[med-svn] [repeatmasker-recon] 01/05: Imported Upstream version 1.08
Olivier Sallou
osallou at debian.org
Sat Aug 22 07:13:28 UTC 2015
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository repeatmasker-recon.
commit b6ca04527102c66892ec4ed4601bc1e9c71eaff7
Author: Olivier Sallou <osallou at debian.org>
Date: Fri Aug 21 20:45:35 2015 +0000
Imported Upstream version 1.08
---
00README | 126 ++
COPYRIGHT | 38 +
Demos/README | 34 +
Demos/input/elegans.msps | 4840 ++++++++++++++++++++++++++++++++++++++++++++++
Demos/input/seqnames | 7 +
Demos/standard/Tc3.list | 26 +
Demos/standard/Tc3.msps | 26 +
INSTALL | 15 +
LICENSE | 339 ++++
scripts/MSPCollect.pl | 67 +
scripts/recon.pl | 101 +
src/Makefile | 123 ++
src/bolts.h | 14 +
src/edgeredef.c | 462 +++++
src/ele.h | 1442 ++++++++++++++
src/eledef.c | 428 ++++
src/eleredef.c | 2409 +++++++++++++++++++++++
src/famdef.c | 260 +++
src/imagespread.c | 98 +
src/msps.h | 225 +++
src/seqlist.h | 72 +
21 files changed, 11152 insertions(+)
diff --git a/00README b/00README
new file mode 100644
index 0000000..79c5e64
--- /dev/null
+++ b/00README
@@ -0,0 +1,126 @@
+RECON -- finding repeat families from biological sequences
+Version 1.08 (Jan 2014)
+Copyright (C) 2001 Washington University School of Medicine
+Copyright (C) 2011-2014 Institute for Systems Biology
+------------------------------------------------------------------
+
+
+About the package
+
+The RECON package implements a de novo algorithm for the
+indentification of repeat families from biological sequences. For
+details about the algorithm, see
+
+Bao Z. and Eddy S.R. (2002) Automated de novo Identification of Repeat
+Sequence Families in Sequenced Genomes. Submitted.
+
+and
+
+http://www.genetics.wustl.edu/eddy/recon
+
+Source code of RECON is freely available under the GNU General Public
+License. For details on the copyright and licensing, see the
+COPYRIGHT and LICENSE file.
+
+This distribution includes two Perl scripts and several C programs.
+Most users only need to run the scripts and the C programs should be
+transparent.
+
+
+What's new?
+
+RECON1.08: Wed Feb 5 14:04:25 PST 2014 - Robert Hubley ISB
+ - New checks in eleredef.c for failed memory allocation/file operations.
+ - A buffer overrun bug fix provided by Stephen Ficklin in eledef.c.
+
+RECON1.07: Wed Jun 8 10:00:55 PDT 2011 - Robert Hubley ISB
+ - Another problem with the eleredef program has appeared a couple
+ of times. A divide by zero error in one of Zhirong's routines.
+ I have applied a workaround to the divide by zero but not a fix
+ to the real problem. The program will now warn the user if
+ the workaround was exercised during a run.
+
+RECON1.06: Tue May 20 15:19:30 PDT 2008 - Robert Hubley ISB
+ - 64 bit compiler fixes: Previous versions of RECON used the "long"
+ data type under the assumption that was 32bits. This caused the
+ program to crash or lock up during analysis.
+
+Bug fix for RECON1.02 in the eleredef program.
+
+
+
+Programs and input
+
+The RECON algorithm defines repeat families on the basis of pairwise
+similarity between the input biological sequences. We do not provide
+pairwise sequence comparison tools in the package. However, we
+provide a tool (MSPCollect) which converts a BLAST output into an
+MSP file, which is used by the package as input. In the MSP file,
+each MSP that BLAST reports is turned into a one-line summary in the
+following format:
+
+score %iden start end query_name start end subject_name \n
+
+The command line format for MSPCollect is
+
+MSPCollect BLAST_output_file > name_of_your_MSP_file
+
+If you have multiple BLAST output files, you have to run MSPCollect
+multiple times and concatenate the result into one MSP file.
+
+
+The recon script drives the running of the package. The command
+line format is as follows:
+
+recon.pl seq_name_list_file MSP_file integer
+
+The seq_name_list_file contains the names of the input sequences, one
+per line. The lines can be just the names, or it may be in the FASTA
+format (starting with ">"). The names should be sorted in lexical
+order. The very first line of file should be an integer which is the
+number of names listed in the file. If the input sequences are stored
+in one FASTA file, one can construct the seq_name_list_file as follows:
+
+grep ">" FASTA_file | sort > name_of_your_seq_name_list_file
+
+One can then add the number of names to the top of the file.
+
+As one of the early steps, the script sort the MSPs. If there are too
+many MSPs in the input, one may consider sorting a subsection at a
+time. The third integer argument specifies how many sections you want
+to divide the sorting process into. The default is 1. (Notice, as
+the file size gets big, the sorting process becomes inefficient, and
+may even cause the process to crash.)
+
+If you know the RECON algorithm, then the names of C programs are self
+explanatory.
+
+
+
+Output of the package
+
+The package generates several directories along the way. All of them,
+except for the summary directory, stores intermediate results. The
+ele_def_res, ele_redef_res and edge_redef_res directories contain
+files for the elements defined at the corresponding step, one file per
+element. Elements are indexed using integers and are named as e123,
+e987, etc.. If you are not interested in the details about the
+elements, you can remove all these directories.
+
+Two files in the summary directory are the "official" output of the
+package -- eles and families. Each line in "eles" is a summary of an
+element defined in the following format:
+
+family_index element_index strand sequence_name start end
+
+Each line in "families" is a summary of a family defined in the
+following format:
+
+family_index copy_number_in_the_family
+
+
+
+The Demo
+
+To get examples of (the format of) the input and output files, see the
+README file in the Demos directory.
diff --git a/COPYRIGHT b/COPYRIGHT
new file mode 100644
index 0000000..159e9c9
--- /dev/null
+++ b/COPYRIGHT
@@ -0,0 +1,38 @@
+RECON -- finding repeat families from biological sequences
+Version 1.01 (Nov 2001)
+Copyright (C) 2001 Washington University School of Medicine
+------------------------------------------------------------------
+
+This suite of programs is free software. You can redistribute it
+and/or modify it under the terms of the GNU General Public License as
+published by the Free Software Foundation; either version 2 of the
+License, or (at your option) any later version.
+
+In other words, you are free to modify, copy, or redistribute this
+source code and its documentation in any way you like, but you must
+distribute all derivative versions as free software under the same
+terms that I've provided my code to you (i.e. the GNU General Public
+License). This precludes any use of the code in proprietary or
+commercial software unless your source code is made freely available.
+
+If you wish to use RECON code under a different Open Source license
+that's not compatible with the GPL (like the Artistic License, BSD
+license, or the Netscape Public License), please contact Sean Eddy
+(eddy at genetics.wustl.edu) for permission.
+
+Incorporation into commercial software under non-GPL terms is possible
+by obtaining a specially licensed version from Washington University
+School of Medicine. Contact Jack Pincus (jhpincus at cris.com) to arrange
+licensing terms.
+
+This software 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
+General Public License for more details.
+
+You should have received a copy of the GNU General Public License
+along with this RECON release, in the file LICENSE; if not, write to
+the Free Software Foundation, Inc., 675 Mass. Ave, Cambridge, MA 02139
+USA.
+
+
diff --git a/Demos/README b/Demos/README
new file mode 100644
index 0000000..6da320e
--- /dev/null
+++ b/Demos/README
@@ -0,0 +1,34 @@
+The Demos directory contains an example from the C. elegans genome.
+You have three directories to start with -- input, standard and output.
+
+The input directory contains two files for the input of the RECON
+package -- the seq_name_list_file "seqnames" and MSP_file
+"elegans.msps". The elegans.msps contains MSPs from an all-vs-all
+comparison of the elegans genome which cover regions similar to Tc3 (a
+transposable element in elegans), directly or by transitive
+similarity. These include both the Tc3 copies in the genome, as well
+as certain Tc3-related but distinct transposable elements.
+
+The standard directory also contains two files -- Tc3.list and
+Tc3.msps. The former file is a manually curated list of Tc3
+copies/fragments in the genome. For the more critical users, the
+latter file is a manually curated list of MSPs from a search with the
+canonical Tc3 against the genome, which we believe are hits to true
+Tc3 copies. You can compare this file with the "elegans.msps" to
+check whether our curation is reasonable.
+
+The empty directory of output is where you can run the RECON package
+on this example (after installation, of course). Within the output
+directory, type
+
+../../scripts/recon.pl ../input/seqnames ../input/elegans.msps 1
+
+The process will generate several directories to store the output. All
+these directories, except for the summary directory stores intermediate
+results (see 00README). You can find that in summary/eles, the Tc3 copies
+are defined as family six. Do
+
+awk '$1==6' summary/eles
+
+to get the list of members in this defined family and compare it to
+standard/Tc3.list to evaluate the result of this automatic clustering.
diff --git a/Demos/input/elegans.msps b/Demos/input/elegans.msps
new file mode 100644
index 0000000..dcb729c
--- /dev/null
+++ b/Demos/input/elegans.msps
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+000648 84.0 01369880 01369694 ChrX 17030575 17030756 ChrX
+000648 84.0 15432752 15432938 ChrX 17030575 17030756 ChrX
+000662 84.5 15431212 15431026 ChrX 17030575 17030756 ChrX
+000601 83.5 11771111 11771291 ChrX 17030585 17030761 ChrX
+000616 83.0 07189104 07189285 ChrX 17030585 17030761 ChrX
+000620 83.5 07187947 07187766 ChrX 17030585 17030761 ChrX
+000651 84.6 11769950 11769769 ChrX 17030585 17030761 ChrX
+000533 82.3 16609724 16609561 ChrX 17030598 17030756 ChrX
+000429 68.7 03600696 03600928 ChrX 17249899 17250131 ChrX
+000409 68.9 03602844 03602620 ChrX 17249907 17250131 ChrX
+002639 96.7 11771340 11770886 ChrX 17249908 17250362 ChrX
+001106 93.4 07921739 07921528 ChrX 17249910 17250119 ChrX
+000432 69.9 16963488 16963270 ChrX 17249913 17250131 ChrX
+000696 86.5 15021806 15021982 ChrX 17249914 17250085 ChrX
+002311 91.4 01369646 01370096 ChrX 17249914 17250363 ChrX
+000405 69.1 16961315 16961531 ChrX 17249915 17250131 ChrX
+000541 77.0 09184177 09183982 ChrX 17249915 17250118 ChrX
+002522 95.5 07187724 07188170 ChrX 17249915 17250362 ChrX
+002686 97.6 11769727 11770175 ChrX 17249915 17250362 ChrX
+000423 78.7 16148839 16148974 ChrX 17249916 17250049 ChrX
+000450 80.1 05417100 05416956 ChrX 17249916 17250059 ChrX
+000548 85.1 12567028 12567167 ChrX 17249916 17250056 ChrX
+000705 82.8 06917364 06917173 ChrX 17249916 17250105 ChrX
+001148 93.8 16609515 16609724 ChrX 17249916 17250125 ChrX
+002216 90.6 15432983 15432537 ChrX 17249916 17250362 ChrX
+002276 91.1 15430980 15431427 ChrX 17249916 17250362 ChrX
+002547 96.0 07189326 07188881 ChrX 17249916 17250362 ChrX
+001015 86.1 07666203 07666464 ChrX 17249938 17250200 ChrX
+000630 83.5 17030761 17030585 ChrX 17249957 17250138 ChrX
+003069 91.0 01370238 01369647 ChrX 17250344 17250935 ChrX
+003491 96.3 07188738 07189330 ChrX 17250344 17250938 ChrX
+003609 97.8 11770743 11771337 ChrX 17250344 17250939 ChrX
+003430 96.4 07188308 07187724 ChrX 17250349 17250935 ChrX
+003571 97.8 11770313 11769727 ChrX 17250349 17250935 ChrX
+002917 90.5 15432408 15432983 ChrX 17250358 17250934 ChrX
+002977 90.8 15431556 15430980 ChrX 17250358 17250934 ChrX
+002690 97.6 17250362 17249911 ChrX 17250487 17250939 ChrX
+001002 85.7 07666464 07666203 ChrX 17250650 17250912 ChrX
+000617 83.0 17030585 17030761 ChrX 17250712 17250893 ChrX
+000401 69.1 16963270 16963486 ChrX 17250719 17250935 ChrX
+001142 93.8 16609724 16609515 ChrX 17250725 17250934 ChrX
+001057 92.8 07921528 07921734 ChrX 17250731 17250935 ChrX
+000518 76.1 09183982 09184178 ChrX 17250732 17250936 ChrX
+000674 81.8 06917173 06917364 ChrX 17250745 17250934 ChrX
+000660 85.3 15021982 15021807 ChrX 17250765 17250935 ChrX
+000452 79.7 05416956 05417107 ChrX 17250791 17250941 ChrX
+000518 83.7 12567167 12567028 ChrX 17250794 17250934 ChrX
diff --git a/Demos/input/seqnames b/Demos/input/seqnames
new file mode 100644
index 0000000..6153df6
--- /dev/null
+++ b/Demos/input/seqnames
@@ -0,0 +1,7 @@
+6
+ChrI
+ChrII
+ChrIII
+ChrIV
+ChrV
+ChrX
diff --git a/Demos/standard/Tc3.list b/Demos/standard/Tc3.list
new file mode 100644
index 0000000..c558ba3
--- /dev/null
+++ b/Demos/standard/Tc3.list
@@ -0,0 +1,26 @@
+-1 ChrI 457418 459754
+-1 ChrI 9599192 9601527
+-1 ChrI 11106922 11109258
+ 1 ChrI 12639993 12640540
+ 1 ChrI 12640672 12640847
+-1 ChrI 12899694 12902028
+-1 ChrII 15997 18331
+ 1 ChrII 466069 468403
+ 1 ChrII 2961941 2964278
+ 1 ChrII 3210901 3213237
+ 1 ChrII 3919512 3921848
+ 1 ChrII 7068733 7071069
+-1 ChrII 7492071 7494407
+ 1 ChrIII 8134615 8136950
+ 1 ChrIV 1196896 1199232
+ 1 ChrIV 12305539 12307875
+ 1 ChrIV 13517358 13519694
+-1 ChrV 17019621 17021957
+ 1 ChrV 18256418 18258754
+ 1 ChrV 18593383 18594138
+ 1 ChrV 18594130 18595566
+ 1 ChrX 2878780 2879615
+ 1 ChrX 2879613 2880344
+ 1 ChrX 13552999 13553907
+ 1 ChrX 13553906 13554419
+ 1 ChrX 2880351 2880552
diff --git a/Demos/standard/Tc3.msps b/Demos/standard/Tc3.msps
new file mode 100644
index 0000000..99215a0
--- /dev/null
+++ b/Demos/standard/Tc3.msps
@@ -0,0 +1,26 @@
+015343 99.8 00002337 00000001 Tc3 00457418 00459754 ChrI
+015343 99.8 00002337 00000001 Tc3 09599192 09601527 ChrI
+015393 99.9 00002337 00000001 Tc3 11106922 11109258 ChrI
+003292 98.2 00001521 00002060 Tc3 12639993 12640540 ChrI
+000868 96.0 00002169 00002337 Tc3 12640672 12640847 ChrI
+015311 99.8 00002337 00000001 Tc3 12899694 12902028 ChrI
+015303 99.8 00002337 00000001 Tc3 00015997 00018331 ChrII
+015317 99.8 00000001 00002337 Tc3 00466069 00468403 ChrII
+015348 99.8 00000001 00002337 Tc3 02961941 02964278 ChrII
+015325 99.7 00000001 00002337 Tc3 03210901 03213237 ChrII
+015425 100 00000001 00002337 Tc3 03919512 03921848 ChrII
+015371 99.9 00000001 00002337 Tc3 07068733 07071069 ChrII
+015411 100 00002337 00000001 Tc3 07492071 07494407 ChrII
+015335 99.8 00000001 00002337 Tc3 08134615 08136950 ChrIII
+015361 99.8 00000001 00002337 Tc3 01196896 01199232 ChrIV
+015407 100 00000001 00002337 Tc3 12305539 12307875 ChrIV
+015329 99.7 00000001 00002337 Tc3 13517358 13519694 ChrIV
+015373 99.8 00002337 00000001 Tc3 17019621 17021957 ChrV
+015373 99.8 00000001 00002337 Tc3 18256418 18258754 ChrV
+004810 99.1 00000001 00000756 Tc3 18593383 18594138 ChrV
+009485 99.9 00000902 00002337 Tc3 18594130 18595566 ChrV
+005365 99.4 00000001 00000837 Tc3 02878780 02879615 ChrX
+004812 100 00001410 00002141 Tc3 02879613 02880344 ChrX
+005900 99.6 00000001 00000910 Tc3 13552999 13553907 ChrX
+003269 99.6 00001823 00002337 Tc3 13553906 13554419 ChrX
+001310 100 00002136 00002337 Tc3 02880351 02880552 ChrX
diff --git a/INSTALL b/INSTALL
new file mode 100644
index 0000000..e178804
--- /dev/null
+++ b/INSTALL
@@ -0,0 +1,15 @@
+The RECON package includes three parts -- the C source code in the src
+directory, the Perl scripts in the scripts directory, and a Demos
+directory containing examplory data.
+
+To install the package, run "make" and then "make install" in the src
+directory. You may have to modify the Makefile in the src directory
+to choose the proper C compliler (cc or gcc).
+
+Before you can use the package, you need one more modification in the
+script "recon.pl" in the scripts directory -- on the third line, add
+the path to the binaries (the bin directory here) between the double
+quotes.
+
+Now the package is up for running. See 00README on how to use the
+package.
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..a43ea21
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,339 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.
+ 675 Mass Ave, Cambridge, MA 02139, USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+ Preamble
+
+ The licenses for most software are designed to take away your
+freedom to share and change it. By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users. This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it. (Some other Free Software Foundation software is covered by
+the GNU Library General Public License instead.) You can apply it to
+your programs, too.
+
+ When we speak of free software, we are referring to freedom, not
+price. Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+ To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+ For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have. You must make sure that they, too, receive or can get the
+source code. And you must show them these terms so they know their
+rights.
+
+ We protect your rights with two steps: (1) copyright the software, and
+(2) offer you this license which gives you legal permission to copy,
+distribute and/or modify the software.
+
+ Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
+software. If the software is modified by someone else and passed on, we
+want its recipients to know that what they have is not the original, so
+that any problems introduced by others will not reflect on the original
+authors' reputations.
+
+ Finally, any free program is threatened constantly by software
+patents. We wish to avoid the danger that redistributors of a free
+program will individually obtain patent licenses, in effect making the
+program proprietary. To prevent this, we have made it clear that any
+patent must be licensed for everyone's free use or not licensed at all.
+
+ The precise terms and conditions for copying, distribution and
+modification follow.
+
+ GNU GENERAL PUBLIC LICENSE
+ TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
+ 0. This License applies to any program or other work which contains
+a notice placed by the copyright holder saying it may be distributed
+under the terms of this General Public License. The "Program", below,
+refers to any such program or work, and a "work based on the Program"
+means either the Program or any derivative work under copyright law:
+that is to say, a work containing the Program or a portion of it,
+either verbatim or with modifications and/or translated into another
+language. (Hereinafter, translation is included without limitation in
+the term "modification".) Each licensee is addressed as "you".
+
+Activities other than copying, distribution and modification are not
+covered by this License; they are outside its scope. The act of
+running the Program is not restricted, and the output from the Program
+is covered only if its contents constitute a work based on the
+Program (independent of having been made by running the Program).
+Whether that is true depends on what the Program does.
+
+ 1. You may copy and distribute verbatim copies of the Program's
+source code as you receive it, in any medium, provided that you
+conspicuously and appropriately publish on each copy an appropriate
+copyright notice and disclaimer of warranty; keep intact all the
+notices that refer to this License and to the absence of any warranty;
+and give any other recipients of the Program a copy of this License
+along with the Program.
+
+You may charge a fee for the physical act of transferring a copy, and
+you may at your option offer warranty protection in exchange for a fee.
+
+ 2. You may modify your copy or copies of the Program or any portion
+of it, thus forming a work based on the Program, and copy and
+distribute such modifications or work under the terms of Section 1
+above, provided that you also meet all of these conditions:
+
+ a) You must cause the modified files to carry prominent notices
+ stating that you changed the files and the date of any change.
+
+ b) You must cause any work that you distribute or publish, that in
+ whole or in part contains or is derived from the Program or any
+ part thereof, to be licensed as a whole at no charge to all third
+ parties under the terms of this License.
+
+ c) If the modified program normally reads commands interactively
+ when run, you must cause it, when started running for such
+ interactive use in the most ordinary way, to print or display an
+ announcement including an appropriate copyright notice and a
+ notice that there is no warranty (or else, saying that you provide
+ a warranty) and that users may redistribute the program under
+ these conditions, and telling the user how to view a copy of this
+ License. (Exception: if the Program itself is interactive but
+ does not normally print such an announcement, your work based on
+ the Program is not required to print an announcement.)
+
+These requirements apply to the modified work as a whole. If
+identifiable sections of that work are not derived from the Program,
+and can be reasonably considered independent and separate works in
+themselves, then this License, and its terms, do not apply to those
+sections when you distribute them as separate works. But when you
+distribute the same sections as part of a whole which is a work based
+on the Program, the distribution of the whole must be on the terms of
+this License, whose permissions for other licensees extend to the
+entire whole, and thus to each and every part regardless of who wrote it.
+
+Thus, it is not the intent of this section to claim rights or contest
+your rights to work written entirely by you; rather, the intent is to
+exercise the right to control the distribution of derivative or
+collective works based on the Program.
+
+In addition, mere aggregation of another work not based on the Program
+with the Program (or with a work based on the Program) on a volume of
+a storage or distribution medium does not bring the other work under
+the scope of this License.
+
+ 3. You may copy and distribute the Program (or a work based on it,
+under Section 2) in object code or executable form under the terms of
+Sections 1 and 2 above provided that you also do one of the following:
+
+ a) Accompany it with the complete corresponding machine-readable
+ source code, which must be distributed under the terms of Sections
+ 1 and 2 above on a medium customarily used for software interchange; or,
+
+ b) Accompany it with a written offer, valid for at least three
+ years, to give any third party, for a charge no more than your
+ cost of physically performing source distribution, a complete
+ machine-readable copy of the corresponding source code, to be
+ distributed under the terms of Sections 1 and 2 above on a medium
+ customarily used for software interchange; or,
+
+ c) Accompany it with the information you received as to the offer
+ to distribute corresponding source code. (This alternative is
+ allowed only for noncommercial distribution and only if you
+ received the program in object code or executable form with such
+ an offer, in accord with Subsection b above.)
+
+The source code for a work means the preferred form of the work for
+making modifications to it. For an executable work, complete source
+code means all the source code for all modules it contains, plus any
+associated interface definition files, plus the scripts used to
+control compilation and installation of the executable. However, as a
+special exception, the source code distributed need not include
+anything that is normally distributed (in either source or binary
+form) with the major components (compiler, kernel, and so on) of the
+operating system on which the executable runs, unless that component
+itself accompanies the executable.
+
+If distribution of executable or object code is made by offering
+access to copy from a designated place, then offering equivalent
+access to copy the source code from the same place counts as
+distribution of the source code, even though third parties are not
+compelled to copy the source along with the object code.
+
+ 4. You may not copy, modify, sublicense, or distribute the Program
+except as expressly provided under this License. Any attempt
+otherwise to copy, modify, sublicense or distribute the Program is
+void, and will automatically terminate your rights under this License.
+However, parties who have received copies, or rights, from you under
+this License will not have their licenses terminated so long as such
+parties remain in full compliance.
+
+ 5. You are not required to accept this License, since you have not
+signed it. However, nothing else grants you permission to modify or
+distribute the Program or its derivative works. These actions are
+prohibited by law if you do not accept this License. Therefore, by
+modifying or distributing the Program (or any work based on the
+Program), you indicate your acceptance of this License to do so, and
+all its terms and conditions for copying, distributing or modifying
+the Program or works based on it.
+
+ 6. Each time you redistribute the Program (or any work based on the
+Program), the recipient automatically receives a license from the
+original licensor to copy, distribute or modify the Program subject to
+these terms and conditions. You may not impose any further
+restrictions on the recipients' exercise of the rights granted herein.
+You are not responsible for enforcing compliance by third parties to
+this License.
+
+ 7. If, as a consequence of a court judgment or allegation of patent
+infringement or for any other reason (not limited to patent issues),
+conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot
+distribute so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you
+may not distribute the Program at all. For example, if a patent
+license would not permit royalty-free redistribution of the Program by
+all those who receive copies directly or indirectly through you, then
+the only way you could satisfy both it and this License would be to
+refrain entirely from distribution of the Program.
+
+If any portion of this section is held invalid or unenforceable under
+any particular circumstance, the balance of the section is intended to
+apply and the section as a whole is intended to apply in other
+circumstances.
+
+It is not the purpose of this section to induce you to infringe any
+patents or other property right claims or to contest validity of any
+such claims; this section has the sole purpose of protecting the
+integrity of the free software distribution system, which is
+implemented by public license practices. Many people have made
+generous contributions to the wide range of software distributed
+through that system in reliance on consistent application of that
+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+ 8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded. In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+ 9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number. If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation. If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+ 10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission. For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this. Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+ NO WARRANTY
+
+ 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+ 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+ END OF TERMS AND CONDITIONS
+
+ Appendix: How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) 19yy <name of author>
+
+ This program is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+
+ This program 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 General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program; if not, write to the Free Software
+ Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+ Gnomovision version 69, Copyright (C) 19yy name of author
+ Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary. Here is a sample; alter the names:
+
+ Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+ `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+ <signature of Ty Coon>, 1 April 1989
+ Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs. If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library. If this is what you want to do, use the GNU Library General
+Public License instead of this License.
diff --git a/scripts/MSPCollect.pl b/scripts/MSPCollect.pl
new file mode 100755
index 0000000..a93aeda
--- /dev/null
+++ b/scripts/MSPCollect.pl
@@ -0,0 +1,67 @@
+#! /usr/bin/perl
+
+if (!@ARGV) {
+ die "usage: MSPCollect BLAST_output_file\n";
+}
+
+open (BLST, "$ARGV[0]") || die "usage: MSPCollect BLAST_output_file\nCan not open the BLAST_output_file $ARGV[0]\n";
+
+$score_cutoff = 0;
+$iden_cutoff = 0;
+
+$score = -1;
+
+
+while (<BLST>) {
+ if (/^Query=\s+(\S+)/) {
+ $query = $1;
+ }
+ elsif (/^>(\S+)/) {
+ $sbjct_current = $1;
+ }
+ elsif (/^\s+Score =\s*(\S+)/) {
+ if (&filter) {
+ &report;
+ }
+ $head_q_boolean = 1;
+ $head_s_boolean = 1;
+ $sbjct = $sbjct_current;
+ $score_string = $1;
+ if ($score_string =~ /(\S+)(e|E)\+(\d+)/) {
+ $score = $1 * exp($3*log(10));
+ }
+ else {$score = $score_string;}
+ }
+ elsif (/^\s+Identities =\s+(\d+)\/(\d+)/) {
+ $iden = $1/$2*100;
+ }
+ elsif (/^Query:\s+(\d+)\s+(\S+)\s+(\d+)/) {
+ if ($head_q_boolean) {
+ $head_query = $1;
+ $head_q_boolean = 0;
+ }
+ $tail_query = $3;
+ }
+ elsif (/^Sbjct:\s+(\d+)\s+(\S+)\s+(\d+)/) {
+ if ($head_s_boolean) {
+ $head_sbjct = $1;
+ $head_s_boolean = 0;
+ }
+ $tail_sbjct = $3;
+ }
+ elsif (/^Parameters:/) {
+ if (&filter) {&report;}
+ $score = -1;
+ }
+}
+
+
+sub filter {
+ if ($score > 0 && $score > $score_cutoff && $iden > $iden_cutoff) {return 1;}
+ return 0;
+}
+
+
+sub report {
+ printf("%06d %03d %05d %05d %s %05d %05d %s \n", $score, $iden, $head_query, $tail_query, $query, $head_sbjct, $tail_sbjct, $sbjct);
+}
diff --git a/scripts/recon.pl b/scripts/recon.pl
new file mode 100755
index 0000000..a3a3f97
--- /dev/null
+++ b/scripts/recon.pl
@@ -0,0 +1,101 @@
+#! /usr/bin/perl
+
+$path = "";
+
+if (!$path) {
+ die "Please modifiy this script to specify the path to the binaries.\n";
+}
+
+if (@ARGV < 2) {
+ die "usage: recon seq_name_list_file MSP_file integer\nSee 00README for details.\n";
+}
+
+open(SEQ, "$ARGV[0]") || die "usage: recon seq_name_list_file MSP_file integer\nCan not open the seq_name_list_file $ARGV[0].\nSee 00README for details.\n";
+close SEQ;
+
+open(MSP, "$ARGV[1]") || die "usage: recon seq_name_list_file MSP_file integer\nCan not open the MSP_file $ARGV[1].\nSee 00README for details.\n";
+close MSP;
+
+
+`rm -f core`;
+
+`rm -rf summary`;
+`mkdir summary`;
+
+
+
+# prepare images
+
+`rm -rf images`;
+`mkdir images`;
+
+`$path/imagespread $ARGV[0] $ARGV[1] $ARGV[2]`;
+
+if ($?) {die "imagespread failed. Exit code $?\n";}
+
+if (@ARGV < 3) {
+ $sect = 1;
+} else {
+ $sect = $ARGV[2];
+}
+
+for ($i=1; $i<=$sect; $i++) {
+ $spread = "images/spread" . $i;
+ `sort -k 3,3 -k 4n,4n -k 5nr,5nr $spread >> images/images_sorted`;
+ if ($?) {die "sort failed for $spread.\n";}
+}
+
+`rm -f images/spread*`;
+
+
+
+# initial definition of elements
+
+`rm -rf ele_def_res`;
+`mkdir ele_def_res`;
+
+`$path/eledef $ARGV[0] $ARGV[1] single`;
+if ($?) {die "eledef failed. Exit code $?\n";}
+
+
+
+# re-defining elements
+
+`rm -rf ele_redef_res`;
+`mkdir ele_redef_res`;
+
+`rm -f tmp tmp2`;
+`ln -s ele_def_res tmp`;
+`ln -s ele_redef_res tmp2`;
+
+`$path/eleredef $ARGV[0]`;
+if ($?) {die "eleredef failed. Exit code $?\n";}
+
+`rm -f tmp tmp2`;
+
+
+
+# re-defining edges
+
+`rm -rf edge_redef_res`;
+`mkdir edge_redef_res`;
+
+`rm -f tmp tmp2`;
+`ln -s ele_redef_res tmp`;
+`ln -s edge_redef_res tmp2`;
+
+`$path/edgeredef $ARGV[0]`;
+if ($?) {die "edgeredef failed. Exit code $?\n";}
+
+
+
+# famdef
+
+`rm -f tmp tmp2`;
+`ln -s edge_redef_res tmp`;
+
+`$path/famdef $ARGV[0]`;
+if ($?) {die "famdef failed. Exit code $?\n";}
+
+`rm -f tmp`;
+
diff --git a/src/Makefile b/src/Makefile
new file mode 100644
index 0000000..3b709c1
--- /dev/null
+++ b/src/Makefile
@@ -0,0 +1,123 @@
+# Makefile for ReCon
+#
+#
+VERSION = 1.08
+
+## where you want things installed
+BINDIR = ../bin
+MANDIR = $(HOME)/man
+
+## sourcefiles
+#SRCDIR = .
