Spectrum (MzJava 1.1.1-SNAPSHOT API)

java.lang.Object
- org.expasy.mzjava.core.ms.spectrum.Spectrum<A>

All Implemented Interfaces:

PeakList<A>

Direct Known Subclasses:

ConsensusSpectrum, GlycanSpectrum, MsnSpectrum, PeptideSpectrum
```
public abstract class Spectrum<A extends PeakAnnotation>
extends Object
implements PeakList<A>
```
Version:

1.0

Author:

Oliver Horlacher

Nested Class Summary
- Nested classes/interfaces inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList
  PeakList.Precision

Constructor Summary

Constructors
Modifier	Constructor and Description
	`Spectrum(int initialCapacity, double constantIntensity, PeakList.Precision precision)` Construct a Spectrum that has a constant intensity.
	`Spectrum(int initialCapacity, PeakList.Precision precision)` Construct a Spectrum that has an initial capacity of `initialCapacity` and a precision of `precision`
`protected`	`Spectrum(Spectrum<A> src, PeakProcessor<A,A> peakProcessor)` Copy constructor
`protected`	`Spectrum(Spectrum<A> src, PeakProcessorChain<A> peakProcessorChain)` Copy constructor

Method Summary

Methods
Modifier and Type	Method and Description
`int`	`add(double mz, double intensity)` Add a mz, intensity pair to the peak list
`int`	`add(double mz, double intensity, A annotation)` Add a mz, intensity pair and associateed annotations to the peak list
`int`	`add(double mz, double intensity, Collection<? extends A> annotations)` Add a mz, intensity pair and associated annotations to the peak list
`void`	`addAnnotation(int index, A annotation)` Add an annotation to the peak at index
`void`	`addAnnotations(int index, Collection<A> annotations)` Set the annotations for the peak at index
`void`	`addPeaks(PeakList<A> peakList)` Add peaks and annotations in `peakList` to this peak list.
`<T extends PeakAnnotation> void`	`addPeaks(PeakList<T> peakList, com.google.common.base.Function<List<T>,List<A>> annotationConverter)` Add peaks (mz, intensity pairs) and optional annotations in `peakList` to this peak list
`<T extends PeakAnnotation> void`	`addPeaksNoAnnotations(PeakList<T> peakList)` Add peaks (without annotations) in `peakList` to this peak list.
`void`	`addSorted(double[] mzs, double[] intensities)` Add the pairs of mz and intensities to this peak list.
`void`	`addSorted(double[] mzs, double[] intensities, int length)` Add the pairs of mz and intensities to this peak list.
`void`	`apply(PeakProcessor<A,A> peakProcessor)` Apply the peakProcessor to the peaks in this PeakList
`void`	`apply(PeakProcessorChain<A> peakProcessorChain)` Apply the peakProcessorChain to the peaks in this PeakList
`double`	`calcVectorLength()` Calculates the vector length of this peak list
`void`	`clear()` Clears the peak list, the size is set to 0 and objects used to store peaks are unreferenced to allow garbage collection
`void`	`clearAnnotations()` Remove all annotations from this PeakList
`void`	`clearAnnotationsAt(int index)` Remove all annotations for the peak at index
`PeakCursor<A>`	`cursor()` Returns a cursor over the peaks in this peak list in proper sequence.
`void`	`ensureCapacity(int minCapacity)` Increases the capacity of this `DoublePeakList` instance, if necessary, to ensure that it can hold at least the number of peaks specified by the minimum capacity argument.
`boolean`	`equals(Object o)`
`int[]`	`getAnnotationIndexes()` Returns an array containing the sorted indexes of the peaks that are annotated.
`List<A>`	`getAnnotations(int index)` Returns an unmodifiable list containing the annotations for the peak at index
`double`	`getBasePeakIntensity()` Get the intensity of the most intense peak
`double`	`getBasePeakMz()` Get the m/z of the most intense peak
`int`	`getClosestIndex(double mz)` Returns the index of the peak that is closest to the supplied mz.
`com.google.common.base.Optional<A>`	`getFirstAnnotation(int index)` Return the first annotation in the list of annotations for the peak at index.
`UUID`	`getId()`
`double[]`	`getIntensities(double[] dest)` Copies an the intensities from this peak list, beginning at 0, to the destination array.
`double[]`	`getIntensities(double[] dest, int destPos)` Copies an the intensities from this peak list, beginning at 0, to the specified position of the destination array.
`double[]`	`getIntensities(int srcPos, double[] dest, int destPos, int length)` Copies an the intensities from this peak list, beginning at the specified position, to the specified position of the destination array.
