4898794edd81be5285ea6e544acbedeaeb31bf78
max
  Tue Nov 23 08:10:57 2021 -0800
Fixing pointers to README file for license in all source code files. refs #27614

diff --git src/hg/lib/mafSummary.c src/hg/lib/mafSummary.c
index 8383cad..6b5064a 100644
--- src/hg/lib/mafSummary.c
+++ src/hg/lib/mafSummary.c
@@ -1,231 +1,231 @@
 /* mafSummary.c was originally generated by the autoSql program, which also 
  * generated mafSummary.h and mafSummary.sql.  This module links the database and
  * the RAM representation of objects. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
- * See README in this or parent directory for licensing information. */
+ * 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 "mafSummary.h"
 
 
 void mafSummaryStaticLoad(char **row, struct mafSummary *ret)
 /* Load a row from mafSummary table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->src = row[3];
 ret->score = atof(row[4]);
 strcpy(ret->leftStatus, row[5]);
 strcpy(ret->rightStatus, row[6]);
 }
 
 struct mafSummary *mafSummaryLoad(char **row)
 /* Load a mafSummary from row fetched with select * from mafSummary
  * from database.  Dispose of this with mafSummaryFree(). */
 {
 struct mafSummary *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->src = cloneString(row[3]);
 ret->score = atof(row[4]);
 strcpy(ret->leftStatus, row[5]);
 strcpy(ret->rightStatus, row[6]);
 return ret;
 }
 
 struct mafSummary *mafSummaryLoadAll(char *fileName) 
 /* Load all mafSummary from a whitespace-separated file.
  * Dispose of this with mafSummaryFreeList(). */
 {
 struct mafSummary *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileRow(lf, row))
     {
     el = mafSummaryLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mafSummary *mafSummaryLoadAllByChar(char *fileName, char chopper) 
 /* Load all mafSummary from a chopper separated file.
  * Dispose of this with mafSummaryFreeList(). */
 {
 struct mafSummary *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[7];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = mafSummaryLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct mafSummary *mafSummaryLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all mafSummary from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with mafSummaryFreeList(). */
 {
 struct mafSummary *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = mafSummaryLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void mafSummarySaveToDb(struct sqlConnection *conn, struct mafSummary *el, char *tableName, int updateSize)
 /* Save mafSummary as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. Strings are automatically escaped to allow insertion into the database. */
 {
 struct dyString *update = newDyString(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%g,'%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->src,  el->score,  el->leftStatus,  el->rightStatus);
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 }
 
 struct mafSummary *mafSummaryCommaIn(char **pS, struct mafSummary *ret)
 /* Create a mafSummary out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new mafSummary */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->src = sqlStringComma(&s);
 ret->score = sqlFloatComma(&s);
 sqlFixedStringComma(&s, ret->leftStatus, sizeof(ret->leftStatus));
 sqlFixedStringComma(&s, ret->rightStatus, sizeof(ret->rightStatus));
 *pS = s;
 return ret;
 }
 
 void mafSummaryFree(struct mafSummary **pEl)
 /* Free a single dynamically allocated mafSummary such as created
  * with mafSummaryLoad(). */
 {
 struct mafSummary *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->src);
 freez(pEl);
 }
 
 void mafSummaryFreeList(struct mafSummary **pList)
 /* Free a list of dynamically allocated mafSummary's */
 {
 struct mafSummary *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     mafSummaryFree(&el);
     }
 *pList = NULL;
 }
 
 void mafSummaryOutput(struct mafSummary *el, FILE *f, char sep, char lastSep) 
 /* Print out mafSummary.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->src);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%g", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->leftStatus);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->rightStatus);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 void mafSummaryTableCreate(struct sqlConnection *conn, char *tableName, int indexSize)
 /* Create a mafSummary table with the given name
  */
 {
 char *createString =
 "#Positions and scores for alignment blocks\n"
 "CREATE TABLE %s (\n"
 "       bin smallint unsigned not null,\n"
 "       chrom varchar(255) not null,	# Chromosome\n"
 "       chromStart int unsigned not null,	# Start position in chromosome\n"
 "       chromEnd int unsigned not null,	# End position in chromosome\n"
 "       src varchar(255) not null,	# Sequence name or database of alignment\n"
 "       score float not null,	# Floating point score (0.0 to 1.0).\n"
 "          #Indices\n"
 "       leftStatus char(1),     # Status WRT preceding block\n"
 "       rightStatus char(1),    # Status WRT following block\n"
 "    INDEX(chrom(%d),bin)\n"
 ")\n";
 struct dyString *dy = newDyString(1024);
 sqlDyStringPrintf(dy, createString, tableName, indexSize, indexSize, indexSize);
 sqlRemakeTable(conn, tableName, dy->string);
 dyStringFree(&dy);
 }
 
 struct mafSummary *mafSummaryMiniLoad(char **row)
 /* Load a mafSummary from row fetched with select * from mafSummary
  * from database, except dummy in the {left,right}Status fields.
  * For use on earlier version of mafSummary tables.
  * Dispose of this with mafSummaryFree(). */
 {
 struct mafSummary *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->src = cloneString(row[3]);
 ret->score = atof(row[4]);
 return ret;
 }