e2ec5ef77645a662ba31c7cfbd7499794975275a
angie
  Fri Mar 23 16:44:07 2012 -0700
Feature #6152 (Variant Annotation Tool): Initial work, squashed infrom origin/annoGrator branch.  Superclasses annoColumn, annoFilter,
annoRow, annoStreamer, annoGrator, and annoFormatter define the core
interfaces for passing data and configuration to and from components.
The annoGrator superclass can join annoRows on position and pass
forward all rows of secondary source.  The annoGratorQuery module
orchestrates the passing of annoRows between the primary source,
annoGrator(s) and annoFormatter(s).  The subclasses annoStreamDb and
annoFormatTab, together with hg/lib/tests/annoGratorTester.c, can join
columns of two database tables such as hg19's pgNA12878 and knownGene
into tab-separated output.

diff --git src/lib/annoFormatter.c src/lib/annoFormatter.c
new file mode 100644
index 0000000..cac50b3
--- /dev/null
+++ src/lib/annoFormatter.c
@@ -0,0 +1,119 @@
+/* annoFormatter -- aggregates, formats and writes output from multiple sources */
+
+#include "annoFormatter.h"
+
+static struct annoFormatterOption *annoFormatterOptionCloneList(struct annoFormatterOption *list)
+/* Return a newly allocated copy of list. */
+{
+struct annoFormatterOption *newList = NULL, *afo;
+for (afo = list;  afo != NULL;  afo = afo->next)
+    {
+    struct annoFormatterOption *newAfo = CloneVar(afo);
+    newAfo->spec.name = cloneString(afo->spec.name);
+    newAfo->value = NULL;
+    unsigned opFlags = opFlags;
+    if (opFlags & OPTION_MULTI)
+	{
+	switch (opFlags & OPTION_TYPE_MASK)
+	    {
+	    case OPTION_STRING:
+		newAfo->value = slNameCloneList((struct slName *)(afo->value));
+		break;
+	    default:
+		errAbort("annoFormatterOptionCloneList: OPTION_MULTI implemented only for "
+			 "OPTION_STRING (not 0x%x)", opFlags);
+	    }
+	}
+    else
+	{
+	switch (opFlags & OPTION_TYPE_MASK)
+	    {
+	    // For numeric singleton values, we are overloading value.
+	    case OPTION_DOUBLE:
+	    case OPTION_FLOAT:
+	    case OPTION_LONG_LONG:
+	    case OPTION_INT:
+	    case OPTION_BOOLEAN:
+		newAfo->value = afo->value;
+		break;
+	    case OPTION_STRING:
+		newAfo->value = cloneString((char *)afo->value);
+		break;
+	    default:
+		errAbort("annoFormatterOptionCloneList: unrecognized op type 0x%x", opFlags);
+	    }
+	}
+    slAddHead(&newList, newAfo);
+    }
+slReverse(&newList);
+return newList;
+}
+
+static void annoFormatterOptionFreeList(struct annoFormatterOption **pList)
+/* Free the same things that we clone above. */
+{
+if (pList == NULL)
+    return;
+struct annoFormatterOption *afo, *nextAfo;
+for (afo = *pList;  afo != NULL;  afo = nextAfo)
+    {
+    nextAfo = afo->next;
+    freeMem(afo->spec.name);
+    unsigned opFlags = opFlags;
+    if (opFlags & OPTION_MULTI)
+	{
+	switch (opFlags & OPTION_TYPE_MASK)
+	    {
+	    case OPTION_STRING:
+		slNameFreeList(&(afo->value));
+		break;
+	    default:
+		errAbort("annoFormatterOptionFreeList: OPTION_MULTI implemented only for "
+			 "OPTION_STRING (not 0x%x)", opFlags);
+	    }
+	}
+    else
+	{
+	switch (opFlags & OPTION_TYPE_MASK)
+	    {
+	    // No need to free overloaded numeric values
+	    case OPTION_DOUBLE:
+	    case OPTION_FLOAT:
+	    case OPTION_LONG_LONG:
+	    case OPTION_INT:
+	    case OPTION_BOOLEAN:
+		break;
+	    case OPTION_STRING:
+		freeMem(afo->value);
+		break;
+	    default:
+		errAbort("annoFormatterOptionFreeList: unrecognized op type 0x%x", opFlags);
+	    }
+	}
+    freeMem(afo);
+    }
+*pList = NULL;
+}
+
+struct annoFormatterOption *annoFormatterGetOptions(struct annoFormatter *self)
+/* Return supported options and current settings.  Callers can modify and free when done. */
+{
+return annoFormatterOptionCloneList(self->options);
+}
+
+void annoFormatterSetOptions(struct annoFormatter *self, struct annoFormatterOption *newOptions)
+/* Free old options and use clone of newOptions. */
+{
+annoFormatterOptionFreeList(&(self->options));
+self->options = annoFormatterOptionCloneList(newOptions);
+}
+
+void annoFormatterFree(struct annoFormatter **pSelf)
+/* Free self. This should be called at the end of subclass close methods, after
+ * subclass-specific connections are closed and resources are freed. */
+{
+if (pSelf == NULL)
+    return;
+annoFormatterOptionFreeList(&((*pSelf)->options));
+freez(pSelf);
+}