4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/makeDb/hgCountAlign/slidingWin.h src/hg/makeDb/hgCountAlign/slidingWin.h index 93f1001..e4423ef 100644 --- src/hg/makeDb/hgCountAlign/slidingWin.h +++ src/hg/makeDb/hgCountAlign/slidingWin.h @@ -1,55 +1,55 @@ /* Copyright (C) 2002 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #ifndef SLIDINGWIN_H #define SLIDINGWIN_H struct slidingWin /* Counts for an overlaping, sliding window, composed of contiguous, * non-overlapping subwindows. This is used to compute the counts for * overlapping windows. New subwindows are added until the the requred number * of subwindows is reached, then windows are circulated head to tail. The * sliding window can be advanced over large blocks without alignments. * Subwindows that invalidated are placed on a free list. The head will have * lowest-positioned subwindow, * the tail the last position counted. */ { char *chrom; unsigned chromSize; /* zero if unknown */ unsigned winSize; unsigned winSlide; /* this is also the subwindow size */ unsigned numSubWins; unsigned curNumSubWins; struct winCounts *head; struct winCounts *tail; struct winCounts *freeSubWins; struct winCounts *sum; }; struct slidingWin *slidingWinNew(char* chrom, unsigned chromSize, unsigned winSize, unsigned winSlide); /* Construct a new sliding window. */ void slidingWinFree(struct slidingWin** win); /* Free a sliding window. */ void slidingWinAdvance(struct slidingWin *win, unsigned winStart); /* Advance forward to the specified window boundry. Existing subwindow * counts are preserved if they overlap the window. Subwindows with * zero counts are added as needed. */ unsigned slidingWinTotalCounts(struct slidingWin *win); /* Calculate the total number of counts represented by these windows */ void slidingWinSum(struct slidingWin *win); /* Sum the subwindows into the sum object */ void slidingWinRemoveFirstWithCounts(struct slidingWin *win); /* Remove the first subwindow that contains counts, which also removes * any preceeding subwindows with no counts. */ void slidingWinRemoveLast(struct slidingWin *win); /* Remove the last subwindow, if it exists. This is used to force recounting * of this window. */ #endif