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* support for local FDR (PEP) * will read in and try to boost on delta score and peptide coverage * searches can be normalized by a version of an interpolated PSM-FDR ** mainly useful for combining searches that have different score-ranges * using fastutil to reduce some memory requirements * support for directional crosslinker has been (partially) removed * bugfix for automatic recognition of column-names fro command-line version * new output column iFDR for interpolated global FDR
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Lutz Fischer
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Sep 3, 2019
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|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| /* | ||
| * Copyright 2019 Lutz Fischer <[email protected]>. | ||
| * | ||
| * 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 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. | ||
| */ | ||
| package org.rappsilber.fdr; | ||
|
|
||
| import java.io.FileNotFoundException; | ||
| import java.sql.SQLException; | ||
| import org.rappsilber.fdr.gui.FDRGUI; | ||
|
|
||
| /** | ||
| * Proxy class that looks at the given arguments and then forwards the whole | ||
| * command-line to the appropriate class. | ||
| * @author Lutz Fischer <[email protected]> | ||
| */ | ||
| public class CommandLine { | ||
|
|
||
| public static void main(String args[]) throws SQLException, FileNotFoundException { | ||
| boolean xicsv = false; | ||
| boolean csv = false; | ||
| boolean gui = true; | ||
| boolean db = false; | ||
| for (String a : args) { | ||
| gui = false; | ||
| if (a.startsWith("--xiconfig=")) { | ||
| xicsv=true; | ||
| } else if (a.startsWith("--dbids=")) { | ||
| db = true; | ||
| } else if (!a.startsWith("-")) { | ||
| csv = true; | ||
| } | ||
| } | ||
| if (db && !csv) { | ||
| DBinFDR.main(args); | ||
| return; | ||
| } | ||
| if (xicsv && !db) { | ||
| XiCSVinFDR.main(args); | ||
| return; | ||
| } | ||
| if (csv && (!db) && (!xicsv)) { | ||
| CSVinFDR.main(args); | ||
| return; | ||
| } | ||
| if (gui) { | ||
| FDRGUI.main(args); | ||
| return; | ||
| } | ||
| new XiCSVinFDR().printUsage(); | ||
| } | ||
| } |
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