int main(int argc, char *argv[]){
/* Input values */
char *inFile = NULL, *forceFile = NULL, *setAlignments = NULL, *matrix = NULL;
int windowSize = -1, gapWindow = -1, simWindow = -1, conWindow = -1;
bool stats_gaps_columns = 0, stats_gaps_dist = 0, stats_simil_columns = 0,
stats_simil_dist = 0, stats_seqs_ident = 0, stats_col_ident_gen = 0,
stats_file_columns = 0, stats_file_dist = 0;
alignment *origAlig = NULL, **compAlig = NULL;
/* Internal variables */
int i = 1, numFiles = 0, maxResidues = 0, referFile = 0, alignDataType = -1;
similarityMatrix *similMatrix = NULL;
char **filesToCompare = NULL;
bool appearErrors = false;
float *compareVect = NULL;
ifstream algsPaths;
string line;
/* ***** ***** ***** ***** ***** Help functions ***** ***** ***** ***** *** */
/* Show help and exit either help flag is set or not arguments are provided */
if((argc == 1) || ((!strcmp(argv[i], "-h") || !strcmp(argv[i], "--help")) &&
(i+1 == argc))) {
show_menu();
show_examples();
return 0;
}
/* Show version and revision if it is asked for */
if((!strcmp(argv[i], "-v") || !strcmp(argv[i], "--version")) &&
(i+1 == argc)) {
cout << endl << "statAl v" << VERSION << ".rev" << REVISION
<< " build[" << BUILD << "]" << endl << endl;
return 0;
}
/* Allocate local memory for input alignment */
origAlig = new alignment;
/* ***** ***** ***** ***** Input parameters loop ***** ***** ***** ***** ** */
while(i < argc) {
/* Get input alignment */
if((!strcmp(argv[i], "-i") || !strcmp(argv[i], "-in")) && (i+1 != argc) &&
(inFile == NULL)) {
/* Try to load input alignment */
inFile = new char[(int) strlen(argv[++i]) + 1];
strcpy(inFile, argv[i]);
if(!origAlig -> loadAlignment(inFile)) {
cerr << endl << "ERROR: Alignment not loaded: \"" << inFile
<< "\" Check input aligmment content." << endl << endl;
appearErrors = true;
}
}
/* Force selection of a specific input alignment as a reference to perform
* alignment comparisons */
else if(!strcmp(argv[i], "-forceselect") && (i+1 != argc) &&
(forceFile == NULL)) {
forceFile = new char[(int) strlen(argv[++i]) + 1];
strcpy(forceFile, argv[i]);
if(!origAlig -> loadAlignment(forceFile)) {
cerr << endl << "ERROR: Alignment not loaded: \"" << forceFile
<< "\" Check input aligmment content." << endl << endl;
appearErrors = true;
}
}
/* Load a set of alignments to perform alignments comparisos among them */
else if(!strcmp(argv[i], "-compareset") && (i+1 != argc) &&
(setAlignments == NULL)) {
setAlignments = new char[(int) strlen(argv[++i]) + 1];
strcpy(setAlignments, argv[i]);
}
/* Load a similarity matrix */
else if(!strcmp(argv[i], "-matrix") && (i+1 != argc) && (matrix == NULL)) {
matrix = new char[int(strlen(argv[++i])) + 1];
strcpy(matrix, argv[i]);
similMatrix = new similarityMatrix();
if(!similMatrix -> loadSimMatrix(matrix)) {
cerr << endl << "ERROR: Similarity Matrix not loaded: \"" << matrix
<< "\" Check input file content." << endl << endl;
appearErrors = true;
}
}
/* Set flags for computing different stats from input alignments */
else if((!strcmp(argv[i], "-sgc")) && (!stats_gaps_columns))
stats_gaps_columns = true;
else if((!strcmp(argv[i], "-sgt")) && (!stats_gaps_dist))
stats_gaps_dist = true;
else if((!strcmp(argv[i], "-ssc")) && (!stats_simil_columns))
stats_simil_columns = true;
else if((!strcmp(argv[i], "-sst")) && (!stats_simil_dist))
stats_simil_dist = true;
else if((!strcmp(argv[i], "-sident")) && (!stats_seqs_ident))
stats_seqs_ident = true;
else if((!strcmp(argv[i], "-scolidentt")) && (!stats_col_ident_gen))
stats_col_ident_gen = true;
else if((!strcmp(argv[i], "-sfc")) && (!stats_file_columns))
stats_file_columns = true;
else if((!strcmp(argv[i], "-sft")) && (!stats_file_dist))
stats_file_dist = true;
/* Windows size parameters. Setting others values than default could affect
* stats computed from selected alignment */
else if(!strcmp(argv[i], "-w") && (i+1 != argc) && (windowSize == -1)) {
if(utils::isNumber(argv[i+1])) {
windowSize = atoi(argv[++i]);
}
else {
cerr << endl << "ERROR: Window size value should be a number\n\n.";
appearErrors = true;
}
if(windowSize < 1) {
cerr << endl << "ERROR: Windows size value should be equal or greater "
<< "than 1. Check your command-line parameter" << endl << endl;
appearErrors = true;
}
}
/* Window size value only affecting stats related to gaps */
else if(!strcmp(argv[i], "-gw") && (i+1 != argc) && (gapWindow == -1)){