`double`	`getIntensity(int index)` Returns the intensity of the peak at index
`int`	`getMostIntenseIndex()` Returns the index of the most intense peak in the peak list or -1 if there are no peaks in this peak list.
`int`	`getMostIntenseIndex(double minMz, double maxMz)` Returns te index of the peak that is most intense in the specified region.
`int`	`getMsLevel()` Returns the ms level that this peak list was measured at
`double`	`getMz(int index)` Returns the mz of the peak at index
`double[]`	`getMzs(double[] dest)` Copies an the mzs from this peak list, beginning at 0, to the destination array.
`double[]`	`getMzs(double[] dest, int destPos)` Copies an the mzs from this peak list, beginning at 0, to the specified position of the destination array.
`double[]`	`getMzs(int srcPos, double[] dest, int destPos, int length)` Copies an the mzs from this peak list, beginning at the specified position, to the specified position of the destination array.
`PeakList.Precision`	`getPrecision()` Return the precision that this PeakList uses to store the peak and intensity values
`Peak`	`getPrecursor()` Returns the precursor peak of this peak list
`double`	`getTotalIonCurrent()` Returns the sum of all intensities
`boolean`	`hasAnnotations()` Returns true if the spectrum has annotations
`boolean`	`hasAnnotationsAt(int index)` Returns true if the spectrum has annotations at peak index
`int`	`hashCode()`
`int`	`indexOf(double mzKey)` Returns the index of the first occurrence of the specified mzKey in this peak list, or (-(insertion point) - 1) if this peak list does not contain the exact mzKey.
`int`	`indexOf(int fromIndex, int toIndex, double mzKey)` Returns the index of the first occurrence of the specified mzKey in the specified range within this peak list, or (-(insertion point) - 1) if this peak list does not contain the exact mzKey.
`boolean`	`isEmpty()` Returns `true` if this peak list contains no peaks.
`boolean`	`removeAnnotation(A annotation, int index)` Remove the annotation from the peak at index
`void`	`setId(UUID id)`
`void`	`setIntensityAt(double intensity, int index)` Replace the intensity at index with intensity
`void`	`setMsLevel(int msLevel)` Set the ms level that this peak list was measured at
`void`	`setPrecursor(Peak precursor)` Set the precursor peak for this peak list
`int`	`size()` Returns the number of peaks in this peak list.
`void`	`sortAnnotations(Comparator<A> comparator)` Sort the annotations for each annotated peak using the `comparator`
`void`	`trimToSize()` Trims the capacity of this `DoublePeakList` instance to be the list's current size.

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList
copy, copy

- Constructor Detail
  - Spectrum
```
protected Spectrum(Spectrum<A> src,
        PeakProcessor<A,A> peakProcessor)
```
    Copy constructor
    
    Parameters:
    src - the Spectrum to copy
    peakProcessor - the processor to process the peaks
  - Spectrum
```
protected Spectrum(Spectrum<A> src,
        PeakProcessorChain<A> peakProcessorChain)
```
    Copy constructor
    
    Parameters:
    src - the Spectrum to copy
    peakProcessorChain - the processor chain to process the peaks
  - Spectrum
```
public Spectrum(int initialCapacity,
        PeakList.Precision precision)
```
    Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision
    
    Parameters:
    initialCapacity - the initial capacity
    precision - the precision
  - Spectrum
```
public Spectrum(int initialCapacity,
        double constantIntensity,
        PeakList.Precision precision)
```
    Construct a Spectrum that has a constant intensity. The precision needs to be either PeakList.Precision.DOUBLE_CONSTANT or PeakList.Precision.FLOAT_CONSTANT. The peak lists initial capacity is set to initialCapacity
    
    Parameters:
    initialCapacity - the initial capacity of the peak list
    constantIntensity - the constant intensity if
    precision - the precision that the peak list is stored at
- Method Detail
  - getId
```
public UUID getId()
```
    Specified by:
    
    getId in interface PeakList<A extends PeakAnnotation>
  - setId
```
public void setId(UUID id)
```
    Specified by:
    
    setId in interface PeakList<A extends PeakAnnotation>
  - addPeaks
```
public void addPeaks(PeakList<A> peakList)
```
    Description copied from interface: PeakList
    
    Add peaks and annotations in peakList to this peak list.
    
