6f75c327bcd0cfc8bf68dfa1227aabb579120698
Merge parents 41b17ce ccb8cb2
kate
  Mon Dec 17 12:37:37 2018 -0800
Merge branch 'master' into interact-multiregion

diff --cc src/hg/hgc/interactClick.c
index 9d1e538,54cd223..87afdb5
--- src/hg/hgc/interactClick.c
+++ src/hg/hgc/interactClick.c
@@@ -1,331 -1,312 +1,331 @@@
  /* Details page for interact type tracks */
  
  /* Copyright (C) 2018 The Regents of the University of California 
   * See README in this or parent directory for licensing information. */
  
  #include "common.h"
  #include "obscure.h"
  #include "hdb.h"
  #include "jksql.h"
  #include "hgc.h"
 +#include "trashDir.h"
  
  #include "interact.h"
  #include "interactUi.h"
  
  struct interactPlusRow
      {
      /* Keep field values in string format, for url processing */
      struct interactPlusRow *next;
      struct interact *interact;
      char **row;
      };
  
  static struct interactPlusRow *getInteractsFromTable(struct trackDb *tdb, char *chrom, 
                                      int start, int end, char *name, char *foot)
  /* Retrieve interact items at this position from track table */
  {
  struct sqlConnection *conn = NULL;
  struct customTrack *ct = lookupCt(tdb->track);
  char *table;
  if (ct != NULL)
      {
      conn = hAllocConn(CUSTOM_TRASH);
      table = ct->dbTableName;
      }
  else
      {
      conn = hAllocConnTrack(database, tdb);
      table = tdb->table;
      }
  if (conn == NULL)
      return NULL;
  
  struct interactPlusRow *iprs = NULL;
  char **row;
  int offset;
  struct sqlResult *sr = hRangeQuery(conn, table, chrom, start, end, NULL, &offset);
  int fieldCount = 0;
  while ((row = sqlNextRow(sr)) != NULL)
      {
      struct interact *inter = interactLoadAndValidate(row+offset);
      // got one, save object and row representation
      struct interactPlusRow *ipr;
      AllocVar(ipr);
      ipr->interact = inter;
      char **fieldVals;
      if (fieldCount == 0)
          fieldCount = sqlCountColumns(sr);
      AllocArray(fieldVals, fieldCount);
      int i;
      for (i = 0; i < fieldCount; i++)
          fieldVals[i] = cloneString(row[i]);
      ipr->row = fieldVals;
      slAddHead(&iprs, ipr);
      }
  sqlFreeResult(&sr);
  hFreeConn(&conn);
  return iprs;
  }
  
  static struct interactPlusRow *getInteractsFromFile(char *file, char *chrom, int start, int end, 
                                                          char *name, char *foot)
  /* Retrieve interact items at this position from big file */
  {
  struct bbiFile *bbi = bigBedFileOpen(file);
  struct lm *lm = lmInit(0);
  struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
  struct interactPlusRow *iprs = NULL;
  
  for (bb = bbList; bb != NULL; bb = bb->next)
      {
      char startBuf[16], endBuf[16];
      int maxFields = 32;
      char *row[maxFields];      // big enough ?
      int fieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, row, maxFields);
      struct interact *inter = interactLoadAndValidate(row);
      if (inter == NULL)
          continue;
  
      // got one, save object and row representation
      struct interactPlusRow *ipr;
      AllocVar(ipr);
      ipr->interact = inter;
      char **fieldVals;
      AllocArray(fieldVals, fieldCount);
      int i;
      for (i = 0; i < fieldCount; i++)
          fieldVals[i] = cloneString(row[i]);
      ipr->row = fieldVals;
      slAddHead(&iprs, ipr);
      }
  return iprs;
  }
  
  static struct interactPlusRow *getInteractions(struct trackDb *tdb, char *chrom, int start, int end, 
                                                  char *name, char *foot, int *retStart, int *retEnd)
  /* Retrieve interact items at this position or name. 
   * Also any others with the same endpoint, if endpoint clicked on.
   * Return full extent of included interactions in returned start, end */
  // NOTE: Consider sortable table of matching interactions
  {
  struct interactPlusRow *ipr, *iprs = NULL, *next, *filtered = NULL;
  char *file = trackDbSetting(tdb, "bigDataUrl");
  char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb);
  if (file != NULL)
      iprs = getInteractsFromFile(file, chrom, start, end, name, foot);
  else
      iprs = getInteractsFromTable(tdb, chrom, start, end, name, foot);
  
