_scan_abbreviated_pairwise_alignment (
        self,
        uhandle,
        consumer,
        )

Sometimes all header information is skipped, leaving only the raw alignments. I believe this is a bug because without the header information, you lose vital information such as score, target sequence id, etc. Format: <PRE> hsp_alignment

_scan_alignments (
        self,
        uhandle,
        consumer,
        )

Check to see whether I'm at an alignment or database report. Possibilities: 1) BLASTP 2.0.14, pairwise alignment <CENTER><b><FONT color="green">Alignments</FONT></b></CENTER> <PRE> ><a name = 121837></a><a href="http://www.ncbi.nlm.nih.gov:80/entre 2) BLASTP 2.0.10, pairwise alignment <PRE> <a name = 120291> </a><a href="http://www.ncbi.nlm.nih.gov:80/entre 3) BLASTP 2.0.10, master-slave <PRE> blast_tmp 1 MFQQIGAVQAKSGTDEPAHPCEKFPPERKCEAVFWKPLPRHEAREILLAARK 4) BLASTP 2.0.10, 2.0.14, database <PRE> Database: Non-redundant SwissProt sequences

_scan_database_report (
        self,
        uhandle,
        consumer,
        )

<PRE> Database: Non-redundant SwissProt sequences Posted date: Dec 18, 1999 8:26 PM Number of letters in database: 29,652,561 Number of sequences in database: 82,258

Lambda K H

Gapped Lambda K H

_scan_header (
        self,
        uhandle,
        consumer,
        )

<b>BLASTP 2.0.10 [Aug-26-1999]</b>

<b><a href="http://www.ncbi.nlm.nih.gov/htbin- post/Entrez/query?uid=9254694&form=6&db=m&Dopt=r">Reference</a>:</b> Altschul, Stephen F., Thomas L. Madden, Alejandro A. Sch&auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database sea programs", Nucleic Acids Res. 25:3389-3402. <p> <b>Query=</b> gi|120291|sp|P21297|FLBT_CAUCR FLBT PROTEIN. (141 letters)

<b>Database:</b> Non-redundant SwissProt sequences 82,258 sequences; 29,652,561 total letters

<p> <p>If you have any problems or questions with the results of this

_scan_hsp_alignment (
        self,
        uhandle,
        consumer,
        )

Query: 11 GRGVSACA-------TCDGFFYRNQKVAVIGGGNTAVEEALYLSNIASEVHLIHRRDGF GRGVS+ TC Y + + V GGG+ + EE L + I R+ Sbjct: 12 GRGVSSVVRRCIHKPTCKE--YAVKIIDVTGGGSFSAEEVQELREATLKEVDILRKVSG

Query: 64 AEKILIKR 71 I +K Sbjct: 70 PNIIQLKD 77 </PRE>

_scan_hsp_header (
        self,
        uhandle,
        consumer,
        )

If the HSP is not the first one within an alignment, includes: <PRE>

_scan_one_pairwise_alignment (
        self,
        uhandle,
        consumer,
        )

Alignment format: <CENTER><b><FONT color="green">Alignments</FONT></b></CENTER> (BLAST 2.0.14) <PRE> alignment_header hsp_header hsp_alignment [...] The hsp_header and hsp_alignment blocks can be repeated.

_scan_parameters (
        self,
        uhandle,
        consumer,
        )

Matrix: BLOSUM62 Number of Hits to DB: 1st pass: 41542626, 2nd pass: 9765 Number of Sequences: 1st pass: 89405, 2nd pass: 84 Number of extensions: 1st pass: 500847, 2nd pass: 6747 Number of successful extensions: 1st pass: 14, 2nd pass: 49 Number of sequences better than 10.0: 20 length of query: 205 length of database: 10,955,950 effective HSP length: 46 effective length of query: 158 effective length of database: 6,843,320 effective search space: 1081244560 effective search space used: 1081244560 frameshift window, decay const: 50, 0.5 T: 13 A: 40 X1: 16 ( 7.3 bits) X2: 0 ( 0.0 bits) S1: 41 (21.7 bits) S2: 52 (26.7 bits)

</PRE>

feed (
        self,
        handle,
        consumer,
        )

1. feed(handle, consumer)

   Feed in a BLAST report for scanning. handle is a file-like object that contains the BLAST report. consumer is a Consumer object that will receive events as the report is scanned.