keyword stringclasses 7
values | repo_name stringlengths 8 98 | file_path stringlengths 4 244 | file_extension stringclasses 29
values | file_size int64 0 84.1M | line_count int64 0 1.6M | content stringlengths 1 84.1M ⌀ | language stringclasses 14
values |
|---|---|---|---|---|---|---|---|
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/CVMappingRule_test.cpp | .cpp | 8,848 | 321 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Andreas Bertsch $
// ------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/FeatureFinderIdentificationAlgorithm_test.cpp | .cpp | 1,229 | 45 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Timo Sachsenberg $
// ----------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/MassDecomposer_test.cpp | .cpp | 1,801 | 67 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Stephan Aiche $
// -------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/ConsensusIDAlgorithmBest_test.cpp | .cpp | 5,877 | 184 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Marc Sturm, Andreas Bertsch, Sven Nahnsen, Hendrik Weisser $
// ... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/XQuestScores_test.cpp | .cpp | 10,952 | 156 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Eugen Netz $
// $Authors: Eugen Netz $
// -----------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/MobilityPeak1D_test.cpp | .cpp | 11,755 | 371 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/TextFile_test.cpp | .cpp | 5,515 | 162 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Marc Sturm, Chris Bielow $
// -------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/BayesianProteinInferenceAlgorithm_test.cpp | .cpp | 10,788 | 225 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// ---------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/ConversionHelper_test.cpp | .cpp | 3,666 | 140 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ---------------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/RibonucleotideDB_test.cpp | .cpp | 3,676 | 110 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// -------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/SpectraSTSimilarityScore_test.cpp | .cpp | 8,533 | 287 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ---------------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/SysInfo_test.cpp | .cpp | 2,153 | 67 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/KroenikFile_test.cpp | .cpp | 2,420 | 84 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// ------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/PeakGroup_test.cpp | .cpp | 10,575 | 393 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Jihyung Kim$
// $Authors: Jihyung Kim$
// -----------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/ProteaseDB_test.cpp | .cpp | 4,149 | 132 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Xiao Liang $
// $Authors: Xiao Liang, Chris Bielow $
// ---------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/ConsensusMapMergerAlgorithm_test.cpp | .cpp | 3,569 | 78 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// ---------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/MSSpectrum_test.cpp | .cpp | 48,747 | 1,565 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Marc Sturm $
// ------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/QTClusterFinder_test.cpp | .cpp | 6,152 | 229 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser $
// -------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/FLASHDeconvSpectrumFile_test.cpp | .cpp | 11,780 | 334 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeong $
// $Authors: Kyowon Jeong $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/SwathQC_test.cpp | .cpp | 5,138 | 192 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/SwathFile_test.cpp | .cpp | 8,133 | 225 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// ------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/PScore_test.cpp | .cpp | 6,691 | 211 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Timo Sachsenberg$
// ------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/Param_test.cpp | .cpp | 58,540 | 1,754 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm, Clemens Groepl $
// -------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/SpecArrayFile_test.cpp | .cpp | 2,389 | 84 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// ------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/FlagSet_test.cpp | .cpp | 8,154 | 341 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/TransitionTSVFile_test.cpp | .cpp | 12,391 | 362 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hannes Roest $
// $Authors: Hannes Roest $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/source/IDBoostGraph_test.cpp | .cpp | 9,656 | 206 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// ---------------------------------------... | C++ |
3D | OpenMS/OpenMS | src/tests/class_tests/openms/data/header_file.h | .h | 384 | 15 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// ----------------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | src/tests/coding/cpplint.py | .py | 262,075 | 6,902 | #!/usr/bin/env python
#
# Copyright (c) 2009 Google Inc. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list... | Python |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProduceQCFigures_tic.R | .R | 716 | 24 | ## This is an R script to produce the figures that are attached to the qcML format
library("ggplot2")
library(scales)
options(warn=-1) #suppress warnings
#options
options(digits=10)
file<-commandArgs(TRUE)[1]
post<-commandArgs(TRUE)[2]
knime.in<-read.csv(file=file,head=TRUE,sep="\t")
names(knime.in)<- c("RT", "TIC")
... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/mzTab2tsv_PSM.R | .R | 2,934 | 105 | ## This is an R script for the conversion of mzTab to a better readable tsv format.
