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/lib/annoGratorQuery.c src/lib/annoGratorQuery.c
index 99aba40..f93d297 100644
--- src/lib/annoGratorQuery.c
+++ src/lib/annoGratorQuery.c
@@ -1,147 +1,150 @@
 /* annoGratorQuery -- framework for integrating genomic annotations from many sources */
 
+/* Copyright (C) 2013 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+
 #include "annoGratorQuery.h"
 #include "dystring.h"
 #include "errabort.h"
 #include "obscure.h"
 
 struct annoGratorQuery
 /* Representation of a complex query: multiple sources, each with its own filters,
  * output data and means of integration, aggregated and output by a formatter. */
     {
     struct annoAssembly *assembly;	// Genome assembly to which annotations belong
     struct annoStreamer *primarySource;	// Annotations to be integrated with other annos.
     struct annoGrator *integrators;	// Annotations & methods for integrating w/primary
     struct annoFormatter *formatters;	// Writers of output collected from primary & intg's
     };
 
 struct annoGratorQuery *annoGratorQueryNew(struct annoAssembly *assembly,
 					   struct annoStreamer *primarySource,
 					   struct annoGrator *integrators,
 					   struct annoFormatter *formatters)
 /* Create an annoGratorQuery from all of its components, and introduce components to each other.
  * integrators may be NULL.  All other inputs must be non-NULL. */
 {
 if (assembly == NULL)
     errAbort("annoGratorQueryNew: assembly can't be NULL");
 if (primarySource == NULL)
     errAbort("annoGratorQueryNew: primarySource can't be NULL");
 if (formatters == NULL)
     errAbort("annoGratorQueryNew: formatters can't be NULL");
 struct annoGratorQuery *query = NULL;
 AllocVar(query);
 query->assembly = assembly;
 query->primarySource = primarySource;
 query->integrators = integrators;
 query->formatters = formatters;
 struct annoFormatter *formatter;
 for (formatter = query->formatters;  formatter != NULL;  formatter = formatter->next)
     formatter->initialize(formatter, primarySource, (struct annoStreamer *)integrators);
 return query;
 }
 
 void annoGratorQuerySetRegion(struct annoGratorQuery *query, char *chrom, uint rStart, uint rEnd)
 /* Set genomic region for query; if chrom is NULL, position is whole genome. */
 {
 if (chrom != NULL)
     {
     uint chromSize = annoAssemblySeqSize(query->assembly, chrom);
     if (rEnd < rStart)
 	errAbort("annoGratorQuerySetRegion: rStart (%u) can't be greater than rEnd (%u)",
 		 rStart, rEnd);
     if (rEnd > chromSize)
 	errAbort("annoGratorQuerySetRegion: rEnd (%u) can't be greater than chrom %s size (%u)",
 		 rEnd, chrom, chromSize);
     if (rEnd == 0)
 	rEnd = chromSize;
     }
 // Alert all streamers that they should now send data from a possibly different region:
 query->primarySource->setRegion(query->primarySource, chrom, rStart, rEnd);
 struct annoStreamer *grator = (struct annoStreamer *)(query->integrators);
 for (;  grator != NULL;  grator = grator->next)
     grator->setRegion(grator, chrom, rStart, rEnd);
 }
 
 void annoGratorQueryExecute(struct annoGratorQuery *query)
 /* For each annoRow from query->primarySource, invoke integrators and pass their annoRows
  * to formatters. */
 {
 struct annoStreamer *primarySrc = query->primarySource;
 struct annoStreamRows *primaryData = annoStreamRowsNew(primarySrc);
 struct annoStreamRows *gratorData = NULL;
 int gratorCount = slCount(query->integrators);
 if (gratorCount > 0)
     {
     struct annoStreamer *gratorStreamList = (struct annoStreamer *)query->integrators;
     gratorData = annoStreamRowsNew(gratorStreamList);
     }
 char *regionChrom = primarySrc->chrom;
 struct annoRow *primaryRow = NULL;
 struct lm *lm = lmInit(0);
 boolean gotPrimaryData = FALSE;
 while ((primaryRow = primarySrc->nextRow(primarySrc, NULL, 0, lm)) != NULL)
     {
     if (regionChrom != NULL && strcmp(primaryRow->chrom, regionChrom) > 0)
 	{
 	// primarySrc's first row is on some chromosome past regionChrom, i.e. it has no
 	// items on regionChrom.
 	break;
 	}
     if (primaryRow->rightJoinFail)
 	continue;
     gotPrimaryData = TRUE;
     primaryData->rowList = primaryRow;
     boolean rjFilterFailed = FALSE;
     int i;
     for (i = 0;  i < gratorCount;  i++)
 	{
 
 	struct annoGrator *grator = (struct annoGrator *)gratorData[i].streamer;
 	gratorData[i].rowList = grator->integrate(grator, primaryData, &rjFilterFailed, lm);
 	if (rjFilterFailed)
 	    break;
 	}
     struct annoFormatter *formatter = NULL;
     for (formatter = query->formatters;  formatter != NULL;  formatter = formatter->next)
 	if (!rjFilterFailed)
 	    formatter->formatOne(formatter, primaryData, gratorData, gratorCount);
     lmCleanup(&lm);
     lm = lmInit(0);
     }
 if (!gotPrimaryData)
     {
     struct dyString *dy = dyStringCreate("No data from %s", primarySrc->name);
     if (regionChrom != NULL)
 	dyStringPrintf(dy, " in range %s:%d-%d; try changing 'region to annotate' to 'genome'",
 		       regionChrom, primarySrc->regionStart, primarySrc->regionEnd);
     struct annoFormatter *formatter = NULL;
     for (formatter = query->formatters;  formatter != NULL;  formatter = formatter->next)
 	formatter->comment(formatter, dy->string);
     dyStringFree(&dy);
     }
 freez(&primaryData);
 freez(&gratorData);
 lmCleanup(&lm);
 }
 
 void annoGratorQueryFree(struct annoGratorQuery **pQuery)
 /* Close and free all inputs and outputs; free self. */
 {
 if (pQuery == NULL)
     return;
 struct annoGratorQuery *query = *pQuery;
 query->primarySource->close(&(query->primarySource));
 struct annoStreamer *grator = (struct annoStreamer *)(query->integrators), *nextGrator;
 for (;  grator != NULL;  grator = nextGrator)
     {
     nextGrator = grator->next;
     grator->close(&grator);
     }
 struct annoFormatter *formatter, *nextFormatter;
 for (formatter = query->formatters;  formatter != NULL;  formatter = nextFormatter)
     {
     nextFormatter = formatter->next;
     formatter->close(&formatter);
     }
 freez(pQuery);
 }