+
+## your compiler
+#CC = cc # for SGI Origin200 compiler#
+CC = gcc
+
+## any special compiler flags you want
+# -pedantic clashes with -DMEMDEBUG??
+#
+#CFLAGS = -g -Wall -pedantic
+CFLAGS = -O
+#CFLAGS = -g
+#CFLAGS = -TARG:exc_max -64 -Ofast=ip27 #specific SGI Origin200 compiler#
+
+## machine specific definitions
+# None should be needed
+#
+# Development:
+# -DASSERT Diagnostics level 1. Assertions.
+# -DVERBOSE Diagnostics level 2. Verbosity. (unused at the moment)
+# -DMEMDEBUG Diagnostics level 3. Memory checking. (maybe slow!)
+# (must link w/ -ldbmalloc)
+# -DLINTING Suppress overzealous warnings from gcc -Wall and lint
+#
+#MDEFS = -DLINTING -DASSERT -DMEMDEBUG
+#MDEFS = -DASSERT
+
+## how to install the man pages
+## cp is fine
+INSTMAN = cp
+MANSUFFIX = 1
+
+## Your compression program
+COMPRESS = gzip # GNU compression (better, smaller)
+#COMPRESS = compress # generic UNIX compress (portable)
+
+#######
+## should not need to modify below this line
+#######
+SHELL = /bin/sh
+LIBS = -lsquid -lm
+#LIBS = -ldbmalloc -lsquid -lm
+
+READMES = README
+#INSTALL COPYING DEMO GNULICENSE FILES
+
+PROGS = imagespread eledef eleredef edgeredef famdef
+
+MANSRC=
+
+DOCS =
+
+HDRS = bolts.h seqlist.h msps.h ele.h
+
+MAIN =
+
+SRC = imagespread.c eledef.c eleredef.c edgeredef.c famdef.c
+
+
+OBJ =
+
+DISTFILES = $(MAIN) $(SRC) $(HDRS) $(MANSRC) $(READMES) $(DOCS)
+
+TESTSUITE =
+
+DEMOS = $(HOME)/Demos
+
+all: $(PROGS)
+
+
+install: $(PROGS)
+ cp $(PROGS) $(BINDIR)/
+
+clean:
+ -rm -f imagespread eledef eleredef edgeredef famdef *.o *~ *.Addrs *.Counts *.pixie Makefile.bak core $(PROGS) TAGS
+
+tags:
+ etags -t $(DISTFILES)
+
+dist:
+ @if test -d recon-$(VERSION); then rm -rf recon-$(VERSION); fi
+ @if test -f recon-$(VERSION).tar.gz; then rm recon-$(VERSION).tar.gz; fi
+ @if test -f recon-$(VERSION).tar.Z; then rm recon-$(VERSION).tar.Z; fi
+ mkdir recon-$(VERSION)/
+ cp $(DISTFILES) recon-$(VERSION)/
+ cp Makefile.dist recon-$(VERSION)/Makefile
+ mkdir recon-$(VERSION)/Testsuite
+ for testfile in $(TESTSUITE); do \
+ cp Testsuite/$$testfile recon-$(VERSION)/Testsuite/;\
+ done
+ mkdir recon-$(VERSION)/Demos
+ for demofile in $(DEMOS); do\
+ cp Demos/$$demofile recon-$(VERSION)/Demos/;\
+ done
+ tar cvf recon-$(VERSION).tar recon-$(VERSION)
+ $(COMPRESS) recon-$(VERSION).tar
+
+test:
+ (cd Testsuite; testsuite.sh)
+
+lint:
+ lint -h -I$(SQUIDDIR) $(RFLAGS) $(MAIN) $(SRC) $(SQUIDDIR)/llib-lsquid.ln /usr/lib/lint/llib-lm.ln
+
+.c.o:
+ $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+
+.m.o:
+ $(CC) $(CFLAGS) $(MDEFS) -I$(SQUIDDIR) -c $<
+
+
+
+
+
diff --git a/src/bolts.h b/src/bolts.h
new file mode 100644
index 0000000..8375ea3
--- /dev/null
+++ b/src/bolts.h
@@ -0,0 +1,14 @@
+/* standard stuff */
+
+#include <stdio.h>
+#include <math.h>
+#include <stdlib.h>
+
+
+#define NAME_LEN 50
+#define DEPTH 3
+
+
+
+int32_t seq_no;
+char **seq_names;
diff --git a/src/edgeredef.c b/src/edgeredef.c
new file mode 100644
index 0000000..e91db3a
--- /dev/null
+++ b/src/edgeredef.c
@@ -0,0 +1,462 @@
+#include "ele.h"
+
+#define CUTOFF3 0.7
+
+
+
+
+void report_redef_stat();
+
+void general_edge_redef(ELE_INFO_t *);
+void build_local_edge_net(ELE_INFO_t *, int, ELE_DATA_t **);
+void local_edge_net_walk(ELE_INFO_t *, EDGE_TREE_t *, int, ELE_DATA_t **);
+void cruise_local_edge_net(ELE_DATA_t *);
+void dissolve_local_edge_net(ELE_DATA_t **);
+void stage_exit(int );
+void edge_filt(ELE_INFO_t *);
+EDGE_TREE_t *find_PPS(ELE_INFO_t *, EDGE_TREE_t *);
+EDGE_TREE_t * edge_update(ELE_INFO_t *, EDGE_TREE_t *, EDGE_TREE_t *);
+
+void edge_repair(ELE_INFO_t *);
+EDGE_TREE_t *best_link(ELE_INFO_t *, EDGE_TREE_t *);
+
+
+
+
+int main (int argc, char *argv[]) {
+ int i, rounds=0, ei, start;
+ short to_march;
+ char line[35], stat;
+ FILE *seq_list, *ele_no, *redef_stat;
+
+ /* processing command line */
+ if (argc == 1) {
+ printf("usage: fam_def seq_list start\n where seq_list is the list of sequence names, start is the index of the element to start defining families. The latter one is optional.\n");
+ exit(1);
+ }
+
+ seq_list = fopen(argv[1], "r");
+ if (!seq_list) {
+ printf("Input file for sequence name list %s not found. Exit.\n", argv[1]);
+ exit(2);
+ }
+ GetSeqNames(seq_list);
+
+ if (argc > 2) start = atoi(argv[2]) - 1;
+ else start = 0;
+
+ ele_no = fopen("summary/redef_ele_no", "r");
+ if(!ele_no) {
+ printf("Can not open redef_ele_no. Exiting\n");
+ exit(1);
+ }
+
+ redef_stat = fopen("tmp/redef_stat", "r");
+ if (!redef_stat) {
+ printf("Can not open redef_stat. Exiting\n");
+ exit(1);
+ }
+
+ log_file = fopen("tmp2/log", "w");
+ if (!log_file) {
+ printf("Can not open log_file. Exiting\n");
+ exit(1);
+ }
+
+ while (fgets(line, 15, ele_no)) {
+ ele_ct = atoi(line);
+ }
+ fclose(ele_no);
+
+ ele_array_size = ele_ct;
+ all_ele = (ELE_INFO_t **) malloc(ele_array_size*sizeof(ELE_INFO_t *));
+
+ for (i=0; i<ele_ct; i++) {
+ *(all_ele+i) = ele_info_init(i+1);
+ }
+
+ ele_ct = 0;
+ while (fgets(line, 35, redef_stat)) {
+ ele_ct ++;
+ /*sscanf(line, "%d %c %d\n", &ei, &stat, &fu);*/
+ /* for some bizzare reason, scanf doesn't work properly here. :( */
+ for (i=0; i<35; i++) {
+ if (line[i] == ' ') break;
+ }
+ ei = atoi(line);
+ stat = line[i+1];
+ (*(all_ele+ei-1))->stat = stat;
+ }
+
+
+ msp_in_mem = 0;
+ msp_left = 0;
+ msp_ct = 0;
+ edge_ct = 0;
+ edge_in_mem = 0;
+ edge_left = 0;
+ files_read = 0;
+ clan_ct = 0;
+ err_no = 0;
+
+ /* update edges, to get rid of PPS */
+
+ for (i=start; i<ele_ct; i++) {
+ if ((*(all_ele+i))->stat != 'O' && (*(all_ele+i))->stat != 'X') {
+ fprintf(log_file, "evaluating edges of element %d\n", (*(all_ele+i))->index);
+ fflush(log_file);
+ if ((*(all_ele+i))->stat == 'v') {
+ general_edge_redef(*(all_ele+i));
+ report_redef_stat();
+ } else if((*(all_ele+i))->stat != 'y') {
+ err_no ++;
+ fprintf(log_file, "ele %d %c not properly defined\n", (*(all_ele+i))->index, (*(all_ele+i))->stat);
+ fflush(log_file);
+ exit(5);
+ }
+ }
+ }
+
+ for (i=start; i<ele_ct; i++) {
+ if ((*(all_ele+i))->stat != 'O' && (*(all_ele+i))->stat != 'X') {
+ fprintf(log_file, "repairing edges of element %d\n", (*(all_ele+i))->index);
+ fflush(log_file);
+ if ((*(all_ele+i))->stat == 'y') {
+ edge_repair(*(all_ele+i));
+ } else {
+ err_no ++;
+ fprintf(log_file, "ele %d %c edges not properly redefined\n", (*(all_ele+i))->index, (*(all_ele+i))->stat);
+ fflush(log_file);
+ exit(5);
+ }
+ }
+ }
+
+ fprintf(log_file, "total numbers: %d elements, %d msps, %d edges\n", ele_ct, msp_index+1, edge_index+1);
+ fprintf(log_file, "%d files read, %d msps seen, %d edges seen\n", files_read, msp_ct, edge_ct);
+ fprintf(log_file, "%d errors, %d msps and %d edges left in memory, \n", err_no, msp_left, edge_left);
+ fflush(log_file);
+ fclose(log_file);
+
+
+ exit(0);
+}
+
+
+
+
+void report_redef_stat() {
+ int i;
+ FILE *redef_stat;
+
+ redef_stat = fopen("tmp2/redef_stat", "w");
+ for (i=0; i<ele_ct; i++) {
+ fprintf(redef_stat, "%d %c %d\n", (*(all_ele+i))->index, (*(all_ele+i))->stat, (*(all_ele+i))->file_updated);
+ }
+
+ fclose(redef_stat);
+}
+
+
+
+
+
+
+
+
+/***********************************
+ ***********************************
+ ** **
+ ** UPDATING THE EDGES **
+ ** **
+ ***********************************
+ ***********************************/
+
+
+
+
+void general_edge_redef(ELE_INFO_t *ele_info) {
+ ELE_DATA_t *local_net=NULL;
+ char *command;
+
+ if (!ele_info->ele) ele_read_in(ele_info, 2);
+
+ if (ele_info->ele->edges) {
+ clan_ct ++;
+ clan_size = 0;
+ clan_core_size = 0;
+ fprintf(log_file, "new clan: %d for ele %d\n", clan_ct, ele_info->index);
+ fflush(log_file);
+ build_local_edge_net(ele_info, 1, &local_net); /*notice level here is 0, not 1 */
+ fprintf(log_file, "clan size: %d, clan core size: %d\n", clan_size, clan_core_size);
+ fflush(log_file);
+ cruise_local_edge_net(local_net);
+ dissolve_local_edge_net(&local_net);
+ } else {
+ ele_info->stat = 'y';
+ ele_cleanup(&ele_info->ele);
+ command = (char *) malloc(80*sizeof(char));
+ sprintf(command, "cp tmp/e%d tmp2/.", ele_info->index);
+ system(command);
+ free(command);
+ }
+}
+
+
+
+
+/* notice the structural similarity and difference b/t the following two functions and the corresponding ones in redef.c */
+/* notice that it's much simpler here */
+
+void build_local_edge_net(ELE_INFO_t *ele_info, int level, ELE_DATA_t **net_p) {
+ ELE_INFO_t *epi;
+ ELE_DATA_t *que;
+ ELEMENT_t *ele;
+
+ clan_size ++;
+ que = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ que->ele_info = ele_info;
+ que->next = *net_p;
+ *net_p = que;
+
+ if (!ele_info->ele) ele_read_in(ele_info, 1);
+ ele = ele_info->ele;
+
+ if (level < DEPTH) {
+ if (ele_info->stat != 'y') {
+ ele->l_hold = 1;
+ clan_core_size ++;
+ /*fprintf(log_file, " %d\n", ele_info->index);
+ fflush(log_file);*/
+ level ++;
+ if (ele->edges) local_edge_net_walk(ele_info, ele->edges, level, net_p);
+ else {
+ err_no ++;
+ fprintf(log_file, "error: edge tree missing in ele %d\n", ele_info->index);
+ fflush(log_file);
+ }
+ } else ele->l_hold = 2;
+ } else ele->l_hold = 2;
+}
+
+
+
+
+
+void local_edge_net_walk(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, int level, ELE_DATA_t **net_p) {
+ ELE_INFO_t *epi;
+ ELEMENT_t *ele=ele_info->ele;
+
+ if (rt->l) local_edge_net_walk(ele_info, rt->l, level, net_p);
+
+ if (rt->to_edge->type == 'p' || rt->to_edge->type == 'S' || rt->to_edge->type == 'P') {
+ epi = linked_ele(ele_info, rt->to_edge);
+ if (!epi->ele) ele_read_in(epi, 2);
+ if (!epi->ele->l_hold) build_local_edge_net(epi, level, net_p);
+ }
+
+ if (rt->r) local_edge_net_walk(ele_info, rt->r, level, net_p);
+}
+
+
+
+
+void cruise_local_edge_net(ELE_DATA_t *local_net) {
+ ELE_DATA_t *que;
+
+ que = local_net;
+ while (que) {
+ /* here, all elements in the local_network are explicitly hung in ques,
+ unlike in the local_network for ele_ref, where some are hung in redef
+ of other elements */
+ /* also, no need to march for a second time, since once edge_filt is done,
+ the status will not be affected by the processing of other elements, so
+ no need to come back and re-do it */
+ if (que->ele_info->ele->l_hold == 1) {
+ if (que->ele_info->stat != 'y') {
+ if (que->ele_info->ele->edges) edge_filt(que->ele_info);
+ else if (que != local_net) {
+ fprintf(log_file, "error: ele %d edge tree missing\n", que->ele_info->index);
+ fflush(log_file);
+ exit(4);
+ }
+ que->ele_info->stat = 'y';
+ }
+ else {
+ fprintf(log_file, "error: ele %d conflicting status in local network\n", que->ele_info->index);
+ fflush(log_file);
+ exit(5);
+ }
+ }
+ que = que->next;
+ }
+}
+
+
+
+
+void dissolve_local_edge_net(ELE_DATA_t **net_p) {
+ ELE_DATA_t *que;
+ char *command;
+ int i, ele_left=0;
+
+ que = *net_p;
+ while (que) {
+ que->ele_info->ele->l_hold = 0;
+ ele_write_out(que->ele_info, 2);
+ ele_cleanup(&que->ele_info->ele);
+ que = que->next;
+ }
+ ele_data_free(net_p);
+
+ if (msp_in_mem) {
+ err_no ++;
+ fprintf(log_file, "error: error in bookkeeping: %d msps total, %d seen, %d left in memory\n", msp_index+1, msp_ct, msp_in_mem);
+ fflush(log_file);
+ msp_left += msp_in_mem;
+
+ }
+
+ if (edge_in_mem) {
+ err_no ++;
+ fprintf(log_file, "error: error in bookkeeping: %d edges total, %d seen, %d left in memory\n", edge_index+1, edge_ct, edge_in_mem);
+ fflush(log_file);
+ edge_left += edge_in_mem;
+ edge_in_mem = 0;
+ }
+
+ for (i=0; i<ele_ct; i++) {
+ if ((*(all_ele+i))->ele) {
+ ele_left ++;
+ err_no ++;
+ fprintf(log_file, "error: element %d not cleaned from memory. stat = %c\n", i+1, (*(all_ele+i))->stat);
+ fflush(log_file);
+ }
+ }
+ if (ele_left) {
+ err_no ++;
+ fprintf(log_file, "error: %d elements left in memory\n", ele_left);
+ fflush(log_file);
+ }
+
+ if (err_no) exit(3);
+
+#if 0
+ command = (char *) malloc(50*sizeof(char));
+ sprintf(command, "mv -f tmp2/clan/e* tmp2/.");
+ if (system(command)) {
+ fprintf(log_file, "error moving files from tmp2/clan/\n");
+ fflush(log_file);
+ stage_exit(6);
+ }
+ free(command);
+#endif
+}
+
+
+
+
+void stage_exit(int code) {
+ char *command = (char *) malloc(50*sizeof(char));
+
+ sprintf(command, "mv -f tmp2/redef_stat tmp2/redef_stat_prev");
+ if (system(command)) {
+ fprintf(log_file, "error in moving tmp2/redef_stat\n");
+ fflush(log_file);
+ exit(code);
+ }
+
+ report_redef_stat();
+ exit(code);
+}
+
+
+
+
+void edge_filt(ELE_INFO_t *ele_info) {
+ EDGE_TREE_t *max;
+
+ max = find_PPS(ele_info, ele_info->ele->edges);
+
+ if (max) {
+ max = edge_update(ele_info, ele_info->ele->edges, max);
+ max->to_edge->type = 'P';
+ }
+}
+
+
+
+EDGE_TREE_t *find_PPS(ELE_INFO_t *ele_info, EDGE_TREE_t *rt) {
+ ELE_INFO_t *epi;
+ EDGE_TREE_t *res=NULL;
+
+ if (rt->to_edge->type == 'p' || rt->to_edge->type == 'S') {
+ epi = linked_ele(ele_info, rt->to_edge);
+ if (((float) ele_info->ele->frag.rb - ele_info->ele->frag.lb)/(epi->ele->frag.rb - epi->ele->frag.lb) < CUTOFF3) res = rt;
+ }
+
+ if (!res && rt->l) res = find_PPS(ele_info, rt->l);
+ if (!res && rt->r) res = find_PPS(ele_info, rt->r);
+
+ return res;
+}
+
+
+
+
+EDGE_TREE_t *edge_update(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, EDGE_TREE_t *ref) {
+ ELE_INFO_t *epi;
+
+ if (rt->l) ref = edge_update(ele_info, rt->l, ref);
+ if (rt->r) ref = edge_update(ele_info, rt->r, ref);
+
+ epi = linked_ele(ele_info, rt->to_edge);
+
+ if (rt->to_edge->type == 'p' || rt->to_edge->type == 'S') {
+ if (((float) ele_info->ele->frag.rb - ele_info->ele->frag.lb)/(epi->ele->frag.rb - epi->ele->frag.lb) < CUTOFF3) {
+ if (rt->to_edge->score > ref->to_edge->score) {
+ ref->to_edge->type = 'S';
+ ref = rt;
+ } else {
+ rt->to_edge->type = 'S';
+ }
+ } else {
+ if (rt->to_edge->type == 'p') rt->to_edge->type = 'S';
+ }
+ }
+
+ return ref;
+}
+
+
+void edge_repair(ELE_INFO_t *ele_info) {
+ EDGE_TREE_t *hanger;
+
+ ele_read_in(ele_info, 2);
+ if (ele_info->ele->edges) {
+ hanger = best_link(ele_info, ele_info->ele->edges);
+ if (!hanger) {
+ fprintf(log_file, "ele %d can not be repaired.\n", ele_info->index);
+ } else if (hanger->to_edge->type == 'S') {
+ hanger->to_edge->type == 'P';
+ ele_write_out(ele_info, 2);
+ }
+ }
+ ele_cleanup(&ele_info->ele);
+}
+
+
+EDGE_TREE_t *best_link(ELE_INFO_t *ele_info, EDGE_TREE_t *rt) {
+ EDGE_TREE_t *res=NULL;
+
+ if (rt->to_edge->type == 'p') res = rt;
+ else if (rt->to_edge->type == 'P' || rt->to_edge->type == 'S') {
+ if (!res || rt->to_edge->score > res->to_edge->score) res = rt;
+ }
+
+ if ((!res || res->to_edge->type != 'p') && rt->l) res = best_link(ele_info, rt->l);
+ if ((!res || res->to_edge->type != 'p') && rt->r) res = best_link(ele_info, rt->r);
+
+ return res;
+}
+
diff --git a/src/ele.h b/src/ele.h
new file mode 100644
index 0000000..1c7aad3
--- /dev/null
+++ b/src/ele.h
@@ -0,0 +1,1442 @@
+#include "msps.h"
+
+
+#define SIZE_LIMIT 500
+#define TANDEM 5
+
+
+
+
+typedef struct cp_list {
+ int32_t cp;
+ struct ele_info *contributor;
+ struct cp_list *next;
+} CP_t;
+
+typedef struct bd_list {
+ int32_t bd;
+ int support;
+ struct bd_list *next;
+} BD_t;
+
+typedef struct edge {
+ int index;
+ char type; /* 'p', 's', 'c' */
+ int direction; /* for clustering elements in consistent directions */
+ int32_t score; /* for edge_filt, to solve the PPS problem */
+ struct ele_info *ele1_info, *ele2_info;
+} EDGE_t;
+
+/* typedef struct edge_list {
+ EDGE_t *to_edge;
+ struct edge_list *next;
+} EDGE_DATA_t; */
+
+typedef struct edge_tree {
+ EDGE_t *to_edge;
+ struct edge_tree *p, *l, *r;
+} EDGE_TREE_t;
+
+typedef struct element {
+ int index;
+ FRAG_t frag;
+ int direction;
+ short update, l_hold;
+ int img_no, flimg_no, edge_no;
+ IMG_TREE_t *to_img_tree;
+ IMG_DATA_t *to_img_data;
+ EDGE_TREE_t *edges;
+ CP_t *PCP;
+ BD_t *TBD;
+ struct ele_list *redef;
+/* IMG_REC_t *ignored, *dissected; */
+} ELEMENT_t;
+
+typedef struct ele_info {
+ int index;
+ ELEMENT_t *ele;
+ char stat; /* 'z', 't', 'v', 'w', 'y', 'x' and 'X' */
+ short file_updated;
+ struct family *to_family;
+ struct ele_info *next;
+} ELE_INFO_t;
+
+typedef struct ele_list {
+ struct ele_info *ele_info;
+ struct ele_list *next;
+} ELE_DATA_t;
+
+
+typedef struct family {
+ int index;
+ char name[10];
+ ELE_DATA_t *members;
+ struct fam_list *relatives;
+} FAMILY_t;
+
+typedef struct fam_list {
+ struct family *to_family;
+ struct fam_list *next;
+} FAM_DATA_t;
+
+
+
+
+
+ELEMENT_t *ele_init(int);
+ELE_INFO_t *ele_info_init(int);
+MSP_t *MSP_malloc();
+void MSP_free(MSP_t *);
+EDGE_t *EDGE_malloc();
+void EDGE_free(EDGE_t *);
+
+ELE_INFO_t *linked_ele(ELE_INFO_t *, EDGE_t *);
+void outthrow_big_tandems(FILE *);
+int int_cmp(const void *, const void *);
+void spit_out_ele(ELE_INFO_t *);
+
+ELEMENT_t *ele_read_in(ELE_INFO_t *, int);
+void img_scan(ELE_INFO_t *, char *, IMAGE_t **, int *);
+void edge_scan(char *, EDGE_t **, ELE_INFO_t *, int *);
+ELE_INFO_t *get_ele_info(int);
+
+void ele_write_out(ELE_INFO_t *, int);
+int img_index_cmp(const void *, const void *);
+int edge_index_cmp(const void *, const void *);
+void write_out_msps(FILE *, IMG_TREE_t *);
+void write_out_edges(FILE *, EDGE_TREE_t *, ELE_INFO_t *);
+
+void build_img_tree(IMG_TREE_t **, IMAGE_t **, int, int);
+int count_img_nodes(IMG_TREE_t *);
+void insert_image(IMG_TREE_t **, IMAGE_t *);
+void delete_image(IMG_TREE_t **, IMAGE_t *);
+IMG_TREE_t *minimal_image(IMG_TREE_t *);
+IMG_TREE_t *find_image(IMG_TREE_t *, int);
+IMG_DATA_t **listify(IMG_TREE_t *, IMG_DATA_t **);
+
+void build_edge_tree(EDGE_TREE_t **, EDGE_t **, int, int);
+int count_edge_nodes(EDGE_TREE_t *);
+int count_total_edges(EDGE_TREE_t *);
+void insert_edge(EDGE_TREE_t **, EDGE_t *);
+void delete_edge(EDGE_TREE_t **, EDGE_t *);
+EDGE_TREE_t *minimal_edge(EDGE_TREE_t *);
+EDGE_TREE_t *find_edge(EDGE_TREE_t *, int);
+
+void ele_info_free(ELE_INFO_t **);
+void ele_cleanup(ELEMENT_t **);
+void BD_free(BD_t **);
+void CP_free(CP_t **);
+void ele_data_free(ELE_DATA_t **);
+void img_data_free (IMG_DATA_t **);
+void img_tree_free(IMG_TREE_t **, ELE_INFO_t *);
+void img_tree_cleanup(IMG_TREE_t **, ELE_INFO_t *);
+void msp_data_free(MSP_DATA_t **);
+void edge_tree_cleanup(ELE_INFO_t *, EDGE_TREE_t **);
+void edge_tree_free(EDGE_TREE_t **);
+void fam_data_free(FAM_DATA_t **);
+void fam_data_cleanup(FAM_DATA_t **);
+void fam_cleanup(FAMILY_t **);
+void frag_data_free(FRAG_DATA_t **);
+void frag_data_cleanup(FRAG_DATA_t **);
+
+void print_ele_info(ELE_INFO_t *rt);
+void print_ele_data(ELE_DATA_t *rt);
+
+/*MSP_DATA_t *all_msps=NULL;
+ EDGE_t *efav=NULL;*/
+ELE_INFO_t **all_ele;
+int ele_ct, ele_array_size, fam_ct;
+int clan_size, clan_core_size;
+int32_t msp_in_mem, msp_left, msp_ct, msp_index;
+int32_t edge_index, edge_in_mem, edge_left, edge_ct;
+int32_t files_read, clan_ct, err_no;
+ELE_INFO_t *ele_info_data, *ele_info_tail;
+FAM_DATA_t *FAMs;
+FILE *err, *new_msps, *eles, *unproc, *combo, *obs, *fams, *log_file;
+
+
+/***************
+ * DEBUG *
+ ***************/
+
+void print_ele_data(ELE_DATA_t *rt) {
+ if (!rt) return;
+ print_ele_info( rt->ele_info );
+ if (rt->next)
+ print_ele_data(rt->next);
+}
+
+void print_ele_info(ELE_INFO_t *rt) {
+ if (!rt) return;
+ printf("ele: index=%d, stat=%c, file_update=%d", rt->index, rt->stat,
+ rt->file_updated );
+ if ( rt->to_family )
+ printf(" family_index=%d,", rt->to_family->index );
+ if ( rt->ele )
+ printf(" ele_index=%d", rt->ele->index );
+ else
+ printf(" ele=NULL");
+ printf("\n");
+}
+
+
+
+
+/***************
+ * Initializer *
+ ***************/
+
+
+
+ELEMENT_t *ele_init(int index) {
+ ELEMENT_t *ele_tmp = (ELEMENT_t *) malloc(sizeof(ELEMENT_t));
+
+ ele_tmp->index = index;
+ ele_tmp->direction = 1;
+ ele_tmp->update = 0;
+ ele_tmp->l_hold = 0;
+ ele_tmp->img_no = 0;
+ ele_tmp->flimg_no = 0;
+ ele_tmp->edge_no = 0;
+ ele_tmp->to_img_data = NULL;
+ ele_tmp->to_img_tree = NULL;
+ ele_tmp->edges = NULL;
+ ele_tmp->PCP = NULL;
+ ele_tmp->TBD = NULL;
+ ele_tmp->redef = NULL;
+
+ return ele_tmp;
+}
+
+
+
+ELE_INFO_t *ele_info_init(int index) {
+ ELE_INFO_t *ele_info_tmp;
+
+ ele_info_tmp = (ELE_INFO_t *) malloc(sizeof(ELE_INFO_t));
+
+ ele_info_tmp->index = index;
+ ele_info_tmp->file_updated = 0;
+ ele_info_tmp->stat = 'z';
+ ele_info_tmp->ele = NULL;
+ ele_info_tmp->to_family = NULL;
+ ele_info_tmp->next = NULL;
+
+ return ele_info_tmp;
+}
+
+
+
+
+MSP_t *MSP_malloc() {
+ MSP_t *msp_tmp = (MSP_t *) malloc(sizeof(MSP_t));
+ /*MSP_DATA_t *new_hanger = (MSP_DATA_t *) malloc(sizeof(MSP_DATA_t *));*/
+
+ msp_in_mem ++;
+ msp_ct ++;
+ /*new_hanger->to_msp = msp_tmp;
+ new_hanger->next = all_msps;
+ all_msps = new_hanger;
+
+ msp_tmp->hanger = new_hanger;*/
+
+ return msp_tmp;
+}
+
+
+
+
+void MSP_free(MSP_t *m) {
+ msp_in_mem --;
+ /*m->hanger->to_msp = NULL;*/
+ free(m);
+}
+
+
+
+
+EDGE_t *EDGE_malloc() {
+ EDGE_t *edge_tmp = (EDGE_t *) malloc(sizeof(EDGE_t));
+
+ edge_in_mem ++;
+ edge_ct ++;
+
+ return edge_tmp;
+}
+
+
+
+
+void EDGE_free(EDGE_t *ed) {
+ edge_in_mem --;
+ free(ed);
+}
+
+
+
+
+/***************
+ * Small Tools *
+ ***************/
+
+
+
+
+ELE_INFO_t *linked_ele(ELE_INFO_t *ele_info, EDGE_t *edge) {
+ if (ele_info->index == edge->ele1_info->index) return edge->ele2_info;
+ return edge->ele1_info;
+}
+
+
+
+
+void outthrow_big_tandems(FILE *size_list){
+ int ei, ino;
+ FILE *ele_file;
+ char ele_name[50], line[150], head[10], *msp = "msp";
+ int id, ele1, ele2;
+ int *partners, i_ct, i, p_id, p_ct;
+ int ratio;
+
+ while (fgets(line, 25, size_list)) {
+ sscanf(line, "%d %d\n", &ei, &ino);
+ if (ino > SIZE_LIMIT) {
+ sprintf(ele_name, "tmp/e%d", ei);
+ ele_file = fopen(ele_name, "r");
+ if (!ele_file) {
+ fprintf(log_file, "Can not open ele file %s. Exit.\n", ele_name);
+ exit(2);
+ }
+ partners = (int *) malloc(ino*sizeof(int));
+ p_ct = 0;
+ i_ct = -1;
+ p_id = -1;
+ while (fgets(line, 150, ele_file)) {
+ sscanf(line, "%s %*s", head);
+ if (!strncmp(head, msp, 3)) {
+ sscanf(line, "msp %d %*c %*d %*f %*d %d %*s %*d %*d %d %*s %*d %*d\n", &id, &ele1, &ele2);
+ i_ct ++;
+ if (id%2) *(partners+i_ct) = ele1;
+ else *(partners+i_ct) = ele2;
+ }
+ }
+ qsort(partners, i_ct+1, sizeof(int), int_cmp);
+ for (i=0; i<=i_ct; i++) {
+ if (*(partners+i) != p_id) {
+ p_id = *(partners+i);
+ p_ct ++;
+ }
+ }
+ if (ino/p_ct > TANDEM) {
+ (*(all_ele+ei-1))->stat = 'O';
+ spit_out_ele(*(all_ele+ei-1));
+ }
+ free(partners);
+ fclose(ele_file);
+ }
+ }
+}
+
+
+
+int int_cmp(const void *i1, const void *i2) {
+ return *((int *) i1) - *((int *) i2);
+}
+
+
+
+void spit_out_ele(ELE_INFO_t *ele_info) {
+ /* char *command = (char *) malloc(100*sizeof(char));*/
+
+ ele_info->file_updated = 1;
+ /* the reason for using ln instead of mv is to avoid changing files in tmp/ */
+#if 0
