Windows: A convenient Windows OS installer executable for MORTAR is available
-(click here to
+(click here to
automatically download the installer .exe of the latest version). Download the installer
executable, start, and follow the instructions to install MORTAR. Note that the installation includes a full
Java Runtime Environment (JRE). After installation, create a shortcut to an appropriate MORTAR start batch file on your
Windows desktop. E.g. for MORTAR to use up to 4 gigabyte of RAM, copy a shortcut to batch file "MORTAR.bat" which is
-located in the MORTAR program folder (default "C:\Program Files\MORTAR\MORTARv1.1.1.0\bin" or the path specified at
+located in the MORTAR program folder (default "C:\Program Files\MORTAR\MORTARv1.2.0.0\bin" or the path specified at
installation). To start MORTAR, double-click the created shortcut. MORTAR can be uninstalled by the provided
Uninstall.exe executable in the MORTAR program folder or standard Windows functions.
@@ -87,21 +87,21 @@ with your chosen initially allocated memory (-Xms) and maximum value (-Xmx) acco
described below. As an alternative way, they should also work on Windows.
Linux and macOS: Every release has the executable Java ARchive (JAR) "MORTAR-fat-1.1.1.0.jar" +
Linux and macOS: Every release has the executable Java ARchive (JAR) "MORTAR-fat-1.2.0.0.jar" attached, which contains the packaged MORTAR code together with all dependencies -(click here to +(click here to automatically download the JAR of the latest version). To run MORTAR (with up to 4 GB of RAM available, e.g.), execute the JAR from the command-line using
-java -jar -Xms512m -Xmx4g [path to]MORTAR-fat-1.1.1.0.jar
java -jar -Xms512m -Xmx4g [path to]MORTAR-fat-1.2.0.0.jar
Please note that MORTAR only supports x64 (on all three platforms) and AArch64 (on macOS and Linux) architectures in general. -For the latter, a special "fat JAR" named "MORTAR-fat-aarch64-1.1.1.0.jar" is available from the distributions attached to the releases and must be used -(click here to +For the latter, a special "fat JAR" named "MORTAR-fat-aarch64-1.2.0.0.jar" is available from the distributions attached to the releases and must be used +(click here to automatically download the AArch64 JAR of the latest version).
Also note that using the Windows Subsystem for Linux (WSL) is not recommended, since a lot of additional configurations have to be made there to run Java GUI applications. @@ -135,7 +135,7 @@ into it (i.e. sub-folders of "AdoptOpenJDK\jdk-21.0.1_12_jre\" need to be "bin", * LibrePDF OpenPDF version 1.3.26 * [OpenPDF GitHub repository](https://github.com/LibrePDF/OpenPDF) * License: GNU Lesser General Public License 2.1 -* Spotless version 6.23 +* Spotless version 6.25 * [Spotless GitHub repository](https://github.com/diffplug/spotless) * License: Apache-2.0 license diff --git a/Tutorial/MORTAR_Tutorial.pdf b/Tutorial/MORTAR_Tutorial.pdf index 089e7e6d..c5405f6d 100644 Binary files a/Tutorial/MORTAR_Tutorial.pdf and b/Tutorial/MORTAR_Tutorial.pdf differ diff --git a/build.gradle b/build.gradle index 146f361b..a23e5d50 100644 --- a/build.gradle +++ b/build.gradle @@ -7,7 +7,7 @@ plugins { } group 'de.unijena.cheminf' -version '1.1.1.0' +version '1.2.0.0' sourceCompatibility = 1.21 diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar index 87b738cb..d64cd491 100644 Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ diff --git a/gradle/wrapper/gradle-wrapper.properties b/gradle/wrapper/gradle-wrapper.properties index a5952066..1af9e093 100644 --- a/gradle/wrapper/gradle-wrapper.properties +++ b/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,7 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists distributionUrl=https\://services.gradle.org/distributions/gradle-8.5-bin.zip +networkTimeout=10000 +validateDistributionUrl=true zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/gradlew b/gradlew index af6708ff..1aa94a42 100644 --- a/gradlew +++ b/gradlew @@ -1,78 +1,127 @@ -#!/usr/bin/env sh +#!