e70152e44cc66cc599ff6b699eb8adc07f3e656a
kent
  Sat May 24 21:09:34 2014 -0700
Adding Copyright NNNN Regents of the University of California to all files I believe with reasonable certainty were developed under UCSC employ or as part of Genome Browser copyright assignment.
diff --git src/hg/lib/altGraph.c src/hg/lib/altGraph.c
index ebcae98..89669d8 100644
--- src/hg/lib/altGraph.c
+++ src/hg/lib/altGraph.c
@@ -1,334 +1,337 @@
 /* altGraph.c was originally generated by the autoSql program, which also 
  * generated altGraph.h and altGraph.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. */
+
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "altGraph.h"
 #include "geneGraph.h"
 
 
 struct altGraph *altGraphLoad(char **row)
 /* Load a altGraph from row fetched with select * from altGraph
  * from database.  Dispose of this with altGraphFree(). */
 {
 struct altGraph *ret;
 int sizeOne;
 
 AllocVar(ret);
 ret->vertexCount = sqlUnsigned(row[5]);
 ret->edgeCount = sqlUnsigned(row[8]);
 ret->mrnaRefCount = sqlSigned(row[11]);
 ret->id = sqlUnsigned(row[0]);
 ret->tName = cloneString(row[1]);
 ret->tStart = sqlSigned(row[2]);
 ret->tEnd = sqlSigned(row[3]);
 strcpy(ret->strand, row[4]);
 sqlUbyteDynamicArray(row[6], &ret->vTypes, &sizeOne);
 assert(sizeOne == ret->vertexCount);
 sqlSignedDynamicArray(row[7], &ret->vPositions, &sizeOne);
 assert(sizeOne == ret->vertexCount);
 sqlSignedDynamicArray(row[9], &ret->edgeStarts, &sizeOne);
 assert(sizeOne == ret->edgeCount);
 sqlSignedDynamicArray(row[10], &ret->edgeEnds, &sizeOne);
 assert(sizeOne == ret->edgeCount);
 sqlStringDynamicArray(row[12], &ret->mrnaRefs, &sizeOne);
 assert(sizeOne == ret->mrnaRefCount);
 return ret;
 }
 
 struct altGraph *altGraphLoadAll(char *fileName) 
 /* Load all altGraph from a tab-separated file.
  * Dispose of this with altGraphFreeList(). */
 {
 struct altGraph *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[13];
 
 while (lineFileRow(lf, row))
     {
     el = altGraphLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct altGraph *altGraphLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all altGraph 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 altGraphFreeList(). */
 {
 struct altGraph *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = altGraphLoad(row);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void altGraphSaveToDb(struct sqlConnection *conn, struct altGraph *el, char *tableName, int updateSize)
 /* Save altGraph 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);
 char  *vTypesArray, *vPositionsArray, *edgeStartsArray, *edgeEndsArray, *mrnaRefsArray;
 vTypesArray = sqlUbyteArrayToString(el->vTypes, el->vertexCount);
 vPositionsArray = sqlSignedArrayToString(el->vPositions, el->vertexCount);
 edgeStartsArray = sqlSignedArrayToString(el->edgeStarts, el->edgeCount);
 edgeEndsArray = sqlSignedArrayToString(el->edgeEnds, el->edgeCount);
 mrnaRefsArray = sqlStringArrayToString(el->mrnaRefs, el->mrnaRefCount);
 sqlDyStringPrintf(update, "insert into %s values ( %u,'%s',%d,%d,'%s',%u,'%s','%s',%u,'%s','%s',%d,'%s')", 
 	tableName,  el->id,  el->tName,  el->tStart,  el->tEnd,  el->strand,  el->vertexCount,  vTypesArray ,  vPositionsArray ,  el->edgeCount,  edgeStartsArray ,  edgeEndsArray ,  el->mrnaRefCount,  mrnaRefsArray );
 sqlUpdate(conn, update->string);
 freeDyString(&update);
 freez(&vTypesArray);
 freez(&vPositionsArray);
 freez(&edgeStartsArray);
 freez(&edgeEndsArray);
 freez(&mrnaRefsArray);
 }
 