if(utils::isNumber(argv[i+1])) {
gapWindow = atoi(argv[++i]);
}
else {
cerr << endl << "ERROR: Gap Window size value should be a number\n\n.";
appearErrors = true;
}
if(gapWindow < 1) {
cerr << endl << "ERROR: Gap Windows size should be equal or greater "
<< "than 1. Check your command-line parameter" << endl << endl;
appearErrors = true;
}
}
/* Window size value only affecting stats related to similarity */
else if(!strcmp(argv[i], "-sw") && (i+1 != argc) && (simWindow == -1)) {
if(utils::isNumber(argv[i+1])) {
simWindow = atoi(argv[++i]);
}
else {
cerr << endl << "ERROR: Similarity Window size should be a number\n\n.";
appearErrors = true;
}
if(simWindow < 1) {
cerr << endl << "ERROR: Similarity Windows size should be equal or "
<< "gretaer than 1. Check your command-line parameter\n\n";
appearErrors = true;
}
}
/* Window size only affecting stats related to alignment comparisons */
else if(!strcmp(argv[i], "-cw") && (i+1 != argc) && (conWindow == -1)) {
if(utils::isNumber(argv[i+1])) {
conWindow = atoi(argv[++i]);
}
else {
cerr << endl << "ERROR: Consistency Window size should be a number\n\n";
appearErrors = true;
}
if(conWindow < 1) {
cerr << endl << "ERROR: Consistency Windows size should be equal or "
<< "gretaer than 1. Check your command-line parameter\n\n";
appearErrors = true;
}
}
else {
cerr << endl << "ERROR: Parameter \"" << argv[i] << "\" not valid\n\n.";
appearErrors = true;
}
i++;
if(appearErrors)
break;
}
/* ***** ***** ***** ** Control input parameters errors ***** ***** ***** * */
if((!appearErrors) && (inFile != NULL)) {
if((stats_file_columns) || (stats_file_dist)) {
cerr << endl << "ERROR: No stats about alignments comparison can be "
<< "obtained from Single Input Alignment" << endl << endl;
appearErrors = true;
}
if((forceFile != NULL) || (setAlignments != NULL)) {
cerr << endl << "ERROR: Incompatibilities detected: Sigle Alignment "
<< "provided as well as Set of Alignments for being compared\n\n";
appearErrors = true;
}
}
if((!appearErrors) && (forceFile != NULL)) {
if(setAlignments == NULL) {
cerr << endl << "ERROR: An alignmnet has been set as reference but it has"
<< "not been defined a set to compare with" << endl << endl;
appearErrors = true;
}
}
if((!appearErrors) && (stats_file_columns || stats_file_dist)) {
if(setAlignments == NULL) {
cerr << endl << "ERROR: A set of alignments should be provided to compute"
<< "stats about its comparison" << endl << endl;
appearErrors = true;
}
}
if((!appearErrors) && (windowSize != -1)) {
if((gapWindow != -1) || (simWindow != -1) || (conWindow != -1)) {
cerr << endl << "ERROR: General and specific windows size specified. Just"
<< " select one of them" << endl << endl;
appearErrors = true;
}
}
if((!appearErrors) && (setAlignments != NULL)) {
/* Open and check whether input file containing the path to alignments for
* being compared is correct or not */
algsPaths.open(setAlignments, ifstream::in);
if(!algsPaths) {
cerr << endl << "ERROR: Check input file \"" << setAlignments
<< "\" containing alignments paths" << endl << endl;
appearErrors = true;
}
/* Count number of alignments */
while(getline(algsPaths, line))
numFiles++;
algsPaths.close();
}
/* ***** ***** ***** ** Input set of alignments: Load it ***** ***** ***** */
if((!appearErrors) && (numFiles != 0)) {
/* allocate memory for input alignments */
filesToCompare = new char*[numFiles];
compAlig = new alignment*[numFiles];
algsPaths.open(setAlignments, ifstream::in);
for(i = 0; (i < numFiles) && (!appearErrors); i++) {
/* Get alignment path */
getline(algsPaths, line);
if(line.size() == 0)
continue;
/* Store alignment path and try to load it */
filesToCompare[i] = new char [line.size() + 1];
strcpy(filesToCompare[i], line.c_str());
/* Check currently load alignment */
compAlig[i] = new alignment;
if(!compAlig[i] -> loadAlignment(filesToCompare[i])) {
cerr << endl << "ERROR: Alignment not loaded: \"" << filesToCompare[i]
<< "\". Check input file content" << endl << endl;
appearErrors = true;
break;
}
/* Check whether each individual alignment is aligned. It is impossible
* to make any comparison with unaligned sequences */
if(!compAlig[i] -> isFileAligned()) {
cerr << endl << "ERROR: Input alignment \"" << filesToCompare[i] << "\""
<< "should have sequences aligned for computing any stats from them."
