+ overlap_weights = 0;
+
+ if( seqnum < 2 ) {
+
+ if( cd_gobics ) {
+ printf("\n\n Something is wrong with your sequence file. Maybe you entered a\n");
+ printf(" MS WORD or RFT file or your file contains only one single sequence.\n");
+ printf(" Please note that our server only accepts plain text files. \n\n");
+ printf(" For more information, please consult our online manual \n");
+ printf(" at the CHAOS/DIALIGN home page:\n\n");
+ printf(" http://dialign.gobics.de/chaos-dialign-manual");
+ }
+
+ else {
+ printf("\n\n Your sequence file containes only a single sequence.\n");
+ printf(" Please make sure your input file contains at least two sequences.\n\n");
+ printf(" For more information, please consult the online manual \n");
+ printf(" at the DIALIGN home page: \n\n");
+ printf(" http://bibiserv.techfak.uni-bielefeld.de/dialign/manual.html ");
+ }
+
+
+
+ printf("\n \n \n \n \n");
+ exit(1);
+ }
+
+ maxlen = 0;
+
+
+
+ if( (pair_score = (float **) calloc( seqnum , sizeof(float *) )) == NULL)
+ {
+ printf(" problems with memory allocation for `pair_score' ! \n \n");
+ exit(1);
+ }
+
+ for(i=0;i<seqnum;i++)
+ if( (pair_score[i] = (float *) calloc( seqnum , sizeof(float) )) == NULL)
+ {
+ printf(" problems with memory allocation for `pair_score' ! \n \n");
+ exit(1);
+ }
+
+
+ if(( cont_it_p = (short **) calloc( seqnum , sizeof( short *))) == NULL ){
+ printf(" problems with memory allocation for `cont_it_p ' ! \n \n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ if( (cont_it_p[i] = (short *) calloc( seqnum , sizeof(short) )) == NULL) {
+ printf(" problems with memory allocation for `cont_it_p' ! \n \n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ for( j = 0 ; j < seqnum ; j++ )
+ cont_it_p[i][j] = 1 ;
+
+
+
+
+
+ for( i = 0 ; i < seqnum ; i++ )
+ {
+ av_len = av_len + seqlen[i];
+
+ if( seqlen[i] == 0 )
+ {
+ printf("\n \n \n WARNING: \n \n");
+ printf(" Sequence %d contains no residues.\n",i+1);
+ printf(" Please inspect the sequence file.\n \n ");
+ printf("\n \n Program terminated \n \n \n " );
+
+ exit(1);
+ }
+
+ if(maxlen < seqlen[i])
+ maxlen = seqlen[i];
+ }
+
+ av_len = av_len / seqnum;
+
+ if ( motifs )
+ seq_parse( mot_regex ) ;
+
+ seq_shift();
+
+
+ if( (glob_sim =
+ (float **) calloc( seqnum , sizeof(float*))) == NULL)
+ {
+ printf("Problems with memory allocation for glob_sim\n");
+ exit(1);
+ }
+
+ for(i=0;i<seqnum;i++)
+ {
+
+ if( (glob_sim[i] =
+ (float *) calloc( seqnum , sizeof(float))) == NULL)
+ {
+ printf("Problems with memory allocation for glob_sim \n");
+ exit(1);
+ }
+
+ }
+
+ strcpy(par_str,"sdfsdf");
+
+ if( argc > 1 )
+ {
+ strcpy(str,par_dir);
+ strcat(str,"/");
+ strcat(str,mat_name);
+ strcpy(mat_name_p,str);
+
+ if( (fp_matrix = fopen(mat_name_p, "r")) == NULL)
+ {
+
+
+ printf("\n\n Cannot find the file %s \n\n", mat_name );
+ printf(" Make sure the environment variable DIALIGN2_DIR points\n");
+ printf(" to a directory containing the files \n\n");
+ printf(" BLOSUM \n tp400_dna\n tp400_prot \n tp400_trans \n\n" );
+ printf(" These files should be contained in the DIALIGN package \n\n\n" ) ;
+ exit(1) ;
+
+
+
+
+ printf("\n \n \n \n ATTENTION ! \n \n");
+ printf("\n There is no similarity matrix `%s'. \n", mat_name);
+ printf(" in the directory \n \n");
+ printf(" %s\n \n", par_dir);
+ exit(1);
+ }
+ }
+
+
+ if( wgt_type != 1 )
+ matrix_read( fp_matrix );
+
+ mem_alloc( );
+
+
+ if( wgt_type != 1 )
+ if( (amino = (int **) calloc( seqnum , sizeof(int *) ) ) == NULL)
+ {
+ printf(" problems with memory allocation");
+ printf(" for `amino' ! \n \n");
+ exit(1);
+ }
+
+ if( wgt_type != 1 )
+ for( i = 0 ; i < seqnum ; i++ )
+ if( (amino[i] = (int *) calloc( ( seqlen[i]+5 ) , sizeof(int) ) ) == NULL)
+ {
+ printf(" problems with memory allocation");
+ printf(" for `amino[%d]' ! \n \n", i);
+ exit(1);
+ }
+
+
+
+
+
+ if( crick_strand ) {
+ if( (amino_c = (int **) calloc( seqnum , sizeof(int *) ) ) == NULL) {
+ printf(" problems with memory allocation");
+ printf(" for `amino_c' ! \n \n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ if( (amino_c[i] = (int *) calloc( ( seqlen[i]+5 ) , sizeof(int) ) ) == NULL) {
+ printf(" problems with memory allocation");
+ printf(" for `amino_c[%d]' ! \n \n", i);
+ exit(1);
+ }
+ }
+
+
+ /******************************************************
+ * *
+ * read file, that contains data of anchored regions *
+ * *
+ ******************************************************/
+
+
+
+if( anchors ) {
+ multi_anc_read( input_name );
+}
+
+if( exclude_frg ) {
+
+ if( ( exclude_list = (int ***) calloc( seqnum , sizeof(int **) )) == NULL) {
+ printf(" problems with memory allocation for 'exclude_list' \n \n");
+ exit(1);
+ }
+
+ for(i = 0 ; i < seqnum ; i++ )
+ if( ( exclude_list[ i ] = (int **) calloc( seqnum , sizeof(int *) )) == NULL) {
+ printf(" problems with memory allocation for 'exclude_list' \n \n");
+ exit(1);
+ }
+
+ for(i = 0 ; i < seqnum ; i++ )
+ for(j = 0 ; j < seqnum ; j++ )
+ if( ( exclude_list[ i ][ j ] = (int *) calloc( seqlen[ i ] + 1 , sizeof(int) )) == NULL) {
+ printf(" problems with memory allocation for 'exclude_list' \n \n");
+ exit(1);
+ }
+
+ exclude_frg_read ( input_name , exclude_list ) ;
+}
+
+
+
+ if( wgt_type == 0 )
+ tp400_read( 0 , tp400_prot);
+ if( wgt_type % 2 )
+ tp400_read( 1 , tp400_dna );
+ if( wgt_type > 1 )
+ tp400_read( 2 , tp400_trans );
+
+
+
+ /****************************\
+ * *
+ * Name of output files *
+ * *
+ \****************************/
+
+ if( default_name )
+ {
+ strcpy( printname , input_name);
+ strcpy( prn , printname);
+ }
+ else
+ {
+ strcpy( printname , output_name );
+ strcpy( prn , printname);
+ }
+
+
+ strcpy(prn2 , prn);
+
+ if( default_name )
+ strcat(prn,".ali");
+
+ strcat(prn2,".fa");
+
+
+
+ strcpy(logname,printname);
+ strcat(logname,".log");
+
+ strcpy(fsm_name , printname);
+ strcat(fsm_name,".fsm");
+
+ if( print_status ) {
+ strcpy( pst_name , printname );
+ strcat( pst_name,".sta");
+ }
+
+ if( afc_file )
+ {
+ strcpy( dia_name , printname );
+ strcat( dia_name , ".afc" );
+ fp_dia = fopen( dia_name , "w" );
+ fprintf(fp_dia,"\n # %s \n\n seq_len: " , input_line );
+ for( i = 0 ; i < seqnum ; i++ )
+ fprintf(fp_dia," %d ", seqlen[i] );
+ fprintf(fp_dia,"\n\n");
+
+ }
+
+ if( col_score ) {
+ strcpy( csc_name , printname );
+ strcat( csc_name , ".csc" );
+ fp_csc = fopen( csc_name , "w" );
+ }
+
+ if( dia_pa_file )
+ {
+ strcpy( dia_pa_name , printname );
+ strcat( dia_pa_name , ".fop" );
+
+ fp_dpa = fopen( dia_pa_name , "w" );
+
+
+ fprintf(fp_dpa,"\n # %s \n\n seq_len: " , input_line );
+ for( i = 0 ; i < seqnum ; i++ )
+ fprintf(fp_dpa," %d ", seqlen[i] );
+ fprintf(fp_dpa,"\n\n");
+ fclose( fp_dpa ) ;
+ }
+
+
+ if( motifs ) {
+ strcpy( mot_file_name , printname );
+ strcat( mot_file_name , ".mot" );
+ fp_mot = fopen( mot_file_name , "w" );
+
+ fprintf(fp_mot,"\n # %s \n\n " , input_line );
+ fprintf(fp_mot," motif: %s \n\n", mot_regex );
+ fprintf(fp_mot," max offset for motifs = %d \n\n", (int) max_mot_offset );
+ fprintf(fp_mot," the following fragments contain the motif: \n\n" );
+ fprintf(fp_mot," seq1 seq2 beg1 beg1 len wgt" );
+ fprintf(fp_mot," # mot mot_wgt \n\n" );
+ }
+
+
+ if( frag_file ) {
+ strcpy( frag_file_name , printname );
+ strcat( frag_file_name , ".frg" );
+ fp_frg = fopen( frag_file_name , "w" );
+
+ fprintf(fp_frg,"\n # %s \n\n seq_len: " , input_line );
+ for( i = 0 ; i < seqnum ; i++ )
+ fprintf(fp_frg," %d ", seqlen[i] );
+ fprintf(fp_frg,"\n sequences: " );
+ for( i = 0 ; i < seqnum ; i++ )
+ fprintf(fp_frg," %s ", seq_name[i] );
+
+ fprintf(fp_frg ,"\n\n");
+ }
+
+
+
+ clos = newAligGraphClosure(seqnum, seqlen, 0, NULL);
+
+ if( (open_pos = (int *** ) calloc( seqnum , sizeof(int **))) == NULL)
+ {
+ printf("Problems with memory allocation for open_pos\n");
+ exit(1);
+ }
+
+ for(i=0;i<seqnum;i++)
+ {
+ if( (open_pos[i] =
+ (int ** ) calloc( seqnum , sizeof(int *))) == NULL)
+ {
+ printf("Problems with memory allocation for open_pos\n");
+ exit(1);
+ }
+ }
+
+
+ for(i=0;i<seqnum;i++)
+ for(j=0;j<seqnum;j++)
+ {
+ if( (open_pos[i][j] =
+ (int * ) calloc( ( seqlen[i]+2) , sizeof(int) ) ) == NULL)
+ {
+ printf("Problems with memory allocation for open_pos\n");
+ exit(1);
+ }
+ }
+
+ for( i = 0 ; i <seqnum ; i++)
+ for( j = 0 ; j <seqnum ; j++)
+ for( hv = 1 ; hv <= seqlen[i] ; hv++)
+ open_pos[i][j][hv] = 1;
+
+
+ /**************************************
+ * *
+ * definition of `amino' *
+ * *
+ **************************************/
+
+
+
+
+ if( wgt_type > 1 )
+ for(hv=0;hv<seqnum;hv++)
+ for(i=1;i<=seqlen[hv]-2;i++)
+ {
+
+
+ if( translate( seq[hv][i],seq[hv][i+1],seq[hv][i+2],hv,i ) == -1)
+ exit(1);
+
+
+ amino[hv][i] = translate( seq[hv][i],seq[hv][i+1],seq[hv][i+2],hv,i);
+
+ if( crick_strand ) {
+ nuc1 = invert( seq[hv][i+2] );
+ nuc2 = invert( seq[hv][i+1] );
+ nuc3 = invert( seq[hv][i] );
+
+ amino_c[hv][i] = translate( nuc1 , nuc2 , nuc3 , hv , i);
+ }
+ }
+
+
+ if( wgt_type == 0 )
+ for(hv=0;hv<seqnum;hv++)
+ for(i=1;i<=seqlen[hv];i++)
+ {
+ if( seq[hv][i] == 'C' ) amino[hv][i] = 1;
+ if( seq[hv][i] == 'S' ) amino[hv][i] = 2;
+ if( seq[hv][i] == 'T' ) amino[hv][i] = 3;
+ if( seq[hv][i] == 'P' ) amino[hv][i] = 4;
+ if( seq[hv][i] == 'A' ) amino[hv][i] = 5;
+ if( seq[hv][i] == 'G' ) amino[hv][i] = 6;
+ if( seq[hv][i] == 'N' ) amino[hv][i] = 7;
+ if( seq[hv][i] == 'D' ) amino[hv][i] = 8;
+ if( seq[hv][i] == 'E' ) amino[hv][i] = 9;
+ if( seq[hv][i] == 'Q' ) amino[hv][i] = 10;
+ if( seq[hv][i] == 'H' ) amino[hv][i] = 11;
+ if( seq[hv][i] == 'R' ) amino[hv][i] = 12;
+ if( seq[hv][i] == 'K' ) amino[hv][i] = 13;
+ if( seq[hv][i] == 'M' ) amino[hv][i] = 14;
+ if( seq[hv][i] == 'I' ) amino[hv][i] = 15;
+ if( seq[hv][i] == 'L' ) amino[hv][i] = 16;
+ if( seq[hv][i] == 'V' ) amino[hv][i] = 17;
+ if( seq[hv][i] == 'F' ) amino[hv][i] = 18;
+ if( seq[hv][i] == 'Y' ) amino[hv][i] = 19;
+ if( seq[hv][i] == 'W' ) amino[hv][i] = 20;
+ }
+
+
+
+ amino_acid[0] = 'X';
+ amino_acid[1] = 'C';
+ amino_acid[2] = 'S';
+ amino_acid[3] = 'T';
+ amino_acid[4] = 'P';
+ amino_acid[5] = 'A';
+ amino_acid[6] = 'G';
+ amino_acid[7] = 'N';
+ amino_acid[8] = 'D';
+ amino_acid[9] = 'E';
+ amino_acid[10] = 'Q';
+ amino_acid[11] = 'H';
+ amino_acid[12] = 'R';
+ amino_acid[13] = 'K';
+ amino_acid[14] = 'M';
+ amino_acid[15] = 'I';
+ amino_acid[16] = 'L';
+ amino_acid[17] = 'V';
+ amino_acid[18] = 'F';
+ amino_acid[19] = 'Y';
+ amino_acid[20] = 'W';
+
+
+
+num_dia_anc = anc_num * (seqnum-1);
+
+
+
+
+if ( anchors ) {
+
+ if( time_stamps )
+ beg_ts = clock() ;
+
+ if ( nas == 0 )
+ if( bubblesort )
+ bubble_sort ( anc_num , anchor_frg ) ;
+ else
+ frag_sort ( anc_num , anchor_frg , 0 ) ;
+
+
+ if( time_stamps) {
+ end_ts = clock() ;
+ time_diff_srt = (float) ( end_ts - beg_ts ) / CLOCKS_PER_SEC ;
+ if( time_stamps )
+ printf (" for anc: time_diff_srt = %f \n", time_diff_srt );
+ }
+
+
+ filter( &anc_num , anchor_frg);
+/* exit(1) ;
+*/
+}
+
+
+if(long_output)
+ {
+ fp_log = fopen(logname,"w");
+ fprintf(fp_log,"\n # %s \n\n " , input_line );
+ }
+
+if(frg_mult_file) {
+ fp_fsm = fopen(fsm_name,"w");
+ fprintf(fp_fsm,"\n # %s \n\n" , input_line );
+}
+
+
+
+
+
+if(
+ ( num_dia_bf = (int *) calloc( ( max_itnum + 1 ) , sizeof( int ) ) )
+ == NULL
+ )
+ {
+ printf(" problems with memory allocation for `num_dia_bf' ! \n \n");
+ exit(1);
+ }
+
+
+if(
+ ( num_dia_af = (int *) calloc( ( max_itnum + 1 ) , sizeof( int ) ) )
+ == NULL
+ )
+ {
+ printf(" problems with memory allocation for `num_dia_af' ! \n \n");
+ exit(1);
+ }
+
+
+all_it_dia = (struct multi_frag *) calloc( 1 , sizeof(struct multi_frag) );
+current_dia = all_it_dia;
+
+
+ strcpy(itname,printname);
+ strcpy(itname2,printname);
+ strcpy(itname3,printname);
+ strcpy(itname4,printname);
+ sprintf(str,".ali");
+
+ if( default_name )
+ strcat(itname,str);
+
+ sprintf(str,".fa");
+ strcat(itname2,str);
+
+
+ if( msf_file )
+ strcat(itname3,".ms");
+
+
+ if( cw_file )
+ strcat(itname4,".cw");
+
+
+
+
+
+
+ if( textual_alignment )
+ fp_ali = fopen(itname,"w");
+
+ if( standard_out )
+ fp_ali = stdout;
+
+
+ if( textual_alignment )
+ if(fasta_file)
+ fp2 = fopen(itname2,"w");
+
+ if(msf_file)
+ fp3 = fopen(itname3,"w");
+
+ if(cw_file)
+ fp4 = fopen(itname4,"w");
+
+ if( textual_alignment )
+ para_print(seq_file , fp_ali);
+
+
+ /***************************\
+ * *
+ * ITERATION START *
+ * *
+ \***************************/
+
+
+
+
+
+
+
+
+
+istep = 0 ;
+ while( ( cont_it == 1 ) && ( istep < max_itnum ) )
+ {
+
+ cont_it = 0 ;
+ istep++ ;
+
+/* printf("\n istep = %d \n", istep ); */
+
+
+ this_it_dia = current_dia;
+
+ strcpy(itname,printname);
+ strcpy(itname2,printname);
+ strcpy(itname3,printname);
+ strcpy(itname4,printname);
+ sprintf(str,".ali");
+
+
+ if( default_name )
+ strcat(itname,str);
+
+ sprintf(str,".fa");
+ strcat(itname2,str);
+
+ if( msf_file )
+ strcat(itname3,".ms");
+
+
+ if( cw_file )
+ strcat(itname4,".cw");
+
+ weight_sum_af = 0;
+ num_dia_bf[ istep ] = 0;
+
+ if( time_stamps )
+ beg_pa = clock();
+
+
+ if( ref_seq == 0 )
+ i_max = seqnum ;
+ else
+ i_max = 1 ;
+
+ for(i = 0 ; i < i_max ; i++)
+ {
+
+ for(j = i + 1 ; j < seqnum ; j++)
+ {
+
+
+ /****************************************\
+ * *
+ * PAIRWISE ALIGNMENT *
+ * *
+ \****************************************/
+
+ if( cont_it_p[ i ][ j] ) {
+
+/*
+ printf("\n out of frc it %d : wgt 20 = %f \n", istep , wgt_dna[ 20 ][ 20 ] ) ;
+*/
+ score = frag_chain( i , j , fp_ali, fp_mot, &num_dia_p );
+ }
+ else {
+ score = 0 ;
+ num_dia_p = 0 ;
+ }
+
+ if( istep == 1 )
+ {
+ pair_score[j][i] = score;
+ pair_score[i][j] = score;
+ }
+
+
+ for(k=0;k<num_dia_p;k++)
+ {
+ *current_dia = pair_dia[k];
+
+ current_dia->next
+ = (struct multi_frag *) calloc( 1 , sizeof(struct multi_frag) );
+ end_dia = current_dia;
+ current_dia = current_dia->next;
+ current_dia->pred = end_dia;
+ }
+
+ num_dia_bf[ istep ] = num_dia_bf[ istep ] + num_dia_p;
+
+ for(hv=0; hv<num_dia_p;hv++)
+ weight_sum_af = weight_sum_af + (pair_dia[hv]).weight;
+
+
+ if(num_dia_p)
+ free(pair_dia);
+
+ } /* for(j = i+1 ; j<seqnum ; j++) */
+
+ } /* for(i = 0 ; i<seqnum ; i++) */
+
+
+ if( time_stamps ) {
+ end_pa = clock();
+
+ time_diff_pa = (float) ( end_pa - beg_pa ) / CLOCKS_PER_SEC ;
+ if( time_stamps )
+ printf (" time_diff_pa = %f \n", time_diff_pa );
+ total_pa_time = total_pa_time + time_diff_pa;
+ }
+
+
+
+
+ if( break1 ) {
+ printf("\n break1\n");
+ exit(1) ;
+ }
+
+
+/*
+ if( pa_only ) {
+ printf("\n\n istep = %d, pa finished - exit \n\n", istep );
+ exit(1);
+ }
+*/
+
+ if(overlap_weights)
+ {
+ diagonal1 = this_it_dia;
+ dia_counter = 0;
+
+ if( diagonal1 != NULL )
+ while( diagonal1->next != NULL )
+ {
+ dia_counter++;
+ if( print_status )
+ if( ( dia_counter % 100 ) == 0 )
+ {
+ fp_st = fopen( pst_name ,"w");
+
+ fprintf(fp_st," dsd %s \n", input_line);
+ fprintf(fp_st,"\n\n\n Status of the program run:\n");
+ fprintf(fp_st," ==========================\n\n");
+ if( seqnum > 2 ) {
+ fprintf(fp_st," iteration step %d in ", istep);
+ fprintf(fp_st,"multiple alignment\n" );
+ }
+ fprintf(fp_st," calculating overlap weight for diagonals\n");
+ fprintf(fp_st," current diagonal = %d\n\n", dia_counter );
+ fprintf(fp_st," total number of");
+ fprintf(fp_st," diagonals: %d\n\n\n\n", num_dia_bf[ istep ]);
+ fclose(fp_st);
+ }
+
+ diagonal2 = diagonal1->next;
+
+ while(diagonal2->next != NULL)
+ {
+ if( diagonal1->trans == diagonal2->trans )
+ ow_add(diagonal1 , diagonal2);
+ diagonal2 = diagonal2->next;
+ }
+ diagonal1 = diagonal1->next;
+ }
+ if( bubblesort )
+ ow_bubble_sort( num_dia_bf[ istep ] , this_it_dia );
+ else
+ frag_sort( num_dia_bf[ istep ] , this_it_dia , overlap_weights );
+ }
+ else /* no overlap_weights */ {
+ beg_ts = clock() ;
+
+ if( bubblesort )
+ bubble_sort( num_dia_bf[ istep ] , this_it_dia );
+ else
+ frag_sort( num_dia_bf[ istep ] , this_it_dia , overlap_weights );
+
+ end_ts = clock() ;
+ time_diff_srt = (float) ( end_ts - beg_ts ) / CLOCKS_PER_SEC ;
+ if( time_stamps )
+ printf (" time_diff_srt = %f \n", time_diff_srt );
+ }
+
+
+ num_dia_af[ istep ] = num_dia_bf[ istep ];
+ weight_sum_bf = weight_sum_af;