  int minStart = iprs->interact->chromStart;
  int maxEnd = iprs->interact->chromEnd;
  for (ipr = iprs; ipr; ipr = next)
      {
      struct interact *inter = ipr->interact;
      next = ipr->next;
      if (!name || sameString(name, "."))
          {
          if (inter->chromStart != start || inter->chromEnd != end)
              continue;
          }
      else
          {
          char *match = inter->name;
          if (clusterMode)
              match = sameString(clusterMode, INTERACT_CLUSTER_SOURCE) ?
                                                  inter->sourceName : inter->targetName;
          if (differentString(name, match))
              {
              if (clusterMode || !foot)
                  continue;
              // if clicked on foot, look at endpoint names
              if (differentString(name, inter->sourceName) && differentString(name, inter->targetName))
                  continue;
              }
          }
      minStart = inter->chromStart <  minStart ? inter->chromStart : minStart;
      maxEnd = inter->chromEnd > maxEnd ? inter->chromEnd : maxEnd;
      slAddHead(&filtered, ipr);
      }
  
  *retStart = minStart;
  *retEnd = maxEnd;
  // consider sorting on score or position
  return filtered;
  }
  
  void doInteractRegionDetails(struct trackDb *tdb, struct interact *inter)
  {
  /* print info for both regions */
  /* Use different labels:
          1) directional (source/target)
          2) non-directional same chrom (lower/upper)
          3) non-directional other chrom (this/other)
  */
  char startBuf[1024], endBuf[1024], sizeBuf[1024];
  printf("<b>Interaction region:</b> ");
  if (interactOtherChrom(inter))
      printf("across chromosomes<br>");
  else
      {
      sprintLongWithCommas(startBuf, inter->chromStart+1);
      sprintLongWithCommas(endBuf, inter->chromEnd);
      sprintLongWithCommas(sizeBuf, inter->chromEnd - inter->chromStart);
      printf("<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a>", 
                  inter->chrom, inter->chromStart, inter->chromEnd,
                  inter->chrom, startBuf, endBuf);
      printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
      }
  printf("<br>");
  char *region1Label = "Source";
  char *region1Chrom = inter->sourceChrom;
  int region1Start = inter->sourceStart;
  int region1End = inter->sourceEnd;
  char *region1Name = inter->sourceName;
  if (isEmptyTextField(inter->sourceName))
      region1Name = "";
  
  char *region2Label = "Target";
  char *region2Chrom = inter->targetChrom;
  int region2Start = inter->targetStart;
  int region2End = inter->targetEnd;
  char *region2Name = inter->targetName;
  if (isEmptyTextField(inter->targetName))
      region2Name = "";
  
  if (!interactUiDirectional(tdb))
      {
      if (interactOtherChrom(inter))
          {
          region1Label = "This";
          region2Label = "Other";
          }
      else
          {
          region1Label = "Lower";
          region2Label = "Upper";
          }
      }
  // format and print
  sprintLongWithCommas(startBuf, region1Start + 1);
  sprintLongWithCommas(endBuf, region1End);
  sprintLongWithCommas(sizeBuf, region1End - region1Start);
  printf("<b>%s region:</b> %s&nbsp;&nbsp;"
                  "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s",
                  region1Label, region1Name, region1Chrom, region1Start+1, region1End,
                  region1Chrom, startBuf, endBuf, 
                  inter->sourceStrand[0] == '.' ? "" : inter->sourceStrand);
  printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
  
  sprintLongWithCommas(startBuf, region2Start+1);
  sprintLongWithCommas(endBuf, region2End);
  sprintLongWithCommas(sizeBuf, region2End - region2Start);
  printf("<b>%s region:</b> %s&nbsp;&nbsp;"
                  "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> %s",
                  region2Label, region2Name, region2Chrom, region2Start+1, region2End,
                  region2Chrom, startBuf, endBuf, 
                  inter->targetStrand[0] == '.' ? "" : inter->targetStrand);
  printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
  int distance = interactRegionDistance(inter);
  if (distance > 0)
      {
      // same chrom
      sprintLongWithCommas(sizeBuf, distance);
      printf("<b>Distance between midpoints:</b> %s bp<br>\n", sizeBuf); 
      }
  