<< endl << endl;
appearErrors = true;
break;
}
/* Check all input alignments contain the same kind of biological data */
if(alignDataType == -1)
alignDataType = compAlig[i] -> getTypeAlignment();
else if(compAlig[i] -> getTypeAlignment() != alignDataType) {
cerr << endl << "ERROR: Check input alignment data-type. Alignment \""
<< filesToCompare[0] << "\" contains a different data-type different "
<< "than \"" << filesToCompare[i] << "\"" << endl << endl;
appearErrors = true;
break;
}
/* Construct residues positions matrix to make possible any comparison */
compAlig[i] -> sequenMatrix();
if(compAlig[i] -> getNumAminos() > maxResidues)
maxResidues = compAlig[i] -> getNumAminos();
}
/* ***** ***** ***** ** Input set of alignments: Compare it ***** ***** * */
if((!appearErrors) && (forceFile == NULL)) {
/* If reference alignment has not been set, just compute the most
* consistent one and choose it as the reference one */
compareVect = new float[maxResidues];
referFile = compareFiles::algorithm(compAlig, filesToCompare, compareVect,
numFiles, true);
origAlig -> loadAlignment(filesToCompare[referFile]);
}
else if((!appearErrors) && (forceFile != NULL)) {
/* Compute consistency vector for the aligment set as the reference one */
compareVect = new float[origAlig -> getNumAminos()];
appearErrors = !(compareFiles::forceComparison(compAlig, numFiles,
origAlig, compareVect));
}
/* Apply any possible windows for future stats */
conWindow = (conWindow != -1) ? conWindow : windowSize;
if((conWindow != -1) && (!appearErrors))
compareFiles::applyWindow(origAlig -> getNumAminos(), conWindow,
compareVect);
/* Deallocate memory for the alignments used to make the comparisons */
for(i = 0; i < numFiles; delete compAlig[i], i++)
delete filesToCompare[i];
}
/* ***** ***** ***** ***** ***** Final Checks ***** ***** ***** ***** ***** */
if((!appearErrors) && (!origAlig -> isFileAligned() && (stats_gaps_columns or
stats_gaps_dist or stats_simil_columns or stats_simil_dist or stats_seqs_ident
or stats_col_ident_gen or stats_file_columns or stats_file_dist))) {
cerr << endl << "ERROR: Reference alignment should aligned to compute any "
<< "stats using it" << endl << endl;
appearErrors = true;
}
/* ***** ***** ***** ***** * Apply input parameters ***** ***** ***** ***** */
if(!appearErrors) {
/* Apply window size to either input single alignment or the most consistent
* one */
gapWindow = (windowSize != -1) ? windowSize : (gapWindow != -1) ?
gapWindow : 0;
simWindow = (windowSize != -1) ? windowSize : (simWindow != -1) ?