+
+ pairalignsum = 0;
+ pairalignlen = 0;
+
+
+ filter( num_dia_af + istep , this_it_dia);
+ num_all_it_dia = num_all_it_dia + num_dia_af[ istep ];
+
+
+/*
+ if( pa_only == 0 ) {
+ printf("\n\n istep = %d, filter finished - exit \n\n", istep );
+ exit(1);
+ }
+*/
+
+
+ weight_sum_af = 0;
+
+ print_log( this_it_dia , fp_log , fp_fsm );
+
+ if( frag_file )
+ print_fragments( this_it_dia , fp_frg );
+
+ throw_out( &weight_sum_af );
+
+ sel_test( );
+
+
+
+ threshold = threshold ;
+
+ if( break2 ) {
+ printf("\n break2\n");
+ exit(1) ;
+ }
+
+
+ } /* while ( cond_it == 1 ) */
+
+
+ /***************************\
+ * *
+ * ITERATION END *
+ * *
+ \***************************/
+
+strcpy( dist_name , printname);
+strcat(dist_name , ".dst");
+
+
+
+
+
+if ( ref_seq == 0 )
+ av_tree_print();
+
+
+
+ if( standard_out )
+ fp_ali = stdout;
+
+if(sf_mat){
+ subst_mat( input_name , num_all_it_dia , all_it_dia ) ;
+}
+
+
+if( textual_alignment )
+ ali_arrange( num_all_it_dia , all_it_dia , fp_ali , fp2, fp3, fp4, fp_csc );
+
+
+if(long_output)
+ {
+/* fprintf(fp_log "\n\n thr = %f , lmax = %d , speed = %f */
+ fprintf(fp_log, "\n\n total sum of weights: %f \n\n\n", tot_weight);
+ fclose(fp_log);
+ }
+
+
+
+
+if( argnum == 1 )
+ {
+ printf("\n Program terminated normally\n");
+ printf(" Results are contained in file `%s' \n \n \n", itname);
+ }
+
+
+av_dia_num = 2 * dia_num ;
+av_dia_num = av_dia_num / ( seqnum * ( seqnum - 1) ) ;
+
+av_max_dia_num = 2 * max_dia_num ;
+av_max_dia_num = av_max_dia_num / ( seqnum * ( seqnum - 1) ) ;
+
+
+
+tmpi1 = av_dia_num ;
+tmpi2 = av_max_dia_num ;
+
+if(pr_av_nd)
+ printf(" %d ", tmpi1 );
+
+if(pr_av_max_nd)
+ printf(" %d ", tmpi2 );
+
+
+
+if(pr_av_nd)
+ fprintf(fp_ali, " %d fragments considered for alignment \n", tmpi1 );
+
+if(pr_av_max_nd)
+ fprintf(fp_ali, " %d fragments simultaneously stored \n\n", tmpi2 );
+
+if( textual_alignment )
+ fclose(fp_ali);
+
+
+ if( time_stamps ){
+ end_ali = clock() ;
+ time_diff_ali = (float) ( end_ali - beg_ali ) / CLOCKS_PER_SEC ;
+
+ perc_pa_time = total_pa_time / time_diff_ali * 100 ;
+ printf (" time_diff_ali = %f \n", time_diff_ali );
+ printf (" total_pa_time = %f \n", total_pa_time );
+ printf (" corresponds to %f percent \n\n", perc_pa_time );
+ }
+} /* main */
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/dialign.h
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/dialign.h 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/dialign.h 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,69 @@
+
+#define PAPER_WIDTH 80
+#define MLINE 1000
+#define MAX_REGEX 1000
+#define NAME_LEN 1000
+#define SEQ_NAME_LEN 12
+#define MAX_SEQNUM 10000
+#define MAX_ITNUM 3
+#define MAX_INPUT_LINE 10000
+#define MIN_MOT_WGT 0.1
+#define MAX_CSC 10
+
+
+ /**************************\
+ * *
+ * default parameters *
+ * *
+ \**************************/
+
+
+#define BETA 0
+#define WEB 0
+#define OVERLAP_THRESHOLD 35
+#define MIN_DIA 1
+#define MAX_DIA 40
+#define MATNAME "BLOSUM"
+#define WEAK_WGT_TYPE_THR 0.5
+#define STRONG_WGT_TYPE_THR 0.75
+
+
+struct pair_frag {int b1, b2, ext; float weight; short trans, cs;
+ struct pair_frag *prec, *last; float sum; };
+ /*
+ fragments in function `pairalign'
+
+ b1, b2: begin of the diagonal
+ ext: length of the diagonal
+ weight: weight of the diagonal
+ prec: preceding diagonal in dot matrix
+ last: last diagonal ending in the same column
+ sum: sum of weights accumulated
+ cs: crick strand
+ trans: translation
+ */
+
+struct multi_frag {int b[2], s[2], ext, it; float weight, ow; short sel, trans;
+ short cs; struct multi_frag *next, *pred;};
+ /*
+ fragments outside function `pairalign'
+
+ b[0], b[1]: begin of the diagonal
+ s[0], s[1]: sequences, to which diagonal belongs
+ ext: length of the diagonal
+ weight: individual weight of the diagonal
+ ow: overlap weight of the diagonal
+ sel: 1, if accepted in filter proces, 0 else
+ trans: translation
+ cs: crick strand
+ it: iteration step
+ *next: next diagonal
+ */
+
+struct leaf {int s1, s2, clade;};
+struct seq_pair {int s1, s2; float weight;};
+
+struct subtree { int member_num, valid ; int *member; char *name ;
+ float depth; };
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/frag_chain.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/frag_chain.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/frag_chain.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,915 @@
+
+ /********************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * frag_chain.c *
+ * *
+ \********************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+extern short **mot_pos ;
+extern float mot_factor , mot_offset_factor , max_mot_offset ;
+extern int self_comparison, ***exclude_list ;
+extern short crick_strand, exclude_frg ;
+extern char pst_name[NAME_LEN];
+extern int wgt_type , dna_speed ;
+extern float **wgt_prot, **wgt_dna, **wgt_trans ;
+extern int istep , lmax;
+extern char *seq[MAX_SEQNUM];
+extern float av_sim_score_pep ;
+extern float av_sim_score_nuc ;
+extern int *seqlen;
+
+/* o.k. with read only global var. */
+
+
+extern int mot_len, motifs, iter_cond_prob , wgt_print , wgt_print_x ;
+extern struct multi_frag *pair_dia;
+extern int afc_file, afc_filex , dia_pa_file ;
+extern int thr_sim_score ;
+extern CLOSURE *clos;
+extern int ***open_pos;
+extern int sim_score[21][21];
+extern int long_output ;
+extern int min_dia, max_dia , strict , seqnum;
+extern int **amino, **amino_c ;
+extern char dia_pa_name[NAME_LEN];
+extern FILE *fp_dia, *fp_dpa, *fp_mot ;
+extern char *seq_name[MAX_SEQNUM];
+extern int print_max_nd , pr_av_max_nd ;
+extern int dia_num, redundant , print_status , dcount, cont_it ;
+extern char input_line[ NAME_LEN ];
+extern int max_dia_num;
+extern float threshold;
+
+ extern float maxf2(float a, float b);
+ extern void rel_wgt_calc( int l1 , int l2 , float **wgt );
+ extern int mini2(int a, int b);
+ extern void weight_print( float **wgt );
+ extern int mini3(int a, int b, int c);
+ extern void wgt_prnt( ) ;
+ extern void wgt_prnt_x( ) ;
+ extern float mot_dist_factor( int offset , float parameter ) ;
+
+float frag_chain( int n1, int n2, FILE *fp1, FILE *fp_m, int *number )
+{
+ /* pairwise alignment */
+
+
+ /* `i' denotes positions in the 1. sequence ( seq[n1] ),
+ `j' denotes positions in the 2. sequence ( seq[n2] ) */
+
+
+ int mot_match[ MAX_DIA * 3 ];
+
+ int mot_match_num , mot_offset ;
+ float mot_wgt_sum , this_mot_wgt ;
+
+ float thr; /* threshold for the weight of fragments starting
+ at a given point (i,j). For any new pair (i,j),
+ thr = 0. However, if a fragment with positive weight w
+ is found starting at (i,j), thr is defined to be w
+ and any further fragment starting at (i,j) is
+ taken into consideration, only if its weight excedes
+ thr. This is, because it is not meaningful to consider
+ a fragment containing another fragment with
+ higher weight. */
+ int i, j, k, l, m, diff1, diff2, diff3, diff4, hv, hv2, numsubseq;
+ int ende2; /* denote the last position considered in the 2nd
+ sequence. Coincides with seqlen[n2], respectively,
+ exept if nucleotide diagonals are translated into
+ peptide diagonals. In this case,
+ ende2 = seqlen[n2]-2 */
+ int start_a ; /* diagonals begining at a position (i,j) are only
+ considered if the similarity-value at (i,j)
+ exceeds a certain threshold, respectively if
+ seq[n1][i] = seq[n2][j]. In this case the value
+ of `start_a' is 1, otherwise the value is 0 */
+ int start_pep, start_pep_c, start_dna, start_dna1 , trpl_start;
+ int match; /* number of matches or sum of similarity values
+ in a given diagonal */
+ int trans , start_count, crick_wgt = 0 ;
+ int match_p, match_p_c, match_d ;
+ int kmaxloc; /* maximum length of diagonals starting at a given
+ position (i,j) of the dot matrix.
+ kmaxloc = min{ max_dia, seqlen[n1]-i+1 , seqlen[n2]-j+1} */
+ int lmax_real ;
+ int mnum = 0; /* number of current diagonal */
+ int *ub_int;
+ int *lb_int;
+ int limit; /* min { ub_int[i] ; ende2 } */
+ int bound_test; /* = 1 , if diagonal under consideration is consistent
+ with ub_int and lb_int.
+ = 0 , if not. */
+ int max_nd = 0 , new_region = 0 , current_nd = 0 ;
+ short accepted;
+ char ch ;
+ float total_sum, wgt_k_match, wgt_k_match_c ;
+
+ float thr2 , mot_wgt ;
+
+ struct pair_frag **diap; /* diap[i] = pointer to last diagonal ending
+ in the (i-1)-th column */
+ struct pair_frag **prec_vec; /* prec_vec[j] = pointer to diagonal with
+ maximum sum of weights accumulated
+ at a given position (i,j) */
+ struct pair_frag *current_dia, *hp, *cp, *cd;
+
+ FILE *fp_st, *nd_fp ;
+
+
+
+/*
+ printf( "\n in frag_chain: iter = %d wgt_type = %d \n\n", istep , wgt_type );
+ printf( "\n in frag_chain: iter = %d wgt_dna 20 = %f \n\n", istep , wgt_dna[ 20 ][ 20 ] );
+*/
+
+ if( print_status )
+ if( seqnum > 20 )
+ {
+ fp_st = fopen( pst_name ,"w");
+
+ fprintf(fp_st,"\n\n\n Status of the program run:\n");
+ fprintf(fp_st," ==========================\n\n");
+ fprintf(fp_st," %s \n\n", input_line);
+ fprintf(fp_st," iteration step %d in multiple alignment\n\n", istep );
+ fprintf(fp_st," aligning seq %d /", n1 + 1 );
+ fprintf(fp_st," seq %d\n", n2 + 1);
+ fprintf(fp_st," total number of");
+ fprintf(fp_st," sequences: %d\n\n", seqnum);
+ fprintf(fp_st,"\n\n\n" );
+
+ fclose(fp_st);
+ }
+
+
+
+
+ if ( (ub_int = (int *) calloc( ( seqlen[n1] + 3 ) , sizeof(int) ) ) == NULL)
+ {
+ printf("problems with memory allocation for ub_int! \n \n");
+ exit(1);
+ }
+
+ if ( (lb_int = (int *) calloc( (seqlen[n1]+3) , sizeof(int) ) ) == NULL)
+ {
+ printf("problems with memory allocation for lb_int! \n \n");
+ exit(1);
+ }
+
+ if ( (prec_vec = (struct pair_frag **)
+ calloc( (seqlen[n2]+3) , sizeof(struct pair_frag *) ) ) == NULL)
+ {
+ printf("problems with memory allocation for prec_vec! \n \n");
+ exit(1);
+ }
+
+ if(
+ (diap = (struct pair_frag **) calloc( (seqlen[n1] + 3) ,
+ sizeof(struct pair_frag *) )) == NULL
+ )
+ {
+ printf("\n \n \n ATTENTION: \n \n \n");
+ printf(" problems with memory allocation\n");
+ printf(" for diagonals! \n");
+ exit(1);
+ }
+
+
+ for( i = 1 ; i<= seqlen[n1] ; i++ )
+ diap[i] = NULL;
+
+
+ if ( (diap[0] = (struct pair_frag *)
+ calloc( 1 , sizeof(struct pair_frag) ) ) == NULL)
+ {
+ printf("problems with memory allocation for diap! \n \n");
+ exit(1);
+ }
+
+ for( j = 1 ; j< seqlen[n2]+3 ; j++ )
+ prec_vec[j] = diap[0];
+
+
+ if( dia_pa_file )
+ fp_dpa = fopen( dia_pa_name , "a" );
+
+ ende2 = seqlen[n2];
+
+/* Calculation of rel_weight */
+
+
+ if( iter_cond_prob == 0 ) {
+ if( wgt_type == 0 )
+ rel_wgt_calc( seqlen[n1] , seqlen[n2] , wgt_prot );
+ if( wgt_type % 2 )
+ rel_wgt_calc( seqlen[n1] , seqlen[n2] , wgt_dna);
+ if( wgt_type > 1 )
+ rel_wgt_calc( seqlen[n1] , seqlen[n2] , wgt_trans);
+
+ if( istep == 1 )
+ if( wgt_print || wgt_print_x ) {
+ wgt_prnt( ) ;
+ if( wgt_print_x )
+ exit(1) ;
+ }
+
+ } /* if( iter_cond_prob == 0 ) */
+
+
+
+
+ for( hv = 1 ; hv <= seqlen[ n1 ] ; hv++ ) {
+ lb_int[ hv ] = predFrontier( clos , n1 , hv , n2 );
+ ub_int[ hv ] = succFrontier( clos , n1 , hv , n2 );
+ if (lb_int[ hv ] != ub_int[ hv ]) {
+ lb_int[ hv ]++; ub_int[ hv ]--;
+ }
+ }
+
+ mnum = 0;
+
+ if( iter_cond_prob || ( istep == 1 ) )
+ new_region = 1;
+
+ /* DP START */
+
+ for( i = 1 ; i <= seqlen[n1] ; i++ )
+ {
+
+ if( open_pos[n1][n2][i] )
+ {
+ if( new_region )
+ {
+
+ diff2 = ( succFrontier(clos, n1, i , n2)
+ - predFrontier(clos, n1, i , n2) -1 );
+
+ if ( diff2 < 0 )
+ diff2 = 0;
+
+ diff1 = ( succFrontier(clos, n2, lb_int[i] , n1)
+ - predFrontier(clos, n2, lb_int[i] , n1) -1 ) ;
+ if ( diff1 < 0 )
+ diff1 = 0;
+
+/*
+ printf(" new region, i = %d diff = %d , %d \n", i, diff1 , diff2 );
+*/
+
+
+ if( iter_cond_prob )
+ if( ( diff1 > 0 ) && ( diff2 > 0 ) ) {
+ if( wgt_type == 0 )
+ rel_wgt_calc( diff1 , diff2 , wgt_prot );
+ if( wgt_type % 2 )
+ rel_wgt_calc( diff1 , diff2 , wgt_dna );
+ if( wgt_type > 1 )
+ rel_wgt_calc( diff1 , diff2 , wgt_trans );
+ }
+
+ }
+
+ limit = mini2( ub_int[i] , ende2 );
+ for( j = lb_int[i] ; j <= limit ; j++ )
+ {
+
+ if( wgt_type != 1 )
+ start_pep = ( sim_score[ amino[n1][i] ][ amino[n2][j] ]
+ >= thr_sim_score );
+
+ if( crick_strand )
+ start_pep_c = ( sim_score[ amino_c[n1][i] ][ amino_c[n2][j] ]
+ >= thr_sim_score );
+
+ if( wgt_type % 2 ) {
+ if( strict )
+ start_dna = ( (seq[n1][i] == seq[n2][j]) &&
+ ( seq[n1][i] == 'A' ||
+ seq[n1][i] == 'C' ||
+ seq[n1][i] == 'T' ||
+ seq[n1][i] == 'G' ||
+ seq[n1][i] == 'U' ) );
+
+ else
+ start_dna = (seq[n1][i] == seq[n2][j]);
+
+ if( dna_speed )
+ if( ( i < seqlen[n1] ) && ( j < limit ) ) {
+ if( strict )
+ start_dna1 = ( (seq[n1][ i + 1 ] == seq[ n2 ][ j + 1 ]) &&
+ ( seq[n1][ i + 1 ] == 'A' ||
+ seq[n1][ i + 1 ] == 'C' ||
+ seq[n1][ i + 1 ] == 'T' ||
+ seq[n1][ i + 1 ] == 'G' ||
+ seq[n1][ i + 1 ] == 'U' ) );
+
+ else
+ start_dna1 = ( seq[ n1 ][ i + 1 ] == seq[ n2 ][ j + 1 ] );
+ start_dna = start_dna * start_dna1 ;
+ }
+
+ }
+
+ if( wgt_type != 1 )
+ start_a = start_pep ;
+ else
+ start_a = start_dna ;
+
+ if( wgt_type == 3 )
+ start_a = start_pep + start_dna ;
+
+ if( crick_strand )
+ start_a = start_a + start_pep_c ;
+
+ if( self_comparison )
+ if( i == j )
+ start_a = 0 ;
+
+ if( exclude_frg )
+ if( j == exclude_list[ n1 ][ n2 ][ i ] )
+ start_a = 0 ;
+
+ if( start_a )
+ {
+
+ match = 0;
+ match_d = 0;
+ match_p = 0;
+ match_p_c = 0;
+ thr = 0;
+/*
+ start_count++ ;
+*/
+ bound_test = 1;
+
+ if( wgt_type > 1 )
+ lmax_real = lmax * 3 ;
+ else
+ lmax_real = lmax ;
+
+ kmaxloc =
+ mini3( lmax_real , seqlen[n1]-i+1 , seqlen[n2]-j+1 );
+
+ if( motifs ) {
+ for( k = 1 ; k <= kmaxloc ; k++ )
+ if( ( mot_pos[ n1 ][ i + k - 1 ] == 1 ) &&
+ ( mot_pos[ n2 ][ j + k - 1 ] == 1 ) ) {
+ mot_match[ k ] = 1 ;
+ /* printf(" match in %d %d %d \n", i, j, k ); */
+ }
+ else
+ mot_match[ k ] = 0 ;
+ }
+
+ /*******************\
+ * *
+ * fragments start *
+ * *
+ \*******************/
+
+ k = 1;
+ mot_match_num = 0;
+ mot_wgt_sum = 0 ;
+
+ while( ( k <= kmaxloc ) && start_a ) {
+ if( motifs ) {
+ if( ( ( i - j ) * ( i - j ) ) < ( max_mot_offset * max_mot_offset ) )
+ if( k >= mot_len )
+ if( mot_match[ k - mot_len + 1] ) {
+ mot_offset = ( i - j ) ;
+ this_mot_wgt = mot_dist_factor( ( i - j ) , mot_offset_factor) ;
+
+/*
+ printf(" i - j = %d , tmw = %f \n", i - j , this_mot_wgt );
+*/
+ mot_wgt_sum = mot_wgt_sum + this_mot_wgt ;
+ mot_match_num++ ;
+
+ }
+ }
+
+ if( open_pos[n1][n2][ i + k - 1 ] )
+ {
+ bound_test = bound_test *
+ ( j + k - 1 >= lb_int[ i + k - 1 ] );
+ bound_test = bound_test *
+ ( j + k - 1 <= ub_int[ i + k - 1 ] );
+
+ trpl_start = 0;
+
+ if( wgt_type < 2 )
+ trans = 0 ;
+ else
+ trans = 1 ;
+
+ if( start_pep ||
+ ( crick_strand && start_pep_c )
+ )
+ if( ( wgt_type > 1 ) && ( ( k % 3 ) == 1 ) ) {
+ trpl_start = 1 ;
+
+ trpl_start = trpl_start *
+ ( j + k >= lb_int[ i + k ] );
+ trpl_start = trpl_start *
+ ( j + k <= ub_int[ i + k ] );
+ trpl_start = trpl_start * open_pos[ n1 ][ n2 ][ i + k ] ;
+
+
+ trpl_start = trpl_start *
+ ( j + k + 1 >= lb_int[ i + k + 1 ] );
+ trpl_start = trpl_start *
+ ( j + k + 1 <= ub_int[ i + k + 1 ] );
+ trpl_start = trpl_start * open_pos[ n1 ][ n2 ][ i + k + 1 ] ;
+ }
+
+
+
+ if(
+ bound_test &&
+ ( ( wgt_type != 2 ) || trpl_start )
+ )
+ {
+ if( start_pep )
+ if(
+ ( wgt_type == 0 ) ||
+ ( ( wgt_type > 1) && trpl_start )
+ )
+ match_p = match_p
+ + sim_score[ amino[ n1 ][ i + k - 1 ] ]
+ [ amino[ n2 ][ j + k - 1 ] ];
+
+ if( crick_strand )
+ if( start_pep_c )
+ if(
+ ( wgt_type == 0 ) ||
+ ( ( wgt_type > 1) && trpl_start )
+ )
+ match_p_c = match_p_c
+ + sim_score[ amino_c[ n1 ][ i + k - 1 ] ]
+ [ amino_c[ n2 ][ j + k - 1 ] ];
+
+
+ if( start_dna )
+ if( wgt_type % 2 )
+ if( !strict ||
+ (seq[n1][i+k-1] == 'A' ||
+ seq[n1][i+k-1] == 'C' ||
+ seq[n1][i+k-1] == 'T' ||
+ seq[n1][i+k-1] == 'G' ||
+ seq[n1][i+k-1] == 'U' ))
+ match_d = match_d +
+ ( seq[n1][i+k-1] == seq[n2][j+k-1] );
+
+ wgt_k_match = 0;
+
+
+ if( wgt_type == 0 )
+ wgt_k_match = wgt_prot[ k ][ match_p ] ;
+ if( wgt_type == 1 )
+ wgt_k_match = wgt_dna[ k ][ match_d ] ;
+
+ if( wgt_type > 1 ) {
+ if( start_pep )