# clear entire workspace
rm(list = ls())
input.file <- commandArgs(TRUE)[1]
output.file <- commandArgs(TRUE)[2]
# find start of the section
startSection <- function(file, section.identifier) {
data <- file(file, "r")
row = 0
wh... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProteomicsLFQ.R | .R | 9,013 | 227 | # example script to perform an MSstats analysis
Sys.setenv(LANG = "en")
library(MSstats)
library(dplyr)
library(tibble)
library(tidyr)
args = commandArgs(trailingOnly=TRUE)
MSstats_input <- args[1]
mzTab_input <- args[2]
mzTab_output <- args[3]
Sys.setenv(LANG = "en")
data <- read.csv(MSstats_input, sep=",", head... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/mzTab2tsv_PEP.R | .R | 2,234 | 82 | ## This is an R script for the conversion of mzTab to a better readable tsv format.
# clear entire workspace
rm(list = ls())
input.file <- commandArgs(TRUE)[1]
output.file <- commandArgs(TRUE)[2]
# find start of the section
startSection <- function(file, section.identifier) {
data <- file(file, "r")
row = 0
wh... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/InternalCalibration_Residuals.R | .R | 2,857 | 69 | ## add default CRAN mirror in case the user's config does not have one
options(repos = list(CRAN="http://cran.rstudio.com/"))
if (!require(ggplot2)) install.packages("ggplot2")
library("ggplot2")
if (!require(reshape2)) install.packages("reshape2")
library("reshape2")
if (!require(plyr)) install.packages("plyr")
libra... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProduceQCFigures_idmap.R | .R | 1,292 | 40 | ## This is an R script to produce the figures that are attached to the qcML format
library("ggplot2")
library(scales)
options(warn=-1) #suppress warnings
#options
options(digits=10)
file_p<-commandArgs(TRUE)[1]
file_id<-commandArgs(TRUE)[2]
post<-commandArgs(TRUE)[3]
png(post)
#file_p<-"/tmp/TOPPAS_out/024-QCExtracto... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProduceQCFigures_setid.R | .R | 510 | 28 | ## This is an R script to produce the figures that are attached to the qcML format
#options
options(digits=10)
file<-commandArgs(TRUE)[1]
post<-commandArgs(TRUE)[2]
######
###setid
######
a<-read.table(file=file, header=TRUE, sep="\t", na.strings="NA", dec=".", strip.white=TRUE)
#####################################... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/Rscript_generic_example.R | .R | 4,366 | 89 | ## This is an exemplary R-Script which can be used in conjunction with TOPP:GenericWrapper (of type: RScript_General)
## In this mode, the GenericWrapper provides four 'in' and six 'out' slots (four single files, two lists), which the user can couple to in/out files as desired
## Slots can be empty, and depending on wh... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ropenms.R | .R | 3,163 | 107 | ################### OpenMS in R ###################
#### Some simple scripts how to use OpenMS in R ####
### if not installed:
### - install pyopenms (https://pyopenms.readthedocs.io/en/latest/installation.html)
### make sure R is using the same python environment as your pyopenms installation
### eg. reticulate:... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProduceQCFigures_inj.R | .R | 954 | 28 | #install.packages("scales")
#install.packages("ggplot2")
## This is an R script to produce the figures that are attached to the qcML format
library("ggplot2")
library(scales)
options(warn=-1) #suppress warnings
file<-commandArgs(TRUE)[1]
post<-commandArgs(TRUE)[2]
#file<-"/tmp/2015-10-28_171407_Cetirizin_2990_1/TOPPA... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/plot_trafo.R | .R | 3,936 | 127 | #!/usr/bin/env Rscript
library(XML)
## utility function:
"%within%" <- function(x, range) {
(x >= range[1]) & (x <= range[2])
}
## read pairs of data points from trafoXML file:
read.pairs <- function(filename) {
pairs <- matrix(nrow=0, ncol=2)
pair.handler <- function(name, attrs) {
pairs <<- rbind(pairs, ... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProduceQCFigures_acc.R | .R | 977 | 29 | library("ggplot2")