simWindow : 0;
origAlig -> setWindowsSize(gapWindow, simWindow);
}
/* ***** ***** ***** ***** * Load Similarity Matrix ***** ***** ***** ***** */
if(!appearErrors) {
if((stats_simil_columns) || (stats_simil_dist)) {
/* Load predefined similarity matrix, if none has been set by the user */
if(matrix == NULL){
similMatrix = new similarityMatrix();
if((origAlig -> getTypeAlignment()) == AAType)
similMatrix -> defaultAASimMatrix();
else
similMatrix -> defaultNTSimMatrix();
}
/* Assign similarity matrix, either predefined one or supply by the user,
* to the alignment that is used to compute stats */
if(!origAlig -> setSimilarityMatrix(similMatrix)) {
cerr << endl << "ERROR: Impossible to associate similarity matrix to "
<< "selected alignment. Check input matrix file content\n\n";
appearErrors = true;
}
}
}
/* ***** ***** ***** ***** ** Compute/Show stats ***** ***** ***** ***** ** */
if(!appearErrors) {
if(stats_gaps_columns) {
cout << endl << "## Gaps scores per column" << endl;
origAlig -> printStatisticsGapsColumns();
}
if(stats_gaps_dist) {
cout << endl << "## Gaps scores distribution" << endl;
origAlig -> printStatisticsGapsTotal();
}
if(stats_simil_columns) {
cout << endl << "## Similarity values per column" << endl;
origAlig -> printStatisticsConservationColumns();
}
if(stats_simil_dist) {
cout << endl << "## Similarity values distribution" << endl;
origAlig -> printStatisticsConservationTotal();
}
if(stats_seqs_ident) {
cout << endl << "## Sequence Identity Values" << endl;
origAlig -> printSeqIdentity();
}
if(stats_col_ident_gen) {
cout << endl << "## Columns Identity Descriptive Statistics" << endl;
origAlig -> printColumnsIdentity_DescriptiveStats();
}
if(stats_file_columns) {
cout << endl << "## Consistency values per column for selected align\n";
compareFiles::printStatisticsFileColumns(origAlig -> getNumAminos(),
compareVect);
}
if(stats_file_dist) {
cout << endl << "## Consistency values distribution for selected align\n";
compareFiles::printStatisticsFileAcl(origAlig -> getNumAminos(),
compareVect);
}
}
/* ***** ***** ***** ***** *** Deallocate memory ***** ***** ***** ***** ** */
delete origAlig;
delete[] compAlig;
delete similMatrix;
delete[] filesToCompare;
delete[] compareVect;
delete[] inFile;
delete[] matrix;
delete[] forceFile;
return (appearErrors == true ? -1 : 0);
}
int main(int argc,char **argv)
{
char
*x,
*y,
buf[BUFSIZ],
encrypted_pass[128], /* 80 bytes actually */
*cipher=NULL,
*option;
int
smtp_info=0,
is_mime=0,
add_dateh=1,
port=(-1),
rc = (-1),
no_cc=1,
no_bcc=1,
i;
char
*address_file=NULL,
*helo_domain=NULL,
*smtp_server=NULL,
*attach_file=NULL,
*msg_body_file=NULL, /* back in 1.17b15 */
*the_msg=NULL,
*custom_header=NULL,
*to=NULL,
*save_to=NULL,
*save_cc=NULL,
*save_bcc=NULL,
*from=NULL,
*sub=NULL,
*cc=NULL,
*bcc=NULL,
*rt=NULL,
*rrr=NULL;
g_verbose=0;
g_connect_timeout = DEFAULT_CONNECT_TIMEOUT; /* 5 secs */
g_quiet=0;
g_wait_for_cr=0;
g_do_auth=0;
g_esmtp=0;
g_auth_plain=0;
g_auth_cram_md5=0;
g_auth_login=0;
g_do_ssl=0;
g_do_starttls=0;
g_log_fp = NULL;
g_show_attachment_in_log = 0;
g_use_protocol = MSOCK_USE_AUTO; /* detect IPv4 or IPv6 */
g_force = MUTILS_FALSE;
memset(g_log_file,0,sizeof(g_log_file));
memset(g_username,0,sizeof(g_username));
memset(g_userpass,0,sizeof(g_userpass));
memset(encrypted_pass, 0, sizeof(encrypted_pass));
memset(g_from_name,0,sizeof(g_from_name));
memset(g_content_type,0,sizeof(g_content_type));
memset(g_attach_sep, 0, sizeof(g_attach_sep));
memset(g_attach_name, 0, sizeof(g_attach_name));
memset(g_content_transfer_encoding, 0, sizeof(g_content_transfer_encoding));
memset(g_mime_type, 0, sizeof(g_mime_type));
memset(g_content_id, 0, sizeof(g_content_id));
/* (void) strcpy(g_content_transfer_encoding,"base64"); */ /* no default */
(void) strcpy(g_content_disposition,"attachment");
(void) strcpy(g_attach_sep,",");
(void) strcpy(g_charset,DEFAULT_CHARSET);
/*
No default for mime_type, we will detect from file extensinon
if no mime type is specified with -mime-type
*/
/*
(void) strcpy(g_mime_type,"text/plain");
*/
for (i=1; i < argc; i++)
{
option=argv[i];
switch (*(option+1))
{
case 'a':
{
if (strncmp("attach",option+1,6) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing file to attach");