+ wgt_k_match = wgt_trans[ ( k + 2 ) / 3 ][ match_p ] ;
+
+ if( crick_strand )
+ if( start_pep_c ) {
+ if( wgt_trans[ ( k + 2 ) / 3 ][ match_p_c ] > wgt_k_match ) {
+ wgt_k_match = wgt_trans[ ( k + 2 ) / 3 ][ match_p_c ] ;
+ crick_wgt = 1 ;
+ }
+ else
+ crick_wgt = 0 ;
+ }
+ }
+
+ if( start_dna )
+ if( wgt_type == 3 )
+ if( k <= lmax )
+ if( wgt_dna[ k ][ match_d ]
+ > wgt_k_match ) {
+ wgt_k_match = wgt_dna[ k ][ match_d ] ;
+ trans = 0 ;
+ }
+
+
+
+ if( wgt_type == 0 )
+ if( match_p <= ( k * av_sim_score_pep ) )
+ start_pep = 0;
+
+ if( wgt_type == 1 )
+ if( match_d <= ( k * av_sim_score_nuc ) )
+ start_dna = 0;
+
+ if( start_pep )
+ if( wgt_type > 1 )
+ if( ( match_p * 3 ) <= ( k * av_sim_score_pep ) )
+ start_pep = 0;
+
+ if( start_pep_c )
+ if( wgt_type > 1 )
+ if( ( match_p_c * 3 ) <= ( k * av_sim_score_pep ) )
+ start_pep_c = 0;
+
+
+ if( wgt_type != 1 )
+ start_a = start_pep ;
+ else
+ start_a = start_dna ;
+
+ if( wgt_type == 3 )
+ start_a = start_pep + start_dna ;
+
+ if( crick_strand )
+ start_a = start_a + start_pep_c ;
+
+ if( exclude_frg )
+ if( exclude_list[ n1 ][ n2 ][ i + k ] == j + k )
+ start_a = 0 ;
+
+
+ if( motifs )
+ if( mot_wgt_sum > 0 ) {
+ fprintf( fp_mot , " %4d %4d ", n1 + 1, n2 + 1);
+ fprintf( fp_mot , " %4d %4d %3d ", i, j, k );
+ fprintf( fp_mot , " %5.2f ", wgt_k_match );
+ mot_wgt = mot_wgt_sum * mot_factor ;
+ wgt_k_match = wgt_k_match + mot_wgt ;
+ fprintf( fp_mot , " %2d ", mot_match_num );
+ fprintf( fp_mot , " %5.2f \n", wgt_k_match );
+ }
+
+/*
+ if( wgt_k_match > 0 ) printf(" k = %d min_dia = %d wgt_k_match = %f thr = %f \n", k, min_dia , wgt_k_match , thr );
+*/
+ if( k >= min_dia )
+ if( wgt_k_match > thr )
+ {
+ if( (current_dia = (struct pair_frag *)
+ calloc(1 , sizeof(struct pair_frag) ))
+ == NULL )
+ {
+ printf("\n \n \n ATTENTION: \n \n \n");
+ printf(" too many diagonals in\n");
+ printf(" pairwise alignment of");
+ printf(" sequences\n");
+ printf(" %s and ", seq_name[n1]);
+ printf("%s\n \n \n \n", seq_name[n2]);
+
+ fprintf(fp1,"\n \n ATTENTION:\n \n");
+ fprintf(fp1," too many diagonals\n");
+ fprintf(fp1," in pairwise alignment");
+ fprintf(fp1," of sequences\n");
+ fprintf(fp1," %s and ", seq_name[n1]);
+ fprintf(fp1,"%s\n \n \n \n", seq_name[n2]);
+
+ exit(1);
+ }
+
+
+
+ current_dia->b1 = i;
+ current_dia->b2 = j;
+ current_dia->ext = k + 2 * trans ;
+ current_dia->weight = wgt_k_match ;
+ current_dia->trans = trans ;
+ current_dia->cs = crick_wgt ;
+ current_dia->sum = current_dia->weight
+ + (prec_vec[j])->sum ;
+ current_dia->prec = prec_vec[j];
+ current_dia->last
+ = diap[ i + (current_dia->ext) ];
+ diap[ i + (current_dia->ext) ] = current_dia;
+
+ mnum++;
+
+ if( print_max_nd )
+ {
+ current_nd++ ;
+ if( current_nd > max_nd )
+ max_nd = current_nd;
+ }
+
+ dia_num++;
+ if( afc_file )
+ {
+ fprintf(fp_dia,"FRG %d ", dia_num );
+ fprintf(fp_dia,"name: %s ", seq_name[ n1 ]);
+ fprintf(fp_dia," %s ", seq_name[ n2 ]);
+ if( seqnum > 2 )
+ {
+ fprintf(fp_dia," seq: %d", n1 + 1 );
+ fprintf(fp_dia," %d" , n2 + 1 );
+ }
+ fprintf(fp_dia," beg: %d %d", i, j );
+ fprintf(fp_dia," len: %d", current_dia->ext );
+ fprintf(fp_dia," wgt: %6.3f", current_dia->weight );
+
+/*
+ if( BETA )
+ if( iter_cond_prob )
+ {
+ fprintf(fp_dia," d1 = %d d2 = %d ", diff1, diff2 );
+ }
+*/
+
+ fprintf(fp_dia," it = %d ", istep );
+ if( ( wgt_type == 3 ) || crick_strand )
+ if( current_dia->trans )
+ fprintf(fp_dia," P-frg" );
+ else
+ fprintf(fp_dia," N-frg" );
+ fprintf(fp_dia,"\n");
+ if( afc_filex ) {
+ fprintf(fp_dia,"SEG1 ");
+ for(hv = 0;hv < current_dia->ext ; hv++){
+ ch = seq[n1][ i + hv ] ;
+ fprintf(fp_dia,"%c" , ch ) ;
+ }
+ fprintf(fp_dia ,"\n");
+ fprintf(fp_dia,"SEG2 ");
+ for(hv = 0;hv < current_dia->ext ; hv++){
+ ch = seq[n2][ j + hv ] ;
+ fprintf(fp_dia,"%c" , ch ) ;
+ }
+ fprintf(fp_dia ,"\n\n");
+ }
+ }
+
+ if( ! redundant )
+ {
+ thr2 = maxf2( thr , ( current_dia->weight ) );
+ thr = thr2 ;
+ }
+
+ } /* if( wgt[k][match] > thr ) */
+ } /* if ( bound_test ) */
+ } /* if( open_pos ... ) */
+ k++;
+ } /* while( ( k <= kmaxloc ) && start_a ) */
+ } /* if( start_a ) */
+ } /* for(j=lb_int[i];j<=limit;j++) */
+ new_region = 0;
+ } /* if( open_pos ) */
+ else
+ if( iter_cond_prob )
+
+ new_region = 1;
+
+
+ if( print_status )
+ if( ( ( seqlen[n1] + seqlen[n2] ) > 1000 ) )
+ if( ! ( i % 100 ) )
+ {
+ fp_st = fopen( pst_name ,"w");
+
+ fprintf(fp_st,"\n\n\n Status of the program run:\n");
+ fprintf(fp_st," ==========================\n\n");
+ fprintf(fp_st," %s \n\n", input_line);
+ if( seqnum > 2 ) {
+ fprintf(fp_st," iteration step %d in" , istep );
+ fprintf(fp_st," multiple alignment\n\n" );
+ }
+ if( seqnum > 2 )
+ {
+ fprintf(fp_st," aligning seq %d /", n1 + 1 );
+ fprintf(fp_st," seq %d\n", n2 + 1);
+ fprintf(fp_st," total number of");
+ fprintf(fp_st," sequences: %d\n\n", seqnum);
+ }
+ fprintf(fp_st," current position in");
+ fprintf(fp_st," sequence %d: %8d\n", n1 + 1, i);
+ fprintf(fp_st," length of seq %d:", n1 + 1 );
+
+ fprintf(fp_st," %8d\n\n", seqlen[n1]);
+
+
+/*
+ if( iter_cond_prob || ( istep == 1 ) )
+ {
+ if( open_pos[n1][n2][i] )
+ {
+ fprintf(fp_st," diff1 = %d \n", diff1 );
+ fprintf(fp_st," diff2 = %d \n", diff2 );
+ }
+ else
+ fprintf(fp_st," position already aligned");
+ }
+*/
+
+ fprintf(fp_st,"\n\n\n" );
+
+ fclose(fp_st);
+ }
+
+
+
+ cp = diap[ i + 1 ];
+ hp = NULL;
+ accepted = 0;
+
+
+ while( cp != NULL )
+ {
+ j = cp->b2 + cp->ext;
+ if( (prec_vec[j])->sum < cp->sum )
+ {
+ prec_vec[j] = cp;
+ accepted = 1;
+
+ hp = cp;
+ cp = cp->last;
+ }
+ else
+ {
+ cp = cp->last;
+
+ if( accepted )
+ {
+ free( hp->last );
+
+
+ hp->last = cp;
+ }
+ else
+ {
+ free( diap[ i + 1 ] );
+ diap[ i + 1 ] = cp;
+ }
+
+ current_nd--;
+
+ }
+ }
+
+ for( hv=2 ; hv < ( seqlen[n2] + 3 ) ; hv++ )
+ if( (prec_vec[hv])->sum < (prec_vec[hv-1])->sum )
+ prec_vec[hv] = prec_vec[hv-1];
+
+
+
+ } /* for(i= ... ) */
+/*
+printf (" start_count = %d \n ", start_count );
+ */
+ if( pr_av_max_nd )
+ if( istep == 1 )
+ {
+ if( ( nd_fp = fopen("nd_file","a")) == NULL)
+ {
+ printf("\n\n nd_fp could not be opened \n\n" );
+ exit(1);
+ }
+
+ fprintf(nd_fp, " %2d/%2d %8d %8d \n", n1 + 1 , n2+ 1 , mnum, max_nd );
+ fclose( nd_fp );
+ }
+
+
+ numsubseq = 0; /* counts diagonals in alignment */
+
+ current_dia = prec_vec[ seqlen[n2] + 1 ];
+ cd = current_dia;
+
+
+ total_sum = cd->sum;
+
+
+ while( cd->prec != NULL )
+ {
+ numsubseq++;
+ cd = cd->prec;
+ }
+
+
+
+ if(numsubseq)
+ {
+ hv = numsubseq - 1;
+
+ if (
+ (
+ pair_dia = (struct multi_frag *)
+ calloc( ( numsubseq + 1 ) , sizeof(struct multi_frag ) )
+ ) == NULL
+ )
+ {
+ printf("problems with memory allocation for `pair_dia'! \n \n");
+ exit(1);
+ }
+
+
+ while(hv>=0)
+ {
+ if( dia_pa_file )
+ {
+ fprintf(fp_dpa, " %3d) " , ++dcount );
+ if( seqnum > 2 )
+ fprintf(fp_dpa, "seq: %3d %3d " , n1 + 1, n2 + 1);
+ fprintf(fp_dpa, " beg: %6d %6d ", current_dia->b1, current_dia->b2);
+ fprintf(fp_dpa, " len: %2d ", current_dia->ext );
+ fprintf(fp_dpa, " weight: %5.2f ", current_dia->weight );
+ fprintf(fp_dpa, " it: %d ", istep );
+ if( ( wgt_type == 3 ) || crick_strand )
+ if( current_dia->trans )
+ fprintf(fp_dpa," P-frg" );
+ else
+ fprintf(fp_dpa," N-frg" );
+ if( current_dia->trans )
+ if( crick_strand){
+ if( current_dia->cs )
+ fprintf(fp_dpa," crick " ) ;
+ else
+ fprintf(fp_dpa," watson " ) ;
+ }
+ fprintf(fp_dpa,"\n");
+ }
+
+
+ (pair_dia[hv]).b[0] = current_dia->b1;
+ (pair_dia[hv]).b[1] = current_dia->b2;
+ (pair_dia[hv]).s[0] = n1;
+ (pair_dia[hv]).s[1] = n2;
+ (pair_dia[hv]).sel = 1;
+ (pair_dia[hv]).ext = current_dia->ext;
+ (pair_dia[hv]).weight = current_dia->weight;
+ (pair_dia[hv]).ow = current_dia->weight;
+ (pair_dia[hv]).trans = current_dia->trans ;
+ if( crick_strand ) {
+ (pair_dia[hv]).cs = current_dia->cs ;
+ }
+ (pair_dia[hv]).it = istep;
+ hv--;
+ current_dia = current_dia->prec;
+ }
+/* if( dia_pa_file )
+ fprintf(fp_dpa, " \n" );
+*/
+
+
+/* modified in LGI-VITRY
+ if( iter_cond_prob )
+*/
+
+ cont_it = 1 ;
+
+ } /* if(numsubseq) */
+
+
+
+ *number = numsubseq;
+
+
+ if( long_output )
+ {
+ printf("Seq. %3d -%3d: ", n1+1, n2+1);
+ printf("T = %2.2f,", threshold);
+ printf(" %3d D. in alignment,", *number);
+ printf("%6d D. in matrix", mnum);
+ printf("\n");
+ }
+
+
+
+ for( hv=0 ; hv < seqlen[n1]+3 ; hv++ )
+ {
+ current_dia = diap[hv];
+
+ while( current_dia != NULL )
+ {
+ hp = current_dia;
+ current_dia = current_dia->last;
+ free(hp);
+ }
+ }
+
+
+ if( istep == 1 )
+ {
+ max_dia_num = max_dia_num + max_nd ;
+ }
+
+ free(diap);
+
+ free(ub_int);
+ free(lb_int);
+ free(prec_vec);
+ if( dia_pa_file ) {
+ fclose( fp_dpa );
+ }
+ return( total_sum);
+
+} /* frag_chain */
Added: trunk/packages/dialign/branches/upstream/current/src/functions.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/functions.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/functions.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,1316 @@
+
+ /*************************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * functions.c *
+ * *
+ \*************************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+
+extern int iter_cond_prob , col_score ;
+extern short **cont_it_p;
+extern char input_name[NAME_LEN];
+extern int anchors ;
+extern int frg_mult_file ;
+extern int frg_mult_file_v ;
+extern short crick_strand ;
+/* extern char dia_pa_name[NAME_LEN]; */
+extern int pr_av_max_nd , wgt_type ;
+extern int mask ;
+extern char prn[ NAME_LEN ];
+extern char input_line[ NAME_LEN ];
+extern int print_status;
+extern char pst_name[NAME_LEN];
+extern char clust_sim[ NAME_LEN ] ;
+extern FILE *fp_dia, *fp_dpa;
+extern float tot_weight, av_len ;
+extern int dia_num, max_dia_num, msf_file, cw_file;
+extern int istep , anc_num;
+extern int fasta_file;
+extern char *upg_str;
+extern int plot_num;
+extern int argnum ;
+extern char *seq[MAX_SEQNUM];
+extern int *seqlen;
+extern char *seq_name[MAX_SEQNUM];
+extern char printname[NAME_LEN];
+extern char amino_acid[22];
+extern int par_count;
+extern int *num_dia_bf;
+extern int *num_dia_af;
+
+extern float pairalignsum;
+extern int pairalignlen ;
+
+extern struct multi_frag *this_it_dia;
+extern struct multi_frag *all_it_dia;
+
+extern CLOSURE *clos;
+extern float **glob_sim;
+
+extern int ***open_pos;
+
+extern float **wgt_prot, **wgt_dna, **wgt_trans ;
+
+extern int sim_score[21][21];
+
+extern int min_dia, max_dia;
+extern int long_output ;
+extern int seqnum;
+extern short dots;
+extern float threshold;
+extern int num_all_it_dia;
+
+extern int num_dia_p, overlap_weights ;
+
+extern int **amino;
+extern int **amino_c;
+
+
+extern int **shift;
+extern double **tp400_prot;
+extern double **tp400_dna;
+extern double **tp400_trans;
+
+
+int num_test( char *cp )
+ {
+ int result = 1;
+ int i;
+ char *strng;
+
+ strng = cp;
+
+ for(i = 0 ; i < strlen(strng) ; i++ )
+ if( ! isdigit(strng[i]) && ( strng[i] != '.' ) )
+ {
+ result = 0;
+ /* printf("\n %c is no digit !!!\n", strng[i]); */
+ }
+
+ return result ;
+ }
+
+
+
+float minf2(float a, float b)
+{
+ if (a<b)
+ return a;
+ else return b;
+}
+
+float maxf2(float a, float b)
+ {
+ if (a>b)
+ return a;
+ else return b;
+ }
+
+
+int mini2(int a, int b)
+ {
+ if(a<b)
+ return a;
+ else
+ return b;
+ }
+
+
+
+
+int maxi2(int a, int b)
+ {
+ if (a>b)
+ return a;
+ else return b;
+ }
+
+int mini3(int a, int b, int c)
+ {
+ return mini2(a, mini2(b,c));
+ }
+
+void minf(float *a, float b)
+ {
+ if (*a > b)
+ *a = b;
+ }
+
+void mini(int *a, int b)
+ {
+ if (*a > b)
+ *a = b;
+ }
+
+void maxf(float *a, float b)
+ {
+ if (*a < b)
+ *a = b;
+ }
+
+void maxi(int *a, int b)
+ {
+ if (*a < b)
+ *a = b;
+ }
+
+
+char invert ( char c1 )
+{
+ char c2 = c1 ;
+
+ if(c1 == 'T')
+ c2 = 'A' ;
+ if(c1 == 'A')
+ c2 = 'T' ;
+ if(c1 == 'C')
+ c2 = 'G' ;
+ if(c1 == 'G')
+ c2 = 'C' ;
+
+ return( c2 );
+
+}
+
+int translate(char c1, char c2 ,char c3, int seqno, int pos)
+{
+ /* translation of triplets into amino acids */
+
+
+ int amac; /* resulting amino acid */
+
+ if(c1 == 'T')
+ {
+ if(c2 == 'T')
+ {
+ if(c3 == 'T') amac = 18;
+ if(c3 == 'C') amac = 18;
+ if(c3 == 'A') amac = 16;
+ if(c3 == 'G') amac = 16;
+ }
+ if(c2 == 'C') amac = 2;
+ if(c2 == 'A')
+ {
+ if(c3 == 'T') amac = 19;
+ if(c3 == 'C') amac = 19;
+ if(c3 == 'A') amac = 0; /* stop codon */
+ if(c3 == 'G') amac = 0;
+ }
+ if(c2 == 'G')
+ {
+ if(c3 == 'T') amac = 1;
+ if(c3 == 'C') amac = 1;
+ if(c3 == 'A') amac = 20;
+
+ if(c3 == 'G') amac = 20;
+ }
+ }
+
+ if(c1 == 'C')
+ {
+ if(c2 == 'T') amac = 16;
+ if(c2 == 'C') amac = 4;
+ if(c2 == 'A')
+ {
+ if(c3 == 'T') amac = 11;
+ if(c3 == 'C') amac = 11;
+ if(c3 == 'A') amac = 10;
+ if(c3 == 'G') amac = 10;
+ }
+ if(c2 == 'G') amac = 12;
+ }
+
+ if(c1 == 'A')
+ {
+ if(c2 == 'T')
+ {
+ if(c3 == 'T') amac = 15;
+ if(c3 == 'C') amac = 15;
+ if(c3 == 'A') amac = 15;
+ if(c3 == 'G') amac = 14;
+ }
+ if(c2 == 'C') amac = 3;
+ if(c2 == 'A')
+ {
+ if(c3 == 'T') amac = 7;
+ if(c3 == 'C') amac = 7;
+ if(c3 == 'A') amac = 13;
+ if(c3 == 'G') amac = 13;
+ }
+ if(c2 == 'G')
+ {
+ if(c3 == 'T') amac = 2;
+ if(c3 == 'C') amac = 2;
+ if(c3 == 'A') amac = 12;
+ if(c3 == 'G') amac = 12;
+ }
+ }
+
+ if(c1 == 'G')
+ {
+ if(c2 == 'T') amac = 17;
+ if(c2 == 'C') amac = 5;
+ if(c2 == 'A')
+ {
+ if(c3 == 'T') amac = 8;
+ if(c3 == 'C') amac = 8;
+ if(c3 == 'A') amac = 9;
+ if(c3 == 'G') amac = 9;
+ }
+ if(c2 == 'G') amac = 6;
+ }
+
+
+if(
+ ( c1 != 'A' && c1 != 'T' && c1 != 'G' && c1 != 'C' ) ||
+ ( c2 != 'A' && c2 != 'T' && c2 != 'G' && c2 != 'C' ) ||
+ ( c3 != 'A' && c3 != 'T' && c3 != 'G' && c3 != 'C' )
+ )
+ return( 0 );
+else
+ return( amac );
+
+ } /* translate */
+
+int int_test(float f)
+{
+ int i = f;
+
+ if(i == f)
+ return (1);
+ else
+ return (0);
+}
+
+
+
+/*==========================================================
+ * OLD SORT FUNCTION (BUBBLE-SORT)
+ *=========================================================*/
+
+
+void change(struct multi_frag *a, struct multi_frag *b)
+{
+ struct multi_frag c, *an, *bn;
+
+ c = *a;
+ an = a->next;
+ bn = b->next;
+
+ *a = *b;
+ *b = c;
+
+ a->next = an;
+ b->next = bn;
+}
+
+
+void pair_change(struct seq_pair *a, struct seq_pair *b)
+{
+ struct seq_pair c;
+
+ c = *a;
+ *a = *b;
+ *b = c;
+}
+
+
+void ow_bubble_sort( int number , struct multi_frag *dp )
+{
+ /* sorting diagonals in multiple alignment according to their
+ overlap weights */
+
+ struct multi_frag *hp;
+ int hv1, hv2;
+
+ FILE *fp_st;
+
+ for( hv1 = 1 ; hv1 < number ; hv1++ )
+ {
+ hp = dp;
+
+ if( print_status )
+ if( ( hv1 % 100 ) == 0 )
+ {
+ fp_st = fopen( pst_name ,"w");
+
+ fprintf(fp_st,"\n\n\n Status of the program run:\n");
+ fprintf(fp_st," ==========================\n\n");
+ fprintf(fp_st," %s \n\n", input_line);
+ fprintf(fp_st," iteration step %d in multiple alignment\n", istep );
+ fprintf(fp_st," overlap weight sorting of diagonals\n");
+ fprintf(fp_st," current diagonal = %d\n\n", hv1 );
+ fprintf(fp_st," total number of");
+ fprintf(fp_st," diagonals: %d\n\n\n\n", number);
+ fclose(fp_st);
+ }
+
+
+ for( hv2 = hv1 ; hv2 < number ; hv2++ )
+ {
+ if( hp->ow < (hp->next)->ow )
+ change( hp , hp->next );
+ hp = hp->next;
+ }
+ }
+} /* ow_bubble_sort */
+
+
+
+
+
+void bubble_sort( int number , struct multi_frag *dp )
+{
+ /* sorting diagonals in multiple alignment according to their
+ individual weights */
+
+ struct multi_frag *hp;
+ int hv1, hv2;
+ FILE *fp_st;
+
+ for( hv1 = 1 ; hv1 < number ; hv1++ )
+ {
+ hp = dp;
+
+ if( print_status )
+ if( ( hv1 % 100 ) == 0 )
+ {
+ fp_st = fopen( pst_name ,"w");
+
+ fprintf(fp_st,"\n\n\n Status of the program run:\n");
+ fprintf(fp_st," ==========================\n\n");
+ fprintf(fp_st," %s \n\n", input_line);
+ fprintf(fp_st," iteration step %d\n", istep );
+ fprintf(fp_st," ind. weight sorting of diagonals\n");
+ fprintf(fp_st," current diagonal = %d\n\n", hv1 );
+ fprintf(fp_st," total number of");
+ fprintf(fp_st," diagonals: %d\n\n\n\n", number);
+ fclose(fp_st);
+ }
+
+
+ for( hv2 = hv1 ; hv2 < number ; hv2++ )
+ {
+ if( hp->weight < (hp->next)->weight )
+ change( hp , hp->next );
+ hp = hp->next;
+ }
+ }
+
+} /* bubble_sort */
+
+
+