/bin/sh + +# +# Copyright © 2015-2021 the original authors. +# +# 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 +# +# https://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +# ############################################################################## -## -## Gradle start up script for UN*X -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null - -APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` -# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. -DEFAULT_JVM_OPTS='"-Xmx64m"' +# This is normally unused +# shellcheck disable=SC2034 +APP_BASE_NAME=${0##*/} +# Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036) +APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit # Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD="maximum" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar + # Determine the Java command to use to start the JVM. if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -81,92 +130,120 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" - which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. + JAVACMD=java + if ! command -v java >/dev/null 2>&1 + then + die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the location of your Java installation." + fi fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked. + # shellcheck disable=SC2039,SC3045 + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. + +# For Cygwin or MSYS, switch paths to Windows format before running java +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) -# For Cygwin, switch paths to Windows format before running java -if $cygwin ; then - APP_HOME=`cygpath --path --mixed "$APP_HOME"` - CLASSPATH=`cygpath --path --mixed "$CLASSPATH"` - JAVACMD=`cygpath --unix "$JAVACMD"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=$((i+1)) + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg done - case $i in - (0) set -- ;; - (1) set -- "$args0" ;; - (2) set -- "$args0" "$args1" ;; - (3) set -- "$args0" "$args1" "$args2" ;; - (4) set -- "$args0" "$args1" "$args2" "$args3" ;; - (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;; - (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;; - (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;; - (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;; - (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=$(save "$@") - -# Collect all arguments for the java command, following the shell quoting and substitution rules -eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS" -# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong -if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then - cd "$(dirname "$0")" +# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. +DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' + +# Collect all arguments for the java command: +# * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments, +# and any embedded shellness will be escaped. +# * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be +# treated as '${Hostname}' itself on the command line. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Stop when "xargs" is not available. +if ! command -v xargs >/dev/null 2>&1 +then + die "xargs is not available" fi +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# + +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' + exec "$JAVACMD" "$@" diff --git a/gradlew.bat b/gradlew.bat index 6d57edc7..93e3f59f 100644 --- a/gradlew.bat +++ b/gradlew.bat @@ -1,4 +1,20 @@ -@if "%DEBUG%" == "" @echo off +@rem +@rem Copyright 2015 the original author or authors. +@rem +@rem Licensed under the Apache License, Version 2.0 (the "License"); +@rem you may not use this file except in compliance with the License. +@rem You may obtain a copy of the License at +@rem +@rem https://www.apache.org/licenses/LICENSE-2.0 +@rem +@rem Unless required by applicable law or agreed to in writing, software +@rem distributed under the License is distributed on an "AS IS" BASIS, +@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +@rem See the License for the specific language governing permissions and +@rem limitations under the License. +@rem + +@if "%DEBUG%"=="" @echo off @rem ########################################################################## @rem @rem Gradle startup script for Windows @@ -9,19 +25,23 @@ if "%OS%"=="Windows_NT" setlocal set DIRNAME=%~dp0 -if "%DIRNAME%" == "" set DIRNAME=. +if "%DIRNAME%"=="" set DIRNAME=. +@rem This is normally unused set APP_BASE_NAME=%~n0 