initial commit from shell

.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="src"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+	<classpathentry kind="output" path="bin"/>
+</classpath>

.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>RawExtractor_v3.6</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.jdt.core.prefs

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+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

bin/.classpath

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+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path=""/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+	<classpathentry kind="output" path=""/>
+</classpath>

bin/.project

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+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>CIUGen Setup</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

bin/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,11 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

src/.classpath

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path=""/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+	<classpathentry kind="output" path=""/>
+</classpath>

src/.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>CIUGen Setup</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>

src/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,11 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode=enabled
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.codegen.unusedLocal=preserve
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.debug.lineNumber=generate
+org.eclipse.jdt.core.compiler.debug.localVariable=generate
+org.eclipse.jdt.core.compiler.debug.sourceFile=generate
+org.eclipse.jdt.core.compiler.problem.assertIdentifier=error
+org.eclipse.jdt.core.compiler.problem.enumIdentifier=error
+org.eclipse.jdt.core.compiler.source=1.8

src/ciugen/imextract/DataVectorInfoObject.java

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+package ciugen.imextract;
+
+/**
+ * Class to hold all information from the data vector/table used in CIUGEN UI. Each object represents
+ * a single analysis (what used to be a single csv file), so each object is one function in MassLynx
+ * @author Dan
+ *
+ */
+public class DataVectorInfoObject {
+	private String rawDataPath;
+	private int function;
+	private boolean selected;
+	private boolean lockmass;
+
+	private double coneCV;
+	private double trapCV;
+	private double transfCV;
+	private double waveHeight;
+	private double waveVel;
+
+	private double[] rangeVals;
+
+	private String rangeName;
+	private String rawDataName;
+	private boolean[] infoTypes;
+
+
+	//(rawDataPath, rawName,function,selected,lockmass,conecv,trapcv,transfcv,wh,wv,rangesArr,rangeFileName
+
+	public DataVectorInfoObject(String myRawDataPath, String myRawName, int myFunction, boolean mySelected,
+			boolean myLockmass, double myConeCV, double myTrapCV, double myTransfCV, double myWH, double myWV,
+			double[] myRangesArr, String myRangeFileName, boolean[] myInfoTypes){
+
+		this.setRawDataPath(myRawDataPath);
+		this.setRawDataName(myRawName);
+		this.setFunction(myFunction);
+		this.setSelected(mySelected);
+
+		this.setLockmass(myLockmass);
+		this.setConeCV(myConeCV);
+		this.setCollisionEnergy(myTrapCV);
+		this.setTransfCV(myTransfCV);
+		this.setWaveHeight(myWH);
+		this.setWaveVel(myWV);
+
+		this.setRangeVals(myRangesArr);
+		this.setRangeName(myRangeFileName);
+		this.setInfoTypes(myInfoTypes);
+	}
+
+	// Deprecated - partial constructors
+//	public DataVectorInfoObject(String myRawPath, String myName, int myFn, boolean mySelected, double myCE, double[] myRangeVals, String myRangeName){
+//		this.setCollisionEnergy(myCE);
+//		this.setFunction(myFn);
+//		this.setRangeVals(myRangeVals);
+//		this.setRawDataPath(myRawPath);
+//		this.setSelected(mySelected);
+//		this.setRangeName(myRangeName);
+//		this.setRawDataName(myName);
+//	}
+//
+//	// Version with no collision energy
+//	public DataVectorInfoObject(String myRawPath, String myName, int myFn, boolean mySelected, double[] myRangeVals, String myRangeName){
+//		this.setFunction(myFn);
+//		this.setRangeVals(myRangeVals);
+//		this.setRawDataPath(myRawPath);
+//		this.setSelected(mySelected);
+//		this.setRangeName(myRangeName);
+//		this.setRawDataName(myName);
+//	}
+	public boolean isSelected() {
+		return selected;
+	}
+
+	public void setSelected(boolean selected) {
+		this.selected = selected;
+	}
+
+	public String getRawDataPath() {
+		return rawDataPath;
+	}
+
+	public void setRawDataPath(String rawDataPath) {
+		this.rawDataPath = rawDataPath;
+	}
+
+	public int getFunction() {
+		return function;
+	}
+
+	public void setFunction(int function) {
+		this.function = function;
+	}
+
+	public double getCollisionEnergy() {
+		return trapCV;
+	}
+
+	public void setCollisionEnergy(double collisionEnergy) {
+		this.trapCV = collisionEnergy;
+	}
+
+	public double[] getRangeVals() {
+		return rangeVals;
+	}
+
+	public void setRangeVals(double[] rangeVals) {
+		this.rangeVals = rangeVals;
+	}
+
+	public double getWaveHeight() {
+		return waveHeight;
+	}
+
+	public void setWaveHeight(double waveHeight) {
+		this.waveHeight = waveHeight;
+	}
+
+	public double getWaveVel() {
+		return waveVel;
+	}
+
+	public void setWaveVel(double waveVel) {
+		this.waveVel = waveVel;
+	}
+
+
+	public String getRangeName() {
+		return rangeName;
+	}
+
+
+	public void setRangeName(String rangeName) {
+		this.rangeName = rangeName;
+	}
+
+
+	public String getRawDataName() {
+		return rawDataName;
+	}
+
+
+	public void setRawDataName(String rawDataName) {
+		this.rawDataName = rawDataName;
+	}
+
+	public boolean isLockmass() {
+		return lockmass;
+	}
+
+	public void setLockmass(boolean lockmass) {
+		this.lockmass = lockmass;
+	}
+
+	public double getConeCV() {
+		return coneCV;
+	}
+
+	public void setConeCV(double coneCV) {
+		this.coneCV = coneCV;
+	}
+
+	public double getTrapCV() {
+		return trapCV;
+	}
+
+	public void setTrapCV(double trapCV) {
+		this.trapCV = trapCV;
+	}
+
+	public double getTransfCV() {
+		return transfCV;
+	}
+
+	public void setTransfCV(double transfCV) {
+		this.transfCV = transfCV;
+	}
+
+	public boolean[] getInfoTypes() {
+		return infoTypes;
+	}
+
+	public void setInfoTypes(boolean[] infoTypes) {
+		this.infoTypes = infoTypes;
+	}
+
+
+}