diff options
Diffstat (limited to 'api/asn2gnb3.c')
| -rw-r--r-- | api/asn2gnb3.c | 102 |
1 files changed, 88 insertions, 14 deletions
diff --git a/api/asn2gnb3.c b/api/asn2gnb3.c index 025c5b77..3fd89877 100644 --- a/api/asn2gnb3.c +++ b/api/asn2gnb3.c @@ -30,7 +30,7 @@ * * Version Creation Date: 10/21/98 * -* $Revision: 1.111 $ +* $Revision: 1.113 $ * * File Description: New GenBank flatfile generator - work in progress * @@ -308,12 +308,6 @@ static void AddWGSMasterCommentString ( if (StringHasNoText (taxname)) { taxname = "?"; } - if (StringHasNoText (first)) { - first = "?"; - } - if (StringHasNoText (last)) { - last = "?"; - } ver [0] = '\0'; acclen = StringLen (wgsname); if (acclen == 12) { @@ -330,15 +324,30 @@ static void AddWGSMasterCommentString ( sprintf (buf, "The %s whole genome shotgun (WGS) project has the project accession %s.", taxname, wgsaccn); FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND); - sprintf (buf, " This version of the project (%s) has the accession number %s,", ver, wgsname); + sprintf (buf, " This version of the project (%s) has the accession number %s", ver, wgsname); FFAddOneString(ffstring, buf, FALSE, FALSE, TILDE_EXPAND); - if (StringCmp (first, last) != 0) { - sprintf (buf, " and consists of sequences %s-%s.", first, last); + if (first == NULL && last == NULL) { + sprintf (buf, "."); FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND); } else { - sprintf (buf, " and consists of sequence %s.", first); - FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND); + if (first != NULL && last == NULL) { + last = first; + } else if (first == NULL && last != NULL) { + first = last; + } + if (StringDoesHaveText (first) && StringDoesHaveText (last)) { + if (StringCmp (first, last) != 0) { + sprintf (buf, ", and consists of sequences %s-%s.", first, last); + FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND); + } else { + sprintf (buf, ", and consists of sequence %s.", first); + FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND); + } + } else { + sprintf (buf, "."); + FFAddOneString(ffstring, buf, TRUE, FALSE, TILDE_EXPAND); + } } } @@ -1295,21 +1304,27 @@ static CharPtr GetStrForTpaOrRefSeqHist ( { Boolean accn; - Char buf [64]; + Char buf [100]; DbtagPtr dbt; Int4 gi; ValNodePtr head = NULL; SeqHistPtr hist; SeqIdPtr id; + Int2 j; + int k; + Int2 max; Boolean minus1; Boolean minus2; + Int4 oldstop = -1; + Uint1 residue; SeqAlignPtr salp; SeqAlignPtr salptmp; + StreamCache sc; SeqIdPtr sip; Int4 start; Int4 stop; CharPtr str; - Char tmp [80]; + Char tmp [120]; if (bsp == NULL) return NULL; hist = bsp->hist; @@ -1344,6 +1359,65 @@ static CharPtr GetStrForTpaOrRefSeqHist ( ValNodeCopyStr (&head, 0, "TPA_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP"); } } + if (isRefSeq && oldstop > -1 && oldstop < start) { + sprintf (tmp, "~%ld-%ld ", + (long) (oldstop + 1), (long) (start)); + tmp [21] = '\0'; + StringCpy (buf, " "); + k = 0; + if (StreamCacheSetup (bsp, NULL, 0, &sc)) { + if (start - oldstop < 15) { + StreamCacheSetPosition (&sc, oldstop); + buf [k] = '"'; + k++; + max = start - oldstop; + for (j = 0; j < max; j++) { + residue = StreamCacheGetResidue (&sc); + buf [k] = (Char) residue; + k++; + } + buf [k] = '"'; + k++; + } else { + StreamCacheSetPosition (&sc, oldstop); + buf [k] = '"'; + k++; + for (j = 0; j < 4; j++) { + residue = StreamCacheGetResidue (&sc); + buf [k] = (Char) residue; + k++; + } + buf [k] = '.'; + k++; + buf [k] = '.'; + k++; + buf [k] = '.'; + k++; + StreamCacheSetPosition (&sc, start - 4); + for (j = 0; j < 4; j++) { + residue = StreamCacheGetResidue (&sc); + buf [k] = (Char) residue; + k++; + } + buf [k] = '"'; + k++; + } + } else { + /* + StringCpy (buf, "inserted base(s)"); + */ + } + buf [k] = '\0'; + StringCat (buf, " "); + buf [18] = '\0'; + StringCat (tmp, buf); + sprintf (buf, " %ld-%ld ", + (long) 1, (long) (start - oldstop)); + buf [21] = '\0'; + StringCat (tmp, buf); + ValNodeCopyStr (&head, 0, tmp); + } + oldstop = stop + 1; if (id != NULL) { SeqIdWrite (id, buf, PRINTID_TEXTID_ACC_VER, sizeof (buf) - 1); if (id->choice == SEQID_GENERAL) { |