library(scales)
options(warn=-1) #suppress warnings
#options
options(digits=10)
file<-commandArgs(TRUE)[1]
post<-commandArgs(TRUE)[2]
#file<-"/tmp/TOPPAS_out/023-QCExtractor-out_csv/old1.csv"
knime.in<-read.csv(file=file,head=TRUE,sep="\t")
names(knime.in)<- c("RT", "MZ", "Score", "PeptideSequence"... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/InternalCalibration_Models.R | .R | 1,511 | 46 | ## add default CRAN mirror in case the user's config does not have one
options(repos = list(CRAN="http://cran.rstudio.com/"))
if (!require(ggplot2)) install.packages("ggplot2")
library("ggplot2")
if (!require(reshape2)) install.packages("reshape2")
library("reshape2")
file.table.in = commandArgs(TRUE)[1] ## file.tabl... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/ProduceQCFigures_rt_acc.R | .R | 904 | 32 | library("ggplot2")
library(scales)
options(warn=-1) #suppress warnings
#options
options(digits=10)
file<-commandArgs(TRUE)[1]
post<-commandArgs(TRUE)[2]
#file<-"/tmp/TOPPAS_out/023-QCExtractor-out_csv/old1.csv"
knime.in<-read.csv(file=file,head=TRUE,sep="\t")
names(knime.in)<- c("RT", "MZ", "Score", "PeptideSequence"... | R |
3D | OpenMS/OpenMS | share/OpenMS/SCRIPTS/mzTab2tsv_PRT.R | .R | 3,771 | 120 | ## This is an R script for the conversion of mzTab to a better readable tsv format.
# clear entire workspace
rm(list = ls())
input.file <- commandArgs(TRUE)[1]
output.file <- commandArgs(TRUE)[2]
# find start of the section
startSection <- function(file, section.identifier) {
data <- file(file, "r")
row = 0
wh... | R |
3D | OpenMS/OpenMS | share/OpenMS/examples/external_code/Main.cpp | .cpp | 560 | 24 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/CHEMISTRY/AASequence.h>
#include "ExampleLibraryFile.h"
using namespace OpenMS;
using namespace OpenMSExternal;
int main(int argc, ... | C++ |
3D | OpenMS/OpenMS | share/OpenMS/examples/external_code/ExampleLibraryFile.h | .h | 541 | 24 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | Unknown |
3D | OpenMS/OpenMS | share/OpenMS/examples/external_code/ExampleLibraryFile.cpp | .cpp | 579 | 21 | // Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// -------------------------------------------------... | C++ |
3D | OpenMS/OpenMS | cmake/Modules/Findcppcheck.cpp | .cpp | 266 | 18 | /**
* \file Findcppcheck.cpp
* \brief Dummy C++ source file used by CMake module Findcppcheck.cmake
*
* \author
* Ryan Pavlik, 2009-2010
* <rpavlik@iastate.edu>
* http://academic.cleardefinition.com/
*
*/
int main(int argc, char* argv[]) {
return 0;
}
| C++ |
3D | OpenMS/OpenMS | cmake/MacOSX/fixdmg.sh | .sh | 2,848 | 105 | #!/bin/bash
# 2012/01/06 - Stephan Aiche
# based on http://stackoverflow.com/questions/96882/how-do-i-create-a-nice-looking-dmg-for-mac-os-x-using-command-line-tools
# bash script to further customize the OpenMS dmg
# if the apple script part fails with "timed out" error try
# defaults write com.apple.Finder AppleSho... | Shell |
3D | OpenMS/OpenMS | cmake/MacOSX/notarize.sh | .sh | 5,847 | 176 | #!/bin/bash
# macOS notarization script using notarytool (requires Xcode 13+ / macOS 11.3+)
# altool was deprecated and unsupported after Fall 2023.
#
# Usage: notarize.sh <bundle_pkg> <bundle_id> <apple_id> <password_env_var> [log_folder]
#
# Arguments:
# bundle_pkg - The package to notarize (.dmg, .pkg, .zip,... | Shell |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/pluginapi.c | .c | 7,045 | 295 | #include <windows.h>
#include "pluginapi.h"
#ifdef _countof
#define COUNTOF _countof
#else
#define COUNTOF(a) (sizeof(a)/sizeof(a[0]))
#endif
unsigned int g_stringsize;
stack_t **g_stacktop;
TCHAR *g_variables;
// utility functions (not required but often useful)
int NSISCALL popstring(TCHAR *str)
{
stack_t *th;... | C |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/afxres.h | .h | 48 | 3 | #include <windows.h>
#define IDC_STATIC (-1)
| Unknown |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/resource.h | .h | 1,860 | 48 | //{{NO_DEPENDENCIES}}
// Microsoft Developer Studio generated include file.
