a44421a79fb36cc2036fe116b97ea3bc9590cd0c
braney
  Fri Dec 2 09:34:39 2011 -0800
removed rcsid (#295)
diff --git src/hg/altGraph/test.c src/hg/altGraph/test.c
index 304338b..2654908 100644
--- src/hg/altGraph/test.c
+++ src/hg/altGraph/test.c
@@ -1,226 +1,225 @@
 #include "common.h"
 #include "ggPrivate.h"
 #include "jksql.h"
 
-static char const rcsid[] = "$Id: test.c,v 1.2 2003/05/06 07:22:13 kate Exp $";
 
 static struct ggAliInfo *makeTestDa(int *data, int dataSize)
 /* Make up ggAliInfo from test data. */
 {
 int vertexCount;
 struct ggAliInfo *da;
 struct ggVertex *v;
 int i;
 
 vertexCount = dataSize;
 AllocVar(da);
 da->vertexCount = vertexCount;
 da->vertices = AllocArray(v, vertexCount);
 for (i=0; i<dataSize; i += 1 )
     {
     v->position = *data++;
     if (i == 0)
 	v->type = ggSoftStart;
     else if (i == dataSize-1)
 	v->type = ggSoftEnd;
     else if (i&1)
 	v->type = ggHardEnd;
     else
 	v->type = ggHardStart;
     ++v;
     }
 return da;
 }
 
 #define RAY_SET
 
 #ifdef JIM_SET
 int rna1[] = {50, 100, 1000, 1150};
 int rna2[] = {25, 100, 1000, 1150};
 int rna3[] = {50, 100, 1000, 1200};
 int rna4[] = {50,  75, 1000, 1150};
 int rna5[] = {50, 100, 1050, 1150};
 int rna6[] = {50, 100, 500, 600, 1000, 1150};
 int rna7[] = {1100, 1250, 1300, 1400};
 int rna8[] = {1075, 1175, 1300, 1400};
 int rna9[] = {1025, 1175, 1300, 1400};
 int rna10[] = {50, 100, 500, 602,};
 int rna11[] = {498, 600, 1000, 1150};
 #endif
 
 #ifdef RAY_SET
 int rna1[] = {0, 100, 150, 500};
 int rna2[] = {50, 100, 150, 200, 250, 550};
 int rna3[] = {300, 700, 750, 800};
 int rna4[] = {350, 600, 650, 700, 750, 850};
 #endif
 
 #ifdef SIMPLE_SET
 //int rna1[] = {0, 100,};
 //int rna2[] = {50, 150,};
 int rna1[] = {110,889, 1045,1118, }; 
 int rna2[] = {111,508}; 
 #endif
 
 #ifdef BIG_SET
 int rna1[] = {109,889, 1045,1118, 1210,1275, 1449,1618, 1703,1736, 4705,4776, 4868,4943, 5111,5283, 5425,5538, 5734,5859, 6073,6157, 6850,6999, 7085,7225, 7526,7612, 7708,7786}; 
 int rna2[] = {110,889, 1045,1118, 1210,1275, 1449,1618, 1703,1736, 4705,4776, 4868,4943, 5111,5283, 5425,5538, 5734,5859, 6073,6157, 6850,6999, 7085,7225, 7526,7612, 7708,7809, 8228,8351, 10897,11011, 11410,11485, 12838,12946, 13030,13068, 13213,13340, 13502,13598, 13960,14007, 19852,20013}; 
 int rna3[] = {111,508}; 
 int rna4[] = {115,397}; 
 int rna5[] = {1096,1118, 1210,1275, 1449,1618, 1703,1736, 4705,4749}; 
 int rna6[] = {1459,1618, 1703,1736, 4705,4776, 4868,4914}; 
 int rna7[] = {1499,1618, 1703,1737}; 
 int rna8[] = {1502,1618, 1703,1736, 4705,4776, 4868,4937}; 
 int rna9[] = {1539,1618, 1703,1736, 4705,4776, 4868,4914}; 
 int rna10[] = {4866,4943, 5111,5283, 5425,5485}; 
 int rna11[] = {5146,5283, 5425,5528}; 
 int rna12[] = {5207,5283, 5425,5538, 5734,5781}; 
 int rna13[] = {5257,5283, 5425,5538, 5734,5859, 6073,6119}; 
 int rna14[] = {5465,5538, 5734,5859, 6073,6117}; 
 int rna15[] = {5772,5859, 6073,6157, 6850,6999, 7085,7225, 7526,7567}; 
 int rna16[] = {6092,6157, 6850,6999, 7085,7176}; 
 int rna17[] = {6946,6999, 7085,7225, 7526,7612, 7708,7809, 8228,8351, 8909,8972}; 
 int rna18[] = {7111,7225, 7526,7612, 7708,7786}; 
 int rna19[] = {7199,7225, 7526,7612, 7722,7807}; 
 int rna20[] = {7537,7612, 7708,7809, 8228,8321}; 
 int rna21[] = {11410,11485, 12838,12946, 13030,13068, 13213,13338}; 
 int rna22[] = {12837,12946, 13030,13068, 13213,13343, 13502,13598, 13960,14007, 19852,19940}; 
 int rna23[] = {12840,12946, 13030,13068, 13213,13346}; 
 int rna24[] = {12884,12946, 13030,13068, 13213,13343, 13502,13598, 13960,14007, 19852,19954}; 
 int rna25[] = {12887,12946, 13030,13068, 13213,13343, 13502,13598, 13960,14007, 19852,19905}; 
 int rna26[] = {12913,12946, 13030,13068, 13213,13343, 13502,13598, 13960,14007, 19852,19972}; 
 #endif /* BIG_SET */
 