rc = 1;
goto ExitProcessing;
}
attach_file=argv[i];
add_attachment_to_list(attach_file);
}
}
else if (strncmp("aname",option+1,5) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing attachment name");
rc = 1;
goto ExitProcessing;
}
mutilsSafeStrcpy(g_attach_name,argv[i],sizeof(g_attach_name)-1);
}
}
else if (strncmp("auth-plain",option+1,
strlen("auth-plain"))==0)
{
if (*option == '-')
{
g_auth_plain=1;
}
}
else if (strncmp("auth-cram-md5",option+1,
strlen("auth-cram-md5"))==0)
{
if (*option == '-')
{
g_auth_cram_md5=1;
}
}
else if (strncmp("auth-login",option+1,
strlen("auth-login"))==0)
{
if (*option == '-')
{
g_auth_login=1;
}
}
else if (strncmp("auth",option+1,
strlen("auth"))==0)
{
if (*option == '-')
{
g_auth_plain=1;
g_auth_login=1;
g_auth_cram_md5=1;
g_auth_login=1;
g_do_auth=1;
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'b':
{
if (strncmp("bcc",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing BCc address/es");
rc = 1;
goto ExitProcessing;
}
bcc=argv[i];
save_bcc=mutilsStrdup(bcc);
/* collapse all spaces to a comma */
mutilsSpacesToChar(bcc,',');
addAddressToList(bcc,"Bcc");
}
else if (*option == '+')
{
no_bcc=1;
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case '4':
{
if (strncmp("4", option + 1,1) == 0)
{
if (*option == '-')
{
g_use_protocol = MSOCK_USE_IPV4;
}
}
break;
}
case '6':
{
if (strncmp("6", option + 1,1) == 0)
{
if (*option == '-')
{
g_use_protocol = MSOCK_USE_IPV6;
}
}
break;
}
case 'c':
{
if (strncmp("cc",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing Cc address/es");
rc = 1;
goto ExitProcessing;
}
cc=argv[i];
save_cc=mutilsStrdup(cc);
/* collapse all spaces to a comma */
mutilsSpacesToChar(cc,',');
addAddressToList(cc,"Cc");
}
else if (*option == '+')
{
no_cc=1;
}
}
else if (strncmp("cs",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing character set");
rc = 1;
goto ExitProcessing;
}
mutilsSafeStrcpy(g_charset,argv[i],sizeof(g_charset)-1);
}
}
else if (strncmp("ct", option + 1, 2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing connect timeout with -ct");
rc = 1;
goto ExitProcessing;
}
g_connect_timeout = atoi(argv[i]);
}
}
else if (strncmp("content-type", option+1, 12)==0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing content-type value");
rc = 1;
goto ExitProcessing;
}
mutilsSafeStrcpy(g_content_type,argv[i],sizeof(g_content_type)-1);
}
}
else if (strncmp("content-disposition", option + 1, 12) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing content-dispostion value");
rc = 1;
goto ExitProcessing;
}
if ((strcmp(argv[i],"inline") == 0) || strcmp(argv[i], "attachment") == 0)
{
mutilsSafeStrcpy(g_content_disposition,argv[i],
sizeof(g_content_disposition)-1);
}
else
{
errorMsg("Invalid value for -content-disposition");
rc = 1;
goto ExitProcessing;
}
}
}
else if (strncmp("content-id", option + 1, 10) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing content-id value");
rc = 1;
goto ExitProcessing;
}
mutilsSafeStrcpy(g_content_id,argv[i],sizeof(g_content_id)-1);
}
}
else if (strncmp("copyright", option + 1, 5) == 0)
{
print_copyright();
rc = 0;
goto ExitProcessing;
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'D':
{
if (strncmp("D",option+1,1) == 0)
{
if (*option == '+')
{
add_dateh=0;
}
}
break;
}
case 'd':
{
if (strncmp("domain",option+1,6) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing domain name");
rc = 1;
goto ExitProcessing;
}
helo_domain=argv[i];
}
}
else if (strncmp("disposition", option + 1, 6) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing content dispostion value");
rc = 1;
goto ExitProcessing;
}
if ((strcmp(argv[i],"inline") == 0) || strcmp(argv[i], "attachment") == 0)
{
mutilsSafeStrcpy(g_content_disposition,argv[i],sizeof(g_content_disposition)-1);
}
else
{
errorMsg("Invalid value for -disposition");
rc = 1;
goto ExitProcessing;
}
}
}
break;
}
case 'e':
{
if (strncmp("example",option+1,2) == 0)
{
if (*option == '-')
{
show_examples();
rc = 1;
goto ExitProcessing;
}
}
else if (strncmp("ehlo",option+1,4) == 0)
{
if (*option == '-')
{
g_esmtp=1;
}
}
else if (strncmp("enc-type",option+1,5) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing encoding type");
rc = 1;
goto ExitProcessing;
