public class JDXSpectrum extends JDXDataObject
JDXSpectrum
implements the Interface Spectrum for the display of
JDX Files.Modifier and Type | Class and Description |
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static class |
JDXSpectrum.IRMode |
Modifier and Type | Field and Description |
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static double |
MAXABS |
dataPointNum, ERROR, fileFirstX, fileLastX, freq2dX, freq2dY, nPointsFile, nucleusX, nucleusY, numDim, observedFreq, observedNucl, offset, SCALE_BOTTOM, SCALE_NONE, SCALE_TOP, SCALE_TOP_BOTTOM, shiftRefType, varName, xFactor, y2DUnits, yFactor
Constructor and Description |
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JDXSpectrum()
Constructor
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Modifier and Type | Method and Description |
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boolean |
addSubSpectrum(JDXSpectrum spectrum,
boolean forceSub)
adds an nD subspectrum and titles it "Subspectrum
|
int |
advanceSubSpectrum(int dir) |
static boolean |
allowSubSpec(JDXSpectrum s1,
JDXSpectrum s2) |
static boolean |
areLinkableX(JDXSpectrum s1,
JDXSpectrum s2) |
static boolean |
areLinkableY(JDXSpectrum s1,
JDXSpectrum s2) |
static boolean |
areXScalesCompatible(JDXSpectrum s1,
JDXSpectrum s2,
boolean isSubspecCheck,
boolean isLinkCheck) |
JDXSpectrum |
copy()
specifically for Abs/Trans conversion.
|
void |
dispose() |
void |
finalize() |
PeakInfo |
findMatchingPeakInfo(PeakInfo pi) |
PeakInfo |
findPeakByCoord(Coordinate coord) |
double |
findXForPeakNearest(double x) |
PeakInfo |
getAssociatedPeakInfo(Coordinate coord) |
java.lang.String |
getAxisLabel(boolean isX)
checks in order: (1) Peaks tag attribute xUnits/yUnits,
then (2) ##XLABEL/##YLABEL,
then (3) ##XUNITS/##YUNITS
|
PeakInfo |
getBasePeakInfo() |
JDXSpectrum |
getConvertedSpectrum() |
JDXSpectrum |
getCurrentSubSpectrum() |
java.util.Map<java.lang.String,java.lang.Object> |
getInfo(java.lang.String key) |
PeakInfo |
getModelPeakInfoForAutoSelectOnLoad() |
java.util.ArrayList<PeakInfo> |
getPeakList() |
java.lang.String |
getPeakTitle() |
double |
getPercentYValueAt(double x) |
PeakInfo |
getSelectedPeak() |
int |
getSubIndex() |
java.util.List<JDXSpectrum> |
getSubSpectra() |
java.lang.String |
getTitleLabel() |
double |
getUserYFactor() |
Coordinate[] |
getXYCoords()
Returns the array of coordinates
|
double |
getYValueAt(double x) |
boolean |
isExportXAxisLeftToRight() |
boolean |
isForcedSubset() |
boolean |
matchesPeakTypeModel(java.lang.String type,
java.lang.String model) |
static JDXSpectrum |
newSpectrum(JDXSpectrum spectrum,
Coordinate[] newXYCoords,
java.lang.String units)
copy spectrum with new coordinates
|
static boolean |
process(java.util.List<JDXSpectrum> specs,
JDXSpectrum.IRMode irMode) |
PeakInfo |
selectPeakByFileIndex(java.lang.String filePath,
java.lang.String index) |
PeakInfo |
selectPeakByFilePathTypeModel(java.lang.String filePath,
java.lang.String type,
java.lang.String model) |
void |
setConvertedSpectrum(JDXSpectrum spectrum) |
int |
setCurrentSubSpectrum(int n) |
void |
setExportXAxisDirection(boolean leftToRight) |
void |
setId(java.lang.String id) |
int |
setNextPeak(Coordinate coord,
int istep) |
int |
setPeakList(java.util.ArrayList<PeakInfo> list,
java.lang.String piUnitsX,
java.lang.String piUnitsY) |
void |
setSelectedPeak(PeakInfo peak) |
void |
setUserYFactor(double userYFactor) |
static JDXSpectrum |
taConvert(JDXSpectrum spectrum,
JDXSpectrum.IRMode mode) |
java.lang.String |
toString() |