+/*==========================================================
+ * NEW SORT FUNCTION (QUICK-SORT)
+ *=========================================================*/
+
+/***********************************************************
+ * change()
+ ***********************************************************/
+void change_struct_el(struct multi_frag **a, int l, int r)
+{
+ struct multi_frag *dummy;
+ dummy = a[l];
+ a[l] = a[r];
+ a[r] = dummy;
+}
+/***********************************************************
+ * change_first()
+ ***********************************************************/
+void change_first(struct multi_frag *a, struct multi_frag *b)
+ {
+ struct multi_frag c, *an, *bn;
+
+ if(a==b)
+ { /* Change the first list-element with the second one (old first-el.). */
+ c = *a;
+ an = a->next;
+ bn = a->next->next;
+
+ *a = *(a->next);
+ a->next = bn;
+
+ *an = c;
+ an->next = a;
+ }
+ else /* Change the new first list-el. with the old first-el. */
+ {
+ c = *a; /* Make a copy of the new first-listelement a. */
+ an = a->next; /* Make a copy of the pointer at the second-el. */
+ bn = b->next->next; /* Make a copy of the pointer old first-el. shows at. */
+
+ *a = *(b->next); /* Whrite the value of the old first-el. on the place of the new first-el.*/
+ a->next = bn; /* Bend his "next" pointer at the next el. of the old first-el. */
+
+ *(b->next) = c; /* Whrite the value of the new fist-el. on the place of the old first-el. */
+ b->next->next = an; /* Bend his "next" pointer at the next el. of the new first-el. */
+
+ b->next = a;
+ }
+ }
+
+
+/***********************************************************
+ * quicksort_ow()
+ ***********************************************************/
+void quicksort_ow(struct multi_frag **array,int left, int right)
+{
+ int l = left, r = right;
+ struct multi_frag *element;
+ element = array[(left+right)/2];
+
+ do
+ {
+ while(array[l]->ow > element->ow) l++;
+ while(element->ow > array[r]->ow) r--;
+
+ if(l < r) change_struct_el(array,l,r);
+ if(l <= r) {l++; r--;}
+ }while(l<=r);
+
+ if(left < r) quicksort_ow(array, left, r);
+ if(l < right) quicksort_ow(array, l, right);
+
+}/*quicksort_ow*/
+
+
+
+/***********************************************************
+ * quicksort_weight()
+ ***********************************************************/
+void quicksort_weight(struct multi_frag **array,int left, int right)
+{
+ int l = left, r = right;
+ struct multi_frag *element;
+ element = array[(left+right)/2];
+
+ do
+ {
+ while(array[l]->weight > element->weight) l++;
+ while(element->weight > array[r]->weight) r--;
+
+ if(l < r) change_struct_el(array,l,r);
+ if(l <= r) {l++; r--;}
+ }while(l<=r);
+
+ if(left < r) quicksort_weight(array, left, r);
+ if(l < right) quicksort_weight(array, l, right);
+
+}/*quicksort_weight*/
+
+
+/***********************************************************
+ * assemble_list()
+ ***********************************************************/
+void assemble_list(struct multi_frag **array, struct multi_frag *dp,int number)
+{
+ int i,index=0;
+ for (i = 0; i< number-1; i++)
+ {
+ if(dp==array[i])
+ index = i;
+ array[i]->next = array[i+1];
+ }
+
+ array[number-1]->next = 0;
+ if(dp==array[number-1])
+ index = number-1;
+
+ if(index!=0)
+ change_first(array[0],array[index-1]);
+} /* assemble_list */
+
+
+/***********************************************************
+* frag_sort()
+************************************************************/
+void frag_sort(int number , struct multi_frag *dp , int olw )
+{
+ int i=1;
+
+ struct multi_frag **array;
+ if((array = (struct multi_frag**)calloc(number+1,sizeof(struct multi_frag*)))==0)
+ {
+ printf(" problems with memory allocation for `all_clades'\n \n");
+ exit(1);
+ }
+
+ array[0] = dp;
+ while(array[i-1]->next)
+ {array[i] = array[i-1]->next; i++;}
+
+ if( olw )
+ quicksort_ow(array,0,number);
+ else
+ quicksort_weight(array,0,number);
+
+
+ assemble_list(array, dp, number+1);
+
+}/* frag_sort */
+
+
+
+void ow_add( struct multi_frag *sm1 , struct multi_frag *sm2 )
+{
+ /* increasing the overlap weights of two diagonals, if they
+ have any overlap */
+
+ int trans, i, j, k, s1, s2, b1, b2, conslen, dif, match;
+ float add_wgt;
+
+ trans = sm1->trans;
+
+ for(i=0;i<2;i++)
+ for(j=0;j<2;j++)
+ if( sm1->s[i] == sm2->s[j] )
+ if( sm1->s[j] != sm2->s[i] )
+ if( sm1->b[i] < sm2->b[j] + sm2->ext &&
+ sm2->b[j] < sm1->b[i] + sm1->ext )
+ {
+ conslen = mini2( sm1->b[i] + sm1->ext, sm2->b[j] + sm2->ext)
+ - maxi2( sm1->b[i] , sm2->b[j] );
+ if(
+ ( trans == 0 ) ||
+ ( ( conslen % 3 ) == 0 )
+ ) {
+
+ s1 = sm1->s[(i+1)%2];
+ s2 = sm2->s[(j+1)%2];
+
+ b1 = sm1->b[(i+1)%2];
+ dif = sm2->b[j] - sm1->b[i];
+ if (dif > 0)
+ b1 = b1 + dif;
+
+ b2 = sm2->b[(j+1)%2];
+ dif = sm1->b[i] - sm2->b[j];
+ if (dif > 0)
+ b2 = b2 + dif;
+
+ match = 0;
+
+ for( k = 0 ; k < conslen ; k++ ) {
+ if(
+ ( wgt_type == 0 ) ||
+ ( trans && ( ( k % 3 ) == 0 ) )
+ )
+ match = match
+ + sim_score[ amino[ s1 ][ b1 + k ] ][ amino[s2][ b2 + k ] ];
+ else
+ match = match + ( seq[ s1 ][ b1 + k ] == seq[ s2 ][ b2 + k ] );
+ }
+
+
+ if( wgt_type == 0 )
+ add_wgt = wgt_prot[ conslen ][ match ];
+ else
+ if( trans )
+ add_wgt = wgt_trans[ conslen / 3 ][ match ] ;
+ else
+ add_wgt = wgt_dna[ conslen ][ match ] ;
+
+ sm1->ow = sm1->ow + add_wgt ;
+ sm2->ow = sm2->ow + add_wgt ;
+
+ }
+ }
+} /* ow_add */
+
+void seq_shift()
+ {
+ int i, hv;
+
+ for(i = 0 ; i < seqnum ; i++)
+ for(hv = seqlen[i]+1 ; hv > 0 ; hv--)
+ seq[i][hv] = seq[i][hv-1];
+ }
+
+
+
+
+void filter(int *number, struct multi_frag *diagonal)
+{
+ /* checks diagonals one by one, if they are consistent with the
+ diagonals already included into the alignment. If a new diagonal
+ is consistent, it is included into the alignment and the frontiers
+ in clos (when GABIOS is used) are changed accordingly */
+
+ int i, j, k, l, sv, hv, ab[2], as[2], ae[2], aext, nv;
+ float awgt ;
+
+ int test; /* = 1 if current diagonal consistent; = 0 otherwise */
+ int number_bf; /* number of diagonals before filter */
+
+ FILE *fp_st, *fp_cap ;
+
+ float lb, ub;
+
+ struct multi_frag *dia;
+ char cap_file_name[ NAME_LEN ] ;
+
+ if( ( istep > 0 ) && ( iter_cond_prob == 0 ) )
+ for( i = 0 ; i < seqnum ; i++ )
+ for( j = 0 ; j < seqnum ; j++ )
+ cont_it_p[i][j] = 0 ;
+
+ dia = diagonal;
+ number_bf = *number;
+
+ if( ( istep == 0 ) && anchors && ( seqnum > 2 ) ) {
+ strcpy( cap_file_name , input_name );
+ strcat( cap_file_name , ".cap" );
+ fp_cap = fopen( cap_file_name ,"w");
+ }
+
+
+ for(nv = 0 ; nv < number_bf ; nv++ )
+ {
+ ab[0] = dia->b[0]; /* begin of n-th diagonal in 1. sequence */
+ ab[1] = dia->b[1]; /* begin of n-th diagonal in 2. sequence */
+ as[0] = dia->s[0]; /* 1. sequence of n-th diagonal */
+ as[1] = dia->s[1]; /* 2. sequence of n-th diagonal */
+ aext = dia->ext; /* length of n-th diagonal */
+ awgt = dia->weight; /* length of n-th diagonal */
+ ae[0] = ab[0] + aext - 1; /* end of n-th diagonal in 1. sequence */
+ ae[1] = ab[1]+aext-1; /* end of n-th diagonal in 2. sequence */
+
+
+ if( print_status )
+ if( ( ( nv + 1 ) % 10 ) == 0 )
+ {
+ fp_st = fopen( pst_name ,"w");
+
+ fprintf(fp_st,"\n\n\n Status of the program run:\n");
+ fprintf(fp_st," ==========================\n\n");
+ fprintf(fp_st," %s \n\n", input_line);
+ fprintf(fp_st," iteration step %d \n", istep );
+ fprintf(fp_st," checking diagonal %d for ", nv + 1);
+ fprintf(fp_st,"consistency\n\n total number of");
+ fprintf(fp_st," diagonals = %d \n\n\n\n", number_bf);
+ fclose(fp_st);
+ }
+
+ test = alignableSegments(clos, as[0], ab[0], as[1], ab[1], aext);
+
+ if(test) /* i.e current diagonal consistent with the diagonals
+ already included into the alignment */
+ {
+
+ addAlignedSegments(clos, as[0], ab[0], as[1], ab[1], aext);
+
+ if( istep )
+ for(hv=0;hv<aext;hv++)
+ for(i=0;i<2;i++)
+ {
+ j = (i+1)%2;
+ open_pos[ as[i] ][ as[j] ][ ab[i]+hv ] = 0;
+ }
+
+ dia->sel = 1;
+ glob_sim[ as[0] ][ as[1] ] =
+ glob_sim[ as[0] ][ as[1] ] + dia->weight;
+
+ if( istep )
+ tot_weight = tot_weight + dia->weight;
+
+
+ } /* if test, i.e. current diagonal consistent */
+ else /* no consistency */
+ {
+ (*number)--;
+ dia->sel = 0;
+ cont_it_p[ as[0] ][ as[1] ] = 1 ;
+ }
+
+ if( ( istep == 0 ) && anchors && ( seqnum > 2 ) ) {
+ fprintf( fp_cap, " anchor %d %d %d %d %d %f " , as[0] + 1, as[1] + 1 , ab[0], ab[1], aext , awgt);
+ if( dia->sel == 0 )
+ fprintf( fp_cap , " inconsistent ");
+ fprintf( fp_cap , "\n");
+ }
+
+
+ dia = dia->next;
+
+ } /* for(hv = 0 ; hv < number_bf ; hv++ ) */
+
+ if( ( istep == 0 ) && anchors && ( seqnum > 2 ) )
+ fclose( fp_cap ) ;
+
+} /* filter( ) */
+
+
+
+
+void sel_test()
+ {
+ int hv;
+ struct multi_frag *hp;
+
+ hp = this_it_dia;
+
+ for( hv = 0 ; hv < num_dia_af[ istep ] ; hv++ )
+ {
+ if( hp->sel == 0 )
+ {
+ printf("\n \n \n WARNING: \n \n \n");
+ printf(" sel[%d] = %d \n", hv, hp->sel);
+ exit(2);
+ }
+ hp = hp->next;
+ }
+ }
+
+
+
+
+
+
+
+
+
+
+void throw_out( float *weight_sum )
+ {
+ int nc;
+ short consist_found = 0;
+
+ struct multi_frag *cp; /* current diagonal */
+ struct multi_frag *hp; /* predecedor of cp */
+
+ hp = ( struct multi_frag *) calloc( 1 , sizeof( struct multi_frag ) );
+ cp = this_it_dia;
+ hp = NULL;
+ *weight_sum = 0;
+
+
+ for( nc = 0 ; nc < num_dia_bf[ istep ] ; nc++ )
+ {
+ if( cp->sel )
+ {
+ *weight_sum = *weight_sum + cp->weight;
+ consist_found = 1;
+
+ hp = cp;
+ cp = cp->next;
+ }
+ else
+ {
+ cp = cp->next;
+ if( consist_found )
+ {
+ free(hp->next);
+ hp->next = cp;
+ }
+ else
+ {
+ free( this_it_dia);
+ this_it_dia = cp;
+ }
+ }
+ }
+ } /* throw_out */
+
+
+
+
+
+
+
+
+
+
+void new_shift(int s, int p, int dif)
+ /* shifts the elements of sequence s starting with position p
+ for dif elements to the right */
+ {
+ int hv;
+ int shift_dif; /* length of a gap (if existing) between position hv
+ and position hv+1. In case of gaps, the function
+ `new_shift' diminishs the lengths of the gaps instead
+ of shifting further sequence elements to the right */
+
+ for(hv=p ; ( hv<seqlen[s]+1 ) && (dif>0) ; hv++)
+ {
+ shift_dif = shift[s][hv+1] - shift[s][hv] - 1;
+ shift[s][hv] = shift[s][hv] + dif;
+ dif = dif - shift_dif;
+ }
+ }
+
+wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+ int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) {
+
+int i, dc, pc, s1, pos;
+
+for( dc = 0 ; dc < num ; dc++ )
+ {
+
+ for( pc = 0 ; pc < dia->ext ; pc++ )
+ {
+ i = dia->b[0] + pc;
+ s1 = dia->s[0];
+ pos = shift[s1][i];
+ if ( dia->trans )
+ if ( dia->cs )
+ minus_cnt[ pos ] = minus_cnt[ pos ] + 1 ;
+ else
+ plus_cnt[ pos ] = plus_cnt[ pos ] + 1 ;
+ else {
+ nuc_cnt[ pos ] = nuc_cnt[ pos ] + 1 ;
+ }
+ frg_inv[ pos ] = frg_inv[ pos ] + 1 ;
+ }
+ dia = dia->next;
+ }
+}
+
+
+
+plot_calc( int num , int e_len, float *w_count, float *pl,
+ struct multi_frag *dia , FILE *fp_csc )
+ {
+ int i, dc, pc, s1, pos;
+ float max_weight = 0; /* maximum value of `weight_count' */
+ float shrink, shrink_csc, hsc ;
+
+ for( dc = 0 ; dc < num ; dc++ )
+ {
+
+ for( pc = 0 ; pc < dia->ext ; pc++ )
+ {
+ i = dia->b[0] + pc;
+ s1 = dia->s[0];
+ pos = shift[s1][i];
+ w_count[ pos ] = w_count[ pos ] + dia->weight;
+ }
+ dia = dia->next;
+ }
+
+
+ for( i = 0 ; i <= e_len ; i++ )
+ if( max_weight < w_count[i] )
+ max_weight = w_count[i];
+
+
+ if( max_weight )
+ {
+ shrink = plot_num / max_weight;
+ shrink_csc = MAX_CSC / max_weight;
+
+ for( i = 0 ; i <= e_len ; i++ )
+ pl[i] = w_count[i] * shrink;
+
+ if( col_score ) {
+ printf(" e_len = %d \n\n", e_len) ;
+ for( i = 0 ; i <= e_len ; i++ ) {
+ hsc = w_count[i] * shrink_csc ;
+ fprintf( fp_csc , "%5.1f\t0\n", hsc ) ;
+ }
+ }
+ }
+ else {
+ for( i = 0 ; i <= e_len ; i++ )
+ pl[i] = 0 ;
+
+ printf(" e_len = %d \n\n", e_len) ;
+ printf(" no max weight\n\n");
+ }
+
+ }
+
+
+
+void av_tree_print()
+ {
+ int i, j, k, connect, max_pair[2], cv, m1, m2;
+ struct subtree *all_clades;
+ double **clade_similarity, new_similarity;
+ double max_sim;
+ char *string, l_name[2][20];
+ char tree_name[NAME_LEN];
+ float max_seq_sim, branch_len[2], depth;
+
+ FILE *t_file;
+
+
+
+ if( (all_clades = (struct subtree *)
+ calloc( seqnum , sizeof( struct subtree ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `all_clades'\n \n");
+ exit(1);
+ }
+
+
+ if( (clade_similarity = (double **)
+ calloc( seqnum , sizeof( double* ) )) == NULL)
+ exit(1);
+
+ for(i = 0 ; i < seqnum ; i++ )
+ if( (clade_similarity[i] = (double *)
+ calloc( seqnum , sizeof( double ) )) == NULL)
+ exit(1);
+
+ if( (string = (char *)
+ calloc( seqnum * 100 , sizeof(char) )) == NULL)
+ {
+ printf(" problems with memory allocation for `string'\n \n");
+ exit(1);
+ }
+
+
+
+
+ for(i = 0 ; i < seqnum ; i++ )
+ {
+ if( (all_clades[i].member = (int *)
+ calloc( seqnum , sizeof( int ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `all_clades'\n \n");
+ exit(1);
+ }
+
+
+ if( (all_clades[i].name = (char *)
+ calloc( seqnum * 100 , sizeof( char ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `all_clades'\n \n");
+ exit(1);
+ }
+
+ strcpy( all_clades[i].name , seq_name[i] );
+ all_clades[i].member_num = 1;
+ all_clades[i].member[0] = i;
+ all_clades[i].valid = 1;
+ all_clades[i].depth = 0;
+ }
+
+
+
+ for(i = 0 ; i < seqnum ; i++ )
+ for(j = i + 1 ; j < seqnum ; j++ )
+ {
+ clade_similarity[i][j] = glob_sim[i][j];
+ clade_similarity[j][i] = glob_sim[i][j];
+ }
+
+
+ for(connect = 1 ; connect < seqnum ; connect++)
+ {
+ max_sim = - 1;
+
+
+
+ for(i = 0 ; i < seqnum ; i++ )
+ for(j = 0 ; j < seqnum ; j++ )
+ if( i != j )
+ if( all_clades[i].valid && all_clades[j].valid )
+ if( clade_similarity[i][j] > max_sim )
+ {
+ max_sim = clade_similarity[i][j];
+ max_pair[0] = i;
+ max_pair[1] = j;
+ }
+
+
+ depth = 1 / ( max_sim + 1 ) ;
+
+ {
+ m1 = max_pair[0];
+ m2 = max_pair[1];
+
+ for( i = 0 ; i < seqnum ; i++ )
+ if( all_clades[i].valid )
+ if( i != m1 )
+ if( i != m2 )
+ {
+ if( ! strcmp(clust_sim , "av") )
+ new_similarity =
+ (
+ clade_similarity[i][m1] * all_clades[m1].member_num +
+ clade_similarity[i][m2] * all_clades[m2].member_num
+ ) /
+ ( all_clades[m1].member_num + all_clades[m2].member_num );
+
+ if( ! strcmp(clust_sim , "max") )
+ new_similarity =
+ maxf2( clade_similarity[i][m1] , clade_similarity[i][m2] );
+
+ if( ! strcmp(clust_sim , "min") )
+ new_similarity =
+ minf2( clade_similarity[i][m1] , clade_similarity[i][m2] );
+
+
+ clade_similarity[i][m1] = new_similarity;
+ clade_similarity[m1][i] = new_similarity;
+ }
+
+
+ all_clades[m2].valid = 0;
+
+ for(k = 0 ; k < all_clades[m2].member_num ; k++)
+ all_clades[m1].member[ all_clades[m1].member_num + k ] =
+ all_clades[m2].member[ k ] ;
+
+ all_clades[m1].member_num =
+ all_clades[m1].member_num + all_clades[m2].member_num;
+
+
+ for(k = 0 ; k < 2 ; k++)
+ {
+ branch_len[k] = depth - all_clades[ max_pair[k] ].depth;
+ sprintf( l_name[k],":%f", branch_len[k]);
+ }
+
+
+ all_clades[m1].depth = depth;
+
+
+ strcpy(string,"(");
+ strcat(string, all_clades[m1].name);
+ strcat(string,l_name[0]);
+/* strcat(string,",\n"); */
+ strcat(string, all_clades[m2].name);
+ strcat(string,l_name[1]);
+ strcat(string,")");
+
+ strcpy( all_clades[m1].name , string );
+ }
+ }
+
+
+ strcat(string, ";");
+
+ i = strlen( string ) + 2;
+
+ if( (upg_str = (char *) calloc( i , sizeof(char) )) == NULL)
+ {
+ printf(" problems with memory allocation for `upg_str'\n \n");
+ exit(1);
+ }
+
+ for(i = 0 ; i <= strlen( string ) ; i++ )
+ upg_str[i] = string[i] ;
+
+
+ } /* av_tree_print */
+
+
+
+void print_log( struct multi_frag *d , FILE *fp_l , FILE *fp_fs )
+ {
+ int i, j, mn, pv, percent, this_frag_trans , frg_count = 0 ;
+ struct multi_frag *diagonal;
+ char hc ;
+
+ if(long_output)
+ {
+ fprintf(fp_l," \n \n Iteration %d:\n", istep );
+
+ if( istep < 10 )
+ fprintf(fp_l," ------------");
+ else
+ fprintf(fp_l," -------------");
+ }
+
+
+ for(i= 0 ; i<seqnum ; i++)
+ for(j= i+1 ; j<seqnum; j++)
+ {
+ if(long_output) {
+ if( seqnum > 2 ) {
+ fprintf(fp_l, "\n \n \n \n Pairwise alignment ");
+ fprintf(fp_l, "%d/%d", i + 1, j + 1);
+ fprintf(fp_l, " (%s / %s) \n" ,seq_name[i] ,seq_name[j] );
+ fprintf(fp_l, " =========================");