+ sprintf(command, "ln -s tmp/e%d unproc/.\n", ele_info->index);
+ if (system(command)) {
+ fprintf(log_file, "error linking tmp/e%d to unproc/\n", ele_info->index);
+ fflush(log_file);
+ exit(6);
+ }
+#endif
+ fprintf(unproc, "%d\n", ele_info->index);
+ /* free(command);*/
+}
+
+
+
+
+
+/**********************
+ * Read in an element *
+ **********************/
+
+
+
+
+ELEMENT_t *ele_read_in(ELE_INFO_t *ele_info, int stage) {
+ char line[200], head[10], rest[150], *fn = (char *) malloc(20*sizeof(char));
+ char fragname[NAME_LEN];
+ int pos;
+ FILE *fp;
+ IMAGE_t **img_array;
+ EDGE_t **edge_array;
+ int holder, img_encountered=0, edge_encountered=0, ct;
+ CP_t *new_pcp;
+ BD_t *new_tbd;
+ ELE_DATA_t *cur_ele_data;
+
+ char *index="index", *stat = "stat", *file_updated="file_updated", *family="family", *direc="direc", *update="update", *l_hold="l_hold", *img_no="img_no", *flimg_no="flimg_no", *edge_no="edge_no", *frag="frag", *pcp="pcp", *tbd="tbd", *redef="redef", *msp="msp", *edge="edge";
+
+ if (ele_info->file_updated) sprintf(fn, "tmp2/e%d", ele_info->index);
+ else sprintf(fn, "tmp/e%d", ele_info->index);
+ fp = fopen(fn, "r");
+ /*if (!fp) {
+ sprintf(fn, "tmp/e%d", ele_info->index);
+ fp = fopen(fn, "r");
+ }*/
+ files_read ++;
+
+ ele_info->ele = ele_init(ele_info->index);
+
+ while (fgets(line, 200, fp)) {
+ sscanf(line, "%s %*s", head);
+/* if (!strncmp(head, index, 10)) sscanf(rest, "%d\n", ele_info->index);
+ if (!strncmp(head, stat, 10)) sscanf(rest, "%c\n", ele_info->stat);
+ if (!strncmp(head, file_updated, 10)) sscanf(rest, "%d\n", ele_info->file_updated); */
+
+ /* if (!strncmp(head, l_hold, 10)) {sscanf(line, "%*s %d\n", &ele_info->ele->l_hold); continue;} */
+ if (!strncmp(head, update, 10)) {sscanf(line, "%*s %hd\n", &ele_info->ele->update); continue;}
+ if (!strncmp(head, direc, 10)) {sscanf(line, "%*s %d\n", &ele_info->ele->direction); continue;}
+ if (!strncmp(head, flimg_no, 10)) {sscanf(line, "%*s %d\n", &ele_info->ele->flimg_no); continue;}
+ if (!strncmp(head, frag, 10)) {
+ sscanf(line, "%*s %s %d %d\n", fragname, &ele_info->ele->frag.lb, &ele_info->ele->frag.rb);
+ pos = GetSeqIndex(0, seq_no-1, fragname);
+ ele_info->ele->frag.seq_name = *(seq_names+pos);
+ if (ele_info->ele->frag.lb > ele_info->ele->frag.rb) {
+ fprintf(log_file, "error: ele %d reversed from read_in\n", ele_info->index);
+ fflush(log_file);
+ exit(3);
+ }
+ continue;
+ }
+ if (!strncmp(head, edge_no, 10)) {
+ sscanf(line, "%*s %d\n", &ele_info->ele->edge_no);
+ if (ele_info->ele->edge_no) edge_array = (EDGE_t **) malloc(ele_info->ele->edge_no*sizeof(EDGE_t *));
+ continue;
+ }
+ if (!strncmp(head, edge, 10)) {
+ if (edge_encountered < ele_info->ele->edge_no) {
+ edge_scan(line, edge_array, ele_info, &edge_encountered);
+ } else {
+ err_no ++;
+ fprintf(log_file, "error: more edges in file for ele %d\n", ele_info->index);
+ fflush(log_file);
+ exit(4);
+ }
+ continue;
+ }
+ if (!strncmp(head, img_no, 10)) {
+ sscanf(line, "%*s %d\n", &ele_info->ele->img_no);
+ if (stage != 3 && ele_info->ele->img_no) img_array = (IMAGE_t **) malloc(ele_info->ele->img_no*sizeof(IMAGE_t *));
+ continue;
+ }
+ if (stage != 3 && !strncmp(head, msp, 10)) {
+ if (img_encountered < ele_info->ele->img_no) {
+ img_scan(ele_info, line, img_array, &img_encountered);
+ } else {
+ err_no ++;
+ fprintf(log_file, "error: more image in file for ele %d\n", ele_info->index);
+ fflush(log_file);
+ exit(2);
+ }
+ continue;
+ }
+ if (stage < 2 && !strncmp(head, pcp, 10)) {
+ new_pcp = (CP_t *) malloc(sizeof(CP_t));
+ sscanf(line, "%*s %d %d\n", &new_pcp->cp, &holder);
+ new_pcp->contributor = get_ele_info(holder);
+ new_pcp->next = ele_info->ele->PCP;
+ ele_info->ele->PCP = new_pcp;
+ continue;
+ }
+ if (!strncmp(head, tbd, 10)) {
+ new_tbd = (BD_t *) malloc(sizeof(BD_t));
+ sscanf(line, "%*s %d %d\n", &new_tbd->bd, &new_tbd->support);
+ new_tbd->next = ele_info->ele->TBD;
+ ele_info->ele->TBD = new_tbd;
+ continue;
+ }
+ if (!strncmp(head, redef, 10)) {
+ sscanf(line, "%*s %d\n", &holder);
+ cur_ele_data = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ cur_ele_data->ele_info = get_ele_info(holder);
+ cur_ele_data->next = ele_info->ele->redef;
+ ele_info->ele->redef = cur_ele_data->next;
+ continue;
+ }
+ }
+
+ fclose(fp);
+ free(fn);
+ if (stage != 3 && img_encountered != ele_info->ele->img_no) {
+ if (ele_info->file_updated) { /* we spit out elements with too many images, so some of their partners might have less images left than img_no */
+ err_no ++;
+ fprintf(log_file, "error: %d: image number not matched.\n", ele_info->index);
+ fflush(log_file);
+ exit(2);
+ }
+ ele_info->ele->img_no = img_encountered;
+ }
+
+ if (edge_encountered != ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: %d: edge number not matched.\n", ele_info->index);
+ fflush(log_file);
+ exit(4);
+ ele_info->ele->edge_no = edge_encountered;
+ }
+
+ /*ele_info->ele->index = ele_info->index;*/
+ if (edge_encountered) {
+ qsort(edge_array, edge_encountered, sizeof(EDGE_t *), edge_index_cmp);
+ build_edge_tree(&ele_info->ele->edges, edge_array, 0, edge_encountered-1);
+ /*ct = count_edge_nodes(ele_info->ele->edges);
+ if (ct != edge_encountered) {
+ err_no ++;
+ fprintf(log_file, "error: trouble building edge tree: %d %d\n", edge_encountered, ct);
+ fflush(log_file);
+ exit(4);
+ }*/
+ free(edge_array);
+ }
+ if (stage != 3 && ele_info->ele->img_no) {
+ qsort(img_array, img_encountered, sizeof(IMAGE_t *), img_index_cmp);
+ build_img_tree(&ele_info->ele->to_img_tree, img_array, 0, img_encountered-1);
+ /*ct = count_img_nodes(ele_info->ele->to_img_tree);
+ if (ct != img_encountered) {
+ err_no ++;
+ fprintf(log_file, "error: trouble building the image tree: %d %d\n", img_encountered, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ free(img_array);
+ }
+ ele_info->file_updated = 1;
+
+ return ele_info->ele;
+}
+
+
+
+
+
+void img_scan(ELE_INFO_t *ele_info, char *line, IMAGE_t **img_array, int *img_encountered_ptr) {
+ MSP_t *msp_tmp = MSP_malloc();
+ int id, ele1, ele2, id2;
+ ELE_INFO_t *epi;
+ IMAGE_t *ip;
+ char qname[NAME_LEN], sname[NAME_LEN];
+ int pos;
+
+
+ /*printf("%s", line);*/
+ sscanf(line, "msp %d %c %d %f %d %d %s %d %d %d %s %d %d\n", &id, &msp_tmp->stat, &msp_tmp->score, &msp_tmp->iden, &msp_tmp->direction, &ele1, qname, &msp_tmp->query.frag.lb, &msp_tmp->query.frag.rb, &ele2, sname, &msp_tmp->sbjct.frag.lb, &msp_tmp->sbjct.frag.rb);
+ pos = GetSeqIndex(0, seq_no-1, qname);
+ msp_tmp->query.frag.seq_name = *(seq_names+pos);
+ pos = GetSeqIndex(0, seq_no-1, sname);
+ msp_tmp->sbjct.frag.seq_name = *(seq_names+pos);
+
+ if (id%2) {
+ epi = get_ele_info(ele1);
+ id2 = id - 1;
+ } else {
+ epi = get_ele_info(ele2);
+ id2 = id + 1;
+ }
+ if (epi->stat == 'O') {
+ MSP_free(msp_tmp);
+ } else {
+ if (ele1 != ele2) {
+ if (epi->ele) {
+ ip = find_image(epi->ele->to_img_tree, id2)->to_image;
+ if (id%2) *(img_array+*img_encountered_ptr) = &ip->to_msp->sbjct;
+ else *(img_array+*img_encountered_ptr) = &ip->to_msp->query;
+ MSP_free(msp_tmp);
+ } else {
+ if (id%2) {
+ msp_tmp->query.index = id2;
+ msp_tmp->sbjct.index = id;
+ *(img_array+*img_encountered_ptr) = &msp_tmp->sbjct;
+ msp_tmp->query.ele_info = epi;
+ msp_tmp->sbjct.ele_info = ele_info;
+ } else {
+ msp_tmp->query.index = id;
+ msp_tmp->sbjct.index = id2;
+ *(img_array+*img_encountered_ptr) = &msp_tmp->query;
+ msp_tmp->query.ele_info = ele_info;
+ msp_tmp->sbjct.ele_info = epi;
+ }
+ msp_tmp->query.to_msp = msp_tmp;
+ msp_tmp->sbjct.to_msp = msp_tmp;
+ /*msp_in_mem ++;*/
+ /*msp_ct ++;*/
+ }
+ (*img_encountered_ptr) ++;
+ } else {
+ if (id%2) {
+ msp_tmp->query.index = id2;
+ msp_tmp->sbjct.index = id;
+ msp_tmp->query.ele_info = epi;
+ msp_tmp->sbjct.ele_info = ele_info;
+ } else {
+ msp_tmp->query.index = id;
+ msp_tmp->sbjct.index = id2;
+ msp_tmp->query.ele_info = ele_info;
+ msp_tmp->sbjct.ele_info = epi;
+ }
+ msp_tmp->query.to_msp = msp_tmp;
+ msp_tmp->sbjct.to_msp = msp_tmp;
+ *(img_array+*img_encountered_ptr) = &msp_tmp->sbjct;
+ (*img_encountered_ptr) ++;
+ *(img_array+*img_encountered_ptr) = &msp_tmp->query;
+ (*img_encountered_ptr) ++;
+ /*msp_in_mem ++;*/
+ /*msp_ct ++;*/
+ }
+ }
+}
+
+
+
+
+
+void edge_scan(char *line, EDGE_t **edge_array, ELE_INFO_t *ele_info, int *edge_encountered_ptr){
+ EDGE_t *new = EDGE_malloc();
+ int ele1, ele2;
+ ELE_INFO_t *epi;
+
+ sscanf(line, "edge %d %c %d %d %d %d\n", &new->index, &new->type, &new->direction, &new->score, &ele1, &ele2);
+
+ if (ele1 != ele2 && new->type != 'c') { /* bullet proof */
+ if (ele_info->index == ele1) {
+ epi = get_ele_info(ele2);
+ new->ele1_info = ele_info;
+ new->ele2_info = epi;
+ } else {
+ epi = get_ele_info(ele1);
+ new->ele1_info = epi;
+ new->ele2_info = ele_info;
+ }
+ if (epi->ele) {
+ *(edge_array+*edge_encountered_ptr) = find_edge(epi->ele->edges, new->index)->to_edge;
+ EDGE_free(new);
+ } else {
+ *(edge_array+*edge_encountered_ptr) = new;
+ }
+ (*edge_encountered_ptr) ++;
+ }else EDGE_free(new);
+}
+
+
+
+
+
+ELE_INFO_t *get_ele_info(int index) {
+ ELE_INFO_t *cur;
+ if (index <= ele_array_size) return *(all_ele+index-1);
+ cur = ele_info_data;
+ while (cur && cur->index < index) {
+ cur = cur->next;
+ }
+ if (cur && cur->index == index) return cur;
+ return NULL;
+}
+
+
+
+
+int img_index_cmp(const void *i1, const void *i2) {
+ return (*((IMAGE_t **) i1))->index - (*((IMAGE_t **) i2))->index;
+}
+
+
+
+
+int edge_index_cmp(const void *ed1, const void *ed2) {
+ return (*((EDGE_t **) ed1))->index - (*((EDGE_t **) ed2))->index;
+}
+
+
+
+
+
+/************************
+ * Write out an element *
+ ************************/
+
+
+
+
+
+void ele_write_out(ELE_INFO_t *ele_info, int stage) {
+ char *fn = (char *) malloc(50*sizeof(char));
+ FILE *fp;
+ CP_t *cur_pcp;
+ BD_t *cur_bd;
+ ELE_DATA_t *cur_ele_data;
+ int ct;
+
+ /* sprintf(fn, "tmp2/clan/e%d", ele_info->index);*/
+ sprintf(fn, "tmp2/e%d", ele_info->index);
+ fp = fopen(fn, "w");
+
+/* fprintf(fp, "index %d\n", ele_info->index);
+ fprintf(fp, "stat %s\n", ele_info->stat);
+ fprintf(fp, "file_updated %d\n", ele_info->file_updated);
+ if (ele_info->to_family) fprintf(fp, "family %d\n", ele_info->to_family->index); */
+
+ fprintf(fp, "frag %s %d %d\n", ele_info->ele->frag.seq_name, ele_info->ele->frag.lb, ele_info->ele->frag.rb);
+ /* if (ele_info->ele->l_hold) fprintf(fp, "l_hold %d\n", ele_info->ele->l_hold); */
+ if (ele_info->ele->direction != 1) fprintf(fp, "direc %d\n", ele_info->ele->direction);
+ if (ele_info->ele->update) fprintf(fp, "update %d\n", ele_info->ele->update);
+ /*ct = count_edge_nodes(ele_info->ele->edges);
+ if (ct > ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: more edges than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->edge_no, ct);
+ fflush(log_file);
+ exit(4);
+ } else if (ct < ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: less edges than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->edge_no, ct);
+ fflush(log_file);
+ exit(4);
+ }*/
+ /*ct = count_img_nodes(ele_info->ele->to_img_tree);
+ if (ct > ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: more images than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ } else if (ct < ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: less images than known: ele %d, %d, %d\n", ele_info->index, ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ fprintf(fp, "img_no %d\n", ele_info->ele->img_no);
+ if (ele_info->ele->flimg_no) fprintf(fp, "flimg_no %d\n", ele_info->ele->flimg_no);
+ fprintf(fp, "edge_no %d\n", ele_info->ele->edge_no);
+ if (ele_info->ele->img_no) write_out_msps(fp, ele_info->ele->to_img_tree);
+ if (ele_info->ele->edge_no) write_out_edges(fp, ele_info->ele->edges, ele_info);
+ if (stage < 2 && ele_info->ele->PCP) {
+ /*fprintf(fp, "PCPs \n");*/
+ cur_pcp = ele_info->ele->PCP;
+ while (cur_pcp) {
+ fprintf(fp, "pcp %d %d\n", cur_pcp->cp, cur_pcp->contributor->index);
+ cur_pcp = cur_pcp->next;
+ }
+ }
+ if (ele_info->ele->TBD) {
+ /*fprintf(fp, "TBDs \n");*/
+ cur_bd = ele_info->ele->TBD;
+ while (cur_bd) {
+ fprintf(fp, "tbd %d %d\n", cur_bd->bd, cur_bd->support);
+ cur_bd = cur_bd->next;
+ }
+ }
+ if (ele_info->ele->redef) {
+ /*fprintf(fp, "redefs \n");*/
+ cur_ele_data = ele_info->ele->redef;
+ while (cur_ele_data) {
+ fprintf(fp, "redef %d\n", cur_ele_data->ele_info->index);
+ cur_ele_data = cur_ele_data->next;
+ }
+ }
+ fclose(fp);
+ free(fn);
+}
+
+
+
+
+void write_out_msps(FILE *fp, IMG_TREE_t *rt) {
+ if (rt->l) write_out_msps(fp, rt->l);
+
+ if (rt->to_image->to_msp->query.ele_info->index != rt->to_image->to_msp->sbjct.ele_info->index || rt->to_image == &rt->to_image->to_msp->sbjct) { /* trick to report self MSPs only once */
+ fprintf(fp, "msp %d ", rt->to_image->index);
+ fprintf(fp, "%c ", rt->to_image->to_msp->stat);
+ fprintf(fp, "%d %3.1f %d ", rt->to_image->to_msp->score, rt->to_image->to_msp->iden, rt->to_image->to_msp->direction);
+ fprintf(fp, "%d %s %d %d ", rt->to_image->to_msp->query.ele_info->index, rt->to_image->to_msp->query.frag.seq_name, rt->to_image->to_msp->query.frag.lb, rt->to_image->to_msp->query.frag.rb);
+ fprintf(fp, "%d %s %d %d\n", rt->to_image->to_msp->sbjct.ele_info->index, rt->to_image->to_msp->sbjct.frag.seq_name, rt->to_image->to_msp->sbjct.frag.lb, rt->to_image->to_msp->sbjct.frag.rb);
+ }
+ if (rt->r) write_out_msps(fp, rt->r);
+}
+
+
+
+
+void write_out_edges(FILE *fp, EDGE_TREE_t *rt, ELE_INFO_t *ele_info) {
+ if (rt->l) write_out_edges(fp, rt->l, ele_info);
+
+ if (rt->to_edge->type != 'c' && rt->to_edge->ele1_info->index != rt->to_edge->ele2_info->index) {
+ fprintf(fp, "edge %d %c %d %d %d %d\n", rt->to_edge->index, rt->to_edge->type, rt->to_edge->direction, rt->to_edge->score, rt->to_edge->ele1_info->index, rt->to_edge->ele2_info->index);
+ } else {
+ fprintf(log_file, "error: illegitimate edges in ele %d\n", ele_info->index);
+ fflush(log_file);
+ exit(4);
+ }
+
+ if (rt->r) write_out_edges(fp, rt->r, ele_info);
+}
+
+
+
+
+
+
+/***************************
+ * manipulating image tree *
+ ***************************/
+
+
+
+
+
+void build_img_tree(IMG_TREE_t **rt_ptr, IMAGE_t **img_array, int ori, int end) {
+ int mid = (ori+end)/2;
+ IMG_TREE_t *new = (IMG_TREE_t *) malloc(sizeof(IMG_TREE_t));
+ new->to_image = *(img_array+mid);
+ new->l = NULL;
+ new->r = NULL;
+ new->p = NULL;
+ *rt_ptr = new;
+ if (mid > ori) {
+ build_img_tree(&new->l, img_array, ori, mid-1);
+ new->l->p = new;
+ }
+ if (mid < end) {
+ build_img_tree(&new->r, img_array, mid+1, end);
+ new->r->p = new;
+ }
+}
+
+
+
+int count_img_nodes(IMG_TREE_t *rt) {
+ int ct=0;
+
+ if (!rt) return 0;
+ if (rt->l) ct += count_img_nodes(rt->l);
+ if (rt->r) ct += count_img_nodes(rt->r);
+
+ ct ++;
+ return ct;
+}
+
+
+
+
+void insert_image(IMG_TREE_t **rt_ptr, IMAGE_t *i) {
+ IMG_TREE_t *new, *x, *y;
+
+ new = (IMG_TREE_t *) malloc(sizeof(IMG_TREE_t));
+ new->to_image = i;
+ new->p = NULL;
+ new->l = NULL;
+ new->r = NULL;
+
+ y = NULL;
+ x = *rt_ptr;
+ while (x) {
+ y = x;
+ if (new->to_image->index < x->to_image->index) x = x->l;
+ else x = x->r;
+ }
+ new->p = y;
+ if (!y) *rt_ptr = new;
+ else {
+ if (new->to_image->index < y->to_image->index) y->l = new;
+ else y->r = new;
+ }
+}
+
+
+
+
+void delete_image(IMG_TREE_t **rt_ptr, IMAGE_t *i) {
+ IMG_TREE_t *x, *y, *z;
+
+ if (!(*rt_ptr)) {
+ err_no ++;
+ fprintf(log_file, "error: Image tree does not exist: %d\n", i->ele_info->index);
+ fflush(log_file);
+ exit(2);
+ return;
+ }
+ z= find_image(*rt_ptr, i->index);
+ if (z) {
+ if (!z->l || !z->r) y = z;
+ else y = minimal_image(z->r);
+ if (y->l) x = y->l;
+ else x = y->r;
+ if (x) x->p = y->p;
+ if (!y->p) *rt_ptr = x;
+ else {
+ if (y == y->p->l) y->p->l = x;
+ else y->p->r = x;
+ }
+ if (y != z) z->to_image = y->to_image;
+ free(y);
+ } else {
+ err_no ++;
+ fprintf(log_file, "error: Can not find the image in the tree: %d %d\n", i->ele_info->index, i->index);
+ fflush(log_file);
+ exit(2);
+ return;
+ }
+}
+
+
+
+IMG_TREE_t *minimal_image(IMG_TREE_t *rt) {
+ while (rt->l) {
+ rt = rt->l;
+ }
+
+ return rt;
+}
+
+
+
+
+
+IMG_TREE_t *find_image(IMG_TREE_t *rt, int index) {
+ while (rt && index != rt->to_image->index) {
+ if (index < rt->to_image->index) rt = rt->l;
+ else rt = rt->r;
+ }
+
+ return rt;
+}
+
+
+
+
+IMG_DATA_t **listify(IMG_TREE_t *rt, IMG_DATA_t **tail_ptr) {
+ IMG_DATA_t *new, **new_tail_ptr;
+
+ if (!rt) return NULL;
+ if (rt->l) tail_ptr = listify(rt->l, tail_ptr);
+ new = (IMG_DATA_t *) malloc(sizeof(IMG_DATA_t));
+ new->to_image = rt->to_image;
+ new->next = NULL;
+ *tail_ptr = new;
+ tail_ptr = &new->next;
+ if (rt->r) tail_ptr = listify(rt->r, tail_ptr);
+ return tail_ptr;
+}
+
+
+
+
+
+/**************************
+ * Manipulating edge tree *
+ **************************/
+
+
+
+
+void build_edge_tree(EDGE_TREE_t **rt_ptr, EDGE_t **edge_array, int ori, int end) {
+ int mid = (ori+end)/2;
+ EDGE_TREE_t *new = (EDGE_TREE_t *) malloc(sizeof(EDGE_TREE_t));
+ new->to_edge = *(edge_array+mid);
+ new->l = NULL;
+ new->r = NULL;
+ new->p = NULL;
+ *rt_ptr = new;
+ if (mid > ori) {
+ build_edge_tree(&new->l, edge_array, ori, mid-1);
+ new->l->p = new;
+ }
+ if (mid < end) {
+ build_edge_tree(&new->r, edge_array, mid+1, end);
+ new->r->p = new;
+ }
+}
+
+
+
+
+int count_edge_nodes(EDGE_TREE_t *rt) {
+ int ct=0;
+
+ if (!rt) return 0;
+ if (rt->l) ct += count_edge_nodes(rt->l);
+ if (rt->r) ct += count_edge_nodes(rt->r);
+
+ if (rt->to_edge->type != 'c' && rt->to_edge->ele1_info->index != rt->to_edge->ele2_info->index) ct ++;
+ return ct;
+}
+
+
+
+
+int count_total_edges(EDGE_TREE_t *rt) {
+ int ct=0;
+
+ if (!rt) return 0;
+ if (rt->l) ct += count_total_edges(rt->l);
+ if (rt->r) ct += count_total_edges(rt->r);
+
+ ct ++;
+ return ct;
+}
+
+
+
+
+
+void insert_edge(EDGE_TREE_t **rt_ptr, EDGE_t *ed) {
+ EDGE_TREE_t *new, *x, *y;
+
+ new = (EDGE_TREE_t *) malloc(sizeof(EDGE_TREE_t));
+ new->to_edge = ed;
+ new->p = NULL;
+ new->l = NULL;
+ new->r = NULL;
+
+ y = NULL;
+ x = *rt_ptr;
+ while (x) {
+ y = x;
+ if (new->to_edge->index < x->to_edge->index) x = x->l;
+ else x = x->r;
+ }
+ new->p = y;
+ if (!y) *rt_ptr = new;
+ else {
+ if (new->to_edge->index < y->to_edge->index) y->l = new;
+ else y->r = new;
+ }
+}
+
+
+
+
+void delete_edge(EDGE_TREE_t **rt_ptr, EDGE_t *ed) {
+ EDGE_TREE_t *x, *y, *z;
+
+ if (!(*rt_ptr)) {
+ err_no ++;
+ fprintf(log_file, "error: edge tree empty: %d %d %d\n", ed->index, ed->ele1_info->index, ed->ele2_info->index);
+ fflush(log_file);
+ exit(4);
+ }
+ z= find_edge(*rt_ptr, ed->index);
+ if (z) {
+ if (!z->l || !z->r) y = z;
+ else y = minimal_edge(z->r);
+ if (y->l) x = y->l;
+ else x = y->r;
+ if (x) x->p = y->p;
+ if (!y->p) *rt_ptr = x;
+ else {
+ if (y == y->p->l) y->p->l = x;
+ else y->p->r = x;
+ }
+ if (y != z) z->to_edge = y->to_edge;
+ free(y);
+ } else {
+ err_no ++;
+ fprintf(log_file, "error: Can not find edge %d between ele %d and %d\n", ed->index, ed->ele1_info->index, ed->ele2_info->index);
+ fflush(log_file);
+ exit(4);
+ }
+}
+
+
+
+
+EDGE_TREE_t *minimal_edge(EDGE_TREE_t *rt) {
+ while (rt->l) {
+ rt = rt->l;
+ }
+
+ return rt;
+}
+
+
+
+
+EDGE_TREE_t *find_edge(EDGE_TREE_t *rt, int index) {
+ while (rt && index != rt->to_edge->index) {
+ if (index < rt->to_edge->index) rt = rt->l;
+ else rt = rt->r;
+ }
+
+ return rt;
+}
+
+
+
+
+
+
+
+
+/************************
+ ************************
+ *** ***
+ *** CLEANING UPS ***
+ *** ***
+ ************************
+ ************************/
+
+
+
+
+void ele_info_free(ELE_INFO_t **ei) {
+ ELE_INFO_t *cur, *next;
+
+ cur = *ei;
+ while (cur) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *ei = NULL;
+}
+
+
+
+void ele_data_free (ELE_DATA_t **e) {
+ ELE_DATA_t *cur, *next;
+
+ cur = *e;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *e = NULL;
+}
+
+
+
+/* void ele_data_cleanup (ELE_DATA_t **e) {
+ ELE_DATA_t *cur, *next, *dangler;
+
+ cur = *e;
+ while (cur != NULL) {
+ next = cur->next;
+ if (cur->ele_info->ele->redef) {
+ ele_data_cleanup(&cur->ele_info->ele->redef);
+ }
+ ele_cleanup(&cur->ele_info->ele);
+ free(cur);
+ cur = next;
+ }
+ *e = NULL;
+} */
+
+
+
+void ele_cleanup(ELEMENT_t **e) {
+ ELE_INFO_t *ele_info;
+ int ct;
+
+ if (!(*e)) return;
+
+ if ((*e)->frag.lb > (*e)->frag.rb) {
+ fprintf(log_file, "error: ele %d reversed before clean up\n", (*e)->index);
+ fflush(log_file);
+ exit(3);
+ }
+ /* reason for finding ele_info here instead of passing it over when
+ calling the function is that this way, ele_cleanup() will be more
+ independent of the ele_info structure */
+ ele_info = get_ele_info((*e)->index);
+ if ((*e)->to_img_data) img_data_free(&(*e)->to_img_data);
+ if ((*e)->PCP) CP_free(&(*e)->PCP);
+ if ((*e)->TBD) BD_free(&(*e)->TBD);
+ if ((*e)->edges) edge_tree_cleanup(ele_info, &(*e)->edges);
+ if ((*e)->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: element %d, %d edges left\n", (*e)->index, (*e)->edge_no);
+ fflush(log_file);
+ exit(4);
+ }
+ if ((*e)->to_img_tree) {
+ /*ct = count_img_nodes((*e)->to_img_tree);
+ if (ct != (*e)->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: image keeping not synchronized: ele %d %d %d\n", (*e)->index, (*e)->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ img_tree_cleanup(&(*e)->to_img_tree, ele_info);
+ if ((*e)->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: element %d, %d images left\n", (*e)->index, (*e)->img_no);
+ fflush(log_file);
+ exit(2);
+ }
+ }
+ if ((*e)->redef) ele_data_free(&(*e)->redef);
+ free(*e);
+ *e = NULL;
+}
+
+
+void BD_free (BD_t **bds) {
+ BD_t *cur, *next;
+
+ cur = *bds;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *bds = NULL;
+}
+
+
+
+void CP_free (CP_t **cps) {
+ CP_t *cur, *next;
+
+ cur = *cps;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *cps = NULL;
+}
+
+
+
+void img_data_free (IMG_DATA_t **i) {
+ IMG_DATA_t *cur, *next;
+
+ cur = *i;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *i = NULL;
+}
+
+
+
+
+void img_tree_cleanup(IMG_TREE_t **rt_p, ELE_INFO_t *ele_info) {
+ ELE_INFO_t *ep;
+
+ if ((*rt_p)->l) img_tree_cleanup(&(*rt_p)->l, ele_info);
+ if ((*rt_p)->r) img_tree_cleanup(&(*rt_p)->r, ele_info);
+
+ ele_info->ele->img_no --;
+ ep = partner((*rt_p)->to_image)->ele_info;
+ if (ep == (*rt_p)->to_image->ele_info) {
+ /* this is a hack here. we cann't simply free self msps 'cuz
+ that way when we run across the second image in the tree, the
+ to_image pointer will be pointing to space already freed. So
+ we mark a self msp by changing its stat when we first see it,
+ and when we see it the second time, which means when a self
+ msp is alredy marked, we free it.