canConvertTransAbs, canIntegrate, canSaveAsJDX, canShowSolutionColor, checkRequiredTokens, copyTo, getDefaultAnnotationInfo, getDeltaX, getFilePath, getFilePathForwardSlash, getFirstX, getFirstY, getHeaderRowDataAsArray, getLastX, getLastY, getMaxX, getMaxY, getMinX, getMinY, getNumberOfPoints, getObservedFreq, getPeakListArray, getPeakPickHash, getTypeLabel, getXFactor, getXUnits, getY2D, getY2DPPM, getYFactor, getYRef, getYUnits, is1D, isAbsorbance, isAutoOverlayFromJmolClick, isContinuous, isHNMR, isHZtoPPM, isImaginary, isInverted, isNMR, isScalable, isStackable, isTransmittance, isXIncreasing, setBlockID, setContinuous, setFilePath, setHZtoPPM, setIncreasing, setMeasurementText, setNucleus, setObservedFreq, setObservedNucleus, setXFactor, setXLabel, setXUnits, setXYCoords, setY2D, setY2DUnits, setYFactor, setYLabel, setYUnits, shouldDisplayXAxisIncreasing
getDataClass, getDataType, getDate, getHeaderRowDataAsArray, getHeaderTable, getJcampdx, getLongDate, getOrigin, getOwner, getQualifiedDataType, getTime, getTitle, setDataClass, setDataType, setDate, setHeaderTable, setJcampdx, setLongDate, setOrigin, setOwner, setTime, setTitle
public static final double MAXABS
public void finalize()
finalize
in class java.lang.Object
public void dispose()
public boolean isForcedSubset()
public void setId(java.lang.String id)
public JDXSpectrum copy()
JDXSpectrum
public Coordinate[] getXYCoords()
public java.util.ArrayList<PeakInfo> getPeakList()
public int setPeakList(java.util.ArrayList<PeakInfo> list, java.lang.String piUnitsX, java.lang.String piUnitsY)
public PeakInfo selectPeakByFileIndex(java.lang.String filePath, java.lang.String index)
public PeakInfo selectPeakByFilePathTypeModel(java.lang.String filePath, java.lang.String type, java.lang.String model)
public boolean matchesPeakTypeModel(java.lang.String type, java.lang.String model)
public void setSelectedPeak(PeakInfo peak)
public PeakInfo getSelectedPeak()
public PeakInfo getModelPeakInfoForAutoSelectOnLoad()
public PeakInfo getAssociatedPeakInfo(Coordinate coord)
public PeakInfo findPeakByCoord(Coordinate coord)
public java.lang.String getPeakTitle()
public java.lang.String getTitleLabel()
public int setNextPeak(Coordinate coord, int istep)
public double getPercentYValueAt(double x)
public double getYValueAt(double x)
public void setUserYFactor(double userYFactor)
public double getUserYFactor()
public JDXSpectrum getConvertedSpectrum()
public void setConvertedSpectrum(JDXSpectrum spectrum)
public static JDXSpectrum taConvert(JDXSpectrum spectrum, JDXSpectrum.IRMode mode)
public static JDXSpectrum newSpectrum(JDXSpectrum spectrum, Coordinate[] newXYCoords, java.lang.String units)
spectrum
- newXYCoords
- units
- public static boolean process(java.util.List<JDXSpectrum> specs, JDXSpectrum.IRMode irMode)
public java.util.List<JDXSpectrum> getSubSpectra()
public JDXSpectrum getCurrentSubSpectrum()
public int advanceSubSpectrum(int dir)
public int setCurrentSubSpectrum(int n)
public boolean addSubSpectrum(JDXSpectrum spectrum, boolean forceSub)
spectrum
- forceSub
- public int getSubIndex()
public void setExportXAxisDirection(boolean leftToRight)
public boolean isExportXAxisLeftToRight()
public java.util.Map<java.lang.String,java.lang.Object> getInfo(java.lang.String key)
public java.lang.String toString()
toString
in class java.lang.Object
public PeakInfo getBasePeakInfo()
public java.lang.String getAxisLabel(boolean isX)
isX
- public double findXForPeakNearest(double x)
public static boolean allowSubSpec(JDXSpectrum s1, JDXSpectrum s2)
public static boolean areXScalesCompatible(JDXSpectrum s1, JDXSpectrum s2, boolean isSubspecCheck, boolean isLinkCheck)
public static boolean areLinkableX(JDXSpectrum s1, JDXSpectrum s2)
public static boolean areLinkableY(JDXSpectrum s1, JDXSpectrum s2)