+ fprintf(fp_l, "===================== ");
+ }
+ fprintf(fp_l, " \n \n \n");
+ }
+
+ pairalignsum = 0;
+ pairalignlen = 0;
+
+ diagonal = d;
+ while(diagonal != NULL)
+ {
+ frg_count++ ;
+ if( diagonal->s[0] == i && diagonal->s[1] == j)
+ {
+ if(diagonal->sel)
+ {
+ if(long_output)
+ {
+ fprintf(fp_l," *");
+ fprintf(fp_l," (%3d,", diagonal->b[0]);
+ }
+
+ pairalignsum = pairalignsum + diagonal->weight;
+ pairalignlen = pairalignlen + diagonal->ext;
+ }
+ else
+ if(long_output)
+ fprintf(fp_l," (%3d,", diagonal->b[0]);
+
+ if(long_output)
+ {
+ fprintf(fp_l,"%3d) ", diagonal->b[1]);
+ fprintf(fp_l," wgt:%7.3f ", diagonal->weight);
+ if(seqnum > 2)
+ if(overlap_weights)
+ fprintf(fp_l," olw:%7.3f ", diagonal->ow);
+ fprintf(fp_l,"len: %2d", diagonal->ext);
+ if( ( wgt_type == 3 ) || crick_strand ) {
+ if( diagonal->trans )
+ fprintf(fp_l," P-frg" );
+ else
+ fprintf(fp_l," N-frg" );
+ }
+
+ if( diagonal->trans )
+ if( crick_strand ) {
+ if( diagonal->cs )
+ fprintf(fp_l,", CRICK strand " );
+ else
+ fprintf(fp_l,", WATSON strand " );
+ }
+
+ }
+
+ if( frg_mult_file_v ) {
+ fprintf(fp_fs,"FRG %d ", frg_count );
+ fprintf(fp_fs,"name: %s %s ", seq_name[i] , seq_name[j] ) ;
+
+ fprintf(fp_fs,"seq: %d %d ", i + 1 , j + 1 ) ;
+ fprintf(fp_fs,"beg: %d %d ", diagonal->b[0], diagonal->b[1]);
+ fprintf(fp_fs,"len: %d ", diagonal->ext);
+
+ fprintf(fp_fs,"wgt:%7.3f ", diagonal->weight);
+ if(diagonal->sel)
+ fprintf(fp_fs," CONS ");
+ else
+ fprintf(fp_fs," NON-CONS ");
+ fprintf(fp_fs,"\n") ;
+ fprintf(fp_fs,"SEG1 ");
+ for(pv = 0 ; pv < diagonal->ext ; pv ++)
+ fprintf(fp_fs,"%c", seq[i][ diagonal->b[0] + pv ] );
+ fprintf(fp_fs,"\n");
+
+ fprintf(fp_fs,"SEG2 ");
+ for(pv = 0 ; pv < diagonal->ext ; pv ++)
+ fprintf(fp_fs,"%c", seq[j][ diagonal->b[1] + pv ] );
+ fprintf(fp_fs,"\n");
+ fprintf(fp_fs,"\n");
+ }
+ if( frg_mult_file & ! frg_mult_file_v ) {
+ if( diagonal->sel ) {
+ fprintf(fp_fs," %d %d ", i + 1 , j + 1 ) ;
+ fprintf(fp_fs," %d %d ", diagonal->b[0], diagonal->b[1]);
+ fprintf(fp_fs," %d \n", diagonal->ext);
+ }
+ }
+
+ if(long_output)
+ {
+ fprintf(fp_l,"\n");
+
+ if(
+ wgt_type == 2 ||
+ ( ( wgt_type == 3 ) && diagonal->trans )
+ )
+ this_frag_trans = 1;
+ else
+ this_frag_trans = 0;
+
+ if( this_frag_trans )
+ {
+ fprintf(fp_l,"\n ");
+ for(pv = 0 ; pv < diagonal->ext ; pv ++)
+ {
+ hc = amino_acid[ amino[i][ diagonal->b[0] + pv - 1 ] ] ;
+ if( crick_strand )
+ if( diagonal->cs )
+ hc = amino_acid[ amino_c[i][ diagonal->b[0] + pv - 1 ] ] ;
+
+ if( ( pv % 3 ) == 0 )
+ fprintf(fp_l,"/");
+ if( ( pv % 3 ) == 1 )
+ fprintf(fp_l,"%c", hc ) ;
+ if( ( pv % 3 ) == 2 )
+ fprintf(fp_l,"\\");
+
+ }
+ }
+
+ fprintf(fp_l,"\n ");
+ for(pv = 0 ; pv < diagonal->ext ; pv ++)
+ fprintf(fp_l,"%c", seq[i][ diagonal->b[0] + pv ] );
+ fprintf(fp_l,"\n");
+
+
+ fprintf(fp_l," ");
+ for(pv = 0 ; pv < diagonal->ext ; pv ++)
+ fprintf(fp_l,"%c", seq[j][ diagonal->b[1] + pv ] );
+
+
+ if( this_frag_trans )
+ {
+ fprintf(fp_l,"\n ");
+ for(pv = 0 ; pv < diagonal->ext ; pv ++)
+ {
+ hc = amino_acid[ amino[j][ diagonal->b[1] + pv - 1 ]
+ ] ;
+ if( crick_strand )
+ if( diagonal->cs )
+ hc = amino_acid[ amino_c[j][ diagonal->b[1] + pv - 1 ] ] ;
+
+ if( ( pv % 3 ) == 0 )
+ fprintf(fp_l,"\\");
+ if( ( pv % 3 ) == 1 )
+ fprintf(fp_l,"%c", hc ) ;
+ if( ( pv % 3 ) == 2 )
+ fprintf(fp_l,"/");
+
+ }
+ }
+
+ fprintf(fp_l,"\n \n");
+ }
+ } /* if( diagonal->s[0] == i && diagonal->s[1] == j) */
+
+ diagonal = diagonal->next;
+
+ } /* while(diagonal != NULL) */
+
+ percent = pairalignlen*100/mini2(seqlen[i],seqlen[j]);
+
+ if(long_output)
+ {
+ fprintf(fp_l,"\n Sum of diagonal scores: %f\n", pairalignsum);
+ fprintf(fp_l," Aligned residues: %d\n", pairalignlen);
+ fprintf(fp_l," (%d percent of the shorter", percent);
+ fprintf(fp_l," sequence aligned)\n");
+ }
+ } /* for(i = 0 ; i < seqnum ; i++)
+ for(j = i + 1 ; j < seqnum ; j++) */
+
+ } /* print_log */
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/input.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/input.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/input.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,396 @@
+
+ /*******************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * input.c *
+ * *
+ \*******************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+extern int max_dia , self_comparison ;
+extern int sim_score[21][21];
+extern int max_sim_score ;
+extern float av_sim_score_pep ;
+extern float av_sim_score_nuc ;
+extern char par_dir[ NAME_LEN ] ;
+extern double **tp400_prot, **tp400_dna, **tp400_trans ;
+extern int *seqlen ;
+extern int seqnum ;
+
+
+int word_count( char *str ) {
+
+ short word = 0 ;
+ int i ;
+ int word_len = 0 ;
+
+ for( i = 0 ; i < strlen( str ) - 1 ; i++ ) {
+ if( ( str[i] != ' ' ) && ( str[i] != '\t' ) ) {
+ if( ! word ) {
+ word_len++ ;
+ word = 1 ;
+ }
+ }
+ else
+ word = 0 ;
+
+ }
+ return( word_len ) ;
+}
+
+
+void exclude_frg_read( char *file_name , int ***exclude_list) {
+
+ char exclude_file_name[ NAME_LEN ] ;
+ FILE *fp;
+ char line[ 10000 ] ;
+ int i, len, beg1, beg2, seq1, seq2;
+ int sv = 0, hv, word_num ;
+
+ strcpy( exclude_file_name , file_name );
+ strcat( exclude_file_name , ".xfr" );
+
+ if( (fp = fopen( exclude_file_name, "r")) == NULL)
+ erreur("\n\n cannot find file with excluded fragments \n\n\n");
+
+
+
+ while( fgets( line , MLINE , fp ) != NULL ) {
+ if( strlen( line ) > 4 ) {
+ sscanf(line,"%d %d %d %d %d", &seq1, &seq2, &beg1, &beg2 , &len );
+
+ if( seq1 > seqnum ){
+ printf ("\n\n exclueded fragment makes no sense!\n\n");
+ printf (" wrong sequence no %d in fragment\n\n", seq1 );
+ printf ("%d %d %d %d %d \n\n ", seq1, seq2, beg1, beg2 , len );
+ exit(1) ;
+ }
+
+ if( seq2 > seqnum ){
+ printf ("\n\n excluded fragment makes no sense!\n\n");
+ printf (" wrong sequence no %d in fragment\n\n", seq2 );
+ printf (" %d %d %d %d %d \n\n", seq1, seq2, beg1, beg2 , len );
+ exit(1) ;
+ }
+
+/*
+ seq1 = seq1 - 1;
+ seq2 = seq2 - 1;
+*/
+
+ if( beg1 + len > seqlen[ seq1 - 1 ] + 1 ){
+ printf ("\n\n excluded fragment makes no sense!\n");
+ printf (" fragment");
+ printf (" \" %d %d %d %d %d \"\n", seq1, seq2, beg1, beg2 , len );
+ printf (" doesn't fit into sequence %d:\n", seq1 );
+ printf (" sequence %d has length = %d\n\n", seq1 , seqlen[ seq1 - 1 ] );
+ exit(1) ;
+ }
+
+
+
+ for( i = 0 ; i < len ; i++ ) {
+ exclude_list[ seq1 - 1 ][ seq2 - 1 ][ beg1 + i ] = beg2 + i ;
+ }
+ }
+ }
+
+} /* excluded_frg_read */
+
+
+
+
+
+
+
+void ws_remove( char *str ) {
+ int pv = 0 ;
+
+ while( ( str[ pv ] == ' ' ) || ( str[ pv ] == '\t' ) ) {
+ pv++ ;
+ }
+
+ strcpy( str , str + pv );
+}
+
+void n_clean( char *str ) {
+ int pv = 0 ;
+ char *char_ptr ;
+
+ while( ( str[ pv ] == ' ' ) ||
+ ( str[ pv ] == '\t' ) ||
+ ( str[ pv ] == '>' ) ) {
+ pv++ ;
+ }
+ strcpy( str , str + pv ) ;
+
+ if( ( char_ptr = strchr( str ,' ') ) != NULL)
+ *char_ptr = '\0';
+ if( ( char_ptr = strchr( str ,'\t') ) != NULL)
+ *char_ptr = '\0';
+ if( ( char_ptr = strchr( str ,'\n') ) != NULL)
+ *char_ptr = '\0';
+
+
+
+
+}
+
+
+void fasta_test( char *seq_file ) {
+
+ int test = 1;
+ int pv = 0;
+ FILE *fp;
+
+ char line[ MAX_INPUT_LINE ] ;
+
+ if( (fp = fopen( seq_file , "r")) == NULL) {
+ printf("\n\n Cannot find sequence file %s \n\n\n", seq_file );
+ exit(1) ;
+ }
+
+ while( test ) {
+ fgets( line , MAX_INPUT_LINE , fp );
+
+ ws_remove( line );
+
+ if( line[0] != '\n' )
+ if( line[0] == '>' )
+ test = 0;
+ else
+ erreur("\n\n file not in FASTA format \n\n");
+ }
+
+ fclose( fp );
+}
+
+
+int seq_read( char *seq_file , char *sq[MAX_SEQNUM] , char **sqn , char **fsqn ) {
+
+ char line[ MAX_INPUT_LINE ] ;
+
+ char *nom_seq;
+ char *char_ptr;
+ int sn, i, j, k , pv , crc ;
+ FILE *fp;
+ int max_char[ MAX_SEQNUM ] ;
+
+ if( (fp = fopen( seq_file , "r")) == NULL) {
+ printf("\n\n Cannot find sequence file %s \n\n\n", seq_file );
+ exit(1) ;
+ }
+ fasta_test( seq_file );
+
+ sn = -1 ;
+ while( fgets( line , MAX_INPUT_LINE , fp ) != NULL ) {
+
+
+ ws_remove( line );
+
+ if( line[0] == '>' ) {
+ sn++;
+
+
+ n_clean( line );
+
+
+ fsqn[ sn ] = ( char * ) calloc( strlen( line ) + 3 , sizeof ( char ) );
+
+ strcpy( fsqn[ sn ] , line ) ;
+
+
+ max_char[ sn ] = 0;
+ sqn[ sn ] = ( char * ) calloc( SEQ_NAME_LEN + 3 , sizeof ( char ) );
+
+ for( crc = 0 ; crc < SEQ_NAME_LEN ; crc++ )
+ if( crc < strlen(line) )
+ sqn[ sn ][ crc ] = line[ crc ] ;
+ else
+ sqn[ sn ][ crc ] = ' ';
+
+ sqn[ sn ][ SEQ_NAME_LEN ] = '\0';
+
+
+
+ }
+
+
+ else
+ max_char[ sn ] = max_char[ sn ] + strlen( line ) - 1 ;
+ }
+
+ for( i = 0 ; i <= sn ; i++ ) {
+ sq[ i ] = ( char * ) calloc( max_char[ i ] + 1 , sizeof ( char ) );
+ }
+
+ if( (seqlen = (int *) calloc( ( sn + 1 ) , sizeof(int) )) == NULL)
+ erreur("\n\n problems with memory allocation for `seqlen' \n\n");
+
+
+ fclose( fp );
+
+
+ /******************************************/
+
+ if( self_comparison == 1 ) {
+ if( sn != 0 ) {
+ printf("\n\n With option \"self comparison\" input file must contain one single sequence \n\n" );
+ exit(1) ;
+ }
+
+ sq[ 1 ] = ( char * ) calloc( max_char[ 0 ] + 1 , sizeof ( char ) );
+
+ sqn[ 1 ] = ( char * ) calloc( strlen( line ) + 3 , sizeof ( char ) );
+ strcpy( sqn[ 1 ] , sqn[ 0 ] ) ;
+ }
+
+ /******************************************/
+
+
+ if( (fp = fopen( seq_file , "r")) == NULL)
+ erreur("\n\n no seq file \n\n");
+
+ sn = -1 ;
+ while( fgets( line , MAX_INPUT_LINE , fp ) != NULL ) {
+ ws_remove( line );
+ if( line[0] == '>' ) {
+ sn++;
+ j = 0;
+ }
+ else
+ for( k = 0 ; k < strlen( line ) ; k++ )
+ if(
+ ( line[ k ] >= 65 ) && ( line[ k ] <= 90 ) ||
+ ( line[ k ] >= 97 ) && ( line[ k ] <= 122 )
+ )
+ sq[ sn ][ j++ ] = toupper( line[ k ] ) ;
+ }
+
+ sn++;
+
+ for( i = 0 ; i < sn ; i++ ) {
+ seqlen[ i ] = strlen ( sq[ i ] ) ;
+ }
+
+ if( self_comparison ) {
+ seqlen[ 1 ] = seqlen[ 0 ] ;
+ for( i = 0 ; i <= seqlen[ 0 ] ; i++ )
+ sq[ 1 ][ i ] = sq[ 0 ][ i ] ;
+ sn++;
+ }
+
+ fclose( fp );
+
+ return( sn );
+}
+
+
+
+void matrix_read( FILE *fp_mat ) {
+ int i, j;
+ char line[MLINE], dummy[MLINE];
+
+ fgets( line , MLINE , fp_mat );
+ fgets( line , MLINE , fp_mat );
+
+
+ for( i = 1 ; i <= 20 ; i++ ) {
+ for(j=i;j<=20;j++) {
+ fscanf( fp_mat , "%d" , &sim_score[i][j]);
+ sim_score[j][i] = sim_score[i][j];
+ if ( sim_score[i][j] > max_sim_score )
+ max_sim_score = sim_score[i][j] ;
+ }
+
+ fscanf( fp_mat, "%s\n", dummy);
+ }
+
+ fclose(fp_mat);
+
+ for( i = 0 ; i <= 20 ; i++ ) {
+ sim_score[i][0] = 0 ;
+ sim_score[0][i] = 0 ;
+ }
+
+/*
+ sim_score[0][0] = max_sim_score ;
+*/
+
+}
+
+
+
+void tp400_read( int w_type , double **pr_ptr ) {
+
+ /* reads probabilities from file */
+ /* w_type = 0 (protein), 1 (dna w/o transl.), 2 (dna with transl.) */
+
+ char line[MLINE], file_name[MLINE], suffix[10], str[MLINE] ;
+ int sum, len, max_sim, i ;
+ double pr;
+
+ FILE *fp;
+
+ if ( w_type == 0 ) {
+ strcpy( suffix , "prot" );
+ }
+
+ if ( w_type == 1 ) {
+ strcpy( suffix , "dna" );
+ }
+
+ if ( w_type == 2 ) {
+ strcpy( suffix , "trans" );
+ }
+
+ strcpy( file_name , par_dir );
+ strcat( file_name , "/tp400_" );
+ strcat( file_name , suffix );
+
+
+ if ( ( fp = fopen( file_name , "r" ) ) == NULL ) {
+ printf("\n\n Cannot find the file %s \n\n", file_name );
+ printf(" Make sure the environment variable DIALIGN2_DIR points\n");
+ printf(" to a directory containing the files \n\n");
+ printf(" BLOSUM \n tp400_dna\n tp400_prot \n tp400_trans \n\n" );
+ printf(" These files should be contained in the DIALIGN package \n\n\n" ) ;
+ exit(1) ;
+ }
+
+
+ if ( fgets( line , MLINE , fp ) == NULL )
+ erreur("\n\n problem with file %s \n\n", file_name );
+ else
+ if( w_type % 2 )
+ av_sim_score_nuc = atof( line );
+ else
+ av_sim_score_pep = atof( line );
+
+
+ while( fgets( line , MLINE , fp ) != NULL )
+ {
+ sscanf(line,"%d %d %s", &len, &sum, str );
+
+ pr = atof(str);
+ pr_ptr[len][sum] = pr;
+
+ }
+
+
+} /* tp400_read */
+
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/makefile
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/makefile 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/makefile 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,55 @@
+
+
+
+ ###############################
+ # #
+ # #
+ # Makefile for DIALIGN #
+ # #
+ # #
+ ###############################
+
+
+CC = gcc
+CFLAGS = -c -O -I$ -DCONS
+#CFLAGS = -g -c -I$ -DCONS
+LIBS = -lm
+#
+
+OBJS = dialign.o functions.o para.o \
+ output.o wgt.o anchor.o regex.o \
+ input.o frag_chain.o \
+ alig_graph_closure.o pratique.o
+
+#
+dialign2-2: $(OBJS)
+ $(CC) $(OBJS) $(LIBS) -o dialign2-2
+# $(CC) -g $(OBJS) $(LIBS) -o dialign2-2_db
+#
+#
+# Subroutines
+#
+
+dialign.o: dialign.c
+ $(CC) $(CFLAGS) dialign.c
+functions.o: functions.c
+ $(CC) $(CFLAGS) functions.c
+input.o: input.c
+ $(CC) $(CFLAGS) input.c
+frag_chain.o: frag_chain.c
+ $(CC) $(CFLAGS) frag_chain.c
+para.o: para.c
+ $(CC) $(CFLAGS) para.c
+output.o: output.c
+ $(CC) $(CFLAGS) output.c
+wgt.o: wgt.c
+ $(CC) $(CFLAGS) wgt.c
+regex.o: regex.c
+ $(CC) $(CFLAGS) regex.c
+anchor.o: anchor.c
+ $(CC) $(CFLAGS) anchor.c
+
+#
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/output.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/output.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/output.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,1065 @@
+
+
+ /*******************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * output.c *
+ * *
+ \*******************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+extern int cd_gobics , wgt_type_plot , col_score ;
+extern int ref_seq, anchors, speed_optimized, online ;
+extern short crick_strand ;
+extern float sf_mat_thr ;
+extern int **amino;
+extern char amino_acid[ 22 ] ;
+extern int quali_num , wgt_plot , mask, lgs_option ;
+extern char input_line[ NAME_LEN ];
+extern char clust_sim[ NAME_LEN ] ;
+extern int msf_file, cw_file;
+extern int lmax;
+extern float threshold;
+extern float av_len ;
+extern int pr_av_max_nd , wgt_type ;
+extern int num_dia_p, overlap_weights ;
+extern int fasta_file;
+extern char *upg_str;
+extern int plot_num;
+extern char *seq[MAX_SEQNUM];
+extern int *seqlen;
+extern int maxlen;
+extern char *seq_name[MAX_SEQNUM];
+extern char *full_name[MAX_SEQNUM];
+extern int **shift;
+
+extern struct multi_frag *pair_dia;
+extern struct multi_frag *this_it_dia;
+extern struct multi_frag *all_it_dia;
+
+extern CLOSURE *clos;
+
+extern int max_sim_score ;
+extern int max_dia;
+extern int seqnum ;
+extern int num_all_it_dia;
+extern int frg_count ;
+
+ extern int mini2(int a, int b) ;
+ extern void new_shift(int s, int p, int dif) ;
+ extern void mini(int *a, int b);
+ extern void maxi(int *a, int b);
+ extern int int_test(float f);
+ extern plot_calc( int num , int e_len, float *w_count, float *pl,
+ struct multi_frag *dia , FILE *fp_csc ) ;
+ extern wgt_type_count( int num , int e_len, int *plus_cnt, int *minus_cnt,
+ int *nuc_cnt , int *frg_inv, struct multi_frag *dia ) ;
+
+
+
+void subst_mat( char *file_name, int fragno , struct multi_frag *frg ) {
+
+ int s0 , s1 , i , j , frg_count ;
+ short a0 , a1 ;
+ int ****sbsmt ;
+ struct multi_frag *frag ;
+ char mat_file_name[ NAME_LEN ] ;
+ FILE *fp_mat;
+
+
+ if( ( sbsmt = (int **** ) calloc( seqnum , sizeof(int ***))) == NULL) {
+ printf("Problems with memory allocation for sbsmt\n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ if( ( sbsmt[i] = (int *** ) calloc( seqnum , sizeof(int **))) == NULL) {
+ printf("Problems with memory allocation for sbsmt\n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ for( j = 0 ; j < seqnum ; j++ )
+ if( ( sbsmt[i][j] = (int ** ) calloc( 21 , sizeof( int* ) ) ) == NULL) {
+ printf("Problems with memory allocation for sbsmt\n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ for( j = 0 ; j < seqnum ; j++ )
+ for( a0 = 0 ; a0 < 21 ; a0++ )
+ if( ( sbsmt[i][j][a0] = (int * ) calloc( 21 , sizeof( int ) ) ) == NULL) {
+ printf("Problems with memory allocation for sbsmt\n");
+ exit(1);
+ }
+
+ for( i = 0 ; i <seqnum ; i++ )
+ for( j = 0 ; j <seqnum ; j++ )
+ for( a0 = 0 ; a0 <= 20 ; a0++ )
+ for( a1 = 0 ; a1 <= 20 ; a1++ )