 +// print link to multi-region view of ends
 +
 +// create bed file in trash directory with end coordinates
 +struct tempName mrTn;
 +trashDirFile(&mrTn, "hgt", "custRgn_interact", ".bed");
 +FILE *f = fopen(mrTn.forCgi, "w");
 +if (f == NULL)
 +    errAbort("can't create temp file %s", mrTn.forCgi);
 +fprintf(f, "%s\t%d\t%d\n"
 +           "%s\t%d\t%d\n",
 +                region1Chrom, region1Start, region1End, 
 +                region2Chrom, region2Start, region2End);
 +fclose(f);
 +printf("<br><a target='_blank' href='hgTracks?"
 +                "virtMode=1"
 +                "&virtModeType=customUrl"
 +                "&multiRegionsBedUrl=%s'"
 +        ">Show both ends of interaction in multi-region browser view</a>",
 +                mrTn.forCgi);
 +
  #ifdef TODO /* TODO: get count and score stats of all interactions in window ?*/
  double *scores;
  AllocArray(scores, count);
  #endif
  }
  
  void doInteractItemDetails(struct trackDb *tdb, struct interactPlusRow *ipr, char *item, 
                                  boolean isMultiple)
  /* Details of interaction item */
  {
  struct interact *inter = ipr->interact;
  struct slPair *fields = getFields(tdb, ipr->row);
- printCustomUrlWithFields(tdb, item, item, TRUE, fields);
+ printCustomUrlWithFields(tdb, inter->name, inter->name, TRUE, fields);
  if (!isEmptyTextField(inter->name))
      printf("<b>Interaction:</b> %s<br>\n", inter->name);
  printf("<b>Score:</b> %d<br>\n", inter->score);
  printf("<b>Value:</b> %0.3f<br>\n", inter->value);
  if (!isEmptyTextField(inter->exp))
      printf("<b>Experiment:</b> %s<br>\n", inter->exp);
  puts("<p>");
  if (!isMultiple)
      doInteractRegionDetails(tdb, inter);
  }
  
  void doInteractDetails(struct trackDb *tdb, char *item)
  /* Details of interaction items */
  {
  char *chrom = cartString(cart, "c");
  int start = cartInt(cart, "o");
  int end = cartInt(cart, "t");
  char *foot = cgiOptionalString("foot");
  int minStart, maxEnd;
  struct interactPlusRow *iprs = getInteractions(tdb, chrom, start, end, item, foot, &minStart, &maxEnd);
  start = minStart;
  end = maxEnd;
  if (iprs == NULL)
      errAbort("Can't find interaction %s", item ? item : "");
  int count = slCount(iprs);
  char *clusterMode = interactUiClusterMode(cart, tdb->track, tdb);
  if (count > 1 || clusterMode)
      {
      printf("<b>Interactions:</b> %d<p>", count);
      if (clusterMode || foot)
          {
          char startBuf[1024], endBuf[1024], sizeBuf[1024];
          sprintLongWithCommas(startBuf, start + 1);
          sprintLongWithCommas(endBuf, end);
          sprintLongWithCommas(sizeBuf, end - start);
          printf("<b>%s interactions region:</b> &nbsp;&nbsp;"
                          "<a href='hgTracks?position=%s:%d-%d' target='_blank'>%s:%s-%s</a> ",
                          item, chrom, start+1, end, chrom, startBuf, endBuf);
          printf("&nbsp;&nbsp;%s bp<br>\n", sizeBuf);
          }
      else
          {
          doInteractRegionDetails(tdb, iprs->interact);
          }
      printf("</p>");
      }
  
  genericHeader(tdb, item);
  static struct interactPlusRow *ipr = NULL;
  for (ipr = iprs; ipr != NULL; ipr = ipr->next)
      {
      if (count > 1)
          printf("<hr>\n");
      doInteractItemDetails(tdb, ipr, item, count > 1);
      if (foot || (clusterMode && count > 1))
          doInteractRegionDetails(tdb, ipr->interact);
      if (count > 1 && !isEmptyTextField(ipr->interact->name) && sameString(ipr->interact->name, item))
          printf("<hr>\n");
      }
 -if (count > 1 && clusterMode)
 -    printf("<hr>\n");
  }