8c908f948b09826c6cb4452ee5b282aca41be85e
galt
  Tue Dec 8 21:52:59 2015 -0800
Multi-region (exonMostly). This work allows people to look at virtual chromosomes from a list of regions and then navigate and perform all of the usual functions on it.

diff --git src/inc/spaceSaver.h src/inc/spaceSaver.h
index a41e62a..a328543 100644
--- src/inc/spaceSaver.h
+++ src/inc/spaceSaver.h
@@ -1,73 +1,102 @@
 /* spaceSaver - routines that help layout 1-D objects into a
  * minimum number of tracks so that no two objects overlap
  * within a single track. 
  *
  * This file is copyright 2000 Jim Kent, but license is hereby
  * granted for all use - public, private or commercial. */
 
 #ifndef SPACESAVER_H
 #define SPACESAVER_H
 
 struct spaceSaver
 /* Help layout 1-D objects onto multiple tracks so that
  * no two objects overlap on a single track. */
     {
     struct spaceSaver *next;	/* Next in list. */
     struct spaceNode *nodeList; /* List of things put in space saver. */
     struct spaceRowTracker *rowList; /* List of rows. */
     int rowCount;             /* Number of rows. */
     int *rowSizes;            /* Height in pixels of each row. 
                                 Used by tracks with variable height items. */
     int winStart,winEnd;      /* Start and end of area we're modeling. */
     int cellsInRow;           /* Number of cells per row. */
     double scale;             /* What to scale by to get to cell coordinates. */
     int maxRows;	      /* Maximum number of rows.  */
     boolean isFull;	      /* Set to true if can't fit data into maxRows. */
+    int vis;                  /* Remember visibility used */
+    void *window;             /* Remember window used */
     };
 
 struct spaceNode
 /* Which row is this one on? */
     {
     struct spaceNode *next;	  /* Next in list. */
     int row;			  /* Which row, starting at zero. */
     void *val;
+    struct spaceSaver *parentSs;  /* Useful for adding to parent spaceSaver with multiple windows */
+    bool noLabel;                 /* Suppress label if TRUE in pack */
     };
 
 struct spaceRowTracker 
 /* Keeps track of how much of row is used. */
     {
     struct spaceRowTracker *next;	/* Next in list. */
     bool *used;                 /* A flag for each spot used. */
     };
 
+struct spaceRange
+/* Specifies start and end of range needed */
+    {
+    struct spaceRange *next;
+    int start;
+    int end;
+    int width;
+    };
+
+
 struct spaceSaver *spaceSaverMaxCellsNew(int winStart, int winEnd, int maxRows, int maxCells);
 /* Create a new space saver around the given window.   */
 
 struct spaceSaver *spaceSaverNew(int winStart, int winEnd, int maxRows);
 /* Create a new space saver around the given window.   */
 
 void spaceSaverFree(struct spaceSaver **pSs);
 /* Free up a space saver. */
 
 struct spaceNode *spaceSaverAdd(struct spaceSaver *ss, int start, int end, void *val);
 /* Add a new node to space saver. */
 
+struct spaceNode *spaceSaverAddMulti(struct spaceSaver *ss, struct spaceRange *rangeList, struct spaceNode *nodeList);
+/* Add new nodes for multiple windows to space saver. */
+
+struct spaceNode *spaceSaverAddOverflowExtended(struct spaceSaver *ss, int start, int end, 
+					void *val, boolean allowOverflow, struct spaceSaver *parentSs, bool noLabel);
+/* Add a new node to space saver. Returns NULL if can't fit item in
+ * and allowOverflow == FALSE. If allowOverflow == TRUE then put items
+ * that won't fit in last row. parentSs allows specification of destination for node from alternate window.*/
 
 struct spaceNode *spaceSaverAddOverflow(struct spaceSaver *ss, int start, int end, 
 					void *val, boolean allowOverflow);
 /* Add a new node to space saver. Returns NULL if can't fit item in
  * and allowOverflow == FALSE. If allowOverflow == TRUE then put items
  * that won't fit in first row (ends up being last row after
  * spaceSaverFinish()). */
 
-int spaceSaverSetRowHeights(struct spaceSaver *ss, int (*itemHeight)(void *item));
+struct spaceNode *spaceSaverAddOverflowMulti(struct spaceSaver *ss, struct spaceRange *rangeList, struct spaceNode *nodeList, 
+					boolean allowOverflow);
+/* Add new nodes for multiple windows to space saver. Returns NULL if can't fit item in
+ * and allowOverflow == FALSE. If allowOverflow == TRUE then put items
+ * that won't fit in first row (ends up being last row after
+ * spaceSaverFinish()). */
+
+void spaceSaverSetRowHeights(struct spaceSaver *ss, struct spaceSaver *holdSs, int (*itemHeight)(void *item));
 /* Determine maximum height of items in a row. Return total height.
    Used by tracks with variable height items */
 
 int spaceSaverGetRowHeightsTotal(struct spaceSaver *ss);
 /* Return height of all rows. Used by tracks with variable height items */
 
 void spaceSaverFinish(struct spaceSaver *ss);
 /* Tell spaceSaver done adding nodes. */
 #endif /* SPACESAVER_H */