diff --git a/pom.xml b/pom.xml
index 0b681685c..4a331131c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -138,7 +138,7 @@
com.google.guava
guava
- 24.1-jre
+ 25.1-jre
org.apache.commons
@@ -294,7 +294,7 @@
uk.ac.ebi.jmzml
jmzml
- 1.7.9
+ 1.7.10
@@ -339,11 +339,6 @@
-
- soap-apis
- metlin-api
- 1.0
-
soap-apis
chemspider-api
diff --git a/src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/onlinedbsearch/databases/MetLinGateway.java b/src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/onlinedbsearch/databases/MetLinGateway.java
deleted file mode 100644
index 07c7c83b9..000000000
--- a/src/main/java/net/sf/mzmine/modules/peaklistmethods/identification/onlinedbsearch/databases/MetLinGateway.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/*
- * Copyright 2006-2015 The MZmine 2 Development Team
- *
- * This file is part of MZmine 2.
- *
- * MZmine 2 is free software; you can redistribute it and/or modify it under the
- * terms of the GNU General Public License as published by the Free Software
- * Foundation; either version 2 of the License, or (at your option) any later
- * version.
- *
- * MZmine 2 is distributed in the hope that it will be useful, but WITHOUT ANY
- * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
- * A PARTICULAR PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with
- * MZmine 2; if not, write to the Free Software Foundation, Inc., 51 Franklin St,
- * Fifth Floor, Boston, MA 02110-1301 USA
- */
-
-package net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.databases;
-
-import java.io.IOException;
-import java.net.URL;
-import java.util.Hashtable;
-import java.util.Map;
-
-import javax.xml.rpc.ServiceException;
-
-import metlin.LineInfo;
-import metlin.MetaboliteSearchRequest;
-import metlin.MetlinPortType;
-import metlin.MetlinServiceLocator;
-import net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.DBCompound;
-import net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.DBGateway;
-import net.sf.mzmine.modules.peaklistmethods.identification.onlinedbsearch.OnlineDatabase;
-import net.sf.mzmine.parameters.ParameterSet;
-import net.sf.mzmine.parameters.parametertypes.tolerances.MZTolerance;
-import net.sf.mzmine.util.RangeUtils;
-
-import org.apache.axis.AxisFault;
-
-import com.google.common.collect.Range;
-
-public class MetLinGateway implements DBGateway {
-
- private static final String adduct[] = { "M" };
-
- private static final String metLinEntryAddress = "http://metlin.scripps.edu/metabo_info.php?molid=";
- private static final String metLinStructureAddress1 = "http://metlin.scripps.edu/structure/";
- private static final String metLinStructureAddress2 = ".mol";
-
- private Map retrievedMolecules = new Hashtable();
-
- public synchronized String[] findCompounds(double mass,
- MZTolerance mzTolerance, int numOfResults, ParameterSet parameters)
- throws IOException {
-
- Range toleranceRange = mzTolerance.getToleranceRange(mass);
-
- MetlinServiceLocator locator = new MetlinServiceLocator();
- MetlinPortType serv;
- try {
- serv = locator.getMetlinPort();
- } catch (ServiceException e) {
- throw (new IOException(e));
- }
-
- // Search mass as float[]
- float searchMass[] = new float[] { (float) RangeUtils
- .rangeCenter(toleranceRange) };
- float searchTolerance = (float) (RangeUtils.rangeLength(toleranceRange) / 2.0);
-
- final String token = parameters.getParameter(
- MetLinParameters.SECURITY_TOKEN).getValue();
-
- MetaboliteSearchRequest searchParams = new MetaboliteSearchRequest(
- token, searchMass, adduct, searchTolerance, "Da");
- LineInfo resultsData[][];
- try {
- resultsData = serv.metaboliteSearch(searchParams);
- } catch (AxisFault e) {
- // For some reason, the METLIN SOAP gateway throws AxisFault caused
- // by ArrayStoreException if no result is found. I suspect their
- // SOAP response is malformed and Axis does not like it.
- resultsData = new LineInfo[1][0];
- }
-
- if (resultsData.length == 0) {
- throw (new IOException("Results could not be retrieved from METLIN"));
-
- }
- final int totalResults = Math.min(resultsData[0].length, numOfResults);
- String metlinIDs[] = new String[totalResults];
-
- for (int i = 0; i < totalResults; i++) {
- LineInfo metlinEntry = resultsData[0][i];
- String metlinID = metlinEntry.getMolid();
- retrievedMolecules.put(metlinID, metlinEntry);
- metlinIDs[i] = metlinID;
- }
-
- return metlinIDs;
-
- }
-
- /**
- * This method retrieves the details about METLIN compound
- *
- */
- public DBCompound getCompound(String ID, ParameterSet parameters)
- throws IOException {
-
- URL entryURL = new URL(metLinEntryAddress + ID);
-
- LineInfo metlinEntry = retrievedMolecules.get(ID);
-
- if (metlinEntry == null) {
- throw new IOException("Unknown ID " + ID);
- }
-
- String compoundName = metlinEntry.getName();
-
- if (compoundName == null) {
- throw (new IOException(
- "Could not parse compound name for compound " + ID));
- }
-
- String compoundFormula = metlinEntry.getFormula();
-
- URL structure2DURL = new URL(metLinStructureAddress1 + ID
- + metLinStructureAddress2);
-
- URL structure3DURL = null;
-
- /*
- DBCompound newCompound = new DBCompound(OnlineDatabase.METLIN, ID,
- compoundName, compoundFormula, entryURL, structure2DURL,
- structure3DURL);
-
- return newCompound;
-
- */
- return null;
-
- }
-}
diff --git a/src/main/lib/soap-apis/metlin-api/1.0/metlin-api-1.0.jar b/src/main/lib/soap-apis/metlin-api/1.0/metlin-api-1.0.jar
deleted file mode 100644
index c20d706d0..000000000
Binary files a/src/main/lib/soap-apis/metlin-api/1.0/metlin-api-1.0.jar and /dev/null differ