+ sbsmt[ i ][ j ][ a0 ][ a1 ] = 0 ;
+
+
+ strcpy( mat_file_name , file_name );
+ strcat( mat_file_name , ".mat" );
+
+ fp_mat = fopen( mat_file_name, "w") ;
+
+
+
+ frag = frg ;
+
+ for( frg_count = 0 ; frg_count < fragno ; frg_count++ ) {
+ if( frag->weight > sf_mat_thr )
+ for( i = 0 ; i < frag->ext ; i++ ) {
+ a0 = amino[ frag->s[0] ][ frag->b[0] + i ] ;
+ a1 = amino[ frag->s[1] ][ frag->b[1] + i ] ;
+ s0 = frag->s[0] ;
+ s1 = frag->s[1] ;
+ sbsmt[ s0 ][ s1 ][ a0 ][ a1 ]++ ;
+ sbsmt[ s1 ][ s0 ][ a1 ][ a0 ]++ ;
+
+ }
+ frag = frag->next ;
+ }
+
+
+ fprintf( fp_mat, "taxanumber: %d ;\n", seqnum) ;
+ fprintf( fp_mat, "description: DIALIGN alignment ;\n" ) ;
+ fprintf( fp_mat, "description: %s;\n", input_line ) ;
+
+
+ for( i = 0 ; i < seqnum ; i++ )
+ fprintf( fp_mat, "taxon: %.3d name: %s ;\n", i + 1 , full_name[i] ) ;
+
+
+ for( s0 = 0 ; s0 < seqnum ; s0++ )
+ for( s1 = s0 + 1 ; s1 < seqnum ; s1++ )
+ for ( a0 = 1 ; a0 <= 20 ; a0++ )
+ for( a1 = 1 ; a1 < 21 ; a1++ ) {
+ fprintf( fp_mat, "pair: %.3d %.3d ", s0 + 1, s1 + 1 );
+ fprintf( fp_mat, " acids: %c%c ", amino_acid[a0] , amino_acid[a1] );
+ fprintf( fp_mat, " number: %d ;\n", sbsmt[ s0 ][ s1 ][ a0 ][ a1 ] );
+ }
+} /* subst_mat */
+
+
+void print_fragments( struct multi_frag *d , FILE *fp_ff2 ) {
+
+ struct multi_frag *fragment ;
+
+ fragment = d;
+ while( fragment != NULL ) {
+ if( fragment->it ){
+ frg_count++ ;
+ fprintf( fp_ff2, "%6d) ", frg_count );
+ fprintf( fp_ff2, "seq: %3d %3d ", fragment->s[0] + 1 , fragment->s[1] + 1 );
+ fprintf( fp_ff2, "beg: %7d %7d ", fragment->b[0] , fragment->b[1] );
+ fprintf( fp_ff2, "len: %3d ", fragment->ext );
+ fprintf( fp_ff2, "wgt: %6.2f ", fragment->weight );
+ fprintf( fp_ff2, "olw: %6.2f ", fragment->ow );
+
+ fprintf( fp_ff2, "it: %d ", fragment->it );
+ if( fragment->sel )
+ fprintf( fp_ff2, "cons " );
+ else
+ fprintf( fp_ff2, "incons " );
+
+ if( ( wgt_type == 3 ) || crick_strand ) {
+ if( fragment->trans )
+ fprintf( fp_ff2, " P-frg" );
+ else
+ fprintf( fp_ff2, " N-frg" );
+ if( fragment->trans )
+ if( crick_strand )
+ if( fragment->cs )
+ fprintf( fp_ff2, " -" );
+ else
+ fprintf( fp_ff2, " +" );
+ }
+
+
+ fprintf( fp_ff2, "\n" );
+ }
+ fragment = fragment->next ;
+ }
+}
+
+
+void weight_print( float **wgt )
+{
+ int i, j , l, s ;
+ FILE *fp;
+
+ fp = fopen("weight_table","w");
+
+
+ fprintf(fp," len1 = %d, len2 = %d\n\n",seqlen[0], seqlen[1] );
+ fprintf(fp," \n %s \n\n", input_line );
+ for( l = 1 ; l <= max_dia ; l++ )
+ for( s = 0 ; s <= l * max_sim_score ; s++ )
+ fprintf(fp," %d %d %7.8f \n", l, s, wgt[l][s] );
+
+ fclose(fp);
+
+} /* weight_print */
+
+
+
+
+
+void ali_arrange( int fragno , struct multi_frag *d, FILE *fp, FILE *fp2, FILE *fp3 , FILE *fp4 , FILE *fp_col_score )
+{
+ int block_no, char_no ;
+ int shift_cond, endlen;
+ int p, pn, i, j, k, l, hv, bc, lc, max_p;
+ int b1, b2, s1, s2, e, dif, sv, lv, add, msf_lines;
+
+ char sim_char;
+ float weak_wgt_type_thr = WEAK_WGT_TYPE_THR ;
+ float strong_wgt_type_thr = STRONG_WGT_TYPE_THR ;
+ float frac_plus, frac_minus, frac_nuc, f_inv ;
+
+ char **endseq;
+ char **hseq;
+ char *clear_seq;
+ float *weight_count;
+ int *plus_count;
+ int *minus_count;
+ int *nuc_count;
+ int *frg_involved;
+ float *plot; /* plot[i] = sum of weights of fragments involved at
+ position i normalizet such that the maximum value */
+
+ char gap_char = '-';
+ char ambi_char = ' ';
+ int *begin, *end, *b_len, *first_pos, pl_int ;
+ int b_size; /* size of fragments */
+ struct multi_frag *fragments, *dia;
+ int **inv_shift;
+ int char_per_line; /* number of residues per line in output file */
+ char aligned;
+ char_per_line = ( ( PAPER_WIDTH - 18 ) / 11) * 10;
+
+ dia = d;
+
+ if( (endseq = (char **) calloc( seqnum , sizeof(char *) )) == NULL)
+ {
+ printf(" problems with memory allocation for `endseq' ! \n \n");
+ exit(1);
+ }
+
+ if( (hseq = (char **) calloc( seqnum , sizeof(char *) )) == NULL)
+ {
+ printf(" problems with memory allocation for `hseq' ! \n \n");
+ exit(1);
+ }
+
+ if( (begin = (int *) calloc( seqnum , sizeof(int) )) == NULL)
+ {
+ printf(" problems with memory allocation for `begin' ! \n \n");
+ exit(1);
+ }
+
+ if( (end = (int *) calloc( seqnum , sizeof(int) )) == NULL)
+ {
+ printf(" problems with memory allocation for `end' ! \n \n");
+ exit(1);
+ }
+
+ if( (b_len = (int *) calloc( seqnum , sizeof(int) )) == NULL)
+ {
+ printf(" problems with memory allocation for `b_len' ! \n \n");
+ exit(1);
+ }
+
+ if( ( first_pos = (int *) calloc( seqnum , sizeof(int) )) == NULL)
+ {
+ printf(" problems with memory allocation for `first_pos' ! \n \n");
+ exit(1);
+ }
+
+ if( (shift = (int **) calloc( seqnum , sizeof(int *) )) == NULL )
+ {
+ printf("not enough memory available for `shift' !!!!\n");
+ fprintf(fp,"not enough memory available for `shift' !\n");
+ exit(1);
+ }
+
+ for(hv=0 ; hv<seqnum ; hv++)
+ if( (shift[hv] = (int *) calloc( (seqlen[hv]+2) , sizeof(int) )) == NULL )
+ {
+ printf("not enough memory available for `shift' !!!!\n");
+ fprintf(fp,"not enough memory available for `shift' !\n");
+ exit(1);
+ }
+
+
+ if( fragno >= 0 )
+ {
+
+ for(hv=0;hv<seqnum;hv++)
+ {
+ begin[hv] = seqlen[hv];
+ end[hv] = 1;
+ }
+
+
+ if( fragno > 0 )
+ if( ( fragments = calloc( fragno , sizeof(struct multi_frag) )) == NULL )
+ {
+ printf("not enough memory available for fragments!\n");
+ fprintf(fp,"not enough memory available for fragments!\n");
+ exit(1);
+ }
+
+ for( hv = 1 ; hv <= fragno ; hv++)
+ {
+ fragments[hv-1] = *dia;
+ dia = dia->next;
+ }
+
+ for( hv = 0 ; hv < fragno ; hv++ )
+ for( j = 0 ; j < 2 ; j++ )
+ {
+ mini( &begin[ fragments[hv].s[j] ] , fragments[hv].b[j] );
+ maxi( &end[ fragments[hv].s[j] ] , fragments[hv].b[j] + fragments[hv].ext );
+ }
+
+ for(hv=0;hv<seqnum;hv++)
+ {
+ begin[hv] = 1;
+ end[hv] = seqlen[hv]+1;
+ }
+
+ b_size = 0;
+
+ for(i=0;i<seqnum;i++)
+ {
+ b_len[i] = end[i] - begin[i];
+ maxi(&b_size,b_len[i]);
+ }
+
+ for(i=0;i<seqnum;i++)
+ for(hv=0;hv<b_len[i];hv++)
+ shift[i][ begin[i]+hv ] = hv;
+
+ shift_cond = 1;
+
+ while(shift_cond)
+ {
+ shift_cond = 0;
+
+ for( hv = 0 ; hv < fragno ; hv++ )
+ for(j=0;j<2;j++)
+ {
+ k = (j+1)%2;
+ s1 = fragments[hv].s[j];
+ s2 = fragments[hv].s[k];
+ b1 = fragments[hv].b[j];
+ b2 = fragments[hv].b[k];
+ e = fragments[hv].ext;
+
+ for(l = e-1;l>=0;l--)
+ {
+ dif = shift[s2][b2+l] - shift[s1][b1+l];
+ if (dif > 0 )
+ {
+ new_shift(s1,b1+l,dif);
+ shift_cond = 1;
+ }
+ }
+ }
+ } /* while (shift_cond) */
+
+
+
+
+
+
+
+ endlen = 0;
+
+ for(hv=0;hv<seqnum;hv++)
+ maxi(&endlen,shift[hv][ end[hv]-1 ] + 1);
+
+ for(hv=0;hv<seqnum;hv++)
+ if( (endseq[hv] = calloc(endlen, sizeof(char) )) == NULL )
+ {
+ printf(" not enough memory available for printing results!\n");
+ fprintf(fp," not enough memory available");
+ fprintf(fp," for printing results!\n");
+ exit(1);
+ }
+
+
+ if( (inv_shift = (int **) calloc( seqnum , sizeof(int *) )) == NULL )
+ {
+ printf("not enough memory available for `inv_shift' !!!!\n");
+ fprintf(fp,"not enough memory available for `inv_shift' !\n");
+ exit(1);
+ }
+
+ for(hv=0 ; hv<seqnum ; hv++)
+ if( (inv_shift[hv] = (int *) calloc( (endlen+2) , sizeof(int) ))
+ == NULL )
+ {
+ printf("not enough memory available for `inv_shift' !!!!\n");
+ fprintf(fp,"not enough memory available for `inv_shift' !\n");
+ exit(1);
+ }
+
+ if( (clear_seq = (char *) calloc( (endlen+1) , sizeof(char) )) == NULL)
+ {
+ printf(" problems with memory allocation for `clear_seq' ! \n \n");
+ exit(1);
+ }
+
+ if( (weight_count =
+ (float *) calloc( ( endlen + 2 ) , sizeof(float) )) == NULL)
+ {
+ printf(" problems with memory allocation for `weight_count' !\n \n");
+ exit(1);
+ }
+
+ if( (plot = (float *) calloc( ( endlen + 2 ) , sizeof(float) )) == NULL)
+ {
+ printf(" problems with memory allocation for `plot' ! \n \n");
+ exit(1);
+ }
+
+ if( (plus_count =
+ (int *) calloc( ( endlen + 2 ) , sizeof( int ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `plus_count' !\n \n");
+ exit(1);
+ }
+
+ if( (minus_count =
+ (int *) calloc( ( endlen + 2 ) , sizeof( int ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `minus_count' !\n \n");
+ exit(1);
+ }
+
+ if( (nuc_count =
+ (int *) calloc( ( endlen + 2 ) , sizeof( int ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `nuc_count' !\n \n");
+ exit(1);
+ }
+
+ if( (frg_involved =
+ (int *) calloc( ( endlen + 2 ) , sizeof( int ) )) == NULL)
+ {
+ printf(" problems with memory allocation for `frg_involved ' !\n \n");
+ exit(1);
+ }
+
+
+
+ for(hv=0 ; hv<seqnum ; hv++)
+ for(p=1 ; p <= seqlen[hv] ; p++)
+ inv_shift[hv][ shift[hv][p] ] = p;
+
+ for(hv=0;hv<seqnum;hv++)
+ if( (hseq[hv] = calloc( (maxlen+1), sizeof(char) )) == NULL )
+ {
+ printf("not enough memory available for printing results! \n");
+ fprintf(fp,"not enough memory available");
+ fprintf(fp," for printing results! \n");
+ exit(1);
+ }
+/*
+printf("endlen = %d \n\n", endlen);
+*/
+
+ for(hv=0;hv<seqnum;hv++)
+ for(i=0;i<endlen;i++)
+ endseq[hv][i] = gap_char;
+
+ for(hv=0;hv<seqnum;hv++)
+ for(i=begin[hv];i<end[hv];i++)
+ hseq[hv][i] = tolower(seq[hv][i]);
+
+ for( hv = 0 ; hv < fragno ; hv++ )
+ for(k=0;k<2;k++)
+ for(i = fragments[hv].b[k] ; i < fragments[hv].b[k] + fragments[hv].ext ; i++)
+ hseq[ fragments[hv].s[k] ][i] = seq[ fragments[hv].s[k] ][i];
+
+ for(hv=0;hv<seqnum;hv++)
+ for(i = begin[hv] ; i < end[hv] ; i++)
+ endseq[hv][ shift[hv][i] ] = hseq[hv][i];
+
+ for(i=0;i<endlen;i++)
+ clear_seq[i] = ' ';
+
+
+
+
+
+
+ for(p=0;p<endlen;p++)
+ {
+ s1 = 0;
+ while(
+ ( endseq[s1][p] == tolower( endseq[s1][p] ) )
+ && (s1 < (seqnum - 1) ) /* no capital letter */
+ )
+ s1++;
+
+ if(s1 < (seqnum - 1) )
+ {
+ for(s2 = s1+1 ; s2 < seqnum ; s2++)
+ {
+ if( endseq[s2][p] != tolower( endseq[s2][p] ) )
+ /* endseq[s2][p] capital letter */
+ {
+ aligned = alignedPositions(clos,s1,inv_shift[s1][p],s2,
+ succFrontier(clos,s1,inv_shift[s1][p],s2));
+
+ if (!aligned)
+ /* i.e.endseq[s1][p] not aligned with end seq[s2][p]*/
+ clear_seq[p] =ambi_char;
+ }
+ }
+ }
+ }
+
+
+ if( mask )
+ for(sv = 0 ; sv < seqnum ; sv++)
+ for(hv = 0 ; hv < endlen ; hv++ )
+ if( endseq[sv][hv] != gap_char )
+ if( endseq[sv][hv] == tolower( endseq[sv][hv] ) )
+ endseq[sv][hv] = '*' ;
+
+
+ if( col_score ){
+ fprintf(fp_col_score , "# 1 %d \n" , endlen );
+ fprintf(fp_col_score,"# %s \n", upg_str);
+ }
+
+ plot_calc( num_all_it_dia , endlen , weight_count , plot , all_it_dia , fp_col_score );
+
+ wgt_type_count( num_all_it_dia , endlen , plus_count, minus_count, nuc_count , frg_involved, all_it_dia );
+
+
+ lc = (endlen-1)/char_per_line;
+ for(hv=0;hv<seqnum;hv++)
+ first_pos[hv] = begin[hv] ;
+
+
+ for( k = 0 ; k <= lc ; k++ )
+ {
+ for( hv = 0 ; hv < seqnum ; hv++ )
+ {
+ fprintf(fp, "%s", seq_name[hv] );
+
+ fprintf(fp,"%8d ", first_pos[hv]);
+
+
+ for(i=0;i<mini2(char_per_line,endlen-k*char_per_line);i++)
+ {
+ if(!(i%10))fprintf(fp, " ");
+ fprintf(fp, "%c",endseq[hv][k*char_per_line+i]);
+ if(endseq[hv][k*char_per_line+i] != gap_char)
+ first_pos[hv]++;
+ }
+ fprintf(fp, " \n");
+ }
+
+ fprintf(fp," ");
+ for( i = 0 ; i < mini2( char_per_line , endlen-k*char_per_line )
+ ; i++ )
+ {
+ if(!(i%10))fprintf(fp, " ");
+ fprintf(fp, "%c",clear_seq[k*char_per_line+i]);
+ }
+
+ if( plot_num )
+ fprintf(fp, " \n");
+
+
+
+ if( quali_num == 0 )
+ for( pn = 0 ; pn < plot_num ; pn ++ )
+ {
+ fprintf(fp," ");
+ for(i=0;i<mini2(char_per_line,endlen-k*char_per_line);i++)
+ {
+ if( !(i%10) )fprintf(fp, " ");
+ if( plot[ k*char_per_line + i ] > pn )
+ fprintf(fp, "*");
+ else
+ fprintf(fp, " ");
+ }
+ fprintf(fp, " \n");
+
+ if( plot_num == 1 )
+ fprintf(fp, " \n");
+ }
+
+
+ if( quali_num ) {
+ for( i = 0 ; i < SEQ_NAME_LEN ; i++ ) {
+ fprintf(fp," ");
+ }
+
+ fprintf(fp," ");
+ for( i = 0 ; i < mini2( char_per_line , endlen-k*char_per_line ) ; i++ ) {
+ if( !(i%10) )fprintf(fp, " ");
+ pl_int = 9 * plot[ k * char_per_line + i ] / plot_num ;
+ fprintf(fp, "%d", pl_int );
+ }
+ fprintf(fp, " \n");
+ }
+
+ /***********************************************************************
+
+ fprintf(fp, " \n");
+ if( wgt_type > 1 ) {
+ for( i = 0 ; i < SEQ_NAME_LEN ; i++ ) {
+ fprintf(fp," ");
+ }
+
+ fprintf(fp," plus ");
+ for( i = 0 ; i < mini2( char_per_line , endlen-k*char_per_line ) ; i++ ) {
+ if( !(i%10) )fprintf(fp, " ");
+ fprintf(fp, "%d", plus_count[ k * char_per_line + i ] );
+ }
+ fprintf(fp, " \n");
+ }
+
+ if( wgt_type > 1 ) {
+ for( i = 0 ; i < SEQ_NAME_LEN ; i++ ) {
+ fprintf(fp," ");
+ }
+
+ fprintf(fp," minus ");
+ for( i = 0 ; i < mini2( char_per_line , endlen-k*char_per_line ) ; i++ ) {
+ if( !(i%10) )fprintf(fp, " ");
+ fprintf(fp, "%d", minus_count[ k * char_per_line + i ] );
+ }
+ fprintf(fp, " \n");
+ }
+
+ if( wgt_type > 1 ) {
+ for( i = 0 ; i < SEQ_NAME_LEN ; i++ ) {
+ fprintf(fp," ");
+ }
+
+ fprintf(fp," nuc ");
+ for( i = 0 ; i < mini2( char_per_line , endlen-k*char_per_line ) ; i++ ) {
+ if( !(i%10) )fprintf(fp, " ");
+ fprintf(fp, "%d", nuc_count[ k * char_per_line + i ] );
+ }
+ fprintf(fp, " \n");
+ fprintf(fp, " \n");
+ }
+
+ ************************************************************************/
+
+ if( wgt_type_plot )
+ if( wgt_type == 3 ) {
+
+ fprintf(fp,"sim. level");
+
+ for( i = 0 ; i < SEQ_NAME_LEN ; i++ ) {
+ fprintf(fp," ");
+ }
+
+ for( i = 0 ; i < mini2( char_per_line , endlen-k*char_per_line ) ; i++ ) {
+ if( !(i%10) )fprintf(fp, " ");
+ sim_char = '.' ;
+
+ if( frg_involved[ k * char_per_line + i ] ) {
+
+ f_inv = frg_involved[ k * char_per_line + i] ;
+ frac_plus = plus_count[ k * char_per_line + i ] / f_inv ;
+ frac_minus = minus_count[ k * char_per_line + i ] / f_inv ;
+ frac_nuc = nuc_count[ k * char_per_line + i ] / f_inv ;
+
+ if ( frac_plus > weak_wgt_type_thr )
+ if( crick_strand )
+ sim_char = 'f' ;
+ else
+ sim_char = 'p' ;
+ if ( frac_plus > strong_wgt_type_thr )
+ if( crick_strand )
+ sim_char = 'F' ;
+ else
+ sim_char = 'P' ;
+ if ( frac_minus > weak_wgt_type_thr )
+ sim_char = 'r' ;
+ if ( frac_minus > strong_wgt_type_thr )
+ sim_char = 'R' ;
+
+ if ( frac_nuc > weak_wgt_type_thr )
+ sim_char = 'n' ;
+ if ( frac_nuc > strong_wgt_type_thr )
+ sim_char = 'N' ;
+
+ }
+ fprintf(fp, "%c", sim_char );
+ }
+ fprintf(fp, " \n");
+ fprintf(fp, " \n");
+ }
+
+
+
+
+
+ fprintf(fp, " \n");
+
+ } /* for(k=0;k<=lc;k++) */
+
+
+ if( fasta_file )
+ {
+ for(sv = 0 ; sv < seqnum ; sv++ )
+ {
+ fprintf(fp2,">%s", full_name[sv]);
+ for(i = 0 ; i < endlen ; i++)
+ {
+ if( ! ( i % 50 ) )
+ fprintf(fp2,"\n");
+ fprintf(fp2,"%c", endseq[sv][i]);
+ }
+
+ fprintf(fp2,"\n ");
+ if( sv < ( seqnum - 1 ) )
+ fprintf(fp2,"\n");
+ }
+ }
+
+
+ if( cw_file )
+ {
+ block_no = 0;
+
+ fprintf(fp4,"DIALIGN 2.1 multiple sequence alignment \n\n");
+ fprintf(fp4,"// \n\n\n");
+
+ while( block_no * 60 < endlen )
+ {
+ char_no = mini2( 60 , ( endlen - block_no * 60 ) ) ;
+ for( sv = 0 ; sv < seqnum ; sv++ )
+ {
+ fprintf(fp4,"%s ", seq_name[sv] );
+ for( i = 0 ; i < char_no ; i++)
+ fprintf(fp4,"%c", endseq[sv][ block_no * 60 + i ] );
+ fprintf(fp4,"\n");
+ }
+ fprintf(fp4,"\n\n");
+ block_no++;
+ }
+
+
+ }
+
+
+ if( msf_file )
+ {
+ msf_lines = endlen / 50;
+ if(endlen % 50)
+ msf_lines = msf_lines + 1;
+
+
+ fprintf(fp3,"DIALIGN 2\n\n\n");
+ fprintf(fp3," MSF: %d \n\n", endlen);
+
+ for( sv = 0 ; sv < seqnum ; sv++ )
+ fprintf(fp3," Name: %s Len: %d \n", seq_name[sv], seqlen[sv] );
+ fprintf(fp3,"\n// \n\n");
+
+ for(lv = 0 ; lv < msf_lines ; lv++ )
+ {
+ add = lv * 50;
+ max_p = mini2( endlen - add , 50 );
+
+ for( sv = 0 ; sv < seqnum ; sv++ )
+ {
+ fprintf(fp3, "%s", seq_name[sv] );
+ for(i=0 ; i < 4 ; i++ )
+ fprintf(fp3, " ");
+
+ for(i = 0 ; i < max_p ; i++)
+ {
+ if( !(i%10) )fprintf(fp3, " ");
+ if( endseq[sv][add + i] == '-' )
+ fprintf(fp3,".");
+ else
+ fprintf(fp3,"%c", endseq[sv][add + i]);
+ }
+ fprintf(fp3,"\n");
+ }
+ fprintf(fp3,"\n\n");
+ }
+
+ }
+
+
+ if( ( seqnum > 2 ) && ( ref_seq == 0 ) )
+ {
+ fprintf(fp,"\n \n \n Sequence tree:\n");
+ fprintf(fp," ==============\n\n");
+
+ if( ! strcmp( clust_sim , "av" ) )
+ fprintf(fp,"Tree constructed using UPGMA");
+ fprintf(fp,"based on DIALIGN fragment weight scores");
+
+ if( ! strcmp( clust_sim , "max" ) )