    Specified by:
    
    addPeaks in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    peakList - containing peaks and annotations which are to be added to this peak list
  - addPeaksNoAnnotations
```
public <T extends PeakAnnotation> void addPeaksNoAnnotations(PeakList<T> peakList)
```
    Description copied from interface: PeakList
    
    Add peaks (without annotations) in peakList to this peak list.
    
    Specified by:
    
    addPeaksNoAnnotations in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    peakList - containing peaks which are to be added to this peak list
  - addPeaks
```
public <T extends PeakAnnotation> void addPeaks(PeakList<T> peakList,
                                       com.google.common.base.Function<List<T>,List<A>> annotationConverter)
```
    Description copied from interface: PeakList
    
    Add peaks (mz, intensity pairs) and optional annotations in peakList to this peak list
    
    Specified by:
    
    addPeaks in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    peakList - containing peaks which are to be added to this peak list
    annotationConverter - convert annotation T to A (annotation will not be added if Optional is absent)
  - addSorted
```
public void addSorted(double[] mzs,
             double[] intensities)
```
    Description copied from interface: PeakList
    
    Add the pairs of mz and intensities to this peak list. The mzs array has to be sorted. If the m/z array is not sorted an IllegalArgumentException will be thrown
    
    Specified by:
    
    addSorted in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mzs - the mz values
    intensities - the intensities
  - addSorted
```
public void addSorted(double[] mzs,
             double[] intensities,
             int length)
```
    Description copied from interface: PeakList
    
    Add the pairs of mz and intensities to this peak list. The mzs array has to be sorted. If the m/z array is not sorted an IllegalArgumentException will be thrown
    
    Specified by:
    
    addSorted in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mzs - the mz values
    intensities - the intensities
    length - the number of pairs to add
  - add
```
public int add(double mz,
      double intensity)
```
    Description copied from interface: PeakList
    
    Add a mz, intensity pair to the peak list
    
    Specified by:
    
    add in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mz - the mz to add
    intensity - the intensity to add
    
    Returns:
    the index at which the peak was added
  - add
```
public int add(double mz,
      double intensity,
      A annotation)
```
    Description copied from interface: PeakList
    
    Add a mz, intensity pair and associateed annotations to the peak list
    
    Specified by:
    
    add in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mz - the mz to add
    intensity - the intensity to add
    annotation - the peaks annotation
    
    Returns:
    the index at which the peak was added
  - add
```
public int add(double mz,
      double intensity,
      Collection<? extends A> annotations)
```
    Description copied from interface: PeakList
    
    Add a mz, intensity pair and associated annotations to the peak list
    
    Specified by:
    
    add in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mz - the mz to add
    intensity - the intensity to add
    annotations - the peaks annotations
    
    Returns:
    the index at which the peak was added
  - size
```
public int size()
```
    Description copied from interface: PeakList
    
    Returns the number of peaks in this peak list.
    
    Specified by:
    
    size in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the number of peaks in this peak list
  - isEmpty
```
public boolean isEmpty()
```
    Description copied from interface: PeakList
    
    Returns true if this peak list contains no peaks.
    