+
+ Same thing for self edges. only we change the type of the edge
+ to 'm' */
+ if ((*rt_p)->to_image->to_msp->stat != 'm') (*rt_p)->to_image->to_msp->stat = 'm';
+ else {
+ MSP_free((*rt_p)->to_image->to_msp);
+ /*msp_in_mem --;*/
+ }
+ } else if (!ep->ele) {
+ MSP_free((*rt_p)->to_image->to_msp);
+ /*msp_in_mem --;*/
+ }
+
+ free(*rt_p);
+ *rt_p = NULL;
+}
+
+
+
+
+void img_tree_free(IMG_TREE_t **rt_p, ELE_INFO_t *ele_info) {
+ if ((*rt_p)->l) img_tree_free(&(*rt_p)->l, ele_info);
+ if ((*rt_p)->r) img_tree_free(&(*rt_p)->r, ele_info);
+
+ ele_info->ele->img_no --;
+ free(*rt_p);
+ *rt_p = NULL;
+}
+
+
+
+
+void edge_tree_cleanup(ELE_INFO_t *ele_info, EDGE_TREE_t **rt_p) {
+ ELE_INFO_t *ep;
+
+ if ((*rt_p)->l) edge_tree_cleanup(ele_info, &(*rt_p)->l);
+ if ((*rt_p)->r) edge_tree_cleanup(ele_info, &(*rt_p)->r);
+
+ if (ele_info->index == (*rt_p)->to_edge->ele1_info->index) ep = (*rt_p)->to_edge->ele2_info;
+ else ep = (*rt_p)->to_edge->ele1_info;
+ if (!ep->ele) EDGE_free((*rt_p)->to_edge);
+
+ ele_info->ele->edge_no --;
+ free(*rt_p);
+ *rt_p = NULL;
+}
+
+
+
+
+void edge_tree_free(EDGE_TREE_t **rt_p) {
+ if ((*rt_p)->l) edge_tree_free(&(*rt_p)->l);
+ if ((*rt_p)->r) edge_tree_free(&(*rt_p)->r);
+
+ free(*rt_p);
+ *rt_p = NULL;
+}
+
+
+
+
+/* void img_data_cleanup (IMG_DATA_t **i) {
+ IMG_DATA_t *cur, *next;
+
+ cur = *i;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur->to_image);
+ free(cur);
+ cur = next;
+ }
+ *i = NULL;
+} */
+
+
+
+
+void fam_data_free(FAM_DATA_t **fd) {
+ FAM_DATA_t *cur, *next;
+
+ cur = *fd;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *fd = NULL;
+}
+
+
+
+
+void fam_data_cleanup(FAM_DATA_t **fd) {
+ FAM_DATA_t *cur, *next;
+
+ cur = *fd;
+ while (cur != NULL) {
+ next = cur->next;
+ fam_cleanup(&cur->to_family);
+ free(cur);
+ cur = next;
+ }
+ *fd = NULL;
+}
+
+
+
+
+void fam_cleanup(FAMILY_t **f) {
+ if ((*f)->members != NULL) ele_data_free(&(*f)->members);
+ if ((*f)->relatives != NULL) fam_data_free(&(*f)->relatives);
+ free(*f);
+ *f = NULL;
+}
+
+
+
+
+/* Unused */
+void msp_data_free(MSP_DATA_t **md) {
+ MSP_DATA_t *cur, *next;
+
+ cur = *md;
+ while (cur != NULL) {
+ next = cur->next;
+ /*if (cur->to_msp) MSP_free(cur->to_msp);*/
+ free(cur);
+ cur = next;
+ }
+ *md = NULL;
+}
+
+
+
+
+/* void edge_data_free(EDGE_DATA_t **ed) {
+ EDGE_DATA_t *cur, *next;
+
+ cur = *ed;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *ed = NULL;
+}
+
+
+
+
+void edge_data_cleanup(EDGE_DATA_t **ed) {
+ EDGE_DATA_t *cur, *next;
+
+ cur = *ed;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur->to_edge);
+ free(cur);
+ cur = next;
+ }
+ *ed = NULL;
+} */
+
+
+
+
+void frag_data_free(FRAG_DATA_t **fd) {
+ FRAG_DATA_t *cur, *next;
+
+ cur = *fd;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur);
+ cur = next;
+ }
+ *fd = NULL;
+}
+
+
+
+
+void frag_data_cleanup(FRAG_DATA_t **fd) {
+ FRAG_DATA_t *cur, *next;
+
+ cur = *fd;
+ while (cur != NULL) {
+ next = cur->next;
+ free(cur->to_frag);
+ free(cur);
+ cur = next;
+ }
+ *fd = NULL;
+}
diff --git a/src/eledef.c b/src/eledef.c
new file mode 100644
index 0000000..6ea3ccf
--- /dev/null
+++ b/src/eledef.c
@@ -0,0 +1,428 @@
+#include "msps.h"
+
+
+#define IMG_CAP 500000
+
+#define INCLUDE_IMAGE if (method == 1) {cov=sing_cov(&ele_frag, &cur->to_image->frag, cutoff);}\
+ else {cov=doub_cov(&ele_frag, &cur->to_image->frag, cutoff);}\
+ if (cov) {\
+ img_ct ++;\
+ if (cur->to_image->index%2) {\
+ (*(all_mprot+cur->to_image->index/2))->se = (*ecp);\
+ } else {\
+ (*(all_mprot+cur->to_image->index/2))->pe = (*ecp);\
+ }\
+ fprintf(img_prot, "%d %d\n", (*ecp), cur->to_image->index);\
+ fflush(img_prot);\
+ if (!cur->next) tail = prev;\
+ if (prev) prev->next = cur->next;\
+ else remain = cur->next;\
+ if (ele_frag.rb < cur->to_image->frag.rb) {\
+ ele_frag.rb = cur->to_image->frag.rb;\
+ free(cur->to_image);\
+ free(cur);\
+ cur = remain;\
+ prev = NULL;\
+ } else {\
+ free(cur->to_image);\
+ free(cur);\
+ if (prev) cur = prev->next;\
+ else cur = remain;\
+ }\
+ } else {\
+ prev = cur;\
+ cur = cur->next;\
+ }
+
+#define ADD_EP ep_tmp = (EPROT_t *) malloc(sizeof(EPROT_t));\
+ ep_tmp->flag = 0;\
+ ep_tmp->index = (*ecp);\
+ ep_tmp->img_no = img_ct;\
+ ep_tmp->frag = ele_frag;\
+ ep_tmp->next = NULL;\
+ if (*all_epp) ep_tail->next = ep_tmp;\
+ else *all_epp = ep_tmp;\
+ ep_tail = ep_tmp;\
+ fprintf(all_ele, "%d %s %d %d\n", (*ecp), ele_frag.seq_name, ele_frag.lb, ele_frag.rb)
+
+#define RITE_THING ritetime = 0;\
+ (*ecp) ++;\
+ img_ct = 1;\
+ ele_frag = cur->to_image->frag;\
+ if (cur->to_image->index%2) {\
+ (*(all_mprot+cur->to_image->index/2))->se = (*ecp);\
+ } else {\
+ (*(all_mprot+cur->to_image->index/2))->pe = (*ecp);\
+ }\
+ fprintf(img_prot, "%d %d\n", (*ecp), cur->to_image->index);\
+ fflush(img_prot);\
+ remain = cur->next;\
+ free(cur->to_image);\
+ free(cur);\
+ prev = NULL;\
+ cur = remain
+
+#define DO_IT if (ele_frag.seq_name == cur->to_image->frag.seq_name /*!strncmp(ele_frag.seq_name, cur->to_image->frag.seq_name, NAME_LEN)*/ && ele_frag.rb - cur->to_image->frag.lb > 10) {\
+ INCLUDE_IMAGE;\
+ } else {\
+ ADD_EP;\
+ ritetime = 1;\
+ break;\
+ }
+
+#define BACK_UP imgp = (IMAGE_t *) malloc(sizeof(IMAGE_t));\
+ *imgp = img;\
+ tmp = (IMG_DATA_t *) malloc(sizeof(IMG_DATA_t));\
+ tmp->to_image = imgp;\
+ tmp->next = NULL;\
+ if (!remain) {\
+ remain = tmp;\
+ } else {\
+ tail->next = tmp;\
+ }\
+ tail = tmp
+
+#define DUMBBELL img_charge(iprot_shadow, iprot_ct, msp_file);\
+ for (i=0; i<iprot_ct; i++) {\
+ if ((*(all_iprot+i))->index%2) {\
+ partner_index = (*(all_mprot+(*(all_iprot+i))->index/2))->pe;\
+ } else {\
+ partner_index = (*(all_mprot+(*(all_iprot+i))->index/2))->se;\
+ }\
+ if ((*(all_iprot+i))->to_msp->score) {\
+ if (!(*(ep_array+((*(all_iprot+i))->ele_index-1)))->flag) {\
+ sprintf(ele_name, "ele_def_res/e%d", (*(all_iprot+i))->ele_index);\
+ freopen(ele_name, "w", all_ele);\
+ fprintf(all_ele, "index %d\n", (*(all_iprot+i))->ele_index);\
+ fprintf(all_ele, "frag %s %d %d\n", (*(ep_array+((*(all_iprot+i))->ele_index-1)))->frag.seq_name, (*(ep_array+((*(all_iprot+i))->ele_index-1)))->frag.lb, (*(ep_array+((*(all_iprot+i))->ele_index-1)))->frag.rb);\
+ fprintf(all_ele, "img_no %d\n", (*(ep_array+((*(all_iprot+i))->ele_index-1)))->img_no);\
+ fprintf(size_list, "%d %d\n", (*(all_iprot+i))->ele_index, (*(ep_array+((*(all_iprot+i))->ele_index-1)))->img_no);\
+ (*(ep_array+((*(all_iprot+i))->ele_index-1)))->flag = 1;\
+ }\
+ if (partner_index != (*(all_iprot+i))->ele_index) {\
+ if ((*(all_iprot+i))->index%2) fprintf(all_ele, "msp %d s %d %.1f %d %d %s %d %d %d %s %d %d\n", (*(all_iprot+i))->index, (*(all_iprot+i))->to_msp->score, (*(all_iprot+i))->to_msp->iden, (*(all_iprot+i))->to_msp->direction, partner_index, (*(all_iprot+i))->to_msp->query.frag.seq_name, (*(all_iprot+i))->to_msp->query.frag.lb, (*(all_iprot+i))->to_msp->query.frag.rb, (*(all_iprot+i))->ele_index, (*(all_iprot+i))->to_msp->sbjct.frag.seq_name, (*(all_iprot+i))->to_msp->sbjct.frag.lb, (* [...]
+ else fprintf(all_ele, "msp %d s %d %.1f %d %d %s %d %d %d %s %d %d\n", (*(all_iprot+i))->index, (*(all_iprot+i))->to_msp->score, (*(all_iprot+i))->to_msp->iden, (*(all_iprot+i))->to_msp->direction, (*(all_iprot+i))->ele_index, (*(all_iprot+i))->to_msp->query.frag.seq_name, (*(all_iprot+i))->to_msp->query.frag.lb, (*(all_iprot+i))->to_msp->query.frag.rb, partner_index, (*(all_iprot+i))->to_msp->sbjct.frag.seq_name, (*(all_iprot+i))->to_msp->sbjct.frag.lb, (*(all_iprot+i))->to_msp->sb [...]
+ } else {\
+ if ((*(all_iprot+i))->index%2) fprintf(all_ele, "msp %d s %d %.1f %d %d %s %d %d %d %s %d %d\n", (*(all_iprot+i))->index, (*(all_iprot+i))->to_msp->score, (*(all_iprot+i))->to_msp->iden, (*(all_iprot+i))->to_msp->direction, partner_index, (*(all_iprot+i))->to_msp->query.frag.seq_name, (*(all_iprot+i))->to_msp->query.frag.lb, (*(all_iprot+i))->to_msp->query.frag.rb, (*(all_iprot+i))->ele_index, (*(all_iprot+i))->to_msp->sbjct.frag.seq_name, (*(all_iprot+i))->to_msp->sbjct.frag.lb, (* [...]