 
 struct ggMrnaCluster *makeTestInput()
 /* Make up nice test set for graph thing. */
 {
 struct ggMrnaCluster *mc;
 AllocVar(mc);
 mc->orientation = 1;
 
 #ifdef BIG_SET
 //slAddTail(&mc->mrnaList, makeTestDa(rna1, ArraySize(rna1)));
 slAddTail(&mc->mrnaList, makeTestDa(rna2, ArraySize(rna2)));
 slAddTail(&mc->mrnaList, makeTestDa(rna3, ArraySize(rna3)));
 #ifdef NEVER
 slAddTail(&mc->mrnaList, makeTestDa(rna4, ArraySize(rna4)));
 slAddTail(&mc->mrnaList, makeTestDa(rna5, ArraySize(rna5)));
 slAddTail(&mc->mrnaList, makeTestDa(rna6, ArraySize(rna6)));
 slAddTail(&mc->mrnaList, makeTestDa(rna7, ArraySize(rna7)));
 slAddTail(&mc->mrnaList, makeTestDa(rna8, ArraySize(rna8)));
 slAddTail(&mc->mrnaList, makeTestDa(rna9, ArraySize(rna9)));
 slAddTail(&mc->mrnaList, makeTestDa(rna10, ArraySize(rna10)));
 slAddTail(&mc->mrnaList, makeTestDa(rna11, ArraySize(rna11)));
 slAddTail(&mc->mrnaList, makeTestDa(rna12, ArraySize(rna12)));
 slAddTail(&mc->mrnaList, makeTestDa(rna13, ArraySize(rna13)));
 slAddTail(&mc->mrnaList, makeTestDa(rna14, ArraySize(rna14)));
 slAddTail(&mc->mrnaList, makeTestDa(rna15, ArraySize(rna15)));
 slAddTail(&mc->mrnaList, makeTestDa(rna16, ArraySize(rna16)));
 slAddTail(&mc->mrnaList, makeTestDa(rna17, ArraySize(rna17)));
 slAddTail(&mc->mrnaList, makeTestDa(rna18, ArraySize(rna18)));
 slAddTail(&mc->mrnaList, makeTestDa(rna19, ArraySize(rna19)));
 slAddTail(&mc->mrnaList, makeTestDa(rna20, ArraySize(rna20)));
 slAddTail(&mc->mrnaList, makeTestDa(rna21, ArraySize(rna21)));
 slAddTail(&mc->mrnaList, makeTestDa(rna22, ArraySize(rna22)));
 slAddTail(&mc->mrnaList, makeTestDa(rna23, ArraySize(rna23)));
 slAddTail(&mc->mrnaList, makeTestDa(rna24, ArraySize(rna24)));
 slAddTail(&mc->mrnaList, makeTestDa(rna25, ArraySize(rna25)));
 slAddTail(&mc->mrnaList, makeTestDa(rna26, ArraySize(rna26)));
 #endif /* NEVER */
 mc->tStart = 0;
 mc->tEnd = 20000;
 #endif /* BIG_SET */
 