    Specified by:
    
    isEmpty in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    true if this peak list contains no peaks
  - getMz
```
public double getMz(int index)
```
    Description copied from interface: PeakList
    
    Returns the mz of the peak at index
    
    Specified by:
    
    getMz in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index
    
    Returns:
    the mz of the peak at index
  - getIntensity
```
public double getIntensity(int index)
```
    Description copied from interface: PeakList
    
    Returns the intensity of the peak at index
    
    Specified by:
    
    getIntensity in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index
    
    Returns:
    the intensity of the peak at index
  - clear
```
public void clear()
```
    Description copied from interface: PeakList
    
    Clears the peak list, the size is set to 0 and objects used to store peaks are unreferenced to allow garbage collection
    
    Specified by:
    
    clear in interface PeakList<A extends PeakAnnotation>
  - getTotalIonCurrent
```
public double getTotalIonCurrent()
```
    Description copied from interface: PeakList
    
    Returns the sum of all intensities
    
    Specified by:
    
    getTotalIonCurrent in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the sum of all intensities
  - getClosestIndex
```
public int getClosestIndex(double mz)
```
    Description copied from interface: PeakList
    
    Returns the index of the peak that is closest to the supplied mz. If mz is exactly equidistant between two peaks the index of the smaller peak is returned
    
    Specified by:
    
    getClosestIndex in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mz - the mz
    
    Returns:
    the index of the peak that is closest to the supplied mz
  - indexOf
```
public int indexOf(double mzKey)
```
    Description copied from interface: PeakList
    
    Returns the index of the first occurrence of the specified mzKey in this peak list, or (-(insertion point) - 1) if this peak list does not contain the exact mzKey. The insertion point is defined as the point at which the key would be inserted into the peak list: the index of the first mzKey greater than the key, or size() if all m/z's in the peak list are less than the specified key. Note that this guarantees that the return value will be >= 0 if and only if the key is found.
    
    Specified by:
    
    indexOf in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    mzKey - the search key
    
    Returns:
    index of the search key, if it is contained in the peak list; otherwise, (-(insertion point) - 1). The insertion point is defined as the point at which the key would be inserted into the peak list: the index of the first mzKey greater than the key, or size() if all m/z's in the peak list are less than the specified key. Note that this guarantees that the return value will be >= 0 if and only if the key is found.
  - indexOf
```
public int indexOf(int fromIndex,
          int toIndex,
          double mzKey)
```
    Description copied from interface: PeakList
    
    Returns the index of the first occurrence of the specified mzKey in the specified range within this peak list, or (-(insertion point) - 1) if this peak list does not contain the exact mzKey. The insertion point is defined as the point at which the key would be inserted into the peak list: the index of the first mzKey greater than the key, or size() if all m/z's in the peak list are less than the specified key. Note that this guarantees that the return value will be >= 0 if and only if the key is found.
    
    Specified by:
    
    indexOf in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    fromIndex - the index of the first peak (inclusive) to be searched
    toIndex - the index of the last peak (exclusive) to be searched
    mzKey - the search key
    
    Returns:
    index of the search key, if it is contained in the peak list; otherwise, (-(insertion point) - 1). The insertion point is defined as the point at which the key would be inserted into the peak list: the index of the first mzKey greater than the key, or size() if all m/z's in the peak list are less than the specified key. Note that this guarantees that the return value will be >= 0 if and only if the key is found.
  - getMostIntenseIndex
```
public int getMostIntenseIndex(double minMz,
                      double maxMz)
```
    Description copied from interface: PeakList
    
    Returns te index of the peak that is most intense in the specified region. Where minMz <= region <= maxMZ.
    
    Specified by:
    
    getMostIntenseIndex in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    minMz - the minMz
    maxMz - the maxMz
    
    Returns:
    the index of the most intense peak or -1 if there is no such peak
  - getMostIntenseIndex
```
public int getMostIntenseIndex()
```
    Description copied from interface: PeakList
    
    Returns the index of the most intense peak in the peak list or -1 if there are no peaks in this peak list.
    