 
 struct altGraph *altGraphCommaIn(char **pS, struct altGraph *ret)
 /* Create a altGraph out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new altGraph */
 {
 char *s = *pS;
 int i;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->id = sqlUnsignedComma(&s);
 ret->tName = sqlStringComma(&s);
 ret->tStart = sqlSignedComma(&s);
 ret->tEnd = sqlSignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->vertexCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->vTypes, ret->vertexCount);
 for (i=0; i<ret->vertexCount; ++i)
     {
     ret->vTypes[i] = sqlUnsignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->vPositions, ret->vertexCount);
 for (i=0; i<ret->vertexCount; ++i)
     {
     ret->vPositions[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->edgeCount = sqlUnsignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->edgeStarts, ret->edgeCount);
 for (i=0; i<ret->edgeCount; ++i)
     {
     ret->edgeStarts[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 s = sqlEatChar(s, '{');
 AllocArray(ret->edgeEnds, ret->edgeCount);
 for (i=0; i<ret->edgeCount; ++i)
     {
     ret->edgeEnds[i] = sqlSignedComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 ret->mrnaRefCount = sqlSignedComma(&s);
 s = sqlEatChar(s, '{');
 AllocArray(ret->mrnaRefs, ret->mrnaRefCount);
 for (i=0; i<ret->mrnaRefCount; ++i)
     {
     ret->mrnaRefs[i] = sqlStringComma(&s);
     }
 s = sqlEatChar(s, '}');
 s = sqlEatChar(s, ',');
 *pS = s;
 return ret;
 }
 
 void altGraphFree(struct altGraph **pEl)
 /* Free a single dynamically allocated altGraph such as created
  * with altGraphLoad(). */
 {
 struct altGraph *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->tName);
 freeMem(el->vTypes);
 freeMem(el->vPositions);
 freeMem(el->edgeStarts);
 freeMem(el->edgeEnds);
 /* All strings in mrnaRefs are allocated at once, so only need to free first. */
 if (el->mrnaRefs != NULL)
     freeMem(el->mrnaRefs[0]);
 freeMem(el->mrnaRefs);
 freez(pEl);
 }
 
 void altGraphFreeList(struct altGraph **pList)
 /* Free a list of dynamically allocated altGraph's */
 {
 struct altGraph *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     altGraphFree(&el);
     }
 *pList = NULL;
 }
 
 void altGraphOutput(struct altGraph *el, FILE *f, char sep, char lastSep) 
 /* Print out altGraph.  Separate fields with sep. Follow last field with lastSep. */
 {
 int i;
 fprintf(f, "%u", el->id);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->tName);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%d", el->tStart);
 fputc(sep,f);
 fprintf(f, "%d", el->tEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->vertexCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vertexCount; ++i)
     {
     fprintf(f, "%u", el->vTypes[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->vertexCount; ++i)
     {
     fprintf(f, "%d", el->vPositions[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%u", el->edgeCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->edgeCount; ++i)
     {
     fprintf(f, "%d", el->edgeStarts[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->edgeCount; ++i)
     {
     fprintf(f, "%d", el->edgeEnds[i]);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(sep,f);
 fprintf(f, "%d", el->mrnaRefCount);
 fputc(sep,f);
 if (sep == ',') fputc('{',f);
 for (i=0; i<el->mrnaRefCount; ++i)
     {
     if (sep == ',') fputc('"',f);
     fprintf(f, "%s", el->mrnaRefs[i]);
     if (sep == ',') fputc('"',f);
     fputc(',', f);
     }
 if (sep == ',') fputc('}',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 
 static boolean isEndVertice(bool **em, int vertexCount, int vertice, 
 	unsigned char *vTypes)
 /* check to see if there are any edges coming out of this vertice */
 {
 int i;
 for(i=0; i<vertexCount; i++)
     {
     if(em[vertice][i] && (vTypes[i] != ggUnused))
 	return FALSE;
     }
 return TRUE;
 }
 
 void countPathsFromVertice(bool **em, unsigned char *vTypes, int vertexCount, int vertice, int *pathCount)
 /* recursively count paths from vertice */
 {
 int i=0;
 /* check for termination */
 if( isEndVertice(em, vertexCount, vertice, vTypes))
     {
     (*pathCount)++;
     }
 else
     {
     /* recursively call for all vertices that are connected to from this vertex */
     for(i = 0; i < vertexCount; i++)
 	{
 	if(em[vertice][i] && vTypes[i] != ggUnused)
 	    {
 	    countPathsFromVertice(em, vTypes, vertexCount, i, pathCount);
 	    }
 	}
     }
 }
 
 int altGraphNumAltSplices(struct altGraph *ag)
 /* Count number of times that exons have more than one edge through them */
 {
 int pathCount=0;
 int i=0;
 int vertexCount = ag->vertexCount;
 bool **em;
 
 /* construct the edge matrix */
 AllocArray(em, vertexCount);
 for (i=0; i<vertexCount; ++i)
     {
     AllocArray(em[i], vertexCount);
     }
 for (i=0; i<ag->edgeCount; ++i)
     em[ag->edgeStarts[i]][ag->edgeEnds[i]] = TRUE;
 
 /* recursively count all possible paths */
 countPathsFromVertice(em, ag->vTypes, vertexCount, 0, &pathCount);
 
 /* clean up */
 for(i = 0; i < vertexCount; i++)
     freez(&em[i]);
 freez(&em);
 
 return pathCount;
 }