// Used by inetc.rc
//
#define IDC_SLOGIN 8
#define IDC_PROGRESS 10
#define IDC_SUBTEXT 11
#define IDC_SPWD 11
#define IDC_ICON1 12
#define... | Unknown |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/nsis_tchar.h | .h | 5,028 | 230 | /*
* nsis_tchar.h
*
* This file is a part of NSIS.
*
* Copyright (C) 1999-2013 Nullsoft and Contributors
*
* This software is provided 'as-is', without any express or implied
* warranty.
*
* For Unicode support by Jim Park -- 08/30/2007
*/
// Jim Park: Only those we use are listed here.
#pragma once
#i... | Unknown |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/api.h | .h | 2,760 | 84 | /*
* apih
*
* This file is a part of NSIS.
*
* Copyright (C) 1999-2013 Nullsoft and Contributors
*
* Licensed under the zlib/libpng license (the "License");
* you may not use this file except in compliance with the License.
*
* Licence details can be found in the file COPYING.
*
* This software is prov... | Unknown |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/crt.cpp | .cpp | 2,167 | 106 | #include <Windows.h>
#if defined(_MSC_VER) && _MSC_VER+0 >= 1400
#if defined(_MSC_FULL_VER) && _MSC_FULL_VER+0 >= 140050727
#include <intrin.h>
#else
EXTERN_C void __stosb(BYTE*,BYTE,size_t);
#endif
#pragma intrinsic(__stosb)
#define CRTINTRINSIC_memset(p,c,s) __stosb((BYTE*)(p),(BYTE)(c),(s))
#endif
extern "C" void*... | C++ |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/inetc.cpp | .cpp | 56,098 | 1,732 | /*******************************************************
* FILE NAME: inetc.cpp
*
* Copyright (c) 2004-2015 Takhir Bedertdinov and NSIS contributors
*
* PURPOSE:
* ftp/http file download plug-in
* on the base of MS Inet API
* 4 GB limit (http support?)
*
* CHANGE HISTORY
*
* Author Date Modificatio... | C++ |
3D | OpenMS/OpenMS | cmake/Windows/Contrib/Inetc/pluginapi.h | .h | 3,076 | 105 | #ifndef ___NSIS_PLUGIN__H___
#define ___NSIS_PLUGIN__H___
#ifdef __cplusplus
extern "C" {
#endif
#include "api.h"
#include "nsis_tchar.h"
#ifndef NSISCALL
# define NSISCALL __stdcall
#endif
#define EXDLL_INIT() { \
g_stringsize=string_size; \
g_stacktop=stacktop; \
g_variabl... | Unknown |
3D | HengCai-NJU/3D2DCT | code/test_util.py | .py | 6,663 | 170 | import h5py
import math
import nibabel as nib
import numpy as np
from medpy import metric
import torch
import torch.nn.functional as F
from tqdm import tqdm
from utils import ramps, losses
def test_all_case(net1, image_list, num_classes, patch_size=(112, 112, 80), stride_xy=18, stride_z=4, save_result=True, test_save... | Python |
3D | HengCai-NJU/3D2DCT | code/test.py | .py | 3,558 | 80 | import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--root_path', type=str, default='../data/2018LA_Seg_Training Set/', help='Name of Experiment')
parser.add_argument('--model', type=str, default='UAMT_unlabel', help='model_name')
parser.add_argument('--gpu', type=str, default='4', help='GPU to us... | Python |
3D | HengCai-NJU/3D2DCT | code/run_2d3d.sh | .sh | 292 | 3 | python train_3d2d.py --dataset mmwhs --max_iteration 6000 --exp whs0 --consistency 0.1 --slice_strategy 12 --split 'train0' --quality_bar 0.98 --ht 0.9 --st 0.7
python test.py --gpu 0 --dataset mmwhs --model whs0 --min_iteration 100 --max_iteration 6000 --iteration_step 100 --split 'valid0'
| Shell |
3D | HengCai-NJU/3D2DCT | code/train_3d2d.py | .py | 12,943 | 307 | import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--root_path', type=str, default='../data/2018LA_Seg_Training Set/', help='Name of Experiment')
parser.add_argument('--exp', type=str, default='MT31', help='model_name')
parser.add_argument('--dataset', type=str, default='effe', help='dataset to use... | Python |
3D | HengCai-NJU/3D2DCT | code/utils/losses.py | .py | 7,196 | 210 | import torch
from torch.nn import functional as F
import numpy as np
import torch.nn as nn
import torch
from torch.autograd import Variable
def multi_dice_loss_weight(outputs_soft1,twod1,twodmask,classnum=7):
loss_seg_dice=0
for i in range(1,classnum+1):
loss_seg_dice += dice_loss_weight(outputs_soft1[... | Python |
3D | HengCai-NJU/3D2DCT | code/utils/util.py | .py | 3,449 | 120 | # Copyright (c) 2017-present, Facebook, Inc.
