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Fixed some deprecation warnings. #30

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Fixed some deprecation warnings. #30

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4 changes: 0 additions & 4 deletions de.openms.knime.importers/src/de/openms/knime/importers/mzml/MzMLChromatogramImporter.java
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Expand Up @@ -13,11 +13,9 @@
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.DataTableSpecCreator;
import org.knime.core.data.RowKey;
import org.knime.core.data.collection.CollectionCellFactory;
import org.knime.core.data.collection.ListCell;
import org.knime.core.data.def.DefaultRow;
import org.knime.core.data.def.DoubleCell;
import org.knime.core.data.def.IntCell;
import org.knime.core.node.BufferedDataTable;
import org.knime.core.node.port.PortObjectSpec;

Expand All @@ -27,8 +25,6 @@
import uk.ac.ebi.jmzml.model.mzml.BinaryDataArray;
import uk.ac.ebi.jmzml.model.mzml.CVParam;
import uk.ac.ebi.jmzml.model.mzml.Chromatogram;
import uk.ac.ebi.jmzml.model.mzml.Scan;
import uk.ac.ebi.jmzml.model.mzml.Spectrum;
import uk.ac.ebi.jmzml.xml.io.MzMLUnmarshaller;

public class MzMLChromatogramImporter implements IDemangler {
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1 change: 0 additions & 1 deletion de.openms.knime.importers/src/de/openms/knime/importers/mzml/MzMLSpectrumImporter.java
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Expand Up @@ -13,7 +13,6 @@
import org.knime.core.data.DataTableSpec;
import org.knime.core.data.DataTableSpecCreator;
import org.knime.core.data.RowKey;
import org.knime.core.data.collection.CollectionCellFactory;
import org.knime.core.data.collection.ListCell;
import org.knime.core.data.def.DefaultRow;
import org.knime.core.data.def.DoubleCell;
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14 changes: 6 additions & 8 deletions de.openms.knime.mzTab/src/de/openms/knime/mztab/MzTabReaderNodeModel.java
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Expand Up @@ -106,14 +106,12 @@ private DataTableSpec createMetaDataSectionSpec() {
* Constructor for the node model.
*/
protected MzTabReaderNodeModel() {
super(new PortType[] { new PortType(IURIPortObject.class) },
new PortType[] {
new PortType(BufferedDataTable.class),
new PortType(BufferedDataTable.class),
new PortType(BufferedDataTable.class),
new PortType(BufferedDataTable.class),
new PortType(BufferedDataTable.class)
});
super(new PortType[] { IURIPortObject.TYPE },
new PortType[] { BufferedDataTable.TYPE,
BufferedDataTable.TYPE,
BufferedDataTable.TYPE,
BufferedDataTable.TYPE,
BufferedDataTable.TYPE});

metaDataRowIdx = 1;
proteinRowIdx = 1;
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4 changes: 2 additions & 2 deletions ...ime.mzTab/src/de/openms/knime/mztab/small_molecule/SmallMoleculeMzTabReaderNodeModel.java
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Expand Up @@ -93,8 +93,8 @@ public class SmallMoleculeMzTabReaderNodeModel extends NodeModel {
* Constructor for the node model.
*/
protected SmallMoleculeMzTabReaderNodeModel() {
super(new PortType[] { new PortType(IURIPortObject.class) },
new PortType[] { new PortType(BufferedDataTable.class) });
super(new PortType[] { IURIPortObject.TYPE },
new PortType[] { BufferedDataTable.TYPE });
}

/**
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2 changes: 1 addition & 1 deletion ...e.qchandling/src/de/openms/knime/qchandling/qcfeaturereader/QCFeatureReaderNodeModel.java
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Expand Up @@ -78,7 +78,7 @@ private static PortType[] getIncomingPorts() {
* @return The outgoing {@link PortType}s of this node.
*/
private static PortType[] getOutgoingPorts() {
return new PortType[] { new PortType(BufferedDataTable.class) };
return new PortType[] { BufferedDataTable.TYPE };
}

/**
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2 changes: 1 addition & 1 deletion ...penms.knime.qchandling/src/de/openms/knime/qchandling/qcidreader/QCIDReaderNodeModel.java
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Expand Up @@ -79,7 +79,7 @@ private static PortType[] getIncomingPorts() {
* @return The outgoing {@link PortType}s of this node.
*/
private static PortType[] getOutgoingPorts() {
return new PortType[] { new PortType(BufferedDataTable.class) };
return new PortType[] { BufferedDataTable.TYPE };
}