+ fprintf(fp,"Tree constructed using maximum linkage clustering");
+
+
+ if( ! strcmp( clust_sim , "min" ) )
+ fprintf(fp,"Tree constructed using minimum linkage clustering");
+
+
+ fprintf(fp,"\n \n%s", upg_str);
+ }
+
+ fprintf(fp,"\n \n \n");
+
+ for(hv=0;hv<seqnum;hv++)
+ free(hseq[hv]);
+
+ for(hv=0;hv<seqnum;hv++)
+ free(endseq[hv]);
+
+ if( fragno > 0 )
+ free( fragments );
+
+ free(plot);
+
+ free(weight_count);
+
+
+ } /* for(bc=0;bc<1;bc++) */
+
+
+ for(hv=0;hv<seqnum;hv++)
+ free(shift[hv]);
+
+
+
+
+
+
+} /* ali_arrange */
+
+
+void para_print( char *s_f, FILE *fpi )
+ {
+ int p_count = 1;
+ int hv, i ;
+
+
+ {
+
+
+
+ if( cd_gobics ) {
+ fprintf(fpi," \n CHAOS / DIALIGN \n");
+ fprintf(fpi," ***************\n \n");
+
+ if( BETA )
+ fprintf(fpi," beta version\n\n");
+
+ fprintf(fpi," Program code written by \n");
+ fprintf(fpi," Burkhard Morgenstern, Said Abdeddaim and Michael Brudno \n\n");
+ fprintf(fpi," e-mail contact: ");
+ fprintf(fpi,"bmorgen (at) gwdg (dot) de \n \n");
+ fprintf(fpi," Published research assisted");
+ fprintf(fpi," by CHAOS / DIALIGN should cite: \n \n");
+ fprintf(fpi," Michael Brudno et al.");
+ fprintf(fpi," (2003)\n");
+ fprintf(fpi," \"Fast and sensitive multiple alignment");
+ fprintf(fpi," of large genomic sequences\" \n");
+ fprintf(fpi," BMC Bioinformatics 4:66 \n");
+ fprintf(fpi," http://www.biomedcentral.com/1471-2105/4/66 \n\n");
+ }
+ else {
+ fprintf(fpi," \n DIALIGN 2.2.1 \n");
+ fprintf(fpi," *************\n \n");
+
+ if( BETA )
+ fprintf(fpi," beta version\n\n");
+
+ fprintf(fpi," Program code written by Burkhard");
+ fprintf(fpi," Morgenstern and Said Abdeddaim \n");
+ fprintf(fpi," e-mail contact: ");
+ fprintf(fpi,"bmorgen (at) gwdg (dot) de \n \n");
+ fprintf(fpi," Published research assisted");
+ fprintf(fpi," by DIALIGN 2 should cite: \n \n");
+ fprintf(fpi," Burkhard Morgenstern");
+ fprintf(fpi," (1999).\n");
+
+ fprintf(fpi," DIALIGN 2: improvement of the");
+ fprintf(fpi," segment-to-segment\n approach");
+ fprintf(fpi," to multiple sequence alignment.\n");
+ fprintf(fpi," Bioinformatics 15,");
+ fprintf(fpi," 211 - 218. \n\n");
+ }
+
+ fprintf(fpi," For more information, please visit");
+ fprintf(fpi," the DIALIGN home page at \n\n ");
+ fprintf(fpi,"http://bibiserv.techfak.uni-bielefeld.de/dialign/");
+ fprintf(fpi," \n \n");
+
+ fprintf(fpi," ************************************************************\n \n");
+ }
+
+/*
+
+ fprintf(fpi," Options:\n");
+ fprintf(fpi," ========\n \n");
+
+
+ if( wgt_type )
+ fprintf(fpi," %2d) nucleic acid sequences aligned \n", p_count++);
+ else
+ fprintf(fpi," %2d) protein sequences aligned \n", p_count++);
+
+ if( wgt_type == 2 )
+ {
+ fprintf(fpi," %2d) translation",p_count++);
+ fprintf(fpi," of nucleotide fragments");
+ fprintf(fpi," into peptide fragments\n");
+ }
+
+ if( wgt_type == 1 )
+ {
+ fprintf(fpi," %2d) no translation of",p_count++);
+ fprintf(fpi," of nucleotide fragments");
+ fprintf(fpi," into peptide fragments\n");
+ }
+
+ if( wgt_type == 3 )
+ {
+ fprintf(fpi," %2d) mixed alignment consisting", p_count++);
+ fprintf(fpi," of P-fragments and N-fragments \n");
+ }
+
+
+ if( seqnum > 2 )
+ if( overlap_weights )
+ fprintf(fpi," %2d) overlap weights used \n", p_count++);
+ else
+ fprintf(fpi," %2d) overlap weights NOT used \n", p_count++);
+
+ if( threshold )
+ {
+ fprintf(fpi," %2d) threshold T =", p_count++);
+ fprintf(fpi," %2.2f\n",threshold);
+ }
+
+ if( mask )
+ {
+ fprintf(fpi," %2d) non-aligned residues masked", p_count++);
+ fprintf(fpi," by `*' \n", p_count++);
+ }
+
+
+ if( lgs_option)
+ {
+ fprintf(fpi," %2d) option for long genomic ", p_count++);
+ fprintf(fpi,"sequences used \n");
+ }
+
+ if( crick_strand )
+ {
+ fprintf(fpi," %2d) translation of Watson and Crick strand \n", p_count++);
+ }
+
+
+
+ if( lmax != MAX_DIA )
+ {
+ fprintf(fpi," %2d) maximum length of fragments = %d", p_count++ , lmax );
+ if( wgt_type == 0)
+ fprintf(fpi," residues ");
+ if( wgt_type == 1)
+ fprintf(fpi," residues ");
+ if( wgt_type == 0)
+ fprintf(fpi," codons ");
+ if( wgt_type == 0)
+ fprintf(fpi," codons / residues ");
+ fprintf(fpi," \n");
+ }
+
+
+
+ if( fasta_file )
+ fprintf(fpi," %2d) separate file in FASTA format \n", p_count++);
+
+ if( msf_file )
+ fprintf(fpi," %2d) separate file in msf format \n", p_count++);
+
+ if( cw_file )
+ fprintf(fpi," %2d) separate file in clustal format \n", p_count++);
+
+ if( plot_num )
+ {
+ fprintf(fpi," %2d) %d \"*\" characters", p_count++, plot_num);
+ fprintf(fpi," for regions of maximum similarity\n");
+ }
+*/
+
+ if( online ) {
+ fprintf(fpi,"\n\n The following options have been used: \n\n") ;
+ fprintf(fpi," - sequences are");
+ if( wgt_type == 0 )
+ fprintf(fpi," protein sequences \n");
+ if( wgt_type == 1 )
+ fprintf(fpi," nucleic acid sequences without translation option\n");
+ if( wgt_type == 2 )
+ fprintf(fpi," nucleic acid sequences with translation option\n");
+ if( speed_optimized )
+ fprintf(fpi," - speed optimized,");
+ fprintf(fpi," see user guide for details \n");
+ if( anchors )
+ fprintf(fpi," - anchor points used\n" );
+ fprintf(fpi,"\n");
+ }
+ else
+ fprintf(fpi,"\n\n %s \n\n", input_line );
+
+ fprintf(fpi," \n");
+
+ fprintf(fpi," Aligned sequences: length:\n");
+ fprintf(fpi," ================== =======\n \n");
+
+ for(hv=0;hv<seqnum;hv++)
+ {
+ fprintf(fpi, " %3d) ", hv + 1 );
+ fprintf(fpi, "%s", seq_name[hv] );
+ fprintf(fpi, " %9d\n",seqlen[hv]);
+ }
+
+
+
+ fprintf(fpi, "\n Average seq. length:" );
+ fprintf(fpi, " %9.1f \n", av_len );
+
+ fprintf(fpi,"\n\n Please note that only upper-case letters are");
+ fprintf(fpi," considered to be aligned. \n");
+
+ fprintf(fpi,"\n\n Alignment (DIALIGN format):\n");
+ fprintf(fpi," ===========================\n \n");
+
+ } /* para_print */
+
Added: trunk/packages/dialign/branches/upstream/current/src/para.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/para.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/para.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,455 @@
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+
+int lgs_option = 0 ;
+float sf_mat_thr = 0 ;
+
+extern int col_score , regex_len , wgt_type_plot, cd_gobics, motifs ;
+extern int bubblesort , nas , ref_seq, speed_optimized , online, time_stamps ;
+extern int thr_sim_score, lmax, redundant, seqnum, strict, sf_mat;
+extern int quali_num , anchors , mask, textual_alignment ;
+extern int pa_only , dna_speed , frg_mult_file , frg_mult_file_v ;
+extern int pr_av_nd, pr_av_max_nd, wgt_print , wgt_print_x ;
+extern int standard_out, self_comparison;
+extern int default_name;
+extern char mot_regex[ MAX_REGEX ] , output_name[ NAME_LEN ], clust_sim[ NAME_LEN ];
+extern int afc_file, afc_filex , frag_file;
+extern int dia_pa_file, iter_cond_prob , fasta_file, cw_file;
+extern int overlap_weights, ow_force, long_output ;
+extern int msf_file, wgt_type, print_status ;
+extern int plot_num , break1, break2 ;
+extern float threshold , mot_factor , mot_offset_factor ;
+extern int num_test( char *cp );
+extern short crick_strand, exclude_frg , max_itnum ;
+
+extern void regex_format_complain() ;
+
+
+void para_read( int num , char ** arg )
+ {
+
+ int an = 1;
+
+
+ while( an < num - 1 )
+ {
+
+ if(
+ strcmp( arg[an] , "-afc") && /* create file containing
+ ALL fragments considered
+ for alignment */
+ strcmp( arg[an] , "-afc_v") && /* like -afc with fragments
+ explicitly printed */
+ strcmp( arg[an] , "-b1") && /* break */
+ strcmp( arg[an] , "-b2") && /* break */
+ strcmp( arg[an] , "-bs") && /* bubble sort */
+ strcmp( arg[an] , "-csc") && /* column score output */
+ strcmp( arg[an] , "-cs") && /* crick strand */
+ strcmp( arg[an] , "-cw") && /* additional output file
+ in clustalw format */
+ strcmp( arg[an] , "-d1w") && /* old weight fkt */
+
+ strcmp( arg[an] , "-ds") &&
+ strcmp( arg[an] , "-fa") && /* separate file with
+ alignment in fasta format */
+ strcmp( arg[an] , "-ff") && /* fragment file */
+ strcmp( arg[an] , "-fn") && /* name of output file */
+ strcmp( arg[an] , "-fop") && /* create file containing
+ fragments selected for
+ optimal pairwise alignment */
+ strcmp( arg[an] , "-fsm") && /* create file containing
+ consistent fragments in
+ multiple alignment (in
+ format needed for -xfr ) */
+ strcmp( arg[an] , "-fsmv") && /* same as -fsm but verbose */
+ strcmp( arg[an] , "-cd_gobics") && /* chaos + dialign @ gobics */
+ strcmp( arg[an] , "-lgs_t") && /* genomic sequences, transl. */
+ strcmp( arg[an] , "-istep") && /* max iteration steps */
+ strcmp( arg[an] , "-it") && /* iteration */
+ strcmp( arg[an] , "-iw") && /* ind. weights */
+ strcmp( arg[an] , "-lgs") && /* genomic sequences */
+ strcmp( arg[an] , "-lgsx") && /* genomic sequences, accurate + textual alignment */
+ strcmp( arg[an] , "-lmax") && /* max. length of diag. */
+ strcmp( arg[an] , "-lo") && /* long output */
+ strcmp( arg[an] , "-ma") && /* mixed weights */
+ strcmp( arg[an] , "-anc") && /* anchor regions */
+ strcmp( arg[an] , "-mask") &&
+ strcmp( arg[an] , "-mat") && /* calc. subst. freq. matrix */
+ strcmp( arg[an] , "-mat_thr") && /* thr for sbst. fr. mat. */
+ strcmp( arg[an] , "-max_link") && /* max. linkage clustering */
+ strcmp( arg[an] , "-min_link") && /* min. linkage clustering */
+ strcmp( arg[an] , "-mot") && /* motifs considered */
+ strcmp( arg[an] , "-msf") && /* separate file with
+ alignment in msf format */
+ strcmp( arg[an] , "-n") && /* DNA/RNA sequences */
+ strcmp( arg[an] , "-nas") && /* no anchor sorting */
+ strcmp( arg[an] , "-nt") && /* DNA/RNA sequences with
+ translation option */
+ strcmp( arg[an] , "-nta") && /* no textual alignment */
+ strcmp( arg[an] , "-o") && /* optimized */
+ strcmp( arg[an] , "-online") && /* online */
+ strcmp( arg[an] , "-ow") && /* overlap weights */
+ strcmp( arg[an] , "-pamnd") && /* print av. max. number of frg. */
+ strcmp( arg[an] , "-pand") && /* print av. number of diag. */
+ strcmp( arg[an] , "-pao") && /* pairw. alignments only */
+ strcmp( arg[an] , "-ref_seq") && /* seq_2, ... , seq_n
+ aligned to seq_1 */
+ strcmp( arg[an] , "-stars")&& /* maximum number of stars under
+ alignment indicating relative similarity*/
+ strcmp( arg[an] , "-pst") && /* print status */
+ strcmp( arg[an] , "-sc") && /* self comparison */
+ strcmp( arg[an] , "-smin") &&
+ strcmp( arg[an] , "-stdo") && /* standard output */
+ strcmp( arg[an] , "-ta") && /* textual alignment*/
+ strcmp( arg[an] , "-thr") && /* threshold */
+ strcmp( arg[an] , "-ts") && /* time stamps */
+ strcmp( arg[an] , "-wgtpr") && /* weight print */
+ strcmp( arg[an] , "-wgtprx") && /* weight print */
+ strcmp( arg[an] , "-wtp") && /* weight type plot */
+ strcmp( arg[an] , "-xfr") /* excluded fragments */
+
+ )
+ {
+ printf("\n \n Arguments in command line make no sense! \n \n");
+ printf("\n Unknown option %s \n \n \n \n", arg[an] );
+ exit(1);
+ }
+
+ if( !strcmp( arg[an] , "-afc") )
+ afc_file = 1;
+
+ if( !strcmp( arg[an] , "-afc_v") ) {
+ afc_file = 1;
+ afc_filex = 1 ;
+ }
+
+ if( !strcmp( arg[an] , "-b1") )
+ break1 = 1;
+
+ if( !strcmp( arg[an] , "-b2") )
+ break2 = 1;
+
+ if( !strcmp( arg[an] , "-bs") )
+ bubblesort = 1;
+
+ if( !strcmp( arg[an] , "-csc") )
+ col_score = 1;
+
+ if( !strcmp( arg[an] , "-cd_gobics") )
+ cd_gobics = 1;
+
+ if( !strcmp( arg[an] , "-cs") )
+ crick_strand = 1;
+
+ if( !strcmp( arg[an] , "-cw") )
+ cw_file = 1;
+
+ if( !strcmp( arg[an] , "-ds") )
+ dna_speed = 1 ;
+
+ if( !strcmp( arg[an] , "-fa") )
+ fasta_file = 1;
+
+ if( !strcmp( arg[an] , "-ff") )
+ frag_file = 1;
+
+ if( !strcmp( arg[an] , "-fop") )
+ dia_pa_file = 1;
+
+ if( !strcmp( arg[an] , "-fsm") )
+ frg_mult_file = 1;
+
+ if( !strcmp( arg[an] , "-fsmv") ) {
+ frg_mult_file = 1;
+ frg_mult_file_v = 1;
+ }
+
+ if( !strcmp( arg[an] , "-it") )
+ iter_cond_prob = 1;
+
+ if( !strcmp( arg[an] , "-iw") )
+ overlap_weights = 0;
+
+ if( !strcmp( arg[an] , "-lgs") ) {
+ wgt_type = 3 ;
+/* iter_cond_prob = 1 ;
+*/
+ threshold = 2.0 ;
+ lmax = 30 ;
+ thr_sim_score = 8 ;
+ strict = 1 ;
+ textual_alignment = 0 ;
+ /* dia_pa_file = 1; */
+ frag_file = 1 ;
+ dna_speed = 1 ;
+ crick_strand = 1 ;
+ lgs_option = 1 ;
+ print_status = 1 ;
+ }
+
+ if( !strcmp( arg[an] , "-lgs_t") ) {
+ wgt_type = 2 ;
+ iter_cond_prob = 1 ;
+ threshold = 0.0 ;
+ lmax = 30 ;
+ thr_sim_score = 8 ;
+ strict = 1 ;
+ textual_alignment = 0 ;
+ dia_pa_file = 1;
+ frag_file = 1 ;
+ dna_speed = 1 ;
+ print_status = 1 ;
+ }
+
+ if( !strcmp( arg[an] , "-lgsx") ) {
+ wgt_type = 3 ;
+ iter_cond_prob = 1 ;
+ strict = 1 ;
+ frag_file = 1 ;
+ crick_strand = 1 ;
+ lgs_option = 1 ;
+ print_status = 1 ;
+ }
+
+ if( !strcmp( arg[an] , "-lo") )
+ long_output = 1;
+
+ if( !strcmp( arg[an] , "-ma") ) {
+ wgt_type = 3;
+ }
+
+ if( !strcmp( arg[an] , "-anc") )
+ anchors = 1;
+
+ if( !strcmp( arg[an] , "-mask") )
+ mask = 1;
+
+ if( !strcmp( arg[an] , "-max_link") )
+ strcpy (clust_sim , "max" );
+
+ if( !strcmp( arg[an] , "-min_link") )
+ strcpy (clust_sim , "min" );
+
+ if( !strcmp( arg[an] , "-msf") )
+ msf_file = 1;
+
+ if( !strcmp( arg[an] , "-n") ) {
+ wgt_type = 1;
+ }
+
+ if( !strcmp( arg[an] , "-nas") ) {
+ nas = 1;
+ }
+
+ if( !strcmp( arg[an] , "-nt") )
+ wgt_type = 2;
+
+ if( !strcmp( arg[an] , "-nta") )
+ textual_alignment = 0;
+
+ if( !strcmp( arg[an] , "-o") )
+ {
+ speed_optimized = 1 ;
+ threshold = 0.5 ;
+ lmax = 30 ;
+ thr_sim_score = 8 ;
+ }
+
+ if( !strcmp( arg[an] , "-ow") )
+ ow_force = 1;
+
+ if( !strcmp( arg[an] , "-pao") )
+ pa_only = 1;
+
+ if( !strcmp( arg[an] , "-pamnd") )
+ pr_av_max_nd = 1;
+
+ if( !strcmp( arg[an] , "-pand") )
+ pr_av_nd = 1;
+
+ if( !strcmp( arg[an] , "-pst") )
+ print_status = 1;
+
+ if( !strcmp( arg[an] , "-red") )
+ redundant = 1;
+
+ if( !strcmp( arg[an] , "-mat") )
+ sf_mat = 1;
+
+ if( !strcmp( arg[an] , "-online") )
+ online = 1;
+
+ if( !strcmp( arg[an] , "-ref_seq") )
+ ref_seq = 1;
+
+ if( !strcmp( arg[an] , "-sc") )
+ self_comparison = 1;
+
+ if( !strcmp( arg[an] , "-stdo") )
+ standard_out = 1;
+
+ if( !strcmp( arg[an] , "-strict") )
+ strict = 1;
+
+ if( !strcmp( arg[an] , "-ta") )
+ textual_alignment = 1 ;
+
+ if( !strcmp( arg[an] , "-ts") )
+ time_stamps = 1 ;
+
+ if( !strcmp( arg[an] , "-wgtpr") )
+ wgt_print = 1 ;
+
+ if( !strcmp( arg[an] , "-wgtprx") )
+ wgt_print_x = 1 ;
+
+ if( !strcmp( arg[an] , "-wtp") )
+ wgt_type_plot = 1 ;
+
+ if( !strcmp( arg[an] , "-xfr") )
+ exclude_frg = 1 ;
+
+
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-fn") )
+ if( an + 2 < num )
+ {
+ strcpy( output_name , arg[++an] );
+ default_name = 0;
+ }
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (Name of output file not properly specified) \n \n");
+ exit(1);
+ }
+
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-istep") )
+ if( ( an + 2 < num ) && num_test( arg[an + 1] ) )
+ max_itnum = atoi( arg[++an] );
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (max_itnum not properly specified) \n \n");
+ exit(1);
+ }
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-lmax") )
+ if( ( an + 2 < num ) && num_test( arg[an + 1] ) )
+ lmax = atoi( arg[++an] );
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (lmax not properly specified) \n \n");
+ exit(1);
+ }
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-stars") )
+ if( ( an + 2 < num ) && num_test( arg[an + 1] ) ) {
+ plot_num = atoi( arg[++an] );
+ quali_num = 0 ;
+ }
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (Number of \"*\" characters not properly specified) \n \n");
+ exit(1);
+ }
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-smin") )
+ if( (an + 2 < num) && num_test( arg[an + 1] ) )
+ thr_sim_score = atoi( arg[++an] );
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (Speed not properly specified) \n \n");
+ exit(1);
+ }
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-thr") )
+ if( (an + 2 < num) && num_test( arg[an + 1] ) )
+ {
+ threshold = atof( arg[++an] );
+ }
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (Threshod not properly specified) \n \n");
+ exit(1);
+ }
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-mat_thr") )
+ if( (an + 2 < num) && num_test( arg[an + 1] ) )