set APP_HOME=%DIRNAME% +@rem Resolve any "." and ".." in APP_HOME to make it shorter. +for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi + @rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. -set DEFAULT_JVM_OPTS="-Xmx64m" +set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m" @rem Find java.exe if defined JAVA_HOME goto findJavaFromJavaHome set JAVA_EXE=java.exe %JAVA_EXE% -version >NUL 2>&1 -if "%ERRORLEVEL%" == "0" goto init +if %ERRORLEVEL% equ 0 goto execute echo. echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. @@ -35,7 +55,7 @@ goto fail set JAVA_HOME=%JAVA_HOME:"=% set JAVA_EXE=%JAVA_HOME%/bin/java.exe -if exist "%JAVA_EXE%" goto init +if exist "%JAVA_EXE%" goto execute echo. echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% @@ -45,38 +65,26 @@ echo location of your Java installation. goto fail -:init -@rem Get command-line arguments, handling Windows variants - -if not "%OS%" == "Windows_NT" goto win9xME_args - -:win9xME_args -@rem Slurp the command line arguments. -set CMD_LINE_ARGS= -set _SKIP=2 - -:win9xME_args_slurp -if "x%~1" == "x" goto execute - -set CMD_LINE_ARGS=%* - :execute @rem Setup the command line set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar + @rem Execute Gradle -"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %CMD_LINE_ARGS% +"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %* :end @rem End local scope for the variables with windows NT shell -if "%ERRORLEVEL%"=="0" goto mainEnd +if %ERRORLEVEL% equ 0 goto mainEnd :fail rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of rem the _cmd.exe /c_ return code! -if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1 -exit /b 1 +set EXIT_CODE=%ERRORLEVEL% +if %EXIT_CODE% equ 0 set EXIT_CODE=1 +if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE% +exit /b %EXIT_CODE% :mainEnd if "%OS%"=="Windows_NT" endlocal diff --git a/settings.gradle b/settings.gradle index 0a398925..24ee57a2 100644 --- a/settings.gradle +++ b/settings.gradle @@ -1,2 +1 @@ -rootProject.name = 'MORTAR' - +rootProject.name = 'MORTAR' \ No newline at end of file diff --git a/src/main/java/de/unijena/cheminf/mortar/controller/MainViewController.java b/src/main/java/de/unijena/cheminf/mortar/controller/MainViewController.java index 82a1713f..3a206a87 100644 --- a/src/main/java/de/unijena/cheminf/mortar/controller/MainViewController.java +++ b/src/main/java/de/unijena/cheminf/mortar/controller/MainViewController.java @@ -96,6 +96,7 @@ import java.util.concurrent.ExecutionException; import java.util.logging.Level; import java.util.logging.Logger; +import java.util.stream.Collectors; /** * MainViewController controls {@link MainView}. @@ -1279,7 +1280,8 @@ private Tab createFragmentsTab(String aFragmentationName){ private Tab createItemsTab(String aFragmentationName){ ItemizationDataTableView tmpItemizationDataTableView = new ItemizationDataTableView(aFragmentationName, this.configuration); tmpItemizationDataTableView.setItemsList( - this.moleculeDataModelList.stream().filter(x -> x.hasMoleculeUndergoneSpecificFragmentation(aFragmentationName)).toList()); + //developers note: a modifiable list is needed for sorting, so don't let SonarCloud tell you that the Collectors are not needed here! + this.moleculeDataModelList.stream().filter(x -> x.hasMoleculeUndergoneSpecificFragmentation(aFragmentationName)).collect(Collectors.toList())); GridTabForTableView tmpItemizationTab = new GridTabForTableView(Message.get("MainTabPane.itemizationTab.title") + " - " + aFragmentationName, TabNames.ITEMIZATION.name(), tmpItemizationDataTableView); this.mainTabPane.getTabs().add(tmpItemizationTab); Pagination tmpPagination = this.createPaginationWithSuitablePageCount(this.moleculeDataModelList.size()); diff --git a/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ErtlFunctionalGroupsFinderFragmenter.java b/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ErtlFunctionalGroupsFinderFragmenter.java index a68ce367..ef1597ea 100644 --- a/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ErtlFunctionalGroupsFinderFragmenter.java +++ b/src/main/java/de/unijena/cheminf/mortar/model/fragmentation/algorithm/ErtlFunctionalGroupsFinderFragmenter.java @@ -754,8 +754,9 @@ public List