/**
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2 changes: 1 addition & 1 deletion ...e/openms/knime/qchandling/qcioninjectiontimereader/QCIonInjectionTimeReaderNodeModel.java
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Expand Up @@ -56,7 +56,7 @@ private static PortType[] getIncomingPorts() {
* @return The outgoing {@link PortType}s of this node.
*/
private static PortType[] getOutgoingPorts() {
return new PortType[] { new PortType(BufferedDataTable.class) };
return new PortType[] { BufferedDataTable.TYPE };
}

/**
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2 changes: 1 addition & 1 deletion ...handling/src/de/openms/knime/qchandling/qcprecursorreader/QCPrecursorReaderNodeModel.java
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Expand Up @@ -76,7 +76,7 @@ private static PortType[] getIncomingPorts() {
* @return The outgoing {@link PortType}s of this node.
*/
private static PortType[] getOutgoingPorts() {
return new PortType[] { new PortType(BufferedDataTable.class) };
return new PortType[] { BufferedDataTable.TYPE };
}

/**
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2 changes: 1 addition & 1 deletion ...knime.qchandling/src/de/openms/knime/qchandling/qcsetidreader/QCSetIdReaderNodeModel.java
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Expand Up @@ -76,7 +76,7 @@ private static PortType[] getIncomingPorts() {
* @return The outgoing {@link PortType}s of this node.
*/
private static PortType[] getOutgoingPorts() {
return new PortType[] { new PortType(BufferedDataTable.class) };
return new PortType[] { BufferedDataTable.TYPE };
}

/**
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2 changes: 1 addition & 1 deletion ...nms.knime.qchandling/src/de/openms/knime/qchandling/qcticreader/QCTICReaderNodeModel.java
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Expand Up @@ -74,7 +74,7 @@ private static PortType[] getIncomingPorts() {
* @return The outgoing {@link PortType}s of this node.
*/
private static PortType[] getOutgoingPorts() {
return new PortType[] { new PortType(BufferedDataTable.class) };
return new PortType[] { BufferedDataTable.TYPE };
}

/**
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9 changes: 2 additions & 7 deletions ...exporter_reader/src/de/openms/knime/consensusTextReader/ConsensusTextReaderNodeModel.java
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Expand Up @@ -43,7 +43,6 @@
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
Expand All @@ -61,16 +60,12 @@
*/
public class ConsensusTextReaderNodeModel extends NodeModel {

// the logger instance
private static final NodeLogger logger = NodeLogger
.getLogger(ConsensusTextReaderNodeModel.class);

/**
* Constructor for the node model.
*/
protected ConsensusTextReaderNodeModel() {
super(new PortType[] { new PortType(IURIPortObject.class) },
new PortType[] { new PortType(BufferedDataTable.class) });
super(new PortType[] { IURIPortObject.TYPE },
new PortType[] { BufferedDataTable.TYPE });
}

/**
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9 changes: 2 additions & 7 deletions ...textexporter_reader/src/de/openms/knime/featureTextReader/FeatureTextReaderNodeModel.java
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Expand Up @@ -13,7 +13,6 @@
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
Expand All @@ -31,16 +30,12 @@
*/
public class FeatureTextReaderNodeModel extends NodeModel {

// the logger instance
private static final NodeLogger logger = NodeLogger
.getLogger(FeatureTextReaderNodeModel.class);

/**
* Constructor for the node model.
*/
protected FeatureTextReaderNodeModel() {
super(new PortType[] { new PortType(IURIPortObject.class) },
new PortType[] { new PortType(BufferedDataTable.class) });
super(new PortType[] { IURIPortObject.TYPE },
new PortType[] { BufferedDataTable.TYPE });
}

/**
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9 changes: 2 additions & 7 deletions ...nms.knime.textexporter_reader/src/de/openms/knime/idTextReader/IDTextReaderNodeModel.java
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Expand Up @@ -43,7 +43,6 @@
import org.knime.core.node.ExecutionContext;
import org.knime.core.node.ExecutionMonitor;
import org.knime.core.node.InvalidSettingsException;
import org.knime.core.node.NodeLogger;
import org.knime.core.node.NodeModel;
import org.knime.core.node.NodeSettingsRO;
import org.knime.core.node.NodeSettingsWO;
Expand All @@ -61,16 +60,12 @@
*/
public class IDTextReaderNodeModel extends NodeModel {

// the logger instance
private static final NodeLogger logger = NodeLogger
.getLogger(IDTextReaderNodeModel.class);

/**
* Constructor for the node model.
*/
protected IDTextReaderNodeModel() {
super(new PortType[] { new PortType(IURIPortObject.class) },
new PortType[] { new PortType(BufferedDataTable.class) });
super(new PortType[] { IURIPortObject.TYPE },
new PortType[] { BufferedDataTable.TYPE });
}

/**
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