# All rights reserved.
#
# This source code is licensed under the license found in the
# LICENSE file in the root directory of this source tree.
#
import os
import pickle
import numpy as np
import torch
from torch.utils.data.sampler import Sampler
import networks
def load... | Python |
3D | HengCai-NJU/3D2DCT | code/utils/ramps.py | .py | 1,319 | 42 | # Copyright (c) 2018, Curious AI Ltd. All rights reserved.
#
# This work is licensed under the Creative Commons Attribution-NonCommercial
# 4.0 International License. To view a copy of this license, visit
# http://creativecommons.org/licenses/by-nc/4.0/ or send a letter to
# Creative Commons, PO Box 1866, Mountain View... | Python |
3D | HengCai-NJU/3D2DCT | code/networks/unetr.py | .py | 8,715 | 223 | # Copyright 2020 - 2021 MONAI Consortium
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# http://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agreed to in wri... | Python |
3D | HengCai-NJU/3D2DCT | code/networks/unet.py | .py | 3,366 | 106 | import torch
import torch.nn as nn
import torch.nn.functional as F
class DoubleConv(nn.Module):
"""(convolution => [BN] => ReLU) * 2"""
def __init__(self, in_channels, out_channels):
super().__init__()
self.double_conv = nn.Sequential(
nn.Conv2d(in_channels, out_channels, kernel_s... | Python |
3D | HengCai-NJU/3D2DCT | code/networks/crn.py | .py | 9,450 | 259 | import torch
from torch import nn
import torch.nn.functional as F
from torch.utils.data import DataLoader
class ConvBlock(nn.Module):
def __init__(self, n_stages, n_filters_in, n_filters_out, normalization='none'):
super(ConvBlock, self).__init__()
ops = []
for i in range(n_stages):
... | Python |
3D | HengCai-NJU/3D2DCT | code/networks/vnet.py | .py | 13,105 | 352 | import torch
from torch import nn
import torch.nn.functional as F
class ConvBlock(nn.Module):
def __init__(self, n_stages, n_filters_in, n_filters_out, normalization='none'):
super(ConvBlock, self).__init__()
ops = []
for i in range(n_stages):
if i==0:
input_cha... | Python |
3D | HengCai-NJU/3D2DCT | code/dataloaders/utils.py | .py | 6,729 | 215 | import os
import torch
import numpy as np
import torch.nn as nn
import matplotlib.pyplot as plt
from skimage import measure
import scipy.ndimage as nd
def recursive_glob(rootdir='.', suffix=''):
"""Performs recursive glob with given suffix and rootdir
:param rootdir is the root directory
:param su... | Python |
3D | HengCai-NJU/3D2DCT | code/dataloaders/mmwhs_preprocessing.py | .py | 11,368 | 288 | import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
import SimpleITK as sitk
import os
from skimage import morphology, exposure
import scipy
from scipy import ndimage
import h5py
import torch
v = "v1"
class CFG:
do_windowing = True
window_width = 2000 # -160
window_center = 350 # 24... | Python |
3D | HengCai-NJU/3D2DCT | code/dataloaders/mmwhs.py | .py | 15,737 | 389 | import os
import torch
import numpy as np
from glob import glob
from torch.utils.data import Dataset
import h5py
import itertools
from torch.utils.data.sampler import Sampler
from torchvision.transforms import Compose
import pdb
class MMWHS(Dataset):
# base_dir="../data/processed_v1_h5"
def __init__(self, bas... | Python |
3D | HengCai-NJU/3D2DCT | code/dataloaders/make_dataset.py | .py | 3,951 | 116 | # -*- coding: utf-8 -*-
import h5py, os
import torch, cv2
import numpy as np
from torch.utils.data import Dataset, DataLoader
import os
from pathlib import Path
import torch
import numpy as np
from glob import glob
