Merge pull request #1498 from SteffenHeu/fix_mztab_errors

remove mztab modules

build.gradle

@@ -108,8 +108,6 @@ repositories {
     maven { url = "https://repo.maven.apache.org/maven2" }
     // local libraries
     maven { url = "file://" + projectDir + "/src/main/lib" }
-    // For jmztab 3.0.9+ (https://github.com/PRIDE-Utilities/jmzTab)
-    maven { url = "https://m.lifs-tools.org/artifactory/libs-release" }
     // For jmzml, etc.
     maven { url = "https://www.ebi.ac.uk/Tools/maven/repos/content/groups/ebi-repo/" }
     // For SIRIUS ID modules
@@ -125,7 +123,6 @@ repositories {
 ext {
     msdkVersion = "0.0.27"
     cdkVersion = "2.5"
-    jmztabVersion = "3.0.9"
     swaggerVersion = "1.5.22"
     okhttpVersion = "2.7.5"
     guavaVersion = "30.1-jre"
@@ -187,8 +184,6 @@ dependencies {
     implementation 'com.github.jbytecode:RCaller:4.0.2'
     implementation "mzmine:jmprojection:1.0"
     implementation "mzmine:gslibml:0.0.1"
-    implementation "uk.ac.ebi.pride:jmztab-modular-model:$jmztabVersion"
-    implementation "uk.ac.ebi.pride:jmztab-modular-util:$jmztabVersion"
     implementation 'org.apache.xmlgraphics:fop:2.6'
     implementation "org.freehep:freehep-graphicsio-emf:2.4"
     implementation "io.github.msdk:msdk-io-mzml:$msdkVersion"

src/main/java/io/github/mzmine/gui/mainwindow/MainMenu.fxml

@@ -290,8 +290,6 @@
   <!-- FEATURE LIST METHODS -->
   <Menu text="Feature list methods">
 <!--    <Menu text="Import feature list">-->
-<!--      <MenuItem text="mzTab" onAction="#runModule"-->
-<!--        userData="io.github.mzmine.modules.io.import_features_mztab.MzTabImportModule"/>-->
 <!--      <MenuItem text="mzTab-m" onAction="#runModule"-->
 <!--        userData="io.github.mzmine.modules.io.import_features_mztabm.MZTabmImportModule"/>-->
 <!--      <MenuItem text="csv" onAction="#runModule"-->
@@ -314,8 +312,6 @@
         userData="io.github.mzmine.modules.io.export_features_venn.VennExportModule"/>
       <MenuItem text="Statistics export (MetaboAnalyst)" onAction="#runModule"
         userData="io.github.mzmine.modules.io.export_features_metaboanalyst.MetaboAnalystExportModule"/>
-      <MenuItem text="mzTab" onAction="#runModule"
-        userData="io.github.mzmine.modules.io.export_features_mztab.MzTabExportModule"/>
       <MenuItem text="mzTab-m" onAction="#runModule"
         userData="io.github.mzmine.modules.io.export_features_mztabm.MZTabmExportModule"/>
       <MenuItem text="SQL Database" onAction="#runModule"

src/main/java/io/github/mzmine/modules/batchmode/BatchModeModulesList.java

@@ -127,7 +127,6 @@
 import io.github.mzmine.modules.io.export_features_metaboanalyst.MetaboAnalystExportModule;
 import io.github.mzmine.modules.io.export_features_mgf.AdapMgfExportModule;
 import io.github.mzmine.modules.io.export_features_msp.AdapMspExportModule;
-import io.github.mzmine.modules.io.export_features_mztab.MzTabExportModule;
 import io.github.mzmine.modules.io.export_features_mztabm.MZTabmExportModule;
 import io.github.mzmine.modules.io.export_features_sirius.SiriusExportModule;
 import io.github.mzmine.modules.io.export_library_analysis_csv.LibraryAnalysisCSVExportModule;
@@ -138,7 +137,6 @@
 import io.github.mzmine.modules.io.export_rawdata_mzml.MzMLExportModule;
 import io.github.mzmine.modules.io.export_rawdata_netcdf.NetCDFExportModule;
 import io.github.mzmine.modules.io.export_scans.ExportScansFromRawFilesModule;
-import io.github.mzmine.modules.io.import_features_mztab.MzTabImportModule;
 import io.github.mzmine.modules.io.import_features_mztabm.MZTabmImportModule;
 import io.github.mzmine.modules.io.import_rawdata_all.AllSpectralDataImportModule;
 import io.github.mzmine.modules.io.import_rawdata_bruker_tdf.TDFImportModule;
@@ -374,12 +372,10 @@ public class BatchModeModulesList {
       AdapMgfExportModule.class, //
       GNPSResultsImportModule.class, //
       AdapMspExportModule.class, //
-      MzTabExportModule.class, //
       MZTabmExportModule.class, //
       NetCDFExportModule.class, //
       SiriusExportModule.class, //
       MZTabmImportModule.class, //
-      MzTabImportModule.class, //
       CSVExportModularModule.class, //
       LegacyCSVExportModule.class, //
       CompoundAnnotationsCSVExportModule.class, //