+ }\
+ }\
+ }
+
+
+
+typedef struct msp_prototype {
+ int pe, se;
+} MPROT_t;
+
+typedef struct img_prototype {
+ int index, ele_index;
+ MSP_t *to_msp;
+} IPROT_t;
+
+typedef struct ele_prototype {
+ short flag;
+ int index, img_no;
+ FRAG_t frag;
+ struct ele_prototype *next;
+} EPROT_t;
+
+
+void ele_def(int, FILE *, float, EPROT_t **, int *, MPROT_t **);
+void img_charge(IPROT_t **, int, FILE *);
+int index_cmp(const void *, const void *);
+
+
+FILE *msp_no, *all_ele, *img_prot, *ele_no, *err, *size_list;
+
+
+int main (int argc, char *argv[]) {
+ int ele_ct=0, msp_ct, i, method;
+ float cutoff;
+ char line[150], *m1="single", *m2="double";
+ MPROT_t **all_mprot;
+ EPROT_t *all_ep=NULL, **ep_array, *ep_tmp;
+
+ IPROT_t **all_iprot, **iprot_shadow;
+ int iprot_ct=0, partner_index;
+ char ele_name[50]; /*name of element used as name of the ele file*/
+
+ FILE *frags, *seq_list, *msp_file;
+
+ /* processing command line */
+ if (argc == 1) {
+ printf("usage: ele_def seq_list msp_file method cut_off\nfor method, choose 'single' or 'double'\ncutoff is optional\n");
+ exit(1);
+ }
+
+ seq_list = fopen(argv[1], "r");
+ if (!seq_list) {
+ printf("Input file for sequence name list %s not found. Exit.\n", argv[1]);
+ exit(2);
+ }
+ GetSeqNames(seq_list);
+
+ msp_file = fopen(argv[2], "r");
+ if (!msp_file) {
+ printf("Input file of MSPs %s not found. Exit.\n", argv[2]);
+ exit(2);
+ }
+
+ if (!strcmp(argv[3], m1)) {method = 1;}
+ else if (!strcmp(argv[3], m2)) {method = 2;}
+ else {
+ printf("please choose single or double to indicate the method to evaluate overlap.\n");
+ printf("%s is not a valid option. Exit.\n", argv[3]);
+ exit(2);
+ }
+
+ if (argc > 4) cutoff = atof(argv[4]);
+ else {
+ if (method == 1) {cutoff = 0.5;}
+ else {cutoff = 0.9;}
+ }
+
+ /* opening files */
+ if (!(frags = fopen("images/images_sorted", "r"))) {
+ printf("Can not open the fragment list file, exiting.\n");
+ exit(1);
+ }
+ if (!(msp_no = fopen("summary/ori_msp_no", "r"))) {
+ printf("Can not open msp_no, exiting.\n");
+ exit(1);
+ }
+ err = fopen("ele_def_res/errors", "w");
+ all_ele = fopen("summary/naive_eles", "w");
+ img_prot = fopen("ele_def_res/img_prot", "w");
+ ele_no = fopen("summary/naive_ele_no", "w");
+ size_list = fopen("ele_def_res/size_list", "w");
+
+ while(fgets(line, 100, msp_no)) {
+ msp_ct = atoi(line);
+ }
+
+ all_mprot = (MPROT_t **) malloc(msp_ct*sizeof(MPROT_t *));
+ for (i=0; i<msp_ct; i++) {
+ *(all_mprot+i) = (MPROT_t *) malloc(sizeof(MPROT_t));
+ (*(all_mprot+i))->pe = 0;
+ (*(all_mprot+i))->se = 0;
+ }
+
+ ele_def(method, frags, cutoff, &all_ep, &ele_ct, all_mprot);
+
+ /*for (i=0; i<msp_ct; i++) {
+ if ((*(all_mprot+i))->pe > ele_ct || (*(all_mprot+i))->se > ele_ct) {
+ printf("not OK\n");
+ exit(1);
+ }
+ }*/
+
+ fclose(ele_no);
+ fclose(img_prot);
+ fclose(msp_no);
+ fclose(frags);
+ img_prot = fopen("ele_def_res/img_prot", "r");
+
+ ep_array = (EPROT_t **) malloc(ele_ct*sizeof(EPROT_t *));
+ ep_tmp = all_ep;
+ i = 0;
+ while (ep_tmp) {
+ *(ep_array+i) = ep_tmp;
+ i ++;
+ ep_tmp = ep_tmp->next;
+ }
+
+ all_iprot = (IPROT_t **) malloc(IMG_CAP*sizeof(IPROT_t *));
+ iprot_shadow = (IPROT_t **) malloc(IMG_CAP*sizeof(IPROT_t *));
+ for (i=0; i<IMG_CAP; i++) {
+ *(all_iprot+i) = (IPROT_t *) malloc(sizeof(IPROT_t));
+ (*(all_iprot+i))->to_msp = (MSP_t *) malloc(sizeof(MSP_t));
+ *(iprot_shadow+i) = *(all_iprot+i);
+ }
+
+ while (fgets(line, 100, img_prot)) {
+ sscanf(line, "%d %d\n", &(*(all_iprot+iprot_ct))->ele_index, &(*(all_iprot+iprot_ct))->index);
+ iprot_ct ++;
+ if (iprot_ct == IMG_CAP) {
+ DUMBBELL;
+ iprot_ct = 0;
+ }
+ }
+
+ if (iprot_ct) {
+ for (i=0; i<iprot_ct; i++) {*(iprot_shadow+i) = *(all_iprot+i);}
+ DUMBBELL;
+ }
+ /* cleaning up */
+ for (i=0; i<IMG_CAP; i++) {
+ free((*(all_iprot+i))->to_msp);
+ free(*(all_iprot+i));
+ }
+ free(all_iprot);
+ free(iprot_shadow);
+
+ for (i=0; i<msp_ct; i++) {
+ free(*(all_mprot+i));
+ }
+ free(all_mprot);
+
+ for (i=0; i<ele_ct; i++) {
+ free(*(ep_array+i));
+ }
+ free(ep_array);
+
+ exit(0);
+}
+
+
+void ele_def(int method, FILE *frags, float cutoff, EPROT_t **all_epp, int *ecp, MPROT_t **all_mprot) {
+ int i, img_ct, cov;
+ char line[100];
+ FRAG_t ele_frag;
+ char fragname[NAME_LEN];
+ int pos;
+ IMAGE_t img, *imgp;
+ IMG_DATA_t *cur, *prev=NULL, *remain=NULL, *tail, *tmp;
+ short ritetime;
+ EPROT_t *ep_tail, *ep_tmp;
+ /*short to_follow, to_finish=1;*/
+
+ ritetime = 1; /* ritetime marks the right time to start a new element */
+ while (fgets(line, 100, frags)) {
+ sscanf(line, "%d %*d %s %d %d\n", &img.index, fragname, &img.frag.lb, &img.frag.rb);
+ pos = GetSeqIndex(0, seq_no-1, fragname);
+ img.frag.seq_name = *(seq_names+pos);
+
+ if (ritetime) { /* starting a new element */
+ ritetime = 0;
+ (*ecp) ++;
+ img_ct = 1;
+ ele_frag = img.frag; /* start the definition of the element */
+ if (img.index%2) {
+ (*(all_mprot+img.index/2))->se = (*ecp);
+ } else {
+ (*(all_mprot+img.index/2))->pe = (*ecp);
+ }
+ fprintf(img_prot, "%d %d\n", (*ecp), img.index);
+ fflush(img_prot);
+ continue;
+ }
+ if (ele_frag.seq_name == img.frag.seq_name /*!strncmp(ele_frag.seq_name, img.frag.seq_name, NAME_LEN)*/ && ele_frag.rb - img.frag.lb > 10) { /* checking possible images */
+ if (method == 1) {cov = sing_cov(&ele_frag, &img.frag, cutoff);}
+ else {cov = doub_cov(&ele_frag, &img.frag, cutoff);}
+ if (cov) { /* a good image */
+ /* include the current frag in the current element*/
+ img_ct ++;
+ if (img.index%2) {
+ (*(all_mprot+img.index/2))->se = (*ecp);
+ } else {
+ (*(all_mprot+img.index/2))->pe = (*ecp);
+ }
+ fprintf(img_prot, "%d %d\n", (*ecp), img.index);
+ fflush(img_prot);
+ /* updating definition of the element if necessary */
+ /* notice that it is a bit complicated than above */
+ if (ele_frag.rb < img.frag.rb) {
+ ele_frag.rb = img.frag.rb;
+ /* time to go back and check if previously unqualified images are now good to be participated to the updated element */
+ cur = remain;
+ prev = NULL;
+ while (cur) {
+ INCLUDE_IMAGE;
+ }
+ }
+ } else { /* current image not good for the current ele, keep it in the remaining list and move on */
+ /*printf("1st backing up\n");*/
+ BACK_UP;
+ }
+ } else { /* time to finish defining of ele_tmp */
+ /* output the element */
+ ADD_EP;
+ /*printf("2nd backing up\n");*/
+ BACK_UP;
+ /* start a new element, finish the remain list */
+ ritetime = 1;
+ /* if (remain) printf("2nd look back\n");
+ else printf("no need for 2nd look back\n"); */
+ while (remain && ritetime) {
+ cur = remain;
+ RITE_THING;
+ while (cur) {
+ DO_IT;
+ }
+ }
+ }
+ }
+
+ ADD_EP;
+ if (remain) ritetime = 1;
+
+ /* add the last element to the list of elements */
+ /* if (remain) printf("finishing\n");
+ else printf("no need to finish\n"); */
+ while (remain) {
+ cur = remain;
+ prev = NULL;
+
+ while (cur) {
+ if (ritetime) {
+ RITE_THING;
+ continue;
+ }
+ DO_IT;
+ }
+ if (!cur) {
+ ADD_EP;
+ ritetime = 1;
+ }
+ }
+
+ fprintf(ele_no, "%d\n", (*ecp));
+}
+
+
+
+
+
+void img_charge(IPROT_t **shadow, int ct, FILE *input) {
+ int i=0, pos=0;
+ char line[151];
+ int scan_flag;
+ MSP_t msp;
+
+ qsort(shadow, ct, sizeof(IPROT_t *), index_cmp);
+ while (fgets(line, 150, input)) {
+ if (pos == (*(shadow+i))->index/2) {
+ scan_flag = scan_msp(&msp, line);
+ if (scan_flag) {
+ (*(shadow+i))->to_msp->score = 0;
+ fprintf(err, "Wrong format in the MSP file line %d for image %d\n", pos, (*(shadow+i))->index);
+ } else {
+ *((*(shadow+i))->to_msp) = msp;
+ }
+ i ++;
+ if (i == ct) break;
+ if (pos == (*(shadow+i))->index/2) {
+ /* in case the next image is from the same MSP line */
+ if (scan_flag) {
+ (*(shadow+i))->to_msp->score = 0;
+ /*(*(shadow+i))->to_msp = NULL;*/
+ fprintf(err, "Wrong format in the MSP file line %d for image %d\n", pos, (*(shadow+i))->index);
+ } else {
+ *((*(shadow+i))->to_msp) = msp;
+ }
+ i ++;
+ if (i == ct) break;
+ }
+ }
+ pos ++;
+ }
+ rewind(input);
+}
+
+
+
+
+
+int index_cmp(const void *i1, const void *i2) {
+ return (*((IPROT_t **) i1))->index - (*((IPROT_t **) i2))->index;
+}
diff --git a/src/eleredef.c b/src/eleredef.c
new file mode 100644
index 0000000..765ca64
--- /dev/null
+++ b/src/eleredef.c
@@ -0,0 +1,2409 @@
+#include <fcntl.h>
+#include <sys/types.h>
+#include <dirent.h>
+
+#include "ele.h"
+
+#define CUTOFF1 0.5
+#define CUTOFF2 0.9
+#define MAX_IMG 1200
+#define TOO_SHORT 30
+#define FUDGE 2
+#define MARGIN 10000
+#define FLURRY 10
+
+
+
+typedef struct img_node {
+ short recorded;
+ IMAGE_t *to_image;
+ struct img_node *sib;
+ struct img_node *children;
+} IMG_NODE_t;
+
+
+
+
+void report_cts();
+void report_redef_stat();
+
+ELE_DATA_t *ele_def(IMG_DATA_t **, float);
+void generate_img_tree(ELEMENT_t *);
+ELE_INFO_t *new_element();
+void add_ele_info(ELE_INFO_t *);
+
+void general_ele_redef(ELE_INFO_t *, IMAGE_t **);
+/*void build_local_network(ELE_INFO_t *, int, ELE_DATA_t **, IMAGE_t **);
+ void local_net_walk(ELE_INFO_t *, int, EDGE_TREE_t *, ELE_DATA_t **, IMAGE_t **);*/
+void build_local_network(ELE_INFO_t *, ELE_DATA_t **, ELE_DATA_t **, IMAGE_t **);
+void recruit(ELE_INFO_t *, EDGE_TREE_t *, ELE_DATA_t **, IMAGE_t **);
+void cruise_local_net(ELE_DATA_t *, IMAGE_t **);
+void local_ele_redef(ELE_INFO_t *, IMAGE_t **, int*);
+void dissolve_local_network(ELE_DATA_t **);
+int emptyDir(char *);
+void stage_exit(int);
+void dismiss_element(ELE_INFO_t *);
+void remove_ele(ELE_INFO_t *);
+
+void ele_redef(ELE_INFO_t *, IMAGE_t **);
+IMG_DATA_t *img_data_sort(IMG_DATA_t *, int);
+void PCP_to_TBDs(ELEMENT_t *);
+BD_t *CP_cluster(CP_t *);
+void CP_sort(CP_t **);
+void BD_sort(BD_t **);
+int span(ELEMENT_t *, int32_t);
+void TBD_merge(ELEMENT_t *);
+
+void dissect(ELE_INFO_t *);
+int too_short(FRAG_t *);
+MSP_t *add_msp(MSP_t *);
+void register_image(IMAGE_t *, ELEMENT_t *);
+void put_image(IMG_DATA_t **, IMAGE_t *);
+void dump_image(IMAGE_t *);
+void remove_image(IMAGE_t *);
+void combo_update(ELE_INFO_t *);
+void combo_edge_update(ELE_INFO_t *, EDGE_TREE_t **);
+void CP_clean(CP_t **, ELE_INFO_t *);
+
+void edges_and_cps(ELE_INFO_t *, IMAGE_t **);
+int full_length(IMAGE_t *, float);
+void add_CP(CP_t **, int32_t, ELE_INFO_t *);
+void add_edge(ELE_INFO_t *, ELE_INFO_t *, char, int32_t, short);
+void adjust_edge_tree(ELE_INFO_t *);
+int charge_edge_array(EDGE_t **, EDGE_TREE_t *, int);
+int consis_tree_build(IMG_NODE_t *, IMAGE_t *, int);
+int consis(IMAGE_t *, IMAGE_t *, float);
+IMG_NODE_t **node_entry(IMG_NODE_t **);
+void consis_tree_free(IMG_NODE_t *);
+/*int find_prim(struct img_node *, float, int32_t, int32_t, short, int32_t *, short *);*/
+int find_prim(IMG_NODE_t *, float, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int32_t, int *, int32_t *, short *);
+
+void combo_output(ELE_INFO_t *);
+void obs_output(ELE_INFO_t *);
+void fprint_ele_obs(FILE *, ELE_INFO_t *);
+
+int frag_cmp(const void *, const void *);
+int partner_cmp(const void *, const void *);
+int CP_cmp(const void *, const void *);
+int BD_cmp(const void *, const void *);
+int fam_cmp(const void *, const void *);
+
+
+
+int main (int argc, char *argv[]) {
+ ELE_INFO_t *cur_ele_info;
+ int i, ele_march, ei, rounds=0, start;
+ char line[35], stat;
+ short fu, to_march;
+ IMAGE_t **img_ptr;
+ FILE *ele_no, *msp_no, *edge_no, *size_list, *new_stat;
+ FILE *seq_list;
+
+ /* processing command line */
+ if (argc == 1) {
+ printf("usage: redef seq_list start clan_ct\n where seq_list is the list of sequence names, start is the index of the element to start redefining, and clan_ct is the number to start counting the number of clans. The latter two are optional.\n");
+ exit(1);
+ }
+
+ seq_list = fopen(argv[1], "r");
+ if (!seq_list) {
+ printf("Input file for sequence name list %s not found. Exit.\n", argv[1]);
+ exit(2);
+ }
+ GetSeqNames(seq_list);
+
+ if (argc > 2) start = atoi(argv[2]) - 1;
+ else start = 0;
+ if (argc > 3) clan_ct = atoi(argv[3]);
+ else clan_ct = 0;
+
+ ele_no = fopen("summary/naive_ele_no", "r");
+ if(!ele_no) {
+ printf("Can not open naive_ele_no. Exiting\n");
+ exit(1);
+ }
+ msp_no = fopen("summary/redef_msp_no", "r");
+ if (!msp_no) msp_no = fopen("summary/ori_msp_no", "r");
+ if (!msp_no) {
+ printf("Can not open msp_no. Exiting\n");
+ exit(1);
+ }
+
+ // May or may not exist. All uses of edge_no first check for
+ // its existence.
+ edge_no = fopen("summary/naive_edge_no", "r");
+
+ // May or may not exist. All uses are checked.
+ size_list = fopen("tmp/size_list", "r");
+
+ // May or may not exist. All uses are checked.
+ new_stat = fopen("tmp2/redef_stat", "r");
+
+ new_msps = fopen("summary/new_msps", "a");
+ if ( !new_msps )
+ {
+ printf("Can not open summary/new_msps for writing! Exiting\n");
+ exit(1);
+ }
+ unproc = fopen("summary/unproc", "a");
+ if ( !unproc )
+ {
+ printf("Can not open summary/unproc for writing! Exiting\n");
+ exit(1);
+ }
+ combo = fopen("summary/combo", "a");
+ if ( !combo )
+ {
+ printf("Can not open summary/combo for writing! Exiting\n");
+ exit(1);
+ }
+ obs = fopen("summary/obsolete", "a");
+ if ( !obs )
+ {
+ printf("Can not open summary/obsolete for writing! Exiting\n");
+ exit(1);
+ }
+ log_file = fopen("tmp2/log", "a");
+ if ( !log_file )
+ {
+ printf("Can not open tmp2/log for writing! Exiting\n");
+ exit(1);
+ }
+
+ while (fgets(line, 15, ele_no)) {
+ ele_ct = atoi(line);
+ }
+ fclose(ele_no);
+
+ while (fgets(line, 15, msp_no)) {
+ msp_index = atoi(line) - 1;
+ }
+ fclose(msp_no);
+
+ if (edge_no) {
+ while (fgets(line, 15, edge_no)) {
+ edge_index = atoi(line) - 1;
+ }
+ } else edge_index = -1;
+
+ ele_array_size = 2*ele_ct;
+ all_ele = (ELE_INFO_t **) malloc(ele_array_size*sizeof(ELE_INFO_t *));
+ for (i=0; i<ele_array_size; i++) {
+ *(all_ele+i) = ele_info_init(i+1);
+ }
+ ele_info_data = NULL;
+
+ /* get rid of large tandem reps */
+ if (size_list && !new_stat) outthrow_big_tandems(size_list);
+ fclose(unproc);
+
+ /* set file_updated / stat for ele_info's */
+ if (new_stat) {
+ ele_ct = 0;
+ while (fgets(line, 35, new_stat)) {
+ ele_ct ++;
+ /*sscanf(line, "%d %c %d\n", &ei, &stat, &fu);*/
+ /* for some bizzare reason, scanf doesn't work properly here. :( */
+ for (i=0; i<35; i++) {
+ if (line[i] == ' ') break;
+ }
+ ei = atoi(line);
+ stat = line[i+1];
+ fu = atoi(&line[i+3]);
+ if (ei<=ele_array_size) {
+ (*(all_ele+ei-1))->stat = stat;
+ (*(all_ele+ei-1))->file_updated = fu;
+ } else {
+ cur_ele_info = ele_info_init(ei);
+ cur_ele_info->stat = stat;
+ cur_ele_info->file_updated = fu;
+ add_ele_info(cur_ele_info);
+ }
+ }
+ }
+
+ msp_in_mem = 0;
+ msp_left = 0;
+ msp_ct = 0;
+ edge_ct = 0;
+ edge_in_mem = 0;
+ edge_left = 0;
+ files_read = 0;
+ err_no = 0;
+
+ /* re-define elements using the syntopy algorithm, and build edges */
+ img_ptr = (IMAGE_t **) malloc(MAX_IMG*sizeof(IMAGE_t *));
+
+ if ( ! img_ptr )
+ {
+ printf("eleredef: Error! Could not allocate memory for img_ptr: %d bytes requested\n", ( MAX_IMG*sizeof(IMAGE_t *) ) );
+ exit(-1);
+ }
+
+ to_march = 1;
+ while (to_march) {
+ to_march = 0;
+ rounds ++;
+ for (i=start; i<ele_ct && i<ele_array_size; i++) {
+ fprintf(log_file, "evaluating definition of element %d\n", (*(all_ele+i))->index);
+ fflush(log_file);
+ if ((*(all_ele+i))->stat == 'z' || (*(all_ele+i))->stat == 'w' || (*(all_ele+i))->stat == 't') {
+ to_march = 1;
+ general_ele_redef(*(all_ele+i), img_ptr);
+#if 0
+ report_redef_stat();
+#endif
+ } /*else if ((*(all_ele+i))->stat == 'O' && !(*(all_ele+i))->file_updated) spit_out_ele(*(all_ele+i));*/
+ }
+
+ start = 0;
+
+ cur_ele_info = ele_info_data;
+ while(cur_ele_info) {
+ fprintf(log_file, "evaluating definition of element %d\n", cur_ele_info->index);
+ fflush(log_file);
+ if (cur_ele_info->stat == 'z' || cur_ele_info->stat == 'w' || cur_ele_info->stat == 't') {
+ to_march = 1;
+ general_ele_redef(cur_ele_info, img_ptr);
+#if 0
+ report_redef_stat();
+#endif
+ } /*else if (cur_ele_info->stat == 'O' && !cur_ele_info->file_updated) spit_out_ele(cur_ele_info);*/
+ cur_ele_info = cur_ele_info->next;
+ }
+ }
+
+ report_cts();
+ report_redef_stat();
+ free(img_ptr);
+
+#if 0
+ for (i=start; i<ele_ct && i<ele_array_size; i++) {
+ if ((*(all_ele+i))->stat == 'X') remove_ele(*(all_ele+i));
+ }
+
+ cur_ele_info = ele_info_data;
+ while(cur_ele_info) {
+ if (cur_ele_info->stat == 'X') remove_ele(cur_ele_info);
+ cur_ele_info = cur_ele_info->next;
+ }
+#endif
+
+ fprintf(log_file, "total numbers: %d elements, %d msps, %d edges\n", ele_ct, msp_index+1, edge_index+1);
+ fprintf(log_file, "%d rounds, %d files read, %d msps seen, %d edges seen\n", rounds, files_read, msp_ct, edge_ct);
+ fprintf(log_file, "%d errors, %d msps and %d edges left in memory, \n", err_no, msp_left, edge_left);
+ fflush(log_file);
+ fclose(log_file);
+
+ exit(0);
+}
+
+
+
+void report_cts() {
+ FILE *fp;
+
+ fp = fopen("summary/redef_ele_no", "w");
+ fprintf(fp, "%d\n", ele_ct);
+ fclose(fp);
+}
+
+
+
+
+void report_redef_stat() {
+ int i, ele_march = ele_ct < ele_array_size ? ele_ct : ele_array_size;
+ FILE *redef_stat, *fp;
+ ELE_INFO_t *cur_ele_info = ele_info_data;
+
+ redef_stat = fopen("tmp2/redef_stat", "w");
+ for (i=0; i<ele_march; i++) {
+ fprintf(redef_stat, "%d %c %d\n", (*(all_ele+i))->index, (*(all_ele+i))->stat, (*(all_ele+i))->file_updated);
+ }
+ while(cur_ele_info) {
+ fprintf(redef_stat, "%d %c %d\n", cur_ele_info->index, cur_ele_info->stat, cur_ele_info->file_updated);
+ cur_ele_info = cur_ele_info->next;
+ }
+ fclose(redef_stat);
+
+ fp = fopen("summary/redef_msp_no", "w");
+ fprintf(fp, "%d\n", msp_index+1);
+ fclose(fp);
+
+ fp = fopen("summary/naive_edge_no", "w");
+ fprintf(fp, "%d\n", edge_index+1);
+ fclose(fp);
+}
+
+
+/***********************************
+ ***********************************
+ ** **
+ ** DEFINING ELEMENTS **
+ ** **
+ ***********************************
+ ***********************************/
+
+
+ELE_DATA_t *ele_def(IMG_DATA_t **img_data_p, float cutoff) {
+ /* this function assumes that the images are SORTED according to frag_cmp.
+ defining elements is in essence partitioning images in the original list.
+ cur_img_data marks the current image under inspection;
+ *img_data_p and prev_img_data are used to maintain the un-participated list;
+ *img_data_p marks the first (un-participated) image in the remaining list;
+ prev_img_data marks the last un-participated image proceding cur_img_data, so that when cur_img_data is removed from the origial list and participated into an element, we know where the tail of the unparticipated list, used to be pointed by cur_img_data->next, should be appended to */
+
+
+ IMG_DATA_t *cur_img_data, *prev_img_data;
+ ELEMENT_t *ele_tmp;
+ ELE_INFO_t *ele_info_tmp;
+ ELE_DATA_t *ele_data=NULL, *ele_data_tmp;
+ short ritetime;
+ int ct;
+
+ while (*img_data_p) {
+
+ cur_img_data = *img_data_p;
+ prev_img_data = NULL;
+ ritetime = 1; /* ritetime marks the right time to start a new element */
+
+ while(cur_img_data != NULL) {
+ if (ritetime) { /* starting a new element */
+ ele_info_tmp = new_element();
+ ele_tmp = ele_info_tmp->ele;
+ /* start the definition of the element */
+ ele_tmp->img_no = 1;
+ ele_tmp->frag = cur_img_data->to_image->frag; /* lst and rst included */
+ /* kick cur_img_data out of the original list */
+ /* notice that whenever we're here, cur_img_data points to the first image in the remaining list, which is also pointed to by *img_data_p */
+ *img_data_p = cur_img_data->next;
+ /* updat the current image and move it to the image list of ele_tmp */
+ /* notice that here it's always the first one for ele_tmp */
+ cur_img_data->to_image->ele_info = ele_info_tmp;
+ cur_img_data->next = NULL;
+ ele_tmp->to_img_data = cur_img_data;
+ /* move pointer cur_img_data to the next one */
+ cur_img_data = *img_data_p;
+ ritetime = 0;
+ continue;
+ }
+ if (/*!strncmp(ele_tmp->frag.seq_name, cur_img_data->to_image->frag.seq_name, NAME_LEN)*/ ele_tmp->frag.seq_name == cur_img_data->to_image->frag.seq_name && ele_tmp->frag.rb - cur_img_data->to_image->frag.lb > 10) { /*checking possible images */
+ if (sing_cov(&ele_tmp->frag, &cur_img_data->to_image->frag, cutoff)) { /* a good image */
+ ele_tmp->img_no ++;
+ /* move cur_img_data from the original list */
+ /* notice that it's a bit more complicated than above */
+ if (prev_img_data != NULL) {
+ prev_img_data->next = cur_img_data->next;
+ } else {
+ *img_data_p = cur_img_data->next;
+ }
+ /* update the current image and move it to the image_list of ele_tmp */
+ cur_img_data->to_image->ele_info = ele_info_tmp;
+ cur_img_data->next = ele_tmp->to_img_data;
+ ele_tmp->to_img_data = cur_img_data;
+
+ /* updating definition of the element if necessary, and move cur_img_data to the right place */
+ /* notice that it is a bit complicated than above */
+ if (ele_tmp->frag.rb < cur_img_data->to_image->frag.rb) {
+ ele_tmp->frag.rb = cur_img_data->to_image->frag.rb;
+ /* ele_tmp->frag.rst = cur_img_data->to_image->frag.rst; */
+ /* time to go back and check if previously unqualified images are now good to be participated to the updated element */
+ cur_img_data = *img_data_p;
+ prev_img_data = NULL;
+ } else {
+ if (prev_img_data != NULL) cur_img_data = prev_img_data->next;
+ else cur_img_data = *img_data_p;
+ }
+ } else { /* current image not good for the ele_tmp, keep it in the remaining list and move on */
+ prev_img_data = cur_img_data;
+ cur_img_data = cur_img_data->next;
+ }
+ } else { /* time to finish defining of ele_tmp */
+ /* add the element to the list of elements */
+ ele_data_tmp = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ ele_data_tmp->ele_info = ele_info_tmp;
+ ele_data_tmp->next = ele_data;
+ ele_data = ele_data_tmp;
+ /* if (!strncmp(ele_tmp->frag.seq_name, target, NAME_LEN)) printf("%d %s %d %d\n", ele_tmp->index, ele_tmp->frag.seq_name, ele_tmp->frag.lb, ele_tmp->frag.rb); */
+ /* time to go back to the head of the remaining list and start a new element */
+ ritetime = 1;
+ cur_img_data = *img_data_p;
+ prev_img_data = NULL;
+ }
+ }
+ /* add the last element to the list of elements */
+ ele_data_tmp = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ ele_data_tmp->ele_info = ele_info_tmp;
+ ele_data_tmp->next = ele_data;
+ ele_data = ele_data_tmp;
+
+ }
+
+ ele_data_tmp = ele_data;
+ while (ele_data_tmp) {
+ if (ele_data_tmp->ele_info->ele->frag.lb > ele_data_tmp->ele_info->ele->frag.rb) {
+ fprintf(log_file, "error: ele %d reversed after ele_def\n", ele_data_tmp->ele_info->index);
+ fflush(log_file);
+ exit(3);
+ }
+ generate_img_tree(ele_data_tmp->ele_info->ele);
+ /*ct = count_img_nodes(ele_data_tmp->ele_info->ele->to_img_tree);
+ if (ct != ele_data_tmp->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble generating image tree for redefed offsprings: ele %d %d %d\n", ele_data_tmp->ele_info->index, ele_data_tmp->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ ele_data_tmp = ele_data_tmp->next;
+ }
+
+ return ele_data;
+}
+
+
+
+
+void generate_img_tree(ELEMENT_t *ele) {
+ IMAGE_t **img_array = (IMAGE_t **) malloc(ele->img_no*sizeof(IMAGE_t *));
+ IMG_DATA_t *cur;
+ int ct=0;
+
+ cur = ele->to_img_data;
+ while (cur) {
+ *(img_array+ct) = cur->to_image;
+ ct ++;
+ cur = cur->next;
+ }
+
+ qsort(img_array, ct, sizeof(IMAGE_t *), img_index_cmp);
+
+ build_img_tree(&ele->to_img_tree, img_array, 0, ct-1);
