00001 #include "format.h"
00002 #include "log.h"
00003 #include "linestream.h"
00004 #include "common.h"
00005 #include "blastParser.h"
00006
00007
00008
00016 static LineStream ls = NULL;
00017
00018
00019
00024 void blastParser_initFromFile (char* fileName)
00025 {
00026 ls = ls_createFromFile (fileName);
00027 ls_bufferSet (ls,1);
00028 }
00029
00030
00031
00032
00033
00038 void blastParser_initFromPipe (char* command)
00039 {
00040 ls = ls_createFromPipe (command);
00041 ls_bufferSet (ls,1);
00042 }
00043
00044
00045
00046
00050 void blastParser_deInit (void)
00051 {
00052 ls_destroy (ls);
00053 }
00054
00055
00056
00057 static void blastParser_freeQuery (BlastQuery *currBlastQuery)
00058 {
00059 int i;
00060 BlastEntry *currBlastEntry;
00061
00062 if (currBlastQuery == NULL) {
00063 return;
00064 }
00065 hlr_free (currBlastQuery->qName);
00066 for (i = 0; i < arrayMax (currBlastQuery->entries); i++) {
00067 currBlastEntry = arrp (currBlastQuery->entries,i,BlastEntry);
00068 hlr_free (currBlastEntry->tName);
00069 }
00070 arrayDestroy (currBlastQuery->entries);
00071 freeMem (currBlastQuery);
00072 }
00073
00074
00075
00076 static void blastParser_processLine (char* line, BlastQuery* currBlastQuery)
00077 {
00078 WordIter w;
00079 BlastEntry *currEntry;
00080
00081 currEntry = arrayp (currBlastQuery->entries,arrayMax (currBlastQuery->entries),BlastEntry);
00082 w = wordIterCreate (line,"\t",0);
00083 currEntry->tName = hlr_strdup (wordNext (w));
00084 currEntry->percentIdentity = atof (wordNext (w));
00085 currEntry->alignmentLength = atoi (wordNext (w));
00086 currEntry->misMatches = atoi (wordNext (w));
00087 currEntry->gapOpenings = atoi (wordNext (w));
00088 currEntry->qStart = atoi (wordNext (w));
00089 currEntry->qEnd = atoi (wordNext (w));
00090 currEntry->tStart = atoi (wordNext (w));
00091 currEntry->tEnd = atoi (wordNext (w));
00092 currEntry->evalue = atof (wordNext (w));
00093 currEntry->bitScore = atof (wordNext (w));
00094 wordIterDestroy (w);
00095 }
00096
00097
00098
00103 BlastQuery* blastParser_nextQuery (void)
00104 {
00105 char *line,*pos;
00106 static char *queryName = NULL;
00107 static char *prevBlastQueryName = NULL;
00108 static BlastQuery *currBlastQuery = NULL;
00109 int first;
00110
00111 if (!ls_isEof (ls)) {
00112 blastParser_freeQuery (currBlastQuery);
00113 currBlastQuery = NULL;
00114 AllocVar (currBlastQuery);
00115 currBlastQuery->entries = arrayCreate (5,BlastEntry);
00116 first = 1;
00117 while (line = ls_nextLine (ls)) {
00118 if (line[0] == '\0') {
00119 continue;
00120 }
00121 pos = strchr (line,'\t');
00122 *pos = '\0';
00123 strReplace (&queryName,line);
00124 if (first == 1 || strEqual (prevBlastQueryName,queryName)) {
00125 blastParser_processLine (pos + 1,currBlastQuery);
00126 }
00127 else {
00128 ls_back (ls,1);
00129 return currBlastQuery;
00130 }
00131 if (first == 1) {
00132 currBlastQuery->qName = hlr_strdup (queryName);
00133 first = 0;
00134 }
00135 strReplace(&prevBlastQueryName,queryName);
00136 }
00137 if (first == 1) {
00138 return NULL;
00139 }
00140 else {
00141 return currBlastQuery;
00142 }
00143 }
00144 blastParser_freeQuery (currBlastQuery);
00145 currBlastQuery = NULL;
00146 return NULL;
00147 }
00148
00149
00150