from torch.utils.data import Dataset
import h5py
import itertools
from torch.utils.data.sampler import S... | Python |
3D | theaidenlab/AGWG-merge | run-asm-pipeline.sh | .sh | 42,279 | 822 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2018 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... | Shell |
3D | theaidenlab/AGWG-merge | JBAT_demo_instructions.md | .md | 3,397 | 28 | # Demo Instructions for the Juicebox Assembly Tools Module
### Overview
Assembly Tools [[1]](https://www.biorxiv.org/content/early/2018/01/28/254797) is a new module in the Juicebox desktop application [[2]](https://www.cell.com/cell-systems/abstract/S2405-4712(15)00054-X) that extends the Juicebox interface for Hi-C ... | Markdown |
3D | theaidenlab/AGWG-merge | run-asm-pipeline-post-review.sh | .sh | 9,382 | 226 | #!/bin/bash
##########
#The MIT License (MIT)
#
# Copyright (c) 2018 Aiden Lab
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
#... | Shell |
3D | theaidenlab/AGWG-merge | lift/lift-edit-asm-annotations-to-original-input-annotations.sh | .sh | 3,181 | 72 | #!/bin/bash
#### Description: Does a series of liftovers to map annotations from an edited assembly to original scaffold/contig input.
#### Usage: lift-edit-asm-annotations-to-original-input-annotations.sh <path_to_original_cprops> <path_to_edited_cprops> <path_to_edited_asm> <path_to_edited_annotation_file>
#### Inpu... | Shell |
3D | theaidenlab/AGWG-merge | lift/lift-input-mnd-to-asm-mnd.sh | .sh | 1,155 | 40 | #!/bin/bash
## Handle options
scale=1
while getopts "s:" opt; do
case $opt in
s) re='^[0-9]+$'
if [[ $OPTARG =~ $re ]]; then
scale=$OPTARG
else
echo ":( Wrong syntax for scale quality. Using the default value ${scale}" >&2
fi
;;
*) echo "$USAGE" >&2
... | Shell |
3D | theaidenlab/AGWG-merge | visualize/juicebox_tools.sh | .sh | 84 | 4 | #!/bin/sh
set -e
java -Xms49152m -Xmx49152m -jar `dirname $0`/juicebox_tools.jar $*
| Shell |
3D | theaidenlab/AGWG-merge | visualize/run-assembly-visualizer.sh | .sh | 9,191 | 205 | #!/bin/bash
#### Description: Script to visualize assemblies: a wrapper around remap-input-mnd-to-asm-mnd.awk and Juicebox pre.
#### Usage: bash ./run-assembly-visualizer.sh [options] <path_to_input_assembly_file> <path_to_input-mnd-file>.
#### Input: assembly file, mnd file.
#### Output: hic file, scaffold and super-... | Shell |
3D | theaidenlab/AGWG-merge | visualize/run-asm-visualizer.sh | .sh | 8,648 | 213 | #!/bin/bash
#### Description: Script to visualize draft assemblies: a wrapper around remap-contig-mnd-to-asm-mnd.awk and Juicebox pre. Also dumps 2D annotation files.
#### Usage: bash ./run-asm-visualizer.sh [options] path_to_cprops path_to_asm <contig-mnd-file>.
#### Input: cprops file, asm file, mnd file.
#### Outpu... | Shell |
3D | theaidenlab/AGWG-merge | polish/run-asm-polisher.sh | .sh | 12,416 | 232 | #!/bin/bash
#### Description: Wrapper script to polish any given assembly. Polish is a process in which a mismatch detector is run and pieces of an assembly between mismatches are treated as an input. Polish cannot insert pieces unlike a typical iterative assembly step but it can avoid some pitfalls caused by very sma... | Shell |
3D | theaidenlab/AGWG-merge | scaffold/run-tiger-scaffolder.sh | .sh | 10,104 | 228 | #!/bin/bash
## TIGer scaffolder wrapper script
## Written by Olga Dudchenko and Sanjit Batra
USAGE="
*****************************************************
This is a wrapper for a Hi-C Tail Iterative Greedy genome assembly (TIGer) algorithm, version date: Dec 7, 2016.