 #ifdef JIM_SET
 slAddTail(&mc->mrnaList, makeTestDa(rna1, ArraySize(rna1)));
 slAddTail(&mc->mrnaList, makeTestDa(rna2, ArraySize(rna2)));
 slAddTail(&mc->mrnaList, makeTestDa(rna3, ArraySize(rna3)));
 slAddTail(&mc->mrnaList, makeTestDa(rna4, ArraySize(rna4)));
 slAddTail(&mc->mrnaList, makeTestDa(rna5, ArraySize(rna5)));
 slAddTail(&mc->mrnaList, makeTestDa(rna6, ArraySize(rna6)));
 slAddTail(&mc->mrnaList, makeTestDa(rna7, ArraySize(rna7)));
 slAddTail(&mc->mrnaList, makeTestDa(rna8, ArraySize(rna8)));
 slAddTail(&mc->mrnaList, makeTestDa(rna9, ArraySize(rna9)));
 slAddTail(&mc->mrnaList, makeTestDa(rna10, ArraySize(rna10)));
 slAddTail(&mc->mrnaList, makeTestDa(rna11, ArraySize(rna11)));
 mc->tStart = 0;
 mc->tEnd = 1400;
 #endif
 
 #ifdef SIMPLE_SET
 slAddTail(&mc->mrnaList, makeTestDa(rna1, ArraySize(rna1)));
 slAddTail(&mc->mrnaList, makeTestDa(rna2, ArraySize(rna2)));
 mc->tStart = 0;
 mc->tEnd = 200;
 #endif
 
 #ifdef RAY_SET
 slAddTail(&mc->mrnaList, makeTestDa(rna1, ArraySize(rna1)));
 slAddTail(&mc->mrnaList, makeTestDa(rna2, ArraySize(rna2)));
 slAddTail(&mc->mrnaList, makeTestDa(rna3, ArraySize(rna3)));
 slAddTail(&mc->mrnaList, makeTestDa(rna4, ArraySize(rna4)));
 mc->tStart = 0;
 mc->tEnd = 1000;
 #endif
 }
 
 
 void smallTest()
 /* Test out stuff. */
 {
 struct ggMrnaCluster *mc = makeTestInput();
 struct geneGraph *gg;
 static struct ggMrnaInput dummyCi;
 
 uglyf("Initial input\n");
 dumpMc(mc);
 uglyf("\n");
 gg = ggGraphCluster(mc, &dummyCi);
 traverseGeneGraph(gg, mc->tStart, mc->tEnd, dumpGgAliInfo);
 errAbort("Done testing");
 }
 
 
 void constraintsForBac(char *bacAcc, char *outDir)
 /* Generate a set of constraint files for bac. */
 {
 struct ggMrnaInput *ci = ggGetMrnaForBac(bacAcc);
 struct ggMrnaCluster *mc, *mcList = ggClusterMrna(ci);
 struct geneGraph *gg;
 
 uglyf("Got %d clusters\n", slCount(mcList));
 for (mc = mcList; mc != NULL; mc = mc->next)
     {
     uglyf("Initial input\n");
     dumpMc(mc);
     uglyf("\n");
     gg = ggGraphCluster(mc, ci);
     uglyf("Constraints\n");
     traverseGeneGraph(gg, mc->tStart, mc->tEnd, dumpGgAliInfo);
     uglyf("\n\n");
     }
 }
 
 void usage()
 /* Describe how to use program and exit. */
 {
 errAbort(
   "test - test alt-splice clustering and \n"
   "Usage:\n"
   "   test bacAccession\n");
 }
 
 int main(int argc, char *argv[])
 {
 char *bacAcc = "AC000001";
 char *outDir = "gff";
 
 
 if (argc < 2)
     usage();
 bacAcc = argv[1];
 
 constraintsForBac(bacAcc, outDir);
 return 0;
 }