    Specified by:
    
    getMostIntenseIndex in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the index of the most intense peak in the peak list
  - getBasePeakMz
```
public double getBasePeakMz()
```
    Description copied from interface: PeakList
    
    Get the m/z of the most intense peak
    
    Specified by:
    
    getBasePeakMz in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the m/z of the most intense peak
  - getBasePeakIntensity
```
public double getBasePeakIntensity()
```
    Description copied from interface: PeakList
    
    Get the intensity of the most intense peak
    
    Specified by:
    
    getBasePeakIntensity in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the intensity of the most intense peak
  - getMzs
```
public double[] getMzs(double[] dest)
```
    Description copied from interface: PeakList
    Copies an the mzs from this peak list, beginning at 0, to the destination array. The number of mzs copied is equal to the size of this peak list. The mzs at positions 0 through size() in this peak list are copied into positions 0 through size(), respectively, of the destination array.
    If dest is null, then a new array with the correct length is created.
    Otherwise, if any of the following is true, an IndexOutOfBoundsException is thrown and the destination is not modified:
    - size() is greater than dest.length, the length of the destination array.
    Specified by:
    
    getMzs in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    dest - the destination array.
    
    Returns:
    dest or the newly created array if dest was null
  - getMzs
```
public double[] getMzs(double[] dest,
              int destPos)
```
    Description copied from interface: PeakList
    Copies an the mzs from this peak list, beginning at 0, to the specified position of the destination array. The number of mzs copied is equal to the size of this peak list. The mzs at positions 0 through size() in this peak list are copied into positions destPos through destPos+length-1, respectively, of the destination array.
    If dest is null, then a new array with the correct length is created.
    Otherwise, if any of the following is true, an IndexOutOfBoundsException is thrown and the destination is not modified:
    - The destPos argument is negative.
    - destPos+size() is greater than dest.length, the length of the destination array.
    Specified by:
    
    getMzs in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    dest - the destination array.
    destPos - starting position in the destination data.
    
    Returns:
    dest or the newly created array if dest was null
  - getMzs
```
public double[] getMzs(int srcPos,
              double[] dest,
              int destPos,
              int length)
```
    Description copied from interface: PeakList
    Copies an the mzs from this peak list, beginning at the specified position, to the specified position of the destination array. A sub-sequence of mzs are copied from this peak list to the destination array referenced by dest. The number of mzs copied is equal to the length argument. The mzs at positions srcPos through srcPos+length-1 in this peak list are copied into positions destPos through destPos+length-1, respectively, of the destination array.
    If dest is null, then a new array with the correct length is created.
    Otherwise, if any of the following is true, an IndexOutOfBoundsException is thrown and the destination is not modified:
    - The srcPos argument is negative.
    - The destPos argument is negative.
    - The length argument is negative.
    - srcPos+length is greater than size(), the size of this.
    - destPos+length is greater than dest.length, the length of the destination array.
    Specified by:
    
    getMzs in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    srcPos - starting position in the mz.
    dest - the destination array.
    destPos - starting position in the destination data.
    length - the number of array elements to be copied.
    
    Returns:
    dest or the newly created array if dest was null
  - getIntensities
```
public double[] getIntensities(double[] dest)
```
    Description copied from interface: PeakList
    Copies an the intensities from this peak list, beginning at 0, to the destination array. The number of intensities copied is equal to the size of this peak list. The intensities at positions 0 through size() in this peak list are copied into positions 0 through size(), respectively, of the destination array.
    If dest is null, then a new array with the correct length is created.
    Otherwise, if any of the following is true, an IndexOutOfBoundsException is thrown and the destination is not modified:
    - size() is greater than dest.length, the length of the destination array.
    Specified by:
    
    getIntensities in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    dest - the destination array.
    
    Returns:
    dest or the newly created array if dest was null
  - getIntensities
```
public double[] getIntensities(double[] dest,
                      int destPos)
```
    Description copied from interface: PeakList
    Copies an the intensities from this peak list, beginning at 0, to the specified position of the destination array. The number of intensities copied is equal to the size of this peak list. The intensities at positions 0 through size() in this peak list are copied into positions destPos through destPos+length-1, respectively, of the destination array.
    If dest is null, then a new array with the correct length is created.
    Otherwise, if any of the following is true, an IndexOutOfBoundsException is thrown and the destination is not modified:
    - The destPos argument is negative.
    - destPos+size() is greater than dest.length, the length of the destination array.
    Specified by:
    
    getIntensities in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    dest - the destination array.
    destPos - starting position in the destination data.
    