}
mutilsSafeStrcpy(g_content_transfer_encoding,
argv[i],
sizeof(g_content_transfer_encoding)-1);
}
}
else if (strncmp("embed-image", option + 1, 7) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing image for -embded-image");
rc = 1;
goto ExitProcessing;
}
add_embed_image_to_attachment_list(argv[i]);
/* TODO */
}
}
break;
}
case 'f':
{
if (strncmp("from",option+1,1) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing From address/es");
rc = 1;
goto ExitProcessing;
}
from=argv[i];
}
}
break;
}
case 'x':
{
if (strncmp("xforce",option+1,1) == 0)
{
if (*option == '-')
{
g_force = MUTILS_TRUE;
}
}
break;
}
case 'h':
{
if (strncmp("help",option+1,1) == 0)
{
usage();
rc = 0;
goto ExitProcessing;
}
/* won't be here */
break;
}
case 'i':
{
if (strncmp("info",option+1,2) == 0)
{
smtp_info=1;
}
break;
}
case 'l':
{
if (strncmp("list_address",option+1,3) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing address list file");
rc = 1;
goto ExitProcessing;
}
address_file=argv[i];
}
}
if (strncmp("log",option+1,3) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing address log file");
rc = 1;
goto ExitProcessing;
}
g_log_fp = fopen(argv[i], "a");
if (g_log_fp == NULL)
{
errorMsg("Could not open log file %s for writing (%s)",
argv[i],
strerror(errno));
rc = 1;
goto ExitProcessing;
}
/*
** tell msock lib to write error message to log file
*/
msock_set_logfp(g_log_fp);
mutilsSafeStrcpy(g_log_file,argv[i],sizeof(g_log_file)-1);
}
}
break;
}
case 'p':
{
if (strncmp("port",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing SMTP Port with -port");
rc = 1;
goto ExitProcessing;
}
port=atoi(argv[i]);
}
}
else if (strncmp("pass",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing password with -pass");
rc = 1;
goto ExitProcessing;
}
(void) snprintf(g_userpass,sizeof(g_userpass)-1,
"%s",argv[i]);
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'H':
{
if (strncmp("Header",option+1,1) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing custom header");
rc = 1;
goto ExitProcessing;
}
custom_header=argv[i];
add_customer_header_to_list(custom_header);
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'M':
{
if (strncmp("Message",option+1,1) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing text message");
rc = 1;
goto ExitProcessing;
}
the_msg=xStrdup(argv[i]);
add_oneline_to_attachment_list(the_msg);
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'm':
{
if (strncmp("mime-type",option+1,9) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing mime type");
rc = 1;
goto ExitProcessing;
}
mutilsSafeStrcpy(g_mime_type,argv[i],sizeof(g_mime_type)-1);
}
}
else if (strncmp("msg-body",option+1,5) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing path of message body file");
rc = 1;
goto ExitProcessing;
}
msg_body_file = argv[i];
add_msg_body_to_attachment_list(argv[i]);
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'n':
{
if (strncmp("name",option+1,3) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing Name with -n");
rc = 1;
goto ExitProcessing;
}
(void) snprintf(g_from_name,sizeof(g_from_name)-1,
"%s",argv[i]);
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 's':
{
if (strncmp("smtp",option+1,3) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing smtp server");
rc = 1;
goto ExitProcessing;
}
smtp_server=argv[i];
}
}
else if (strncmp("subject",option+1,3) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing subject with -sub");
rc = 1;
goto ExitProcessing;
}
sub=argv[i];
}
}
else if (strncmp("ssl", option + 1, 3) == 0)
{
#ifdef HAVE_OPENSSL
g_do_ssl=1;
#else
(void) fprintf(stderr,"Error: '-ssl' not available, not compiled with OpenSSL\n");
rc = 1;
goto ExitProcessing;
#endif /* HAVE_OPENSSL */
}
else if (strncmp("starttls",option+1,3) == 0)
{
#ifdef HAVE_OPENSSL
g_do_starttls=1;
#else
(void) fprintf(stderr,"Error: '-starttls' not available, not compiled with OpenSSL\n");
rc = 1;
goto ExitProcessing;
#endif /* HAVE_OPENSSL */
}
else if (strncmp("show-attach", option + 1, 9) == 0)
{
g_show_attachment_in_log = 1;
}
else if (strncmp("show-mime-types",option+1,9) == 0)
{
show_mime_types();
rc = 0;
goto ExitProcessing;
}
else if (strncmp("separator", option + 1, 4) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing separator");
