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Copyright (c) 1996,1997,1998,1999,2000,2001,2004,2006
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Whitehead Institute for Biomedical Research, Steve Rozen
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(http://jura.wi.mit.edu/rozen), and Helen Skaletsky
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are
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* Redistributions of source code must retain the above copyright
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notice, this list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above
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copyright notice, this list of conditions and the following disclaimer
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in the documentation and/or other materials provided with the
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* Neither the names of the copyright holders nor contributors may
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be used to endorse or promote products derived from this software
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without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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OWNERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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/* Print the melting tm of an oligo on stdout. */
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char *msg = "Usage: %s [-k salt-conc] [-d template-conc] oligo\n\n"
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"where oligo is an oligonucleotide sequence of between 2 and 36 bases.\n"
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"(Bases in oligo must be uppercase.)\n"
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"salt-conc is mM salt (usually K) concentration; defaults to 50mM\n"
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"template-conc is nM template concentration\n; defaults to 50nM\n"
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"Prints oligo's melting temperature on stdout.\n";
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if (argc < 2 || argc > 6) {
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fprintf(stderr, msg, argv[0]);
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for (i=1; i < argc; ++i) {
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if (!strncmp("-k", argv[i], 2)) {
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k = strtol(argv[i+1], &endptr, 10);
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if ('\0' != *endptr) {
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fprintf(stderr, msg, argv[0]);
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} else if (!strncmp("-d", argv[i], 2)) {
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d = strtol(argv[i+1], &endptr, 10);
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if ('\0' != *endptr) {
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fprintf(stderr, msg, argv[0]);
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} else if (!strncmp("-", argv[i], 1)) {
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fprintf(stderr, msg, argv[0]);
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break; /* all args processed. go on to sequences. */
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tm = oligotm(argv[i], d, k);
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if (OLIGOTM_ERROR == tm) {
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"%s: length of %s is less than 2 or it contains an illegal character\n",
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fprintf(stdout, "%f\n", tm);
added
removed
src/oligotm_main.c
