src/hg/blastToPsl/pslBuild.h 1.1

Index: src/hg/blastToPsl/pslBuild.h
===================================================================
RCS file: src/hg/blastToPsl/pslBuild.h
diff -N src/hg/blastToPsl/pslBuild.h
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/blastToPsl/pslBuild.h	8 Feb 2010 03:04:24 -0000	1.1
@@ -0,0 +1,32 @@
+/* object using in building a PSL from a blast record */
+#ifndef pslBuild_h
+#define pslBuild_h
+
+enum
+/* flags for build, including blast algorithm */
+{
+    blastn    = 0x01,   // blast algorithms
+    blastp    = 0x02,
+    blastx    = 0x04,
+    tblastn   = 0x10,
+    tblastx   = 0x20,
+    psiblast  = 0x40,
+    bldPslx   = 0x80,   // construct a PSLx with sequence
+};
+
+/* score file header */
+extern char *pslBuildScoreHdr;
+
+unsigned pslBuildGetBlastAlgo(char *program);
+/* determine blast algorithm flags */
+
+struct psl *pslBuildFromHsp(char *qName, int qSize, int qStart, int qEnd, char qStrand, char *qAln,
+                            char *tName, int tSize, int tStart, int tEnd, char tStrand, char *tAln,
+                            unsigned flags);
+/* construct a new psl from an HSP.  Chaining is left to other programs. */
+
+void pslBuildWriteScores(FILE* scoreFh, struct psl *psl, double bitScore, double eValue);
+/* write scores for a PSL */
+
+#endif
+