From a5238624f111abb40c83bb62acca1dae19d3d5b5 Mon Sep 17 00:00:00 2001 From: efischer Date: Thu, 24 Feb 2022 15:14:28 -0600 Subject: [PATCH] Change default graph caching behavior to false --- readme.md | 6 +----- src/main/java/BiGpairSEQ.java | 4 ++-- 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/readme.md b/readme.md index 41accf0..be0133c 100644 --- a/readme.md +++ b/readme.md @@ -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 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 ### 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. 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 consist of any number of distinct "T cells." Every cell contains diff --git a/src/main/java/BiGpairSEQ.java b/src/main/java/BiGpairSEQ.java index 8448c13..af6577d 100644 --- a/src/main/java/BiGpairSEQ.java +++ b/src/main/java/BiGpairSEQ.java @@ -12,8 +12,8 @@ public class BiGpairSEQ { private static String graphFilename = null; private static boolean cacheCells = false; private static boolean cachePlate = false; - private static boolean cacheGraph = true; - private static String priorityQueueHeapType = "PAIRING"; + private static boolean cacheGraph = false; + private static String priorityQueueHeapType = "FIBONACCI"; public static void main(String[] args) { if (args.length == 0) {