Usage: ./run-tiger-scaffolder.sh [-h] [-s minimal_... | Shell |
3D | theaidenlab/AGWG-merge | scaffold/run-liger-scaffolder.sh | .sh | 10,086 | 228 | #!/bin/bash
## LIGer scaffolder wrapper script
## Written by Olga Dudchenko and Sanjit Batra
USAGE="
*****************************************************
This is a wrapper for a Hi-C Limitless Iterative Greedy genome assembly (LIGer) algorithm, version date: Dec 7, 2016.
Usage: ./run-liger-scaffolder.sh [-h] [-s min... | Shell |
3D | theaidenlab/AGWG-merge | merge/align-nearby-sequences-and-filter-overlaps.sh | .sh | 5,679 | 152 | #!/bin/bash
## Part of the merge segment of the diploid pipeline.
## Requires LASTZ in path! Requires PARALLEL in path!
## TODO: Add scaling for annotations? Or fully switch to bpe? Add warning!!
## Written by: Olga Dudchenko
USAGE="
*****************************
./run-pairwise-alignment.sh [options] <path_to_cprops... | Shell |
3D | theaidenlab/AGWG-merge | merge/run-asm-merger.sh | .sh | 4,202 | 104 | #!/bin/bash
## Wrapper script to do the merging block in the diploid pipeline workflow to merge assembly errors due to undercollapsed heterozygosity.
## Requires LASTZ aligner in path
## The idea is that sequence similarities identified via LASTZ alignments need to be long enough and with high enough identity score to... | Shell |
3D | theaidenlab/AGWG-merge | merge/merge-tiled-asm.sh | .sh | 7,181 | 196 | #!/bin/bash
## Wrapper script to merge contigs inside clusters as indicated by the annotated asm file.
## Requires LASTZ
## Written by: OD
USAGE="
*****************************************************
USAGE: merge-tiled-asm.sh -a <tiled-annotations> <path-to-cprops> <path-to-annotated-asm> <path-to-fasta-split-folder... | Shell |
3D | theaidenlab/AGWG-merge | merge/tile-assembly-based-on-overlaps.sh | .sh | 1,166 | 21 | #!/bin/bash
## Sandboxing part of the merge pipeline that performs connected component analysis and tiling based on pairwise alignment data
## USAGE: bash ./merge/tile-assembly-based-on-overlaps.sh <cprops> <asm> <overlaps-from-alignment-2D-annotation-file>
## Input: cprops, asm, overlaps 2D annotation files
## Output:... | Shell |
3D | theaidenlab/AGWG-merge | split_chrom_aware/run-asm-splitter.sh | .sh | 6,070 | 164 | #!/bin/bash
#### Description: Wrapper script to split megascaffold into individual chromosome-length scaffolds.
#### Written by: Sanjit Batra - sanjit.batra@bcm.edu. Version date 12/19/2016.
pipeline=`cd "$( dirname $0)" && cd .. && pwd`
USAGE="
*****************************************************
This is a wrapper... | Shell |
3D | theaidenlab/AGWG-merge | split_chrom_aware/recursive-chromosome-splitter.py | .py | 6,047 | 233 | import numpy as np
#import matplotlib.pyplot as plt
import sys
from scipy.sparse import *
import math
# #First we define a function that takes in a matrix and computes the point where
# #S(i) is minimized, splits the matrix at that position and makes two recursive
# #calls to itself on both submatrices
# #This funct... | Python |
3D | theaidenlab/AGWG-merge | split_chrom_aware/mnd-dump.sh | .sh | 1,601 | 52 | #!/bin/bash
#### Description: Script to dump matrix data from mnd.
#### Written by: Olga Dudchenko - olga.dudchenko@bcm.edu.
#TODO: Add usage
## Set defaults
mapq=1
## Handle options
while getopts "q:" opt; do
case $opt in
q) re='^[0-9]+$'