+
+ free(img_array);
+}
+
+
+
+
+
+ELE_INFO_t *new_element() {
+ ELE_INFO_t *ele_info_tmp;
+
+ ele_ct ++;
+
+ if (ele_ct <= ele_array_size) ele_info_tmp = *(all_ele+ele_ct-1);
+ else {
+ ele_info_tmp = ele_info_init(ele_ct);
+ add_ele_info(ele_info_tmp);
+ }
+
+ ele_info_tmp->ele = ele_init(ele_ct);
+ ele_info_tmp->file_updated = 1;
+
+ return ele_info_tmp;
+}
+
+
+
+
+void add_ele_info(ELE_INFO_t *ele_info_tmp) {
+
+ if (!ele_info_data) ele_info_data = ele_info_tmp;
+ else ele_info_tail->next = ele_info_tmp;
+
+ ele_info_tail = ele_info_tmp;
+}
+
+
+
+
+
+/***********************************
+ ***********************************
+ ** **
+ ** REDEFINING THE ELEMENTS **
+ ** **
+ ***********************************
+ ***********************************/
+
+
+
+
+/**********************************************
+ * Organizing the traverse of the local graph *
+ **********************************************/
+
+
+
+
+
+void general_ele_redef(ELE_INFO_t *ele_info, IMAGE_t **img_ptr) {
+ ELE_DATA_t *local_net=NULL, *local_net_tail=NULL;
+
+ if (!ele_info->ele) ele_read_in(ele_info, 1);
+
+ /* an element could have lost all its images during the re-evaluation of its partners */
+ if (!ele_info->ele->img_no) {
+ combo_update(ele_info);
+ remove_ele(ele_info);
+ ele_cleanup(&ele_info->ele);
+ } else {
+ /* redefining cur_ele and its adjacent neighbors */
+ fprintf(new_msps, "new clan for ele %d\n", ele_info->index);
+ fflush(new_msps);
+ fprintf(combo, "new clan for ele %d\n", ele_info->index);
+ fflush(combo);
+ fprintf(obs, "new clan for ele %d\n", ele_info->index);
+ fflush(obs);
+ /* set up the local network */
+ clan_ct ++;
+ clan_size = 0;
+ clan_core_size = 0;
+ fprintf(log_file, "new clan: %d for ele %d\n", clan_ct, ele_info->index);
+ fflush(log_file);
+ build_local_network(ele_info, &local_net, &local_net_tail, img_ptr);
+ if ( ele_info->index == 362 || ele_info->index == 10 )
+ {
+ printf("Printing local net for 362\n");
+ print_ele_data( local_net );
+ }
+ fprintf(log_file, "clan size: %d, clan core size: %d\n", clan_size, clan_core_size);
+ fflush(log_file);
+ /* redefining elements in the local network */
+ /* local_ele_redef(ele_info, img_ptr); */
+ cruise_local_net(local_net, img_ptr);
+ /* clearing up the local network */
+ fflush(new_msps);
+ fflush(combo);
+ fflush(obs);
+ dissolve_local_network(&local_net);
+ }
+}
+
+
+
+
+#if 0
+void build_local_network(ELE_INFO_t *ele_info, int level, ELE_DATA_t **net_p, IMAGE_t **img_ptr) {
+ ELEMENT_t *ele;
+ ELE_DATA_t *que;
+
+ clan_size ++;
+ que = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ que->ele_info = ele_info;
+ que->next = *net_p;
+ *net_p = que;
+
+ if (!ele_info->ele) ele_read_in(ele_info, 1);
+ ele = ele_info->ele;
+
+ if (level < DEPTH) {
+ ele->l_hold = 1;
+ clan_core_size ++;
+ /*fprintf(log_file, " %d\n", ele_info->index);
+ fflush(log_file);*/
+ if (ele_info->stat != 'v') {
+ if (ele_info->stat == 'z') edges_and_cps(ele_info, img_ptr);
+ level ++;
+ if (ele->edges) local_net_walk(ele_info, level, ele->edges, net_p, img_ptr);
+ } else {
+ if (ele->edges) local_net_walk(ele_info, DEPTH, ele->edges, net_p, img_ptr);
+ }
+ } else ele->l_hold = 2;
+}
+
+
+
+
+void local_net_walk(ELE_INFO_t *ele_info, int level, EDGE_TREE_t *edge_node, ELE_DATA_t **net_p, IMAGE_t **img_ptr) {
+ ELE_INFO_t *epi;
+
+ if (edge_node->l) local_net_walk(ele_info, level, edge_node->l, net_p, img_ptr);
+
+ /*if (edge_node->to_edge->type == 'p' || edge_node->to_edge->type == 's') {*/
+ epi = linked_ele(ele_info, edge_node->to_edge);
+ if (!epi->ele) ele_read_in(epi, 1);
+ if (!epi->ele->l_hold) build_local_network(epi, level, net_p, img_ptr);
+ else if (epi->ele->l_hold == 2 && level < DEPTH) {
+ epi->ele->l_hold = 1;
+ clan_core_size ++;
+ /*fprintf(log_file, " %d\n", epi->index);
+ fflush(log_file);*/
+ if (epi->stat == 'z') edges_and_cps(epi, img_ptr);
+ if (epi->ele->edges) local_net_walk(epi, level+1, epi->ele->edges, net_p, img_ptr);
+ }
+ /*}*/
+
+ if (edge_node->r) local_net_walk(ele_info, level, edge_node->r, net_p, img_ptr);
+}
+#endif
+
+
+
+
+
+void build_local_network(ELE_INFO_t *ele_info, ELE_DATA_t **net_p, ELE_DATA_t **net_tail_p, IMAGE_t **img_ptr) {
+ ELEMENT_t *ele;
+ ELE_DATA_t *que;
+
+ /* seed the network with the first element */
+ que = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ que->ele_info = ele_info;
+ que->next = NULL;
+ *net_p = que;
+ *net_tail_p = que;
+
+ ele_info->ele->l_hold = 1;
+
+ /* breadth first search */
+ while (que) {
+ clan_size ++;
+ if (que->ele_info->ele->l_hold <= DEPTH) {
+ clan_core_size ++;
+ if (que->ele_info->stat == 'z') edges_and_cps(que->ele_info, img_ptr);
+ if (que->ele_info->ele->edges) recruit(que->ele_info, que->ele_info->ele->edges, net_tail_p, img_ptr);
+ /* else {
+ fprintf(log_file, "error: ele %d edge tree missing. Exit.\n", que->ele_info->index);
+ fflush(log_file);
+ exit(4);
+ }*/
+ }
+ que = que->next;
+ }
+}
+
+
+
+
+void recruit(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, ELE_DATA_t **net_tail_p, IMAGE_t **img_ptr) {
+ ELE_INFO_t *epi;
+ ELE_DATA_t *member;
+
+ if (rt->l) recruit(ele_info, rt->l, net_tail_p, img_ptr);
+
+ epi = linked_ele(ele_info, rt->to_edge);
+ if (!epi->ele) ele_read_in(epi, 1);
+ if (!epi->ele->l_hold) {
+ epi->ele->l_hold = ele_info->ele->l_hold + 1;
+ if (epi->stat == 'v' && epi->ele->l_hold < DEPTH) epi->ele->l_hold = DEPTH;
+ member = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ member->ele_info = epi;
+ member->next = NULL;
+ (*net_tail_p)->next = member;
+ *net_tail_p = member;
+ }
+
+ if (rt->r) recruit(ele_info, rt->r, net_tail_p, img_ptr);
+}
+
+
+
+
+void cruise_local_net(ELE_DATA_t *local_net, IMAGE_t **img_ptr) {
+ ELE_DATA_t *que;
+ int to_march = 1;
+
+ while (to_march) {
+ to_march = 0;
+ que = local_net;
+ while (que) {
+ if (que->ele_info->ele->l_hold <= DEPTH) {
+ local_ele_redef(que->ele_info, img_ptr, &to_march);
+ }
+ que = que->next;
+ }
+ }
+}
+
+
+
+
+void local_ele_redef(ELE_INFO_t *ele_info, IMAGE_t **img_ptr, int *march_p) {
+ ELE_DATA_t *new_ele_data;
+ ELEMENT_t *ele = ele_info->ele;
+
+ if (ele->redef != NULL) {
+ new_ele_data = ele->redef;
+ while (new_ele_data != NULL) {
+ local_ele_redef(new_ele_data->ele_info, img_ptr, march_p);
+ new_ele_data = new_ele_data->next;
+ }
+ } else {
+ if (ele_info->stat != 'v' && ele_info->stat != 'X') {
+ if (ele->PCP) {
+ *march_p = 1;
+ ele_redef(ele_info, img_ptr);
+ } else ele_info->stat = 'v';
+ }
+ }
+}
+
+
+
+
+
+void dissolve_local_network(ELE_DATA_t **net_p) {
+ ELE_DATA_t *que, *new_ele_data;
+ int i, ele_left=0;
+ char *command;
+ /*MSP_DATA_t *md;*/
+
+ int j, in_clan;
+ FILE *fp;
+ ELE_INFO_t *cur_ele_info;
+
+ /* output results to tmp2/clan, which holds results temporily and clean up memory */
+ que = *net_p;
+ while (que) {
+ dismiss_element(que->ele_info);
+ que = que->next;
+ }
+
+ if (msp_in_mem) {
+ err_no ++;
+ fprintf(log_file, "error: error in bookkeeping: %d msps total, %d seen, %d left in memory\n", msp_index+1, msp_ct, msp_in_mem);
+ fflush(log_file);
+ msp_left += msp_in_mem;
+ /*md = all_msps;
+ while (md) {
+ if (md->to_msp) {
+ fprint_msp(log_file, md->to_msp);
+ fflush(log_file);
+ MSP_free(md->to_msp);
+ }
+ md = md->next;
+ }
+ if (msp_in_mem) {
+ fprintf(log_file, "error: further discrepency: %d msps left\n", msp_in_mem);
+ msp_in_mem = 0;
+ }*/
+ }
+
+ if (edge_in_mem) {
+ err_no ++;
+ fprintf(log_file, "error: error in bookkeeping: %d edges total, %d seen, %d left in memory\n", edge_index+1, edge_ct, edge_in_mem);
+ fflush(log_file);
+ edge_left += edge_in_mem;
+ edge_in_mem = 0;
+ }
+
+#if 0
+ for (i=0; i<ele_ct; i++) {
+ if ((*(all_ele+i))->ele) {
+ ele_left ++;
+ err_no ++;
+ fprintf(log_file, "error: element %d not cleaned from memory. stat = %c\n", i+1, (*(all_ele+i))->stat);
+ fflush(log_file);
+ if ((*(all_ele+i))->stat != 'O' && (*(all_ele+i))->stat != 'X') ele_write_out(*(all_ele+i), 1);
+ ele_cleanup(&(*(all_ele+i))->ele);
+ }
+ }
+ if (ele_left) {
+ err_no ++;
+ fprintf(log_file, "error: %d elements left in memory\n", ele_left);
+ fflush(log_file);
+ /*system(command);*/
+ }
+#endif
+
+ if (err_no) exit(3);
+
+#if 0
+ /* move files from tmp2/clan, i.e. finalize the result */
+ command = (char *) malloc(50*sizeof(char));
+
+ sprintf(command, "tmp2/clan/combos");
+ if (!emptyDir(command)) {
+ sprintf(command, "mv -f tmp2/clan/combos combos/clan%d", clan_ct);
+ if (system(command)) {
+ fprintf(log_file, "error moving tmp2/clan/combos/\n");
+ fflush(log_file);
+ stage_exit(6);
+ } else {
+ sprintf(command, "mkdir tmp2/clan/combos");
+ if (system(command)) {
+ fprintf(log_file, "error generating dir tmp2/clan/combos/\n");
+ fflush(log_file);
+ stage_exit(6);
+ }
+ }
+ }
+
+ sprintf(command, "tmp2/clan/obsolete");
+ if (!emptyDir(command)) {
+ sprintf(command, "mv -f tmp2/clan/obsolete obsolete/clan%d", clan_ct);
+ if (system(command)) {
+ fprintf(log_file, "error moving tmp2/clan/obsolete/\n");
+ fflush(log_file);
+ stage_exit(6);
+ } else {
+ sprintf(command, "mkdir tmp2/clan/obsolete");
+ if (system(command)) {
+ fprintf(log_file, "error generating dir tmp2/clan/obsolete\n");
+ fflush(log_file);
+ stage_exit(6);
+ }
+ }
+ }
+
+ sprintf(command, "mv -f tmp2/clan/e* tmp2/.");
+ if (system(command)) {
+ /*fprintf(log_file, "error moving files from tmp2/clan/\n");
+ fflush(log_file);
+ stage_exit(6);*/
+ j = ele_ct < ele_array_size ? ele_ct : ele_array_size;
+ for (i=0; i<=j; i++) {
+ sprintf(command, "tmp2/clan/e%d", i+1);
+ if (fp = fopen(command, "r")) in_clan = 1;
+ else in_clan = 0;
+ fclose(fp);
+ if (in_clan) {
+ sprintf(command, "mv -f tmp2/clan/e%d tmp2/.", i+1);
+ if (system(command)) {
+ fprintf(log_file, "error doing %s\n", command);
+ fflush(log_file);
+ stage_exit(6);
+ }
+ }
+ }
+ cur_ele_info = ele_info_data;
+ while (cur_ele_info) {
+ sprintf(command, "tmp2/clan/e%d", cur_ele_info->index);
+ if (fp = fopen(command, "r")) in_clan = 1;
+ else in_clan = 0;
+ fclose(fp);
+ if (in_clan) {
+ sprintf(command, "mv -f tmp2/clan/e%d tmp2/.", cur_ele_info->index);
+ if (system(command)) {
+ fprintf(log_file, "error doing %s\n", command);
+ fflush(log_file);
+ stage_exit(6);
+ }
+ }
+ cur_ele_info = cur_ele_info->next;
+ }
+ }
+
+ free(command);
+#endif
+
+ /* remove arkaine ele files, now done in main()
+ que = *net_p;
+ while (que) {
+ if (que->ele_info->stat == 'X') remove_ele(que->ele_info);
+ que = que->next;
+ } */
+
+ ele_data_free(net_p);
+}
+
+
+
+#if 0
+int emptyDir(char *dir_name) {
+ int res = 1;
+ DIR *cur_dir;
+ struct dirent *dp;
+
+ cur_dir = opendir(dir_name);
+ while (cur_dir && res && (dp = readdir(cur_dir))) {
+ if (strcmp(dp->d_name, ".") && strcmp(dp->d_name, "..")) res = 0;
+ }
+ closedir(cur_dir);
+ return res;
+}
+
+
+
+
+void stage_exit(int code) {
+ char *command = (char *) malloc(50*sizeof(char));
+
+ sprintf(command, "mv -f tmp2/redef_stat tmp2/redef_stat_prev");
+ if (system(command)) {
+ fprintf(log_file, "error in moving tmp2/redef_stat\n");
+ fflush(log_file);
+ exit(code);
+ }
+
+ sprintf(command, "mv -f tmp2/msp_no tmp2/msp_no_prev");
+ if (system(command)) {
+ fprintf(log_file, "error in moving tmp2/msp_no\n");
+ fflush(log_file);
+ exit(code);
+ }
+
+ sprintf(command, "mv -f tmp2/edge_no tmp2/edge_no_prev");
+ if (system(command)) {
+ fprintf(log_file, "error in moving tmp2/edge_no\n");
+ fflush(log_file);
+ exit(code);
+ }
+
+ report_redef_stat();
+ exit(code);
+}
+#endif
+
+
+
+void dismiss_element(ELE_INFO_t *ele_info) {
+ ELE_DATA_t *new_ele_data;
+
+ if (ele_info->ele->redef) {
+ new_ele_data = ele_info->ele->redef;
+ while (new_ele_data) {
+ dismiss_element(new_ele_data->ele_info);
+ new_ele_data = new_ele_data->next;
+ }
+ }
+ /*printf("clearing ele %d\n", ele_info->index);*/
+ ele_info->ele->l_hold = 0;
+ if (ele_info->stat != 'X') {
+ if (!ele_info->ele->img_no) {
+ ele_info->stat = 'X';
+ if (ele_info->ele->redef) combo_output(ele_info);
+ else obs_output(ele_info);
+ } else ele_write_out(ele_info, 1);
+ }
+ ele_cleanup(&ele_info->ele);
+}
+
+
+
+
+void remove_ele(ELE_INFO_t *ele_info) {
+ char *command;
+
+ command = (char *) malloc(50*sizeof(char));
+ sprintf(command, "rm -f tmp2/e%d", ele_info->index);
+ if (system(command)) {
+ fprintf(log_file, "error removing file tmp2/e%d\n", ele_info->index);
+ fflush(log_file);
+ exit(6);
+ }
+ free(command);
+}
+
+
+
+
+
+
+/******************************
+ * Redefining a given element *
+ ******************************/
+
+
+
+void ele_redef(ELE_INFO_t *ele_info, IMAGE_t **img_ptr) {
+ ELE_DATA_t *new_ele_data;
+ ELEMENT_t *cur_ele = ele_info->ele;
+ BD_t *pbd;
+ CP_t *cur;
+ short to_dissect=0;
+ IMG_DATA_t *cur_img_data;
+
+ if (!cur_ele->to_img_data) listify(cur_ele->to_img_tree, &cur_ele->to_img_data);
+ cur_ele->to_img_data = img_data_sort(cur_ele->to_img_data, cur_ele->img_no);
+
+ /* find TBDs for the element */
+ if (cur_ele->PCP) {
+ PCP_to_TBDs(cur_ele);
+ }
+ if (cur_ele->TBD) {
+ TBD_merge(cur_ele);
+ }
+ if (cur_ele->TBD) {
+#if 0
+ to_dissect = 1;
+ if (cur_ele->TBD->bd - cur_ele->frag.lb <= FLURRY || cur_ele->TBD->bd - cur_ele->frag.rb >= -FLURRY) {
+ if (!cur_ele->TBD->next) {
+ to_dissect = 0;
+ if (cur_ele->TBD->bd - cur_ele->frag.lb <= FLURRY) cur_ele->frag.lb = cur_ele->TBD->bd;
+ else cur_ele->frag.rb = cur_ele->TBD->bd;
+ BD_free(&cur_ele->TBD);
+ } else {
+ if (cur_ele->TBD->next->bd - cur_ele->frag.rb >= -FLURRY) {
+ if (!cur_ele->TBD->next->next) {
+ to_dissect = 0;
+ cur_ele->frag.lb = cur_ele->TBD->bd;
+ cur_ele->frag.rb = cur_ele->TBD->next->bd;
+ BD_free(&cur_ele->TBD);
+ }
+ }
+ }
+ }
+#endif
+ pbd = cur_ele->TBD;
+ while (pbd) {
+ /*if (pbd->bd-cur_ele->frag.lb<-(FLURRY+5) || pbd->bd-cur_ele->frag.rb>(FLURRY+5)) {
+ fprintf(log_file, "error: ele %d TBD outside ele bound\n", ele_info->index);
+ fflush(log_file);
+ exit(3);
+ }*/
+ if (pbd->bd-cur_ele->frag.lb>FLURRY && pbd->bd-cur_ele->frag.rb<-FLURRY) {
+ to_dissect ++;
+ }
+ pbd = pbd->next;
+ }
+
+ if (!to_dissect) {
+ pbd = cur_ele->TBD;
+ while (pbd) {
+ if (/*pbd->bd-cur_ele->frag.lb>0 &&*/ pbd->bd-cur_ele->frag.lb<=FLURRY) {
+ cur_ele->frag.lb = pbd->bd;
+ } else if (/*pbd->bd-cur_ele->frag.rb<0 &&*/ pbd->bd-cur_ele->frag.rb>=-FLURRY) {
+ cur_ele->frag.rb = pbd->bd;
+ }
+ pbd = pbd->next;
+ }
+ BD_free(&cur_ele->TBD);
+ } else {
+ /* dissect all images according to the TBDs */
+ dissect(ele_info);
+ /* redefine elements according to the dissected images, if any left */
+ if (cur_ele->img_no) {
+ cur_ele->to_img_data = img_data_sort(cur_ele->to_img_data, cur_ele->img_no);
+ cur_ele->redef = ele_def(&cur_ele->to_img_data, CUTOFF1);
+ }
+ /* clear unnecessary memory, 'v'->'w' and update CPs for w's */
+ combo_update(ele_info);
+ /* ele_redef() for offspring elements. we finish redefinition of all offsprings before pulling in partners, because the combo may have > 1 copy of the same family, which means other members' CPs won't be fully updated until all offsprings are processed */
+ new_ele_data = cur_ele->redef;
+ while (new_ele_data != NULL) {
+ new_ele_data->ele_info->ele->update = 1;
+ new_ele_data->ele_info->ele->l_hold = cur_ele->l_hold;
+ if (new_ele_data->ele_info->ele->to_img_tree) {
+ edges_and_cps(new_ele_data->ele_info, img_ptr);
+ if (new_ele_data->ele_info->ele->PCP) ele_redef(new_ele_data->ele_info, img_ptr);
+ else new_ele_data->ele_info->stat = 'v';
+ } else {
+ if (new_ele_data->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: image tree missing in newly redefed offspring %d\n", new_ele_data->ele_info->index);
+ fflush(log_file);
+ exit(2);
+ } else {
+ combo_output(new_ele_data->ele_info);
+ }
+ }
+ new_ele_data = new_ele_data->next;
+ }
+ }
+ }
+ if (cur_ele->img_no > 0) {
+ ele_info->stat = 'v';
+ } else if (!to_dissect) combo_update(ele_info);
+
+ /*img_data_free(&cur_ele->to_img_data);*/
+}
+
+
+
+
+
+IMG_DATA_t *img_data_sort(IMG_DATA_t *img_data, int ct) {
+ IMG_DATA_t **img_data_ptr;
+ int i;
+
+ if (!ct) return NULL;
+ img_data_ptr = (IMG_DATA_t **) malloc(ct*sizeof(IMG_DATA_t *));
+ for (i=0; i<ct; i++) {
+ *(img_data_ptr+i) = img_data;
+ img_data = img_data->next;
+ }
+ qsort(img_data_ptr, ct, sizeof(IMAGE_t *), frag_cmp);
+ img_data = *img_data_ptr;
+ ct --;
+ for (i=0; i<ct; i++) {
+ (*(img_data_ptr+i))->next = *(img_data_ptr+i+1);
+ }
+ (*(img_data_ptr+ct))->next = NULL;
+ free(img_data_ptr);
+ return img_data;
+}
+
+
+
+
+/***************************
+ * Determine possible TBDs *
+ ***************************/
+
+
+
+void PCP_to_TBDs(ELEMENT_t *ele) {
+ int s = 0, left;
+ BD_t *pbd_tmp, *pbd_prev, *pbd, *pbds;
+ CP_t *cp;
+
+ /* sort the PCP list according to cp */
+ CP_sort(&ele->PCP);
+ /*clustering the PCPs into PBDs */
+ pbds = CP_cluster(ele->PCP);
+ /* identify TBP from PBDs */
+ /* TBDs are removed from PBDs, what is left in PBDs are those unsuccessful ones */
+ pbd_tmp = pbds;
+ pbd_prev = NULL;
+ while (pbd_tmp != NULL) {
+ /* s is the KEY! */
+ s = span(ele, pbd_tmp->bd);
+ if (pbd_tmp->support >= s) {
+ if (pbd_prev == NULL) {
+ pbds = pbd_tmp->next;
+ pbd_tmp->next = ele->TBD;
+ ele->TBD = pbd_tmp;
+ pbd_tmp = pbds;
+ } else {
+ pbd_prev->next = pbd_tmp->next;
+ pbd_tmp->next = ele->TBD;
+ ele->TBD = pbd_tmp;
+ pbd_tmp = pbd_prev->next;
+ }
+ } else {
+ pbd_prev = pbd_tmp;
+ pbd_tmp = pbd_tmp->next;
+ }
+ }
+
+ BD_free(&pbds);
+}
+
+
+
+#if 0
+BD_t *CP_cluster(CP_t *cps) {
+ int32_t first = cps->cp, last = cps->cp, sum = 0;
+ int cpct = 0;
+ BD_t *bds = NULL, *bd_tmp;
+
+ while (cps != NULL) {
+ if (cps->cp - last <= 10) {
+ sum += cps->cp - first;
+ cpct ++;
+ } else {
+ bd_tmp = (BD_t *) malloc(sizeof(BD_t));
+ bd_tmp->bd = sum/cpct + first;
+ bd_tmp->support = cpct;
+ bd_tmp->next = bds;
+ bds = bd_tmp;
+ first = cps->cp;
+ sum = 0;
+ cpct = 1;
+ }
+ if (cps->next == NULL) {
+ bd_tmp = (BD_t *) malloc(sizeof(BD_t));
+ bd_tmp->bd = sum/cpct + first;
+ bd_tmp->support = cpct;
+ bd_tmp->next = bds;
+ bds = bd_tmp;
+ }
+ last = cps->cp;
+ cps = cps->next;
+ }
+ return bds;
+}
+#endif
+
+
+
+BD_t *CP_cluster(CP_t *cps) {
+ int32_t first = cps->cp, last = cps->cp, sum = 0;
+ CP_t *begin = cps;
+ int cpct = 0;
+ BD_t *bds = NULL, *bd_tmp;
+
+ while (cps != NULL) {
+ if (cps->cp - first <= 20 && cps->cp - last <= 10) {
+ sum += cps->cp - first;
+ cpct ++;
+ last = cps->cp;
+ cps = cps->next;
+ } else {
+ bd_tmp = (BD_t *) malloc(sizeof(BD_t));
+ bd_tmp->bd = sum/cpct + first;
+ bd_tmp->support = cpct;
+ bd_tmp->next = bds;
+ bds = bd_tmp;
+ if (cps->cp - last <= 10) begin = cps;
+ else begin = begin->next;
+ if (begin) {
+ first = begin->cp;
+ last = first;
+ }
+ sum = 0;
+ cpct = 0;
+ cps = begin;
+ }
+ }
+
+ bd_tmp = (BD_t *) malloc(sizeof(BD_t));
+ bd_tmp->bd = sum/cpct + first;
+ bd_tmp->support = cpct;
+ bd_tmp->next = bds;
+ bds = bd_tmp;
+
+ return bds;
+}
+
+
+
+void CP_sort(CP_t **CP_ptr) {
+ int i=0, j;
+ CP_t *cur, **CPs;
+
+ cur = *CP_ptr;
+ while (cur != NULL) {
+ i ++;
+ cur = cur->next;
+ }
+ CPs = (CP_t **) malloc(i*sizeof(CP_t *));
+ i = 0;
+ cur = *CP_ptr;
+ while (cur != NULL) {
+ *(CPs+i) = cur;
+ i ++;
+ cur = cur->next;
+ }
+ qsort(CPs, i, sizeof(CP_t *), CP_cmp);
+ i --;
+ for (j=0; j<i; j++) {
+ (*(CPs+j))->next = *(CPs+j+1);
+ }
+ (*(CPs+i))->next = NULL;
+ *CP_ptr = *CPs;
+
+ free(CPs);
+}
+
+
+
+
+void BD_sort(BD_t **BD_ptr) {
+ int i=0, j;
+ BD_t *cur, **BDs;
+
+ cur = *BD_ptr;
+ while (cur != NULL) {
+ i ++;
+ cur = cur->next;
+ }
+
+ BDs = (BD_t **) malloc(i*sizeof(BD_t*));
+ i = 0;
+ cur = *BD_ptr;;
+ while (cur != NULL) {
+ *(BDs+i) = cur;
+ i ++;
+ cur = cur->next;
+ }
+
+ qsort(BDs, i, sizeof(BD_t *), BD_cmp);
+
+ i --;
+ for (j=0; j<i; j++) {
+ (*(BDs+j))->next = *(BDs+j+1);
+ }
+ (*(BDs+i))->next = NULL;;
+ *BD_ptr = *BDs;
+
+ free(BDs);
+}
+
+
+
+
+int span(ELEMENT_t *ele, int32_t cut) {
+ /* span requires PCP sorted according to cp_cmp and images sorted according to frag_cmp */
+ int left=0, rite=0;
+ IMG_DATA_t *id;
+
+ id = ele->to_img_data;
+ while (id && id->to_image->frag.lb <= cut-10) {
+ left ++;
+ if (id->to_image->frag.rb <= cut+10) rite ++;
+ id = id->next;
+ }
+ return (left-rite)*FUDGE;
+}
+
+
+
+
+
+void TBD_merge(ELEMENT_t *ele) {
+ BD_t *prev=NULL, *cur, *next;
+
+ BD_sort(&ele->TBD);
+ cur = ele->TBD;
+ next = cur->next;
+ while (next != NULL) {
+ if (next->bd - cur->bd <= 10) {
+ if (cur->support < next->support) {
+ if (prev == NULL) {
+ ele->TBD = next;
+ } else {
+ prev->next = next;
+ }
+ free(cur);
+ cur = next;
+ } else {
+ cur->next = next->next;
+ free(next);
+ }
+ if (cur) next = cur->next;
+ else next = NULL;
+ } else {
+ prev = cur;
+ cur = next;
+ next = cur->next;
+ }
+ }
+}
+
+
+
+
+
+/**************************
+ * Dissecting the element *
+ **************************/
+
+
+
+void dissect(ELE_INFO_t *ele_info) {
+ IMG_DATA_t *cur_img_data, *img_data_tmp, *next;
+ MSP_t *msp_tmp, *msp_ori;
+ IMAGE_t *img_partner, *target_img, *target_partner;
+ ELEMENT_t *ele_partner, *cur_ele = ele_info->ele;
+ BD_t *tbd_tmp, *new_tbd;
+ short dissected;
+
+ cur_img_data = cur_ele->to_img_data;
+ while (cur_img_data != NULL) {
+ next = cur_img_data->next;
+ dissected = 0;
+ img_partner = partner(cur_img_data->to_image);
+ ele_partner = img_partner->ele_info->ele;
+ if (full_length(img_partner, CUTOFF2)){
+ ele_partner->flimg_no --;
+ }
+ tbd_tmp = cur_ele->TBD;
+ while (tbd_tmp != NULL) {
+ if (tbd_tmp->bd > cur_img_data->to_image->frag.lb || !tbd_tmp->next) {
+ if (tbd_tmp->bd > cur_img_data->to_image->frag.lb && tbd_tmp->bd < cur_img_data->to_image->frag.rb) {
+ if (tbd_tmp->bd - cur_img_data->to_image->frag.lb <= TOO_SHORT) {
+ cur_img_data->to_image->to_msp->score = (int32_t) (cur_img_data->to_image->frag.rb-tbd_tmp->bd+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score;
+ if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.lb += tbd_tmp->bd - cur_img_data->to_image->frag.lb;
+ else img_partner->frag.rb -= tbd_tmp->bd - cur_img_data->to_image->frag.lb;
+ cur_img_data->to_image->frag.lb = tbd_tmp->bd;
+ } else if (tbd_tmp->bd - cur_img_data->to_image->frag.rb >= -TOO_SHORT) {
+ cur_img_data->to_image->to_msp->score = (int32_t) (tbd_tmp->bd-cur_img_data->to_image->frag.lb+1.)/(cur_img_data->to_image->frag.rb-cur_img_data->to_image->frag.lb+1.)*cur_img_data->to_image->to_msp->score;
+ if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.rb -= cur_img_data->to_image->frag.rb - tbd_tmp->bd;
+ else img_partner->frag.lb += cur_img_data->to_image->frag.rb - tbd_tmp->bd;
+ cur_img_data->to_image->frag.rb = tbd_tmp->bd;
+ } else {
+ dissected = 1;
+ /* create a new MSP to hold the left products of the dissection */
+ msp_tmp = add_msp(cur_img_data->to_image->to_msp);
+ /* upgrade the content of the new MSP */
+ if (cur_img_data->to_image == &cur_img_data->to_image->to_msp->query) {
+ target_img = &msp_tmp->query;
+ target_partner = &msp_tmp->sbjct;
+ } else {
+ target_img = &msp_tmp->sbjct;
+ target_partner = &msp_tmp->query;
+ }
+ msp_tmp->score = (int32_t) (tbd_tmp->bd-target_img->frag.lb+1.)/(target_img->frag.rb-target_img->frag.lb+1.)*msp_tmp->score;
+ if (msp_tmp->direction == 1) {
+ // RMH: When tracking down the divide by zero problem I ended up signaling this
+ // spot in the code as the likely place where things went initially wrong.
+ // Explore further.