+ {
+ sf_mat_thr = atof( arg[++an] );
+ }
+ else
+ {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (subst. mat. threshod not properly specified) \n \n");
+ exit(1);
+ }
+
+
+ /********************************************************************/
+
+
+ if( !strcmp( arg[an] , "-mot") )
+ if( ( an + 4 < num ) &&
+ num_test( arg[ an + 2 ] ) &&
+ num_test( arg[ an + 3 ] )
+ )
+ {
+ motifs = 1 ;
+ strcpy( mot_regex , arg[++an] );
+ mot_factor = atof( arg[++an] ) ;
+ mot_offset_factor = atof( arg[++an] ) ;
+ regex_len = strlen( mot_regex ) ;
+ }
+ else
+ regex_format_complain();
+
+ /********************************************************************/
+
+ an++;
+ }
+ }
+
+
+
+
Added: trunk/packages/dialign/branches/upstream/current/src/pratique.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/pratique.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/pratique.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,173 @@
+#include <stdio.h>
+#include <ctype.h>
+#include "pratique.h"
+
+/* ------------------------------------------------------------*/
+
+void erreur(char *message)
+{
+printf("%s\n", message);
+exit(1);
+}
+
+/* ------------------------------------------------------------*/
+
+void *allouer(size_t taille)
+{
+void *pointeur;
+
+if (taille == 0) taille = 1;
+
+pointeur = (void *) malloc(taille);
+
+if (pointeur==NULL)
+ erreur("out of memory");
+ else return(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+void *reallouer(void *pointeur, size_t taille)
+{
+void *p;
+
+p = pointeur;
+
+pointeur = (void *) realloc(pointeur, taille);
+
+if (pointeur==NULL)
+ erreur("out of memory");
+else return(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+void liberer(void *pointeur)
+{
+
+free(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+void **callouer_mat(size_t t_elt, size_t nb_lig, size_t nb_col)
+{
+void **pointeur;
+int i;
+
+pointeur = (void **) allouer(nb_lig * sizeof(void *));
+
+for (i=0; i < nb_lig; i++)
+ pointeur[i] = (void *) allouer(nb_col * t_elt);
+
+return(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+void **recallouer_mat(void **pointeur, size_t t_elt, size_t anc_nb_lig,
+ size_t nb_lig, size_t nb_col)
+{
+int i;
+
+if (anc_nb_lig == nb_lig) return(pointeur);
+
+for (i=nb_lig; i < anc_nb_lig; i++)
+ liberer(pointeur[i]);
+
+pointeur = (void **) reallouer(pointeur, nb_lig * sizeof(void *));
+
+for (i=anc_nb_lig; i < nb_lig; i++)
+ pointeur[i] = (void *) allouer(nb_col * t_elt);
+
+return(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+void **recallouer_mat2(void **pointeur, size_t t_elt,
+ size_t anc_nb_lig, size_t nb_lig, size_t nb_col)
+{
+int i;
+for (i=nb_lig; i < anc_nb_lig; i++)
+ liberer(pointeur[i]);
+
+pointeur = (void **) reallouer(pointeur, nb_lig * sizeof(void *));
+
+for (i=0; i < min(anc_nb_lig, nb_lig); i++)
+ pointeur[i] = (void *) reallouer(pointeur[i], nb_col * t_elt);
+
+for (i=anc_nb_lig; i < nb_lig; i++)
+ pointeur[i] = (void *) allouer(nb_col * t_elt);
+
+return(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+void liberer_mat(void **pointeur, size_t nb_lig)
+{
+int i;
+
+for (i=0; i < nb_lig; i++)
+ liberer(pointeur[i]);
+
+liberer(pointeur);
+}
+
+/* ------------------------------------------------------------*/
+
+FILE *ouvrir(char *nomfich, char *mode)
+{
+FILE *f;
+
+if ((f = fopen(nomfich, mode)) == NULL)
+ {
+ printf("fopen(\"%s\",\"%s\"): ", nomfich, mode);
+ erreur("enable to open file");
+ }
+else return f;
+}
+
+/* ------------------------------------------------------------*/
+
+void fermer(FILE *f)
+{
+if (fclose(f) == EOF)
+ erreur("enable to close file");
+}
+
+/* ------------------------------------------------------------*/
+
+void fcopie(FILE *fdestination, FILE *fsource)
+{
+char line[TAILLE_MAX_LIGNE_FICHIER];
+
+while (fgets(line, TAILLE_MAX_LIGNE_FICHIER, fsource) != NULL)
+ fputs(line, fdestination);
+
+fflush(fdestination);
+}
+
+/* ------------------------------------------------------------*/
+
+void strmin(char *p)
+{
+char c;
+
+for (; (c=*p); p++)
+ *p = tolower(c);
+}
+
+/* ------------------------------------------------------------*/
+
+void strmaj(char *p)
+{
+char c;
+
+for (; (c=*p); p++)
+ *p = toupper(c);
+}
+
+/* ------------------------------------------------------------*/
+
Added: trunk/packages/dialign/branches/upstream/current/src/pratique.h
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/pratique.h 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/pratique.h 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,32 @@
+#ifndef _PRATIQUE_H
+#define _PRATIQUE_H
+
+#include <stdio.h>
+#include <stdlib.h>
+
+#define true 1
+#define false 0
+
+#define min(a,b) ((a)<(b)?(a):(b))
+#define max(a,b) ((a)>(b)?(a):(b))
+
+#define TAILLE_MAX_LIGNE_FICHIER 10000
+
+void erreur(char *message);
+
+void *allouer(size_t taille);
+void *reallouer(void *pointeur, size_t taille);
+void liberer(void *pointeur);
+void **callouer_mat(size_t t_elt, size_t nb_lig, size_t nb_col);
+void **recallouer_mat(void **pointeur, size_t t_elt, size_t anc_nb_lig, size_t nb_lig, size_t nb_col);
+void **recallouer_mat2(void **pointeur, size_t t_elt, size_t anc_nb_lig, size_t nb_lig, size_t nb_col);
+void liberer_mat(void **pointeur, size_t nb_lig);
+
+FILE *ouvrir(char *nomfich, char *mode);
+void fermer(FILE *f);
+void fcopie(FILE *fdestination, FILE *fsource);
+
+void strmin(char *p);
+void strmaj(char *p);
+
+#endif /* _PRATIQUE_H */
Added: trunk/packages/dialign/branches/upstream/current/src/regex.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/regex.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/regex.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,236 @@
+
+ /*******************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * regex.c *
+ * *
+ \*******************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+extern float max_mot_offset , mot_offset_factor , mot_factor ;
+extern int char_num[ MAX_REGEX ] ;
+extern int regex_len , mot_len ;
+extern char *mot_char[ MAX_REGEX ] ;
+extern int seqnum, *seqlen ;
+extern char *seq[MAX_SEQNUM];
+extern short **mot_pos ;
+extern FILE *fp_mot ;
+
+void regex_complain( char *regex ) {
+ printf("\n bracket structure in regular expression makes no sense \n");
+ printf("\n %s \n\n", regex) ;
+ printf(" program terminated\n\n");
+ exit(1);
+}
+
+void struc_check( char *regex ) {
+ int p, bracket_count = 0 ;
+
+ for( p = 0 ; p < MAX_REGEX; p++ ) {
+ char_num[ p ] = 0 ;
+ }
+
+ for( p = 0 ; p < regex_len ; p++ ) {
+
+ if( regex[ p ] == '[' )
+ bracket_count++ ;
+
+ if( ( regex[ p ] != '[' ) && ( regex[ p ] != ']' ) ) {
+ char_num[ mot_len ]++ ;
+ regex[ p ] = toupper( regex[ p ] ) ;
+ }
+
+ if( regex[ p ] == ']' )
+ bracket_count-- ;
+
+ if( ( regex[ p ] == ']' ) || ( bracket_count == 0 ) )
+ mot_len++ ;
+
+
+ if( ( bracket_count < 0 ) || ( bracket_count > 1 ) )
+ regex_complain( regex ) ;
+
+
+ }
+
+ if( bracket_count != 0 )
+ regex_complain( regex ) ;
+
+}
+
+
+void regex_parse( char *mot_regex ) {
+
+ int i, p , mp = 0 ;
+ int in_bracket = 0;
+ int char_c = 0 ;
+
+
+ if( ( mot_pos = ( short ** ) calloc( seqnum , sizeof( short *) ) ) == NULL) {
+ printf(" problems with memory allocation");
+ printf(" for `mot_pos' ! \n \n");
+ exit(1);
+ }
+
+ for( i = 0 ; i < seqnum ; i++ )
+ if( ( mot_pos[i] = ( short *) calloc( ( seqlen[i] + 2 ) , sizeof( short ) ) ) == NULL) {
+ printf(" problems with memory allocation");
+ printf(" for `mot_pos[%d]' ! \n \n", i);
+ exit(1);
+ }
+
+
+
+
+ struc_check( mot_regex ) ;
+
+/*
+ printf(" \n regex_len = %d\n", regex_len) ;
+ printf(" mot_len = %d\n", mot_len) ;
+ printf("\n");
+
+ for( p = 0 ; p < mot_len ; p++ ) {
+ printf(" %d ", char_num[ p ] );
+ }
+ printf("\n\n");
+*/
+
+ for( p = 0 ; p < mot_len ; p++ ) {
+ mot_char[ p ] = (char *) calloc( char_num[ p ] , sizeof(char) );
+ }
+
+
+ /* PROBLEM */
+
+
+ for( p = 0 ; p < regex_len ; p++ ) {
+
+ if( mot_regex[ p ] == '[' ) {
+ in_bracket = 1 ;
+ }
+
+ if( mot_regex[ p ] == ']' ) {
+ in_bracket = 0 ;
+ char_c = 0 ;
+ mp++ ;
+ }
+
+ if( ( mot_regex[ p ] != '[' ) && ( mot_regex[ p ] != ']' ) ) { /* char */
+ if( in_bracket ) {
+ mot_char[ mp ][ char_c ] = mot_regex[ p ] ;
+ char_c++;
+ }
+ else { /* not in bracket */
+ char_c = 0 ;
+ mot_char[ mp ][ 0 ] = mot_regex[ p ] ;
+ mp++ ;
+ }
+ }
+ }
+
+/*
+ for( mp = 0 ; mp < mot_len ; mp++ ) {
+ printf(" position %d ", mp + 1 );
+ for( p = 0 ; p < char_num[ mp ] ; p++ ) {
+ printf(" %c ", mot_char[ mp ][ p ] ) ;
+ }
+ printf("\n");
+ }
+*/
+
+}
+
+seq_parse( char *mot_regex ) {
+ int sn, ok , i ;
+ int sp, ap, rp, hv, match;
+ max_mot_offset = sqrt ( - log ( 0.1 ) * 10 / mot_factor ) * mot_offset_factor;
+
+
+ for( sn = 0 ; sn < seqnum ; sn++ )
+ for( sp = 0 ; sp < ( seqlen[ sn ] - mot_len + 1 ) ; sp++ ) {
+ ok = 1 ;
+ rp = 0 ;
+ while( ok && ( rp < mot_len ) ) {
+ if( mot_char[ rp ][ 0 ] != 'X' ) {
+ match = 0 ;
+ for( hv = 0 ; hv < char_num[ rp ] ; hv++ ) {
+ if( mot_char[ rp ][ hv ] == seq[ sn ][ sp + rp ] ) {
+ match = 1 ;
+ }
+ }
+ }
+ ok = match ;
+ rp++;
+ }
+ if( ok ) {
+ printf( " motif in seq %d at pos %d \n", sn + 1 , sp + 1 ) ;
+ mot_pos[ sn ][ sp + 1 ] = 1 ;
+ }
+ else
+ mot_pos[ sn ][ sp + 1 ] = 0 ;
+ }
+
+
+ printf("\n") ;
+
+/*
+ for( sn = 0 ; sn < seqnum ; sn++ ) {
+ printf(" %s \n", seq[ sn ] ) ;
+ printf(" ");
+ for( i = 1 ; i <= seqlen[ sn ] ; i++ ) {
+
+
+ if( mot_pos[ sn ][ i ] )
+ printf("*");
+ else
+ printf(" ");
+ }
+ printf("\n\n" ) ;
+ }
+ printf("\n" ) ;
+*/
+
+}
+
+
+void regex_format_complain() {
+ printf("\n \n Arguments in command line don't make sense! \n");
+ printf(" (Motifs not properly specified) \n \n");
+ printf(" With the motif-search option, the program call is:\n\n");
+ printf(" ./dialign2-2 [para] -mot <regex> <fct1> <fct2> ");
+ printf("[para] <seq> \n\n");
+ printf(" where \n <regex> is a regular expression,");
+ printf(" e.g. \"AT[CG]XT\",\n");
+ printf(" <fct1> is a weighting factor \n");
+ printf(" <fct2> is a weighting factor \n");
+ printf(" <seq> is the input sequence file and \n");
+ printf(" [para] are (optional)");
+ printf(" additional program parameters\n\n" );
+ exit(1);
+}
+
+float mot_dist_factor( int offset , float parameter ) {
+ float mdf , parameter2, factor1 ;
+ int offset2 ;
+
+ offset2 = offset * offset ;
+ parameter2 = parameter * parameter ;
+
+ factor1 = (float) offset2 / ( parameter2 * 10 ) ;
+ mdf = exp( - ( offset2 ) / ( parameter2 * 10 ) ) ;
+
+ return mdf ;
+
+}
+
Added: trunk/packages/dialign/branches/upstream/current/src/wgt.c
===================================================================
--- trunk/packages/dialign/branches/upstream/current/src/wgt.c 2006-04-09 10:21:57 UTC (rev 15)
+++ trunk/packages/dialign/branches/upstream/current/src/wgt.c 2006-04-18 12:55:28 UTC (rev 16)
@@ -0,0 +1,250 @@
+
+
+ /*******************\
+ * *
+ * DIALIGN 2 *
+ * *
+ * wgt.c *
+ * *
+ \*******************/
+
+
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <math.h>
+#include <string.h>
+#include <ctype.h>
+#include "define.h"
+#include "dialign.h"
+#include "alig_graph_closure.h"
+
+extern int max_sim_score, istep, *seqlen ;
+extern float **min_weight , threshold , av_sim_score_pep , av_sim_score_nuc ;
+extern int max_dia , wgt_type ;
+extern double **tp400_prot, **tp400_dna, **tp400_trans;
+extern float **wgt_prot, **wgt_dna, **wgt_trans;
+extern char par_dir[NAME_LEN];
+
+void rel_wgt_calc( int l1 , int l2 , float **rel_wgt )
+ {
+ int l , m, mss;
+ float ent, factor, l1f, l2f, **wgt , av_sim_score ;
+ double t_pr, pr400, **tpr ;
+
+/*
+ printf(" it %d, rel_wgt_calc: len = %d , %d \n", istep , l1 , l2 );
+*/
+
+ if( rel_wgt == wgt_prot ) {
+ tpr = tp400_prot ;
+ mss = max_sim_score ;
+ av_sim_score = av_sim_score_pep ;
+ }
+
+ if( rel_wgt == wgt_dna ) {
+ tpr = tp400_dna ;
+ mss = 1 ;
+ av_sim_score = av_sim_score_nuc ;
+ }
+
+ if( rel_wgt == wgt_trans ) {
+ tpr = tp400_trans ;
+ mss = max_sim_score ;
+ av_sim_score = av_sim_score_pep ;
+ }
+
+
+
+ l1f = l1;
+ l2f = l2;
+
+ factor = ( l1f * l2f ) / 400.00;
+
+
+ for( l = 1 ; l <= max_dia ; l++ )
+ for( m = 0 ; m <= l * mss ; m++ )
+ {
+ rel_wgt[l][m] = 0;
+
+
+ if( tpr[l][m] )
+ if( m > av_sim_score * l )
+
+ {
+ pr400 = tpr[l][m];
+
+ if( pr400 > 0.0000000001 )
+ t_pr = 1 - pow( 1 - pr400 , factor );
+ else
+ t_pr = pr400 * factor;
+
+ ent = 0;
+
+ if(t_pr)
+ ent = -log( t_pr );
+
+ if( ent > threshold )
+ rel_wgt[l][m] = ent;
+ }
+ }
+ } /* rel_wgt_calc */
+
+
+
+
+void wgt_prnt_prot( ) {
+ int i, j ;
+ printf(" \n\n weight scores for PROTEIN fragments\n\n" );
+ printf(" sequence lengths = %d , %d \n\n", seqlen[0] , seqlen[1] ) ;
+ for( i = 1 ; i <= max_dia ; i++ ) {
+ for( j = 0 ; j <= ( i * 15 ) ; j++ )
+ printf(" %3d %3d %f \n", i , j , wgt_prot[ i ][ j ] );
+ }
+}
+
+void wgt_prnt_dna( ) {
+ int i, j ;
+ printf(" \n\n weight scores for NON-TRANSLATED DNA fragments\n\n" );
+ printf(" sequence lengths = %d , %d \n\n", seqlen[0] , seqlen[1] ) ;
+ for( i = 1 ; i <= max_dia ; i++ ) {
+ for( j = 0 ; j <= i ; j++ )
+ printf(" %3d %3d %f \n", i , j , wgt_dna[ i ][ j ] );
+ }
+}
+
+
+void wgt_prnt_trans( ) {
+ int i, j ;
+ printf(" \n\n weight scores for TRANSLATED DNA fragments\n\n" );
+ printf(" sequence lengths = %d , %d \n\n", seqlen[0] , seqlen[1] ) ;
+ for( i = 1 ; i <= max_dia ; i++ ) {
+ for( j = 0 ; j <= ( i * 15 ) ; j++ )
+ printf(" %3d %3d %f \n", i , j , wgt_trans[ i ][ j ] );
+ }
+}
+
+
+
+void wgt_prnt( ) {
+ if (wgt_type == 0 )
+ wgt_prnt_prot( );
+
+ if (wgt_type % 2 )
+ wgt_prnt_dna( );
+
+ if (wgt_type > 1 )
+ wgt_prnt_trans( );
+}
+
+
+
+void mem_alloc( ) {
+ /* allocates memory for `tp400_xxx', `wgt_xxx' */
+
+ int i;
+
+ if( wgt_type == 0 ) {
+ if( (tp400_prot = (double **) calloc( ( max_dia + 1 ) , sizeof(double*) ))
+ == NULL) {
+ printf(" problems with memory allocation for `tp400_prot' ! \n \n");
+ exit(1);
+ }
+
+ if( ( wgt_prot = (float **) calloc( (max_dia+1) , sizeof(float*) ))
+ == NULL) {
+ printf(" problems with memory allocation for `weights' ! \n \n");
+ exit(1);
+ }
+ }
+
+ if( wgt_type % 2 ) {
+ if( (tp400_dna = (double **) calloc( ( max_dia + 1 ) , sizeof(double*) ))
+ == NULL) {
+ printf(" problems with memory allocation for `tp400_dna' ! \n \n");
+ exit(1);
+ }
+
+ if( ( wgt_dna = (float **) calloc( (max_dia+1) , sizeof(float*) ))
+ == NULL) {
+ printf(" problems with memory allocation for `weights' ! \n \n");
+ exit(1);
+ }
+ }
+
+
+ if( wgt_type > 1 ) {
+ if( (tp400_trans = (double **) calloc( ( max_dia + 1 ) , sizeof(double*) ))
+ == NULL) {
+ printf(" problems with memory allocation for `tp400_trans' ! \n \n");
+ exit(1);
+ }
+
+ if( ( wgt_trans = (float **) calloc( (max_dia+1) , sizeof(float*) ))
+ == NULL) {
+ printf(" problems with memory allocation for `weights' ! \n \n");
+ exit(1);
+ }
+ }
+
+ for( i = 1 ; i <= max_dia ; i++ ){
+
+
+ if( wgt_type == 0 ) {
+ if( (tp400_prot[i] =
+ (double *) calloc( ((i + 1) * max_sim_score ) , sizeof(double) ))
+ == NULL) {
+ printf(" problems with memory allocation for `tp400_prot' ! \n \n");
+ exit(1);
+ }
+
+ if( (wgt_prot[i] =
+ (float *) calloc( ((i+1) * max_sim_score ) , sizeof(float) ))
+ == NULL) {
+ printf(" problems with memory allocation for `weights'!\n\n");
+ exit(1);
+ }
+ }
+
+
+ if( wgt_type % 2 ) {
+ if( (tp400_dna[i] =
+ (double *) calloc( ((i + 1) ) , sizeof(double) ))
+ == NULL) {
+ printf(" problems with memory allocation for `tp400_dna' ! \n \n");
+ exit(1);
+ }
+
+ if( (wgt_dna[i] =
+ (float *) calloc( ((i+1) ) , sizeof(float) ))
+ == NULL) {
+ printf(" problems with memory allocation for `weights'!\n\n");
+ exit(1);
+ }
+ }
+
+
+ if( wgt_type > 1 ) {
+ if( (tp400_trans[i] =
+ (double *) calloc( ((i + 1) * max_sim_score ) , sizeof(double) ))
+ == NULL) {
+ printf(" problems with memory allocation for `tp400_trans' %d ! \n \n", i);
+ exit(1);
+ }
+
+ if( (wgt_trans[i] =
+ (float *) calloc( ((i+1) * max_sim_score ) , sizeof(float) ))
+ == NULL) {
+ printf(" problems with memory allocation for `weights'!\n\n");
+ exit(1);
+ }
+ }
+ }
+} /* void memory_allocation */
+
+
+
+
+
+
+
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