rc = 1;
goto ExitProcessing;
}
(void) snprintf(g_attach_sep,sizeof(g_attach_sep)-1,"%s",argv[i]);
if (strlen(g_attach_sep) != 1)
{
errorMsg("Invalid separator character specified");
rc = 1;
goto ExitProcessing;
}
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'u':
{
if (strncmp("user",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
errorMsg("Missing smtp server");
rc = 1;
goto ExitProcessing;
}
(void) snprintf(g_username,sizeof(g_username)-1,
"%s",argv[i]);
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'v':
{
if (strncmp("verbose",option+1,1) == 0)
{
if (*option == '-')
{
g_verbose=1;
msock_set_debug(g_verbose);
}
}
break;
}
case 'q':
{
if (strncmp("quiet",option+1,1) == 0)
{
if (*option == '-')
{
g_quiet=1;
}
}
break;
}
case 'V':
{
(void) fprintf(stderr,"mailsend Version: %.1024s\n",MAILSEND_VERSION);
#ifdef HAVE_OPENSSL
(void) fprintf(stderr,"Compiled with OpenSSL: %s\n",
SSLeay_version(SSLEAY_VERSION));
#else
(void) fprintf(stderr,"Not Compiled OpenSSL, some auth methods will be unavailable\n");
#endif /* ! HAVE_OPENSSL */
rc = 0;
goto ExitProcessing;
break;
}
case 't':
{
if (strncmp("to",option+1,1) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
(void) fprintf(stderr,"Error: missing to addresses\n");
rc = 1;
goto ExitProcessing;
}
to=argv[i];
save_to=mutilsStrdup(to);
if (save_to == NULL)
{
errorMsg("memory allocation problem for -to");
rc = 1;
goto ExitProcessing;
}
save_to=fix_to(save_to);
to=fix_to(to);
/* collapse all spaces to a comma */
mutilsSpacesToChar(to,',');
/* add addresses to a singly linked list */
addAddressToList(to,"To");
/* Note: to is modifed now! */
}
}
break;
}
case 'r':
{
if (strncmp("rrr",option+1,3) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
(void) fprintf(stderr,"Error: missing to addresses for -rrr\n");
rc = 1;
goto ExitProcessing;
}
rrr=mutilsStrdup(argv[i]);
if (rrr == NULL)
{
errorMsg("memory allocation problem for -rrr");
rc = 1;
goto ExitProcessing;
}
}
}
else if (strncmp("rt",option+1,2) == 0)
{
if (*option == '-')
{
i++;
if (i == argc)
{
(void) fprintf(stderr,"Error: missing to addresses for -rt\n");
rc = 1;
goto ExitProcessing;
}
rt=mutilsStrdup(argv[i]);
if (rt == NULL)
{
errorMsg("memory allocation problem for -rt");
rc = 1;
goto ExitProcessing;
}
}
}
else
{
errorMsg("Unknown flag: %s\n",option);
rc = 1;
goto ExitProcessing;
}
break;
}
case 'w':
{
if (strncmp("wait",option+1,1) == 0)
{
if (*option == '-')
{
g_wait_for_cr=1;
}
}
break;
}
default:
{
(void) fprintf(stderr,"Error: Unrecognized option: %s\n",
option);
rc = 1;
goto ExitProcessing;
}
}
}
x=getenv("SMTP_USER_PASS");
y=NULL;
if (x && y)
{
(void) fprintf(stderr,"SMTP_USER_PASS and SMTP_USER_PASS_ENC can not be set. Exiting..\n");
rc = 1;
goto ExitProcessing;
}
if (x)
{
if (*g_userpass == '\0')
{
(void) snprintf(g_userpass,sizeof(g_userpass)-1,"%s",x);
}
}
#ifdef HAVE_OPENSSL
if (g_do_ssl && g_do_starttls)
{
(void) fprintf(stderr,"Options -ssl and -starttls are mutually exclusive\n");
rc = 1;
goto ExitProcessing;
}
#endif /* HAVE_OPENSSL */
initialize_openssl(cipher);
if (port == -1)
port=MAILSEND_SMTP_PORT;
if (smtp_info)
{
if (smtp_server == NULL)
smtp_server="localhost";
}
if (smtp_info && smtp_server)
{
if (helo_domain == NULL)
helo_domain="localhost";
rc = show_smtp_info(smtp_server,port,helo_domain);
if (rc < 0)
rc = 1;
goto ExitProcessing;
}
/*
print_attachment_list();
print_oneline_attachment_list();
*/
/*
** attaching a file or a one line message will make the mail a
** MIME mail
*/
if (attach_file || the_msg || msg_body_file)
{
is_mime=1;
}
if (smtp_server == NULL)
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"SMTP server address/IP: ",EMPTY_NOT_OK);
if (x)
smtp_server=xStrdup(x);
}
if (helo_domain == NULL)
{
/*
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"Domain: ",EMPTY_NOT_OK);
if (x)
helo_domain=xStrdup(x);
*/
/* use localhost */
helo_domain=xStrdup("localhost");
}
if (from == NULL)
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"From: ",EMPTY_NOT_OK);
if (x)
from=xStrdup(x);
}
/* if address file specified, add the addresses to the list as well */
if (address_file != NULL)
{
addAddressesFromFileToList(address_file);
printAddressList();