if [[ $OPTARG =~ $re ]]; then
mapq=$OPTARG
... | Shell |
3D | theaidenlab/AGWG-merge | seal/seal-asm.sh | .sh | 1,837 | 57 | #!/bin/bash
## Wrapper script to analyze the assembly and place fragments from among the small scaffolds back into the assembly
## NOTE: now is run after splitting but for diploid pipeline could be run for for tiled assembly
## NOTE: Relies on standard annotations :::fragment_ and :::debris!
## NOTE: Probably should be... | Shell |
3D | theaidenlab/AGWG-merge | finalize/construct-fasta-from-asm.sh | .sh | 1,575 | 71 | #!/bin/bash
## Wrapper script to generate a fasta from internal datatypes: cprops and asm
## Input: internally consistent cprops, asm and fasta
## TODO: parallelize for speed
## Prints into STDOUT
USAGE="
*****************************************************
USAGE: construct-fasta-from-asm.sh <path-to-cprops> <path-to... | Shell |
3D | theaidenlab/AGWG-merge | finalize/remove-N-overhangs-from-asm.sh | .sh | 2,698 | 64 | #!/bin/bash
#### Description: Script to create an equivalent to a given assembly output (cprops asm fasta) but without N overhangs in the input contigs/scaffolds.
#### Usage: bash remove-N-overhangs-from-asm.sh <(modified) input cprops> <(modified) input asm> <(modified) input-fasta-file>
#### Input: cprops, asm, fast... | Shell |
3D | theaidenlab/AGWG-merge | finalize/finalize-output-w-stats.sh | .sh | 7,826 | 183 | #!/bin/bash
## Wrapper script to generate final fasta as well as various component fastas (unprompted)
## Adds 500bp gaps between assembly components scaffolded via Hi-C
## TODO: make gap length a parameter
## Written by OD
pipeline=`cd "$( dirname $0)" && cd .. && pwd`
## unprompted
gap_size=500
#subtiny_size=100... | Shell |
3D | theaidenlab/AGWG-merge | finalize/finalize-output.sh | .sh | 7,681 | 182 | #!/bin/bash
## Wrapper script to generate final fasta as well as various component fastas (unprompted)
## Adds 500bp gaps between assembly components scaffolded via Hi-C
## TODO: make gap length a parameter
## Written by OD
pipeline=`cd "$( dirname $0)" && cd .. && pwd`
## unprompted
gap_size=500
subtiny_size=1000
#... | Shell |
3D | theaidenlab/AGWG-merge | edit/reconstruct-edits-from-cprops.sh | .sh | 550 | 9 | #!/bin/bash
pipeline=`cd "$( dirname $0)" && cd .. && pwd`
orig_cprops=$1
current_cprops=$2
awk 'BEGIN{OFS="\t"; print "chr1", "x1", "x2", "chr2", "y1", "y2", "color", "id", "X1", "X2", "Y1", "Y2"}$1~/:::debris/{print $1, 0, $3, $1, 0, $3, "0,0,0", "debris", 0, $3, 0, $3}' ${current_cprops} | awk -f ${pipeline}/lift... | Shell |
3D | theaidenlab/AGWG-merge | edit/edit-asm-according-to-new-cprops.sh | .sh | 1,396 | 14 | #!/bin/bash
# Script to make an equivalent of the old asm file in terms of new cprops if contigs/scaffolds were edited
# Written by OD
new_cprops=$1
old_cprops=$2
old_asm=$3
pipeline=`cd "$( dirname $0)" && cd .. && pwd`
## TODO: SAFEGUARDS
((awk 'BEGIN{OFS="\t"; print "chr1", "x1", "x2", "chr2", "y1", "y2", "color... | Shell |
3D | theaidenlab/AGWG-merge | edit/run-coverage-analyzer.sh | .sh | 3,975 | 94 | #!/bin/bash
#### Description: Wrapper script to annotate likely repeats. Analyzes normalization vector at a specified resolution (default 25kb).
#### Usage: run-mismatch-detector.sh -w <bin_size> <path-to-hic-file>
#### Dependencies: Juicebox_tools
#### Input: Juicebox hic file.
#### Output: "Wide" bed file highlightin... | Shell |
3D | theaidenlab/AGWG-merge | edit/edit-mnd-according-to-new-cprops.sh | .sh | 919 | 22 | #!/bin/bash
# Wrapper around gnu parallel for editing the mnd in case all of apply-edits is not needed. Not employed at the moment.
# Written by: OD
## GNU Parallel Dependency
parallel="false"
if hash parallel 2>/dev/null; then
ver=`parallel --version | awk 'NR==1{print \$3}'`
[ $ver -ge 20150322 ] && ... | Shell |
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