+ target_partner->frag.rb -= target_img->frag.rb - tbd_tmp->bd;
+ }
+ else {
+ target_partner->frag.lb += target_img->frag.rb - tbd_tmp->bd;
+ }
+ target_img->frag.rb = tbd_tmp->bd;
+ fprint_msp(new_msps, msp_tmp);
+ /* keep or ignore the new msp */
+ register_image(target_img, cur_ele);
+
+ /* create the right product */
+ /* we cheat here. instead of generating a new MSP, we change the content of the original one, then output it into new_msp when finished. in the meantime, the index of the MSP is unchanged, which points to the oringinal MSP */
+ cur_img_data->to_image->to_msp->score -= msp_tmp->score;
+ if (cur_img_data->to_image->to_msp->direction == 1) img_partner->frag.lb += tbd_tmp->bd - cur_img_data->to_image->frag.lb + 1;
+ else img_partner->frag.rb -= tbd_tmp->bd - cur_img_data->to_image->frag.lb + 1;
+ cur_img_data->to_image->frag.lb = tbd_tmp->bd +1;
+ }
+ }
+ if (tbd_tmp->bd >= cur_img_data->to_image->frag.rb || !tbd_tmp->next) { /* end of this image */
+ if (dissected) {
+ fprint_msp(new_msps, cur_img_data->to_image->to_msp);
+ }
+ if (too_short(&cur_img_data->to_image->frag) || too_short(&img_partner->frag)) {
+ if (next && next->to_image->to_msp == cur_img_data->to_image->to_msp) next = next->next;
+ dump_image(cur_img_data->to_image);
+ }
+ break;
+ }
+ }
+ tbd_tmp = tbd_tmp->next;
+ }
+ cur_img_data = next;
+ }
+ /* the reason for not generating new elements according to the TBDs and then dissect and partition the images is that there's no gaining in time, it's virtually the same thing */
+}
+
+
+
+
+int too_short(FRAG_t *f) {
+ if (f->rb - f->lb <= TOO_SHORT) return 1;
+ return 0;
+}
+
+
+MSP_t *add_msp(MSP_t *m) {
+ MSP_t *msp_tmp;
+ /*MSP_DATA_t *hanger;*/
+
+ msp_tmp = MSP_malloc();
+ /*hanger = msp_tmp->hanger;*/
+ *msp_tmp = *m;
+ /*msp_tmp->hanger = hanger;*/
+ msp_index ++;
+ msp_tmp->query.to_msp = msp_tmp;
+ msp_tmp->query.index = 2*msp_index;
+ msp_tmp->sbjct.to_msp = msp_tmp;
+ msp_tmp->sbjct.index = 2*msp_index+1;
+ msp_tmp->stat = 's';
+ /*msp_in_mem ++;*/
+ /*msp_ct ++;*/
+
+ return msp_tmp;
+}
+
+
+
+
+void register_image(IMAGE_t *i, ELEMENT_t *ele) {
+ IMAGE_t *ip = partner(i);
+ int ct;
+
+ if (too_short(&i->frag)) {
+ /* rec_image(&i->ele_info->ele->ignored, i);
+ rec_image(&ip->ele_info->ele->ignored, ip); */
+ /* the msp here havn't been added to the corresponding elements, so we can simply free it */
+ MSP_free(i->to_msp);
+ } else {
+ /*ct = count_img_nodes(i->ele_info->ele->to_img_tree);
+ if (ct != i->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: image tree changed before inserting a new image: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ insert_image(&i->ele_info->ele->to_img_tree, i);
+ i->ele_info->ele->img_no ++;
+ /*ct = count_img_nodes(i->ele_info->ele->to_img_tree);
+ if (ct != i->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble inserting a new image: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ if (i->ele_info->ele->to_img_data) put_image(&i->ele_info->ele->to_img_data, i);
+ /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree);
+ if (ct != ip->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: tree changed before inserting a new image: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ insert_image(&ip->ele_info->ele->to_img_tree, ip);
+ ip->ele_info->ele->img_no ++;
+ /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree);
+ if (ct != ip->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble inserting a new image: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ if (ip->ele_info->ele->to_img_data) put_image(&ip->ele_info->ele->to_img_data, ip);
+ }
+}
+
+
+
+
+
+void put_image(IMG_DATA_t **idp, IMAGE_t *i) {
+ IMG_DATA_t *img_data_tmp;
+
+ img_data_tmp = (IMG_DATA_t *)malloc(sizeof(IMG_DATA_t));
+ img_data_tmp->to_image = i;
+ img_data_tmp->next = *idp;
+ *idp = img_data_tmp;
+}
+
+
+
+
+void dump_image(IMAGE_t *i) {
+ IMAGE_t *ip = partner(i);
+ int ct;
+
+ if (i->ele_info->ele->to_img_data) remove_image(i);
+ if (ip->ele_info->ele->to_img_data) remove_image(ip);
+
+ /*ct = count_img_nodes(i->ele_info->ele->to_img_tree);
+ if (ct != i->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: image tree changed before deleting a node: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ delete_image(&i->ele_info->ele->to_img_tree, i);
+ i->ele_info->ele->img_no --;
+ /*ct = count_img_nodes(i->ele_info->ele->to_img_tree);
+ if (ct != i->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble deleting an image node: ele %d %d %d\n", i->ele_info->index, i->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+
+ /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree);
+ if (ct != ip->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: image tree changed before deleting a node: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+ delete_image(&ip->ele_info->ele->to_img_tree, ip);
+ ip->ele_info->ele->img_no --;
+ /*ct = count_img_nodes(ip->ele_info->ele->to_img_tree);
+ if (ct != ip->ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble deleting an image node: ele %d %d %d\n", ip->ele_info->index, ip->ele_info->ele->img_no, ct);
+ fflush(log_file);
+ exit(2);
+ }*/
+
+ MSP_free(i->to_msp);
+}
+
+
+
+
+void remove_image(IMAGE_t *i) {
+ IMG_DATA_t *prev_img_data=NULL, *cur_img_data;
+
+ cur_img_data = i->ele_info->ele->to_img_data;
+ while (cur_img_data != NULL) {
+ if (cur_img_data->to_image == i) {
+ if (prev_img_data != NULL) {
+ prev_img_data->next = cur_img_data->next;
+ } else {
+ i->ele_info->ele->to_img_data = cur_img_data->next;
+ }
+ free(cur_img_data);
+ break;
+ }
+ prev_img_data = cur_img_data;
+ cur_img_data = cur_img_data->next;
+ }
+}
+
+
+
+
+/*****************************
+ *updating dissected element *
+ *****************************/
+
+
+
+
+
+void combo_update(ELE_INFO_t *ele_info) {
+ if (ele_info->ele->img_no < 0) {
+ err_no ++;
+ fprintf(log_file, "error: combo ele %d has %d images\n", ele_info->index, ele_info->ele->img_no);
+ fflush(log_file);
+ exit(2);
+ }
+ ele_info->stat = 'X';
+ if (ele_info->ele->edges) combo_edge_update(ele_info, &ele_info->ele->edges);
+ if (ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: combo_ele %d, %d edge_node left\n", ele_info->index, ele_info->ele->edge_no);
+ fflush(log_file);
+ exit(4);
+ }
+ ele_info->ele->flimg_no = 0;
+ if (ele_info->ele->PCP) CP_free(&ele_info->ele->PCP);
+ if (ele_info->ele->redef) {
+ if (ele_info->ele->to_img_data) {
+ err_no ++;
+ fprintf(log_file, "error re-defining ele %d, still images left\n", ele_info->index);
+ fflush(log_file);
+ exit(5);
+ }
+ /* all images and msps are relocated to offsprings, so img_tree_free() is enough */
+ if (ele_info->ele->to_img_tree) img_tree_free(&ele_info->ele->to_img_tree, ele_info);
+ if (ele_info->ele->img_no) {
+ err_no ++;
+ fprintf(log_file, "error: combo_ele %d, %d img_node left\n", ele_info->index, ele_info->ele->img_no);
+ fflush(log_file);
+ ele_info->ele->img_no = 0;
+ exit(2);
+ }
+ combo_output(ele_info);
+ } else {
+ if (ele_info->ele->img_no || ele_info->ele->to_img_data || ele_info->ele->to_img_tree) {
+ err_no ++;
+ fprintf(log_file, "error: images not cleaned in obs ele %d\n", ele_info->index);
+ fflush(log_file);
+ exit(2);
+ }
+ else obs_output(ele_info);
+ }
+}
+
+
+
+
+
+void combo_edge_update(ELE_INFO_t *ele_info, EDGE_TREE_t **edge_node_p) {
+ ELE_INFO_t *epi;
+ EDGE_TREE_t *edge_node = *edge_node_p;
+ ELEMENT_t *ele = ele_info->ele;
+
+ if (edge_node->l) combo_edge_update(ele_info, &(*edge_node_p)->l);
+
+ if (edge_node->r) combo_edge_update(ele_info, &(*edge_node_p)->r);
+
+ epi = linked_ele(ele_info, edge_node->to_edge);
+ if (epi->stat == 'v') epi->stat = 'w';
+ if (epi->ele->PCP) CP_clean(&epi->ele->PCP, ele_info);
+ delete_edge(&epi->ele->edges, edge_node->to_edge);
+ epi->ele->edge_no --;
+
+ EDGE_free(edge_node->to_edge);
+
+ ele_info->ele->edge_no --;
+ free(edge_node);
+ *edge_node_p = NULL;
+}
+
+
+
+
+
+void CP_clean(CP_t **cps_p, ELE_INFO_t *cont) {
+ /*int res=0;*/
+ CP_t *cp_cur, *cp_prev;
+
+ cp_cur = *cps_p;
+ cp_prev = NULL;
+ while (cp_cur != NULL) {
+ if (cp_cur->contributor == cont) {
+ if (cp_prev == NULL) {
+ *cps_p = cp_cur->next;
+ free(cp_cur);
+ cp_cur = *cps_p;
+ } else {
+ cp_prev->next = cp_cur->next;
+ free(cp_cur);
+ cp_cur = cp_prev->next;
+ }
+ /*res ++;*/
+ } else {
+ cp_prev = cp_cur;
+ cp_cur = cp_cur->next;
+ }
+ }
+ /*return res;*/
+}
+
+
+
+
+
+/****************************************************
+ ****************************************************
+ ** functions for finding PCPs and set up edges **
+ ****************************************************
+ ****************************************************/
+
+
+
+void edges_and_cps(ELE_INFO_t *ele_info, IMAGE_t **img_ptr) { /* the core function in this part, calls everything below */
+ int eff_img_ct, i, prim;
+ int j, riteplace;
+ short ritetime;
+ MSP_t *prim_p;
+
+ IMG_DATA_t *cur_img_data;
+ ELEMENT_t *ele_partner, *cur_ele = ele_info->ele;
+ ELE_INFO_t *epi;
+ IMAGE_t *img_partner, *cur_img;
+
+ IMAGE_t *token_image;
+ int token_mark=0;
+ IMG_NODE_t *consis_rt, *cur_consis_nd;
+ ELE_DATA_t *ele_data_tmp;
+ IMG_DATA_t *scovs;
+
+ int32_t max_score=0;
+ short dir;
+
+ /* sort unprocessed images according to their partner element, and then their left bounds */
+ /* to allocate proper amount of memory */
+ /* when update is 1, it means the element is an offspring of a combo, in which case all the images need to be processed; when update is 0, those images whose partner is 'v' or 'w' should be omitted */
+ /* no self-images are accepted to generate pcps or edges, updating or not */
+ if (!cur_ele->to_img_data) listify(cur_ele->to_img_tree, &cur_ele->to_img_data);
+ cur_img_data = cur_ele->to_img_data;
+ eff_img_ct = 0;
+ while(cur_img_data != NULL) {
+ epi = partner(cur_img_data->to_image)->ele_info;
+ if (epi->index != ele_info->index) {
+ if (cur_ele->update || epi->stat == 'z') eff_img_ct ++;
+ }
+ cur_img_data = cur_img_data->next;
+ }
+
+ if (eff_img_ct) {
+ token_image = (IMAGE_t *) malloc(sizeof(IMAGE_t));
+ token_image->frag.lb = 0;
+ token_image->frag.rb = 0;
+ token_image->to_msp = NULL;
+ token_image->ele_info = NULL;
+ consis_rt = (IMG_NODE_t *) malloc(sizeof(IMG_NODE_t));
+ consis_rt->to_image = token_image;
+ consis_rt->children = NULL;
+ consis_rt->sib = NULL;
+
+ if (eff_img_ct > MAX_IMG) {
+ img_ptr = (IMAGE_t **) malloc(eff_img_ct*sizeof(IMAGE_t *));
+ }
+
+ cur_img_data = cur_ele->to_img_data;
+ eff_img_ct = 0;
+ while(cur_img_data != NULL) {
+ epi = partner(cur_img_data->to_image)->ele_info;
+ if (epi->index != ele_info->index) {
+ if (cur_ele->update || epi->stat == 'z') {
+ *(img_ptr+eff_img_ct) = cur_img_data->to_image;
+ eff_img_ct ++;
+ }
+ }
+ cur_img_data = cur_img_data->next;
+ }
+ qsort(img_ptr, eff_img_ct, sizeof(IMAGE_t *), partner_cmp);
+
+ /* recognizing full-length images, and put partial and secondary images into a consistency tree, in which images connected are consistent with each other (look at the consis() function of definition of consistency) */
+ ritetime = 1;
+ for (i=0; i<eff_img_ct; i++) {
+ cur_img = *(img_ptr+i);
+ img_partner = partner(cur_img);
+ if (ritetime) { /* new ele_partner begins */
+ epi = img_partner->ele_info;
+ ritetime = 0;
+ if (!epi->ele) ele_read_in(epi, 1);
+ ele_partner = epi->ele;
+ riteplace = i;
+ prim = 0;
+ prim_p = NULL;
+ max_score = 0;
+ }
+ if (img_partner->ele_info->index == epi->index) { /* still the same partner element */
+ /* full length */
+ if (full_length(cur_img, CUTOFF2)) {
+ /*cur_img->to_msp->stat = 'p';*/
+ prim = 1;
+ cur_ele->flimg_no ++;
+ }
+ if (full_length(img_partner, CUTOFF2)) {
+ /*cur_img->to_msp->stat = 'p';*/
+ prim = 1;
+ ele_partner->flimg_no ++;
+ }
+ /*if (cur_img->to_msp->stat == 'p') {*/
+ if (prim == 1) {
+ prim = 0;
+ if (cur_img->to_msp->iden > max_score) {
+ max_score = cur_img->to_msp->iden;
+ dir = cur_img->to_msp->direction;
+ prim_p = cur_img->to_msp;
+ }
+ }
+ if (!prim_p) { /* non-fl, and no fl found yet */
+ consis_tree_build(consis_rt, cur_img, 1);
+ }
+ }
+ if (img_partner->ele_info->index != epi->index || i == eff_img_ct-1) { /* reached the end of the current ele_partner */
+ /* start a new ele_partner */
+ ritetime = 1;
+ if (img_partner->ele_info->index != epi->index) i --;
+ /* finish the current ele_partner */
+ if (prim_p) {
+ prim_p->stat = 'p';
+ prim = 1;
+ } else { /* if no fl, find partial primary images */
+ /*prim = find_prim(consis_rt, CUTOFF2, 0, 0, 0, &max_score, &dir);*/
+ prim = find_prim(consis_rt->children, CUTOFF2, ele_info->ele->frag.lb, -1, 0, 0, 0, 0, 0, &token_mark, &max_score, &dir);
+ }
+ /* build edge */
+ if (prim) {
+ if (ele_info->index != epi->index) add_edge(ele_info, epi, 'p', max_score, dir);
+ else {
+ err_no ++;
+ fprintf(log_file, "error: self edge seen: ele %d\n", ele_info->index);
+ fflush(log_file);
+ }
+ for (j=riteplace; j<=i; j++) {
+ if ((*(img_ptr+j))->to_msp->stat == 'p') {
+ cur_img = *(img_ptr+j);
+ img_partner = partner(cur_img);
+ add_CP(&cur_ele->PCP, cur_img->frag.lb, epi);
+ add_CP(&cur_ele->PCP, cur_img->frag.rb, epi);
+ add_CP(&ele_partner->PCP, img_partner->frag.lb, ele_info);
+ add_CP(&ele_partner->PCP, img_partner->frag.rb, ele_info);
+ }
+ }
+ } else { /* no primary images, full-length or partial */
+ if (ele_info->index != epi->index) add_edge(ele_info, epi, 's', 0, 0);
+ else {
+ err_no ++;
+ fprintf(log_file, "error: self edge seen: ele %d\n", ele_info->index);
+ fflush(log_file);
+ }
+ }
+ if (consis_rt->children != NULL) {
+ consis_tree_free(consis_rt->children);
+ consis_rt->children = NULL;
+ }
+ }
+ }
+
+ if (eff_img_ct > MAX_IMG) {
+ free(img_ptr);
+ }
+ free(consis_rt);
+ free(token_image);
+ }
+
+ if (ele_info->ele->edges) adjust_edge_tree(ele_info);
+
+ cur_ele->update = 0;
+ ele_info->stat = 't';
+}
+
+
+
+/* NOTE: Due to the difference in computational precesion between 32bit
+ * and 64 bit processors the following function may return differing
+ * results.
+ */
+int full_length(IMAGE_t *i, float cutoff) {
+ if (!i->ele_info->ele) {
+ err_no ++;
+ fprintf(log_file, "error: element %d not in memory\n", i->ele_info->index);
+ fflush(log_file);
+ exit(3);
+ ele_read_in(i->ele_info, 1);
+ }
+ if (i->frag.lb-i->ele_info->ele->frag.lb < 10 && i->frag.rb-i->ele_info->ele->frag.rb > -10 && ((float) i->frag.rb-i->frag.lb)/(i->ele_info->ele->frag.rb-i->ele_info->ele->frag.lb) > cutoff) {
+ return 1;
+ }
+ return 0;
+}
+
+
+
+void add_CP(CP_t **CP_ptr, int32_t cp, ELE_INFO_t *cont) {
+ CP_t *new = (CP_t *) malloc(sizeof(CP_t));
+ new->cp = cp;
+ new->contributor = cont;
+ new->next = *CP_ptr;
+ *CP_ptr = new;
+}
+
+
+
+void add_edge(ELE_INFO_t *ele1_info, ELE_INFO_t *ele2_info, char type, int32_t score, short dir) {
+ EDGE_t *new = EDGE_malloc();
+ int ct;
+
+ edge_index ++;
+ new->index = edge_index;
+ new->ele1_info = ele1_info;
+ new->ele2_info = ele2_info;
+ new->type = type;
+ new->score = score;
+ new->direction = dir;
+ /*ct = count_edge_nodes(ele1_info->ele->edges);
+ if (ct != ele1_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble before inserting edge\n");
+ fflush(log_file);
+ exit(4);
+ }*/
+ ele1_info->ele->edge_no ++;
+ insert_edge(&ele1_info->ele->edges, new);
+ /*ct = count_edge_nodes(ele1_info->ele->edges);
+ if (ct != ele1_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble after inserting edge\n");
+ fflush(log_file);
+ exit(4);
+ }*/
+ if (ele1_info->index != ele2_info->index) {
+ /*ct = count_edge_nodes(ele2_info->ele->edges);
+ if (ct != ele2_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble before inserting edge\n");
+ fflush(log_file);
+ exit(4);
+ }*/
+ ele2_info->ele->edge_no ++;
+ insert_edge(&ele2_info->ele->edges, new);
+ /*ct = count_edge_nodes(ele2_info->ele->edges);
+ if (ct != ele2_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble after inserting edge\n");
+ fflush(log_file);
+ exit(4);
+ }*/
+ }
+}
+
+
+
+
+void adjust_edge_tree(ELE_INFO_t *ele_info) {
+ EDGE_t **edge_array;
+ int ct, ct1;
+
+ /*ct = count_edge_nodes(ele_info->ele->edges);
+ if (ct != ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble before adjusting the edge tree: ele %d %d %d\n", ele_info->index, ele_info->ele->edge_no, ct);
+ fflush(log_file);
+ exit(4);
+ }
+ ct = count_total_edges(ele_info->ele->edges);
+ if (ct != ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: illegitimate edge in ele %d\n", ele_info->index);
+ fflush(log_file);
+ exit(5);
+ }*/
+ ct = ele_info->ele->edge_no;
+ edge_array = (EDGE_t **) malloc(ct*sizeof(EDGE_t *));
+ ct1 = charge_edge_array(edge_array, ele_info->ele->edges, 0);
+ if (ct1 != ct) {
+ err_no ++;
+ fprintf(log_file, "error: trouble charging the edge array in ele %d: %d charged, %d expected\n", ele_info->index, ct1, ct);
+ fflush(log_file);
+ exit(4);
+ }
+ edge_tree_free(&ele_info->ele->edges);
+ build_edge_tree(&ele_info->ele->edges, edge_array, 0, ct-1);
+ /*ct = count_edge_nodes(ele_info->ele->edges);
+ if (ct != ele_info->ele->edge_no) {
+ err_no ++;
+ fprintf(log_file, "error: trouble adjusting the edge tree: ele %d %d %d\n", ele_info->index, ele_info->ele->edge_no, ct);
+ fflush(log_file);
+ exit(4);
+ }*/
+ free(edge_array);
+}
+
+
+
+
+int charge_edge_array(EDGE_t **edge_array, EDGE_TREE_t *rt, int pos) {
+ if (rt->l) pos = charge_edge_array(edge_array, rt->l, pos);
+
+ *(edge_array+pos) = rt->to_edge;
+ pos ++;
+
+ if (rt->r) pos = charge_edge_array(edge_array, rt->r, pos);
+
+ return pos;
+}
+
+
+
+
+/******************************************
+ * functions for building the consis_tree *
+ ******************************************/
+
+
+int consis_tree_build(IMG_NODE_t *rt, IMAGE_t *im, int prequal) {
+ int sum=0;
+ IMG_NODE_t *nex_rt, *node;
+ if (prequal || consis(rt->to_image, im, CUTOFF2)) {
+ nex_rt = rt->children;
+ while (nex_rt != NULL) {
+ sum += consis_tree_build(nex_rt, im, 0);
+ nex_rt = nex_rt->sib;
+ }
+ if (!sum) {
+ node = (IMG_NODE_t *) malloc(sizeof(IMG_NODE_t));
+ node->recorded = 0;
+ node->to_image = im;
+ node->sib = NULL;
+ node->children = NULL;
+ *node_entry(&rt->children) = node;
+ sum = 1;
+ }
+ }
+ return sum;
+}
+
+
+int consis(IMAGE_t *i1, IMAGE_t *i2, float cutoff) {
+ int res = 0;
+ IMAGE_t *ip1 = partner(i1), *ip2 = partner(i2);
+ if (i1->ele_info->index == i2->ele_info->index && ip1->ele_info->index == ip2->ele_info->index && i1->to_msp->direction == i2->to_msp->direction) {
+ if (i1->to_msp->direction == 1) {
+ if ((i1->frag.lb - i2->frag.lb)*(ip1->frag.lb - ip2->frag.lb) > 0) {
+ if (!sing_cov(&i1->frag, &i2->frag, 1.0-cutoff) && !sing_cov(&ip1->frag, &ip2->frag, 1.0-cutoff)) {
+ res = 1;
+ }
+ }
+ } else {
+ if ((i1->frag.lb - i2->frag.lb)*(ip1->frag.rb - ip2->frag.rb) < 0) {
+ if (!sing_cov(&i1->frag, &i2->frag, 1.0-cutoff) && !sing_cov(&ip1->frag, &ip2->frag, 1.0-cutoff)) {
+ res = 1;
+ }
+ }
+ }
+ }
+ return res;
+}
+
+
+
+IMG_NODE_t ** node_entry(IMG_NODE_t **node_pp) {
+ if (*node_pp != NULL) {
+ return node_entry(&(*node_pp)->sib);
+ }
+ return node_pp;
+}
+
+
+
+
+void consis_tree_free(IMG_NODE_t *rt) {
+ if (rt->sib != NULL) {
+ consis_tree_free(rt->sib);
+ }
+ if (rt->children != NULL) {
+ consis_tree_free(rt->children);
+ }
+ free(rt);
+}
+
+
+
+
+/*****************************************
+ * functions for parsing the consis_tree *
+ *****************************************/
+
+/*
+ I. function for finding primary images from the consis_tree
+*/
+
+#if 0
+int find_prim(IMG_NODE_t *nd, float cutoff, int32_t score, int32_t hist, short which, int32_t *sc, short *d) {
+ IMG_NODE_t *nex_node;
+ int sum = 0;
+ short level, further = 0;
+ IMAGE_t *img_partner;
+
+ if (!hist) level = 1;
+ hist += nd->to_image->frag.rb - nd->to_image->frag.lb;
+
+ if (level && hist) { /* if first image in a path isn't EOE, forget the path */
+ if (nd->to_image->frag.lb - nd->to_image->ele_info->ele->frag.lb < MARGIN) {
+ which = 1;
+ }
+ img_partner = partner(nd->to_image);
+ if (nd->to_image->to_msp->direction == 1) {
+ if (img_partner->frag.lb - img_partner->ele_info->ele->frag.lb < MARGIN) {
+ which += 2;
+ }
+ } else {
+ if (img_partner->frag.rb - img_partner->ele_info->ele->frag.rb > -MARGIN) {
+ which += 2;
+ }
+ }
+ if (!which) return 0;
+ }
+
+ if (nd->children != NULL) {
+ nex_node = nd->children;
+ while (nex_node != NULL) {
+ sum += find_prim(nex_node, cutoff, score, hist, which, sc, d);
+ nex_node = nex_node->sib;
+ }
+ if (sum && hist) {
+ nd->to_image->to_msp->stat = 'p'; /* p stands for primary, NOT partial */
+ }
+ } else { /* the last image goes to EOE on the same element as the first image in the path */
+ if ((which == 1 || which == 3) && nd->to_image->frag.rb - nd->to_image->ele_info->ele->frag.rb > -MARGIN && (float) hist/(nd->to_image->ele_info->ele->frag.rb - nd->to_image->ele_info->ele->frag.lb) > cutoff) {
+ further = 1;
+ } else {
+ img_partner = partner(nd->to_image);
+ if ((which == 2 || which == 3) && (float) hist/(img_partner->ele_info->ele->frag.rb - img_partner->ele_info->ele->frag.lb) > cutoff) {
+ if (nd->to_image->to_msp->direction == 1) {
+ if (img_partner->frag.rb - img_partner->ele_info->ele->frag.rb > -MARGIN) further = 1;
+ } else {
+ if (img_partner->frag.lb - img_partner->ele_info->ele->frag.lb < MARGIN) further = 1;
+ }
+ }
+ }
+ if (further) {
+ nd->to_image->to_msp->stat = 'p';
+ score += nd->to_image->to_msp->score;
+ if (score > *sc) {
+ *sc = score;
+ *d = nd->to_image->to_msp->direction;
+ }
+ sum = 1;
+ } else {sum = 0;}
+ }
+
+ return sum;
+}
+#endif
+
+
+
+int find_prim(IMG_NODE_t *nd, float cutoff, int32_t end1, int32_t end2, int32_t efl1, int32_t efl2, int32_t al1, int32_t al2, int32_t score, int *pmarkp, int32_t *sc, short *d) {
+ int sum = 0, mark=0;
+ int32_t skip1, skip2, len1, len2;
+ IMAGE_t *ipt;
+
+ if (nd->sib) sum += find_prim(nd->sib, cutoff, end1, end2, efl1, efl2, al1, al2, score, pmarkp, sc, d);
+
+ ipt = partner(nd->to_image);
+ if (end2 < 0) { /*first alignment in the group*/
+ if (nd->to_image->to_msp->direction == 1) end2 = ipt->ele_info->ele->frag.lb;
+ else end2 = ipt->ele_info->ele->frag.rb;
+ }
+
+ skip1 = nd->to_image->frag.lb - end1;
+ if (nd->to_image->to_msp->direction == 1) skip2 = ipt->frag.lb - end2;
+ else skip2 = end2 - ipt->frag.rb;
+ if (skip1>10 && skip2>10) {
+ efl1 += skip1;
+ efl2 += skip2;
+ }
+ len1 = nd->to_image->frag.rb - nd->to_image->frag.lb;
+ len2 = ipt->frag.rb - ipt->frag.lb;
+ efl1 += len1;
+ efl2 += len2;
+ al1 += len1;
+ al2 += len2;
+ score += ((int32_t) nd->to_image->to_msp->iden)*(len1+len2)/2;
+
+ if (nd->children) {
+ end1 = nd->to_image->frag.rb;
+ if (nd->to_image->to_msp->direction == 1) end2 = ipt->frag.rb;
+ else end2 = ipt->frag.lb;
+ sum += find_prim(nd->children, cutoff, end1, end2, efl1, efl2, al1, al2, score, &mark, sc, d);
+ } else { /*last alignment in group*/
+ skip1 = nd->to_image->ele_info->ele->frag.rb - nd->to_image->frag.rb;
+ if (nd->to_image->to_msp->direction == 1) skip2 = ipt->ele_info->ele->frag.rb - ipt->frag.rb;
+ else skip2 = ipt->frag.lb - ipt->ele_info->ele->frag.lb;
+ if (skip1>10 && skip2>10) {
+ efl1 += skip1;
+ efl2 += skip2;
+ }
+ /*if (1.0*al1/efl1 > cutoff || 1.0*al2/efl2 > cutoff) {*/
+ if ( (1.0*al1/efl1 > cutoff || 1.0*al2/efl2 > cutoff) && (efl1-al1 < 30 || efl2-al2 < 30) ) {
+ sum = 1;
+ mark = 1;
+ if ( (al1+al2) == 0 )
+ {
+ // RMH: A divide by zero error has occured a few times at this point.
+ // I looked extensively through the code and cannot determine what
+ // is causing this -- although I have a reliable test case to
+ // explore this further. For now this is the only workaround.
+ // If al1 & al2 are zero then simply set them to 1.