}
/*
** The To address must be speicifed, even if the file with the list of
** addresses is specified. The specified To will be shown in the
** envelope. None of the To, Cc and Bcc from the address list file will
** be shown anywhre.. that's how I like it. I hate long To, Cc or Bcc.
** [email protected], Thu Mar 29 11:56:45 EST 2001
*/
if (save_to == NULL)
{
/* don't ask for To add addresses are specified with -l file */
if (getAddressList() == NULL)
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"To: ",EMPTY_NOT_OK);
if (x)
{
save_to=xStrdup(x);
addAddressToList(x,"To");
}
}
}
/*
** if msg file specified, dont ask for unneeded things, as it could
** be used from other programs, and it will wait for input
** [email protected] Tue Apr 10 18:02:12 EST 2001
*/
#ifdef WINNT
if (attach_file == NULL && isInConsole(_fileno(stdin)))
#else
if (attach_file == NULL && isatty(fileno(stdin)))
#endif /* WINNT */
{
if (save_cc == NULL && !no_cc)
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"Carbon copy: ",EMPTY_OK);
if (x)
{
save_cc=xStrdup(x);
addAddressToList(x,"Cc");
}
}
if (save_bcc == NULL && ! no_bcc)
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"Blind Carbon copy: ",EMPTY_OK);
if (x)
{
save_bcc=xStrdup(x);
addAddressToList(x,"BCc");
}
}
if (sub == NULL)
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"Subject: ",EMPTY_OK);
if (x)
sub=xStrdup(x);
}
if (g_do_ssl || g_do_starttls)
{
if (*g_username == '\0')
{
memset(buf,0,sizeof(buf));
x=askFor(buf,sizeof(buf)-1,"Auth user: "******"%s",x);
}
}
if (*g_userpass == '\0')
{
(void) fprintf(stderr,"\nPlease specify auth password with -pass\n");
(void) fprintf(stderr,"Or by environment variable SMTP_USER_PASS\n");
rc = 1;
goto ExitProcessing;
}
}
}
rc=validateMusts(from,save_to,smtp_server,helo_domain);
if (rc != 0)
{
rc = 1;
goto ExitProcessing;
}
#ifdef UNIX
signal(SIGPIPE,SIG_IGN);
#endif /* UNIX */
#if 0
{
MutilsTime
mt;
char
timebuf[64];
mutils_time_now(&mt);
mutils_time_fmt(&mt, timebuf, sizeof(timebuf));
(void) fprintf(stderr,"timebuf: %s\n",timebuf);
return 1;
}
#endif /* 0 */
write_log("mailsend v%s\n",MAILSEND_VERSION);
rc=send_the_mail(from,save_to,save_cc,save_bcc,sub,smtp_server,port,
helo_domain,attach_file,msg_body_file,the_msg,is_mime,rrr,rt,add_dateh);
if (rc == 0)
{
if (isInteractive())
{
if (!g_quiet)
{
(void) printf("Mail sent successfully\n");
(void) fflush(stdout);
}
}
if (!g_quiet)
{
write_log("Mail sent successfully\n");
}
}
else
{
if (isInteractive())
{
(void) printf("Could not send mail\n");
}
write_log("Could not send mail\n");
}
if (isInteractive())
{
if (g_wait_for_cr)
{
printf("\nPress Enter to Exit: ");
x=fgets(buf,sizeof(buf)-1,stdin);
}
}
if (rc != 0)
{
rc = 1;
}
ExitProcessing:
close_log();
return (rc);
}
