312002c4b4015a4e5acedd47dad9e5d6b8d3c1b1
markd
  Mon Nov 22 18:38:59 2021 -0800
move rmskAlign and rmskJoined to lib so it they can be used by programs

diff --git src/hg/cgilib/rmskAlign.c src/hg/cgilib/rmskAlign.c
deleted file mode 100644
index 8348b92..0000000
--- src/hg/cgilib/rmskAlign.c
+++ /dev/null
@@ -1,212 +0,0 @@
-/* rmskAlign.c was originally generated by the autoSql program, which also 
- * generated rmskAlign.h and rmskAlign.sql.  This module links the database and
- * the RAM representation of objects. */
-
-/* Copyright (C) 2014 The Regents of the University of California 
- * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
-
-#include "common.h"
-#include "linefile.h"
-#include "dystring.h"
-#include "jksql.h"
-#include "rmskAlign.h"
-
-
-void rmskAlignStaticLoad(char **row, struct rmskAlign *ret)
-/* Load a row from rmskAlign table into ret.  The contents of ret will
- * be replaced at the next call to this function. */
-{
-
-ret->swScore = sqlUnsigned(row[0]);
-ret->milliDiv = sqlUnsigned(row[1]);
-ret->milliDel = sqlUnsigned(row[2]);
-ret->milliIns = sqlUnsigned(row[3]);
-ret->genoName = row[4];
-ret->genoStart = sqlUnsigned(row[5]);
-ret->genoEnd = sqlUnsigned(row[6]);
-ret->genoLeft = sqlSigned(row[7]);
-safecpy(ret->strand, sizeof(ret->strand), row[8]);
-ret->repName = row[9];
-ret->repClass = row[10];
-ret->repFamily = row[11];
-ret->repStart = sqlSigned(row[12]);
-ret->repEnd = sqlUnsigned(row[13]);
-ret->repLeft = sqlSigned(row[14]);
-ret->id = sqlUnsigned(row[15]);
-ret->alignment = row[16];
-}
-
-struct rmskAlign *rmskAlignLoad(char **row)
-/* Load a rmskAlign from row fetched with select * from rmskAlign
- * from database.  Dispose of this with rmskAlignFree(). */
-{
-struct rmskAlign *ret;
-
-AllocVar(ret);
-ret->swScore = sqlUnsigned(row[0]);
-ret->milliDiv = sqlUnsigned(row[1]);
-ret->milliDel = sqlUnsigned(row[2]);
-ret->milliIns = sqlUnsigned(row[3]);
-ret->genoName = cloneString(row[4]);
-ret->genoStart = sqlUnsigned(row[5]);
-ret->genoEnd = sqlUnsigned(row[6]);
-ret->genoLeft = sqlSigned(row[7]);
-safecpy(ret->strand, sizeof(ret->strand), row[8]);
-ret->repName = cloneString(row[9]);
-ret->repClass = cloneString(row[10]);
-ret->repFamily = cloneString(row[11]);
-ret->repStart = sqlSigned(row[12]);
-ret->repEnd = sqlUnsigned(row[13]);
-ret->repLeft = sqlSigned(row[14]);
-ret->id = sqlUnsigned(row[15]);
-ret->alignment = cloneString(row[16]);
-return ret;
-}
-
-struct rmskAlign *rmskAlignLoadAll(char *fileName) 
-/* Load all rmskAlign from a whitespace-separated file.
- * Dispose of this with rmskAlignFreeList(). */
-{
-struct rmskAlign *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[17];
-
-while (lineFileRow(lf, row))
-    {
-    el = rmskAlignLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct rmskAlign *rmskAlignLoadAllByChar(char *fileName, char chopper) 
-/* Load all rmskAlign from a chopper separated file.
- * Dispose of this with rmskAlignFreeList(). */
-{
-struct rmskAlign *list = NULL, *el;
-struct lineFile *lf = lineFileOpen(fileName, TRUE);
-char *row[17];
-
-while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
-    {
-    el = rmskAlignLoad(row);
-    slAddHead(&list, el);
-    }
-lineFileClose(&lf);
-slReverse(&list);
-return list;
-}
-
-struct rmskAlign *rmskAlignCommaIn(char **pS, struct rmskAlign *ret)
-/* Create a rmskAlign out of a comma separated string. 
- * This will fill in ret if non-null, otherwise will
- * return a new rmskAlign */
-{
-char *s = *pS;
-
-if (ret == NULL)
-    AllocVar(ret);
-ret->swScore = sqlUnsignedComma(&s);
-ret->milliDiv = sqlUnsignedComma(&s);
-ret->milliDel = sqlUnsignedComma(&s);
-ret->milliIns = sqlUnsignedComma(&s);
-ret->genoName = sqlStringComma(&s);
-ret->genoStart = sqlUnsignedComma(&s);
-ret->genoEnd = sqlUnsignedComma(&s);
-ret->genoLeft = sqlSignedComma(&s);
-sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
-ret->repName = sqlStringComma(&s);
-ret->repClass = sqlStringComma(&s);
-ret->repFamily = sqlStringComma(&s);
-ret->repStart = sqlSignedComma(&s);
-ret->repEnd = sqlUnsignedComma(&s);
-ret->repLeft = sqlSignedComma(&s);
-ret->id = sqlUnsignedComma(&s);
-ret->alignment = sqlStringComma(&s);
-*pS = s;
-return ret;
-}
-
-void rmskAlignFree(struct rmskAlign **pEl)
-/* Free a single dynamically allocated rmskAlign such as created
- * with rmskAlignLoad(). */
-{
-struct rmskAlign *el;
-
-if ((el = *pEl) == NULL) return;
-freeMem(el->genoName);
-freeMem(el->repName);
-freeMem(el->repClass);
-freeMem(el->repFamily);
-freeMem(el->alignment);
-freez(pEl);
-}
-
-void rmskAlignFreeList(struct rmskAlign **pList)
-/* Free a list of dynamically allocated rmskAlign's */
-{
-struct rmskAlign *el, *next;
-
-for (el = *pList; el != NULL; el = next)
-    {
-    next = el->next;
-    rmskAlignFree(&el);
-    }
-*pList = NULL;
-}
-
-void rmskAlignOutput(struct rmskAlign *el, FILE *f, char sep, char lastSep) 
-/* Print out rmskAlign.  Separate fields with sep. Follow last field with lastSep. */
-{
-fprintf(f, "%u", el->swScore);
-fputc(sep,f);
-fprintf(f, "%u", el->milliDiv);
-fputc(sep,f);
-fprintf(f, "%u", el->milliDel);
-fputc(sep,f);
-fprintf(f, "%u", el->milliIns);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->genoName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%u", el->genoStart);
-fputc(sep,f);
-fprintf(f, "%u", el->genoEnd);
-fputc(sep,f);
-fprintf(f, "%d", el->genoLeft);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->strand);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->repName);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->repClass);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->repFamily);
-if (sep == ',') fputc('"',f);
-fputc(sep,f);
-fprintf(f, "%d", el->repStart);
-fputc(sep,f);
-fprintf(f, "%u", el->repEnd);
-fputc(sep,f);
-fprintf(f, "%d", el->repLeft);
-fputc(sep,f);
-fprintf(f, "%u", el->id);
-fputc(sep,f);
-if (sep == ',') fputc('"',f);
-fprintf(f, "%s", el->alignment);
-if (sep == ',') fputc('"',f);
-fputc(lastSep,f);
-}
-
-/* -------------------------------- End autoSql Generated Code -------------------------------- */
-