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Change default graph caching behavior to false

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efischer
2022-02-24 15:14:28 -06:00
parent d8ba42b801
commit a5238624f1
2 changed files with 3 additions and 7 deletions
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6
readme.md
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@@ -29,10 +29,6 @@ Unfortunately, it's a fairly new algorithm, and not yet implemented by the graph
So this program instead uses the Fibonacci heap-based algorithm of Fredman and Tarjan (1987), which has a worst-case So this program instead uses the Fibonacci heap-based algorithm of Fredman and Tarjan (1987), which has a worst-case
runtime of **O(n (n log(n) + m))**. The algorithm is implemented as described in Melhorn and Näher (1999). runtime of **O(n (n log(n) + m))**. The algorithm is implemented as described in Melhorn and Näher (1999).
The current version of the program uses a pairing heap instead of a Fibonacci heap for its priority queue,
which has lower theoretical efficiency but also lower complexity overhead, and is often equivalently performant
in practice.
## USAGE ## USAGE
### RUNNING THE PROGRAM ### RUNNING THE PROGRAM
@@ -91,7 +87,7 @@ or caching is turned off for that file type. The program checks whether it needs
filenames as entered by the user. On encountering a new filename, the program flushes its cache and reads in the new file. filenames as entered by the user. On encountering a new filename, the program flushes its cache and reads in the new file.
The program's caching behavior can be controlled in the Options menu. By default, caching for cell sample and The program's caching behavior can be controlled in the Options menu. By default, caching for cell sample and
sample plate files is OFF, and caching for graph/data files is ON. sample plate files is OFF, and caching for graph/data files is OFF.
#### Cell Sample Files #### Cell Sample Files
Cell Sample files consist of any number of distinct "T cells." Every cell contains Cell Sample files consist of any number of distinct "T cells." Every cell contains

4
src/main/java/BiGpairSEQ.java
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@@ -12,8 +12,8 @@ public class BiGpairSEQ {
private static String graphFilename = null; private static String graphFilename = null;
private static boolean cacheCells = false; private static boolean cacheCells = false;
private static boolean cachePlate = false; private static boolean cachePlate = false;
private static boolean cacheGraph = true; private static boolean cacheGraph = false;
private static String priorityQueueHeapType = "PAIRING"; private static String priorityQueueHeapType = "FIBONACCI";
public static void main(String[] args) { public static void main(String[] args) {
if (args.length == 0) { if (args.length == 0) {