+ printf("eleredef warning: Divide by zero averted -- setting al1 to 1.\n");
+ al1 = 1;
+ }
+ score = score*2/(al1+al2);
+ if (score > *sc) {
+ *sc = score;
+ *d = nd->to_image->to_msp->direction;
+ }
+ }
+ }
+ if (mark) {
+ nd->to_image->to_msp->stat = 'p';
+ *pmarkp = 1;
+ }
+ return sum;
+}
+
+
+
+
+
+
+/************************
+ ************************
+ *** ***
+ *** OUTPUT ***
+ *** ***
+ ************************
+ ************************/
+
+
+
+
+
+void combo_output(ELE_INFO_t *ele_info) {
+ char *ele_name;
+ FILE *ele_fp;
+ ELE_DATA_t *cur_ele_data;
+
+ fprintf(combo, "%d %s %d %d \n", ele_info->index, ele_info->ele->frag.seq_name, ele_info->ele->frag.lb, ele_info->ele->frag.rb);
+ fflush(combo);
+
+#if 0
+ /* no ele_read_in() needed, 'cuz where this function is called, both the combo and its offsprings are in the memory */
+ ele_name = (char *) malloc(30*sizeof(char));
+ sprintf(ele_name, "tmp2/clan/combos/e%d", ele_info->index);
+ ele_fp = fopen(ele_name, "w");
+
+ fprintf(ele_fp, "ele %d\n", ele_info->index);
+ fprintf(ele_fp, "offsprings \n");
+ cur_ele_data = ele_info->ele->redef;
+ while (cur_ele_data != NULL) {
+ if (cur_ele_data->ele_info->ele->direction == 1) fprintf(ele_fp, "%6d %10s %8d %8d\n", cur_ele_data->ele_info->index, cur_ele_data->ele_info->ele->frag.seq_name, cur_ele_data->ele_info->ele->frag.lb, cur_ele_data->ele_info->ele->frag.rb);
+ else fprintf(ele_fp, "%6d %10s %8d %8d\n", cur_ele_data->ele_info->index, cur_ele_data->ele_info->ele->frag.seq_name, cur_ele_data->ele_info->ele->frag.rb, cur_ele_data->ele_info->ele->frag.lb);
+ cur_ele_data = cur_ele_data->next;
+ }
+
+ fclose(ele_fp);
+ free(ele_name);
+ /* remove_ele(ele_info);*/
+#endif
+}
+
+
+
+
+
+void obs_output(ELE_INFO_t *ele_info) {
+ char *ele_name;
+ FILE *ele_fp;
+
+ fprintf(obs, "%d %s %d %d \n", ele_info->index, ele_info->ele->frag.seq_name, ele_info->ele->frag.lb, ele_info->ele->frag.rb);
+ fflush(obs);
+
+#if 0
+ ele_name = (char *) malloc(30*sizeof(char));
+ sprintf(ele_name, "tmp2/clan/obsolete/e%d", ele_info->index);
+ ele_fp = fopen(ele_name, "w");
+ fprint_ele_obs(ele_fp, ele_info);
+ fclose(ele_fp);
+ free(ele_name);
+ /* remove_ele(ele_info);*/
+#endif
+}
+
+
+
+
+void fprint_ele_obs(FILE *fp, ELE_INFO_t *ele_info) {
+ int i;
+ BD_t *cur_bd;
+ ELEMENT_t *ele=ele_info->ele;
+
+ fprintf(fp, "ele %d\n", ele_info->index);
+ fprintf(fp, "%s %d %d \n", ele->frag.seq_name, ele->frag.lb, ele->frag.rb);
+ if (ele->TBD != NULL) {
+ fprintf(fp, "cutting points\n");
+ i = 0;
+ cur_bd = ele->TBD;
+ while (cur_bd != NULL) {
+ fprintf(fp, "%d ", cur_bd->bd);
+ i ++;
+ if (i%10 == 0) fprintf(fp, "\n");
+ cur_bd = cur_bd->next;
+ }
+ }
+}
+
+
+
+
+
+
+/**************************************
+ **************************************
+ * *
+ * comparison fucntions for qsort() *
+ * *
+ **************************************
+ **************************************/
+
+
+
+
+
+
+int frag_cmp(const void *i1, const void *i2) {
+ int res = (*(IMG_DATA_t **)i1)->to_image->frag.seq_name - (*(IMG_DATA_t **)i2)->to_image->frag.seq_name; /*strncmp((*(IMG_DATA_t **)i1)->to_image->frag.seq_name, (*(IMG_DATA_t **)i2)->to_image->frag.seq_name, NAME_LEN)*/
+ if (res == 0) {
+ res = (*(IMG_DATA_t **)i1)->to_image->frag.lb - (*(IMG_DATA_t **)i2)->to_image->frag.lb;
+ if (res == 0) {
+ res = (*(IMG_DATA_t **)i1)->to_image->frag.rb - (*(IMG_DATA_t **)i2)->to_image->frag.rb;
+ }
+ }
+ return res;
+}
+
+
+int partner_cmp(const void *i1, const void *i2) {
+ int res = partner(*((IMAGE_t **)i1))->ele_info->index - partner(*((IMAGE_t **)i2))->ele_info->index;
+ if (res == 0) {
+ res = (*((IMAGE_t **)i1))->to_msp->direction - (*((IMAGE_t **)i2))->to_msp->direction;
+ }
+ if (res == 0) {
+ res = (*((IMAGE_t **)i1))->frag.lb - (*((IMAGE_t **)i2))->frag.lb;
+ }
+ if (res == 0) {
+ res = (*((IMAGE_t **)i1))->frag.rb - (*((IMAGE_t **)i2))->frag.rb;
+ }
+ return res;
+}
+
+
+int CP_cmp(const void *cp1, const void *cp2) {
+ return (*((CP_t **) cp1))->cp - (*((CP_t **) cp2))->cp;
+}
+
+
+int BD_cmp(const void *bd1, const void *bd2) {
+ return (*((BD_t **) bd1))->bd - (*((BD_t **) bd2))->bd;
+}
+
+
+int fam_cmp(const void *fd1, const void *fd2) {
+ return (*((FAM_DATA_t **) fd1))->to_family->index - (*((FAM_DATA_t **) fd2))->to_family->index;
+}
diff --git a/src/famdef.c b/src/famdef.c
new file mode 100644
index 0000000..afc86f7
--- /dev/null
+++ b/src/famdef.c
@@ -0,0 +1,260 @@
+#include "ele.h"
+
+
+typedef struct Dirs {
+ int dir;
+ struct Dirs *next;
+} Dirs_t;
+
+
+FAMILY_t *new_family();
+void build_family(FAMILY_t *, ELE_INFO_t *, short, int *);
+void recruit_partner(ELE_INFO_t *, EDGE_TREE_t *, ELE_DATA_t **, Dirs_t *, Dirs_t **);
+
+
+
+
+
+
+int main (int argc, char *argv[]) {
+ int i, rounds=0, ei;
+ char line[35], stat;
+ FAM_DATA_t *fam;
+ FAMILY_t *family;
+ FILE *seq_list, *ele_no, *redef_stat;
+ FILE *fam_no, *final_ele_no;
+ int tot_ele;
+
+ /* processing command line */
+ if (argc == 1) {
+ printf("usage: famdef seq_list\n where seq_list is the list of sequence names.\n");
+ exit(1);
+ }
+
+ seq_list = fopen(argv[1], "r");
+ if (!seq_list) {
+ printf("Input file for sequence name list %s not found. Exit.\n", argv[1]);
+ exit(2);
+ }
+ GetSeqNames(seq_list);
+
+ ele_no = fopen("summary/redef_ele_no", "r");
+ if(!ele_no) {
+ printf("Can not open redef_ele_no. Exiting\n");
+ exit(2);
+ }
+
+ redef_stat = fopen("tmp/redef_stat", "r");
+ if (!redef_stat) {
+ printf("Can not open redef_stat. Exiting\n");
+ exit(2);
+ }
+
+ eles = fopen("summary/eles", "w");
+ fams = fopen("summary/families", "w");
+ fam_no = fopen("summary/fam_no", "w");
+ final_ele_no = fopen("summary/ele_no", "w");
+
+ log_file = fopen("tmp/log2", "w");
+
+ while (fgets(line, 15, ele_no)) {
+ ele_ct = atoi(line);
+ }
+ fclose(ele_no);
+
+ ele_array_size = ele_ct;
+ all_ele = (ELE_INFO_t **) malloc(ele_array_size*sizeof(ELE_INFO_t *));
+
+ for (i=0; i<ele_ct; i++) {
+ *(all_ele+i) = ele_info_init(i+1);
+ }
+
+ ele_ct = 0;
+ while (fgets(line, 35, redef_stat)) {
+ ele_ct ++;
+ /*sscanf(line, "%d %c %d\n", &ei, &stat, &fu);*/
+ /* for some bizzare reason, scanf doesn't work properly here. :( */
+ for (i=0; i<35; i++) {
+ if (line[i] == ' ') break;
+ }
+ ei = atoi(line);
+ stat = line[i+1];
+ (*(all_ele+ei-1))->stat = stat;
+ }
+
+
+ msp_in_mem = 0;
+ msp_left = 0;
+ msp_ct = 0;
+ edge_ct = 0;
+ edge_in_mem = 0;
+ edge_left = 0;
+ files_read = 0;
+ clan_ct = 0;
+ err_no = 0;
+
+ /* define families */
+ fam_ct = 0;
+ tot_ele = 0;
+
+ fprintf(eles, "# fam ele dir sequence start end\n");
+ fprintf(fams, "# fam cp-no name\n");
+
+ for (i=0; i<ele_ct; i++) {
+ if ((*(all_ele+i))->stat != 'O' && (*(all_ele+i))->stat != 'X') {
+ fprintf(log_file, "evaluating family membership of element %d\n", (*(all_ele+i))->index);
+ fflush(log_file);
+ if ((*(all_ele+i))->stat == 'y') { /* starting a new family! */
+ family = new_family();
+ build_family(family, *(all_ele+i), 1, &tot_ele);
+ } else if ((*(all_ele+i))->stat != 'x') {
+ err_no ++;
+ fprintf(log_file, "ele %d %c not properly filtered\n", (*(all_ele+i))->index, (*(all_ele+i))->stat);
+ fflush(log_file);
+ exit(5);
+ }
+ }
+ }
+
+ fprintf(fam_no, "%d\n", fam_ct);
+ fclose(fam_no);
+
+ fprintf(final_ele_no, "%d\n", tot_ele);
+ fclose(final_ele_no);
+
+ fprintf(log_file, "total numbers: %d elements, %d msps, %d edges\n", ele_ct, msp_index+1, edge_index+1);
+ fprintf(log_file, "%d files read, %d msps seen, %d edges seen\n", files_read, msp_ct, edge_ct);
+ fprintf(log_file, "%d errors, %d msps and %d edges left in memory, \n", err_no, msp_left, edge_left);
+ fflush(log_file);
+ fclose(log_file);
+
+
+ exit(0);
+}
+
+
+
+
+
+
+
+/**************************************
+ **************************************
+ ** **
+ ** CLUSTERING, YEAH BABY YEAH! **
+ ** **
+ **************************************
+ **************************************/
+
+
+
+
+
+
+FAMILY_t *new_family() {
+ FAMILY_t *fam;
+ FAM_DATA_t *fam_data;
+
+ fam_ct ++;
+ fam = (FAMILY_t *) malloc(sizeof(FAMILY_t));
+ fam->index = fam_ct;
+ fam->members = NULL;
+ fam->relatives = NULL;
+
+ return fam;
+}
+
+
+
+
+
+void build_family(FAMILY_t *fam, ELE_INFO_t *ele_info, short dir, int *te) {
+ /* standard breath first traverse for connected components */
+ ELE_DATA_t *mem_tail, *seed, *cur_mem;
+ ELE_INFO_t *cei;
+ int mem_ct = 0;
+ Dirs_t *dirs, *dirs_t, *cur_dir;
+
+
+ ele_info->stat = 'x';
+ seed = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ seed->ele_info = ele_info;
+ seed->next = NULL;
+ fam->members = seed;
+ mem_tail = seed;
+ dirs = (Dirs_t *) malloc(sizeof(Dirs_t));
+ dirs->dir = 1;
+ dirs->next = NULL;
+ dirs_t = dirs;
+
+ /* recruiting new members */
+ cur_mem = fam->members;
+ cur_dir = dirs;
+ while (cur_mem) {
+ mem_ct ++;
+ cei = cur_mem->ele_info;
+ if (cei->ele) {
+ fprintf(log_file, "ele %d is in memory unexpectedly\n", cei->index);
+ fflush(log_file);
+ exit(3);
+ } else ele_read_in(cei, 4);
+
+ cei->to_family = fam;
+
+ /* output the element */
+ /* to the list of all elements */
+ /*fprintf(eles, "%6d %6d %2d %10s %8d %8d \n", fam->index, cei->index, cei->ele->direction, cei->ele->frag.seq_name, cei->ele->frag.lb, cei->ele->frag.rb);*/
+ fprintf(eles, "%6d %6d %2d %10s %8d %8d \n", fam->index, cei->index, cur_dir->dir, cei->ele->frag.seq_name, cei->ele->frag.lb, cei->ele->frag.rb);
+
+ /* recruit its partners (that have not been recruited) */
+ if (cei->ele->edges) recruit_partner(cei, cei->ele->edges, &mem_tail, cur_dir, &dirs_t);
+ else if (cur_mem != seed) {
+ fprintf(log_file, "error: ele %d edge tree missing\n", cei->index);
+ fflush(log_file);
+ exit(4);
+ }
+ ele_cleanup(&cei->ele);
+ cur_mem = cur_mem->next;
+ cur_dir = cur_dir->next;
+ }
+
+ fprintf(fams, "%d %d unknown \n", fam->index, mem_ct);
+ fflush(fams);
+
+ *te += mem_ct;
+
+ fprintf(log_file, "new family with %d members\n", mem_ct);
+ fflush(log_file);
+
+ fam_cleanup(&fam);
+}
+
+
+
+
+void recruit_partner(ELE_INFO_t *ele_info, EDGE_TREE_t *rt, ELE_DATA_t **tail, Dirs_t *cur_dir, Dirs_t **dtail){
+ ELE_INFO_t *epi;
+ ELE_DATA_t *new_mem;
+ Dirs_t *new_dir;
+
+ if (rt->l) recruit_partner(ele_info, rt->l, tail, cur_dir, dtail);
+
+ if (rt->to_edge->type == 'p' || rt->to_edge->type == 'P') {
+ epi = linked_ele(ele_info, rt->to_edge);
+ if (epi->stat == 'y') {
+ epi->stat = 'x';
+ new_mem = (ELE_DATA_t *) malloc(sizeof(ELE_DATA_t));
+ new_mem->ele_info = epi;
+ new_mem->next = NULL;
+ (*tail)->next = new_mem;
+ *tail = new_mem;
+ new_dir = (Dirs_t *) malloc(sizeof(Dirs_t));
+ new_dir->dir = cur_dir->dir * rt->to_edge->direction;
+ new_dir->next = NULL;
+ (*dtail)->next = new_dir;
+ *dtail = new_dir;
+ }
+ }
+
+ if (rt->r) recruit_partner(ele_info, rt->r, tail, cur_dir, dtail);
+}
diff --git a/src/imagespread.c b/src/imagespread.c
new file mode 100644
index 0000000..798773b
--- /dev/null
+++ b/src/imagespread.c
@@ -0,0 +1,98 @@
+
+#include "msps.h"
+
+
+int GetOutputInterval(char *, int, int);
+
+
+
+int main (int argc, char *argv[]) {
+ FILE *msp_file, *seq_list; /* input files */
+ FILE **output, *err, *msp_no; /* output files */
+ int noof=1, i; /* noof == Number Of Output Files */
+ char line[150], output_name[50];
+ MSP_t cur;
+ int img_ct=-1;
+
+ /* checking command line */
+ if (argc < 3) {
+ printf("usage:\n imagespread seq_name_list msp_list number_of_output_files\nlast parameter optional with default of 1\n");
+ exit(1);
+ }
+
+ /* checking input */
+ seq_list = fopen(argv[1], "r");
+ if (!seq_list) {
+ printf("Input file for sequence name list %s not found. Exit.\n", argv[1]);
+ exit(2);
+ }
+ msp_file = fopen(argv[2], "r");
+ if (!msp_file) {
+ printf("Input MSP file %s not found. Exit.\n", argv[2]);
+ exit(2);
+ }
+ if (argc == 4) {noof = atoi(argv[3]);}
+ if (noof < 1) noof = 1;
+
+ /*files for output */
+ err = fopen("images/errors", "w");
+ if (!err) {
+ printf("Can not open images/errors for output. Exit.\n");
+ exit(3);
+ }
+ msp_no = fopen("summary/ori_msp_no", "w");
+ if (!msp_no) {
+ printf("Can not open images/msp_no for output. Exit.\n");
+ exit(3);
+ }
+ output = (FILE **) malloc(noof*sizeof(FILE *));
+ for (i=0; i<noof; i++) {
+ sprintf(output_name, "images/spread%d", i+1);
+ *(output+i) = fopen(output_name, "w");
+ if (!*(output+i)) {
+ printf("Can not open %s for output. Exit.\n", output_name);
+ exit(3);
+ }
+ }
+
+ /* get the list sequence names */
+ GetSeqNames(seq_list);
+
+ /* spread the MSPs */
+ while (fgets(line, 150, msp_file)) {
+ if (scan_msp(&cur, line)) {
+ fprintf(err, "Wrong format:\n%s", line);
+ continue;
+ }
+ img_ct ++;
+ i = GetOutputInterval(cur.query.frag.seq_name, seq_no, noof);
+ if (i < 0) {
+ fprintf(err, "Sequence name %s not found in the given list of sequences. Exit.\n", cur.query.frag.seq_name);
+ exit(4);
+ }
+ fprintf(*(output+i), "%d %d %s %d %d \n", img_ct, cur.score, cur.query.frag.seq_name, cur.query.frag.lb, cur.query.frag.rb);
+ img_ct ++;
+ i = GetOutputInterval(cur.sbjct.frag.seq_name, seq_no, noof);
+ if (i < 0) {
+ fprintf(err, "Sequence name %s not found in the given list of sequences. Exit.\n", cur.query.frag.seq_name);
+ exit(4);
+ }
+ fprintf(*(output+i), "%d %d %s %d %d \n", img_ct, cur.score, cur.sbjct.frag.seq_name, cur.sbjct.frag.lb, cur.sbjct.frag.rb);
+ }
+
+ fprintf(msp_no, "%d\n", img_ct/2+1);
+
+ exit(0);
+}
+
+
+int GetOutputInterval(char *seq_name, int seq_no, int noof) {
+ int interval;
+ interval = GetSeqIndex(0, seq_no-1, seq_name)/(seq_no/noof);
+ if (interval < 0) {
+ printf("Sequence name %s not found in the given list of sequences. Exit.\n", seq_name);
+ }
+ if (interval > noof-1) interval=noof-1; /* the last few ones */
+
+ return interval;
+}
diff --git a/src/msps.h b/src/msps.h
new file mode 100644
index 0000000..91818d9
--- /dev/null
+++ b/src/msps.h
@@ -0,0 +1,225 @@
+/* standard stuff */
+
+#include "bolts.h"
+#include "seqlist.h"
+
+/* A collection of structures and functions to handle MSPs */
+
+/* BASIC structures */
+
+typedef struct frag {
+ char *seq_name;
+ int32_t lb, rb;
+/* char lst, rst; type of ends, can be used to mark physical ends */
+} FRAG_t;
+
+typedef struct frag_list {
+ FRAG_t *to_frag;
+ struct frag_list *next;
+} FRAG_DATA_t;
+
+typedef struct image {
+ int index;
+ FRAG_t frag;
+ struct msp *to_msp;
+ struct ele_info *ele_info;
+} IMAGE_t;
+
+typedef struct image_list {
+ IMAGE_t *to_image;
+ struct image_list *next;
+} IMG_DATA_t;
+
+typedef struct img_tree {
+ IMAGE_t *to_image;
+ struct img_tree *p, *l, *r;
+} IMG_TREE_t;
+
+/*typedef struct img_rec {
+ int msp_index;
+ struct img_rec *next;
+} IMG_REC_t; */
+
+typedef struct msp {
+ /*struct msp_list *hanger;*/
+ char stat; /* 'p', 's' */
+ int32_t score;
+ float iden;
+ int direction;
+ IMAGE_t query, sbjct;
+} MSP_t;
+
+typedef struct msp_list {
+ MSP_t *to_msp;
+ struct msp_list *next;
+} MSP_DATA_t;
+
+
+
+
+
+
+
+/* funtions prototypes */
+
+int print_msp(MSP_t *);
+int fprint_msp(FILE *, MSP_t *);
+int scan_msp(MSP_t *, char *);
+int merge_msp(MSP_t *, MSP_t *);
+IMAGE_t *partner(IMAGE_t *);
+int doub_cov(FRAG_t *, FRAG_t *, float);
+int sing_cov(FRAG_t *, FRAG_t *, float);
+
+int print_msp(MSP_t *m) {
+ if (m->direction == 1) {
+ if (printf("%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.lb, m->query.frag.rb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (m->direction == -1) {
+ if (printf("%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.rb, m->query.frag.lb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else {
+ return 1;
+ }
+}
+
+
+int fprint_msp(FILE *ofp, MSP_t *m) {
+ if (m->direction == 1) {
+ if (fprintf(ofp, "%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.lb, m->query.frag.rb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else if (m->direction == -1) {
+ if (fprintf(ofp, "%06d %3.1f %08d %08d %s %08d %08d %s \n", m->score, m->iden, m->query.frag.rb, m->query.frag.lb, m->query.frag.seq_name, m->sbjct.frag.lb, m->sbjct.frag.rb, m->sbjct.frag.seq_name) > 0) {
+ return 0;
+ } else {
+ return 1;
+ }
+ } else {
+ return 1;
+ }
+}
+
+
+int scan_msp(MSP_t *m, char *line) {
+ int32_t bd_tmp;
+ char qname[NAME_LEN], sname[NAME_LEN];
+ int pos;
+
+ if (sscanf(line, "%ld %f %ld %ld %s %ld %ld %s \n", &(m->score), &(m->iden), &(m->query.frag.lb), &(m->query.frag.rb), qname, &(m->sbjct.frag.lb), &(m->sbjct.frag.rb), sname) != 8) {
+ return 1;
+ } else {
+ pos = GetSeqIndex(0, seq_no-1, qname);
+ if (pos<0) {return pos;}
+ m->query.frag.seq_name = *(seq_names+pos);
+ pos = GetSeqIndex(0, seq_no-1, sname);
+ if (pos<0) {return pos;}
+ m->sbjct.frag.seq_name = *(seq_names+pos);
+
+ m->direction = 1;
+ m->stat = 's';
+ /*m->score = m->score;*/
+ m->query.to_msp = m;
+ m->sbjct.to_msp = m;
+ /* indices and ele_info pointer are not taken care of here */
+ /* m->query.frag.lst = 'n';
+ m->query.frag.rst = 'n';
+ m->sbjct.frag.lst = 'n';
+ m->sbjct.frag.rst = 'n'; */
+ if (m->query.frag.lb > m->query.frag.rb) {
+ m->direction *= -1;
+ bd_tmp = m->query.frag.lb;
+ m->query.frag.lb = m->query.frag.rb;
+ m->query.frag.rb = bd_tmp;
+ }
+ if (m->sbjct.frag.lb > m->sbjct.frag.rb) {
+ m->direction *= -1;
+ bd_tmp = m->sbjct.frag.lb;
+ m->sbjct.frag.lb = m->sbjct.frag.rb;
+ m->sbjct.frag.rb = bd_tmp;
+ }
+ return 0;
+ }
+}
+
+/* archaine */
+#if 0
+int merge_msp(MSP_t *m1, MSP_t *m2) { /* merge two MSPs into the first one */
+ int32_t l1, l2;
+
+ /* no need for changing direction */
+ /* iden */
+ l1 = m1->sbjct.frag.rb - m1->sbjct.frag.lb;
+ l2 = m2->sbjct.frag.rb - m2->sbjct.frag.lb;
+ m1->iden = (m1->iden*l1 + m2->iden*l2)/(l1+l2);
+ /* query */
+ /* links and seq_name do not need to change */
+ /* query boundaries */
+ m1->query.frag.lb = m2->query.frag.lb < m1->query.frag.lb ? m2->query.frag.lb : m1->query.frag.lb;
+ m1->query.frag.rb = m2->query.frag.rb > m1->query.frag.rb ? m2->query.frag.rb : m1->query.frag.rb;
+ /* sbjct */
+ /* links and seq_name do not need to change */
+ /* sbjct boundaries */
+ m1->sbjct.frag.lb = m2->sbjct.frag.lb < m1->sbjct.frag.lb ? m2->sbjct.frag.lb : m1->sbjct.frag.lb;
+ m1->sbjct.frag.rb = m2->sbjct.frag.rb > m1->sbjct.frag.rb ? m2->sbjct.frag.rb : m1->sbjct.frag.rb;
+ /* score */
+ if (m1->score == 999999 || m2->score == 999999) {
+ m1->score = 999999;
+ } else {
+ m1->score = (m1->score%800000 + m2->score%800000)*(m1->sbjct.frag.rb - m1->sbjct.frag.lb)/(l1+l2); /* notice that the boundaries of m1 are now for the merged MSP */
+ if (m1->score + 800000 < 999999) {
+ m1->score += 800000;
+ } else {
+ m1->score = 999999;
+ }
+ }
+
+ return 0;
+}
+#endif
+
+IMAGE_t *partner(IMAGE_t *i) {
+ if (i == &(i->to_msp->query)) {
+ return &(i->to_msp->sbjct);
+ }
+ return &(i->to_msp->query);
+}
+
+
+int sing_cov(FRAG_t *f1, FRAG_t *f2, float cutoff) {
+ int32_t l1, l2, l, lb, rb;
+ if (f1->seq_name == f2->seq_name /*!strncmp(f1->seq_name, f2->seq_name, NAME_LEN)*/) {
+ l1 = f1->rb - f1->lb;
+ l2 = f2->rb - f2->lb;
+ lb = f1->lb > f2->lb ? f1->lb : f2->lb;
+ rb = f1->rb < f2->rb ? f1->rb : f2->rb;
+ l = rb - lb;
+ if ( (float) l/l1 >= cutoff || (float) l/l2 >= cutoff) {
+ return 1;
+ }
+ }
+ return 0;
+}
+
+
+int doub_cov(FRAG_t *f1, FRAG_t *f2, float cutoff) {
+ int32_t l1, l2, l, lb, rb;
+ if (f1->seq_name == f2->seq_name /*!strncmp(f1->seq_name, f2->seq_name, NAME_LEN)*/) {
+ l1 = f1->rb - f1->lb;
+ l2 = f2->rb - f2->lb;
+ lb = f1->lb > f2->lb ? f1->lb : f2->lb;
+ rb = f1->rb < f2->rb ? f1->rb : f2->rb;
+ l = rb - lb;
+ if ( (float) l/l1 >= cutoff && (float) l/l2 >= cutoff) {
+ return 1;
+ }
+ }
+ return 0;
+}
diff --git a/src/seqlist.h b/src/seqlist.h
new file mode 100644
index 0000000..9ee9558
--- /dev/null
+++ b/src/seqlist.h
@@ -0,0 +1,72 @@
+
+#include "bolts.h"
+#include "string.h"
+
+#ifndef _seqlist_h
+#define _seqlist_h
+
+void GetSeqNames(FILE *);
+int GetSeqIndex(int, int, char *);
+
+
+
+void GetSeqNames(FILE *seq_list) {
+ char line[256];
+ int seq_ct = -1;
+ char *name_start;
+
+ /* get the number of sequences in the list, and generates an array of proper size to hold the list */
+ fgets(line, 255, seq_list);
+ seq_no = atoi(line);
+ if (!seq_no) {
+ printf("First line in the list of sequences must be an integer,\nwhich is the number of sequences in the list. Exit\n");
+ exit(2);
+ }
+ seq_names = (char **) malloc(seq_no*sizeof(char *));
+
+ /* get the names of the sequences */
+ while (fgets(line, 255, seq_list)) {
+ seq_ct ++;
+ if (seq_ct == seq_no) {
+ printf("More sequence names than indicated at the begining of the file. Exit.\n");
+ exit(2);
+ }
+ *(seq_names+seq_ct) = (char *) malloc(NAME_LEN*sizeof(char));
+ /* skip the '>' and possilbe spaces following it at the beginning of the line, in case the name is grepped directly from a fasta file */
+ name_start = line;
+ if (line[0] == '>') {
+ name_start++;
+ while (isspace(*name_start)) name_start++;
+ }
+ strncpy(*(seq_names+seq_ct), name_start, NAME_LEN-1);
+ /* mark the end of the string */
+ name_start = *(seq_names+seq_ct);
+ while (/**name_start != EOF &&*/ !isspace(*name_start)) name_start++;
+ *name_start = '\0';
+ }
+
+ /* we assume that the list is already sorted lexically, which is done in get-names.pl */
+}
+
+
+
+
+/* binary search of a sorted list of sequence names */
+/* returns position in the array if found */
+/* returns -1 if not found */
+int GetSeqIndex(int left, int right, char *seq_name) {
+ int pos, dir;
+
+ if (left <= right) {
+ pos = (left+right)/2;
+ dir = strncmp(seq_name, *(seq_names+pos), NAME_LEN);
+ if (dir < 0) return GetSeqIndex(left, pos-1, seq_name);
+ else if (dir > 0) return GetSeqIndex(pos+1, right, seq_name);
+ else return pos;
+ } else {
+ return -1;
+ }
+}
+
+
+#endif
--
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