    Returns:
    dest or the newly created array if dest was null
  - getIntensities
```
public double[] getIntensities(int srcPos,
                      double[] dest,
                      int destPos,
                      int length)
```
    Description copied from interface: PeakList
    Copies an the intensities from this peak list, beginning at the specified position, to the specified position of the destination array. A sub-sequence of intensities are copied from this peak list to the destination array referenced by dest. The number of intensities copied is equal to the length argument. The intensities at positions srcPos through srcPos+length-1 in this peak list are copied into positions destPos through destPos+length-1, respectively, of the destination array.
    If dest is null, then a new array with the correct length is created.
    Otherwise, if any of the following is true, an IndexOutOfBoundsException is thrown and the destination is not modified:
    - The srcPos argument is negative.
    - The destPos argument is negative.
    - The length argument is negative.
    - srcPos+length is greater than size(), the size of this.
    - destPos+length is greater than dest.length, the length of the destination array.
    Specified by:
    
    getIntensities in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    srcPos - starting position in the mz.
    dest - the destination array.
    destPos - starting position in the destination data.
    length - the number of array elements to be copied.
    
    Returns:
    dest or the newly created array if dest was null
  - getPrecision
```
public PeakList.Precision getPrecision()
```
    Description copied from interface: PeakList
    
    Return the precision that this PeakList uses to store the peak and intensity values
    
    Specified by:
    
    getPrecision in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the precision that this PeakList uses to store the peak and intensity values
  - setIntensityAt
```
public void setIntensityAt(double intensity,
                  int index)
```
    Description copied from interface: PeakList
    
    Replace the intensity at index with intensity
    
    Specified by:
    
    setIntensityAt in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    intensity - the new intensity
    index - the index for which the intensity is to be set
  - trimToSize
```
public void trimToSize()
```
    Description copied from interface: PeakList
    
    Trims the capacity of this DoublePeakList instance to be the list's current size. An application can use this operation to minimize the storage of a DoublePeakList instance.
    
    Specified by:
    
    trimToSize in interface PeakList<A extends PeakAnnotation>
  - ensureCapacity
```
public void ensureCapacity(int minCapacity)
```
    Description copied from interface: PeakList
    
    Increases the capacity of this DoublePeakList instance, if necessary, to ensure that it can hold at least the number of peaks specified by the minimum capacity argument.
    
    Specified by:
    
    ensureCapacity in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    minCapacity - the desired minimum capacity
  - addAnnotation
```
public void addAnnotation(int index,
                 A annotation)
```
    Description copied from interface: PeakList
    
    Add an annotation to the peak at index
    
    Specified by:
    
    addAnnotation in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index of the peak
    annotation - the annotation to add
  - addAnnotations
```
public void addAnnotations(int index,
                  Collection<A> annotations)
```
    Description copied from interface: PeakList
    
    Set the annotations for the peak at index
    
    Specified by:
    
    addAnnotations in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index of the peak
    annotations - the list of annotations
  - removeAnnotation
```
public boolean removeAnnotation(A annotation,
                       int index)
```
    Description copied from interface: PeakList
    
    Remove the annotation from the peak at index
    
    Specified by:
    
    removeAnnotation in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    annotation - the annotation to remove
    index - the index of the peak
    
    Returns:
    true if an annotation was removed as a result of this call
  - clearAnnotationsAt
```
public void clearAnnotationsAt(int index)
```
    Description copied from interface: PeakList
    
    Remove all annotations for the peak at index
    
    Specified by:
    
    clearAnnotationsAt in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index of the peak
  - clearAnnotations
```
public void clearAnnotations()
```
    Description copied from interface: PeakList
    
    Remove all annotations from this PeakList
    
    Specified by:
    
    clearAnnotations in interface PeakList<A extends PeakAnnotation>
  - hasAnnotations
```
public boolean hasAnnotations()
```
    Description copied from interface: PeakList
    
    Returns true if the spectrum has annotations
    
    Specified by:
    
    hasAnnotations in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    true if the spectrum has annotations
  - getAnnotationIndexes
```
public int[] getAnnotationIndexes()
```
    Description copied from interface: PeakList
    
    Returns an array containing the sorted indexes of the peaks that are annotated.
    If this peak list has no annotated peaks an clear array is returned
    
    Specified by:
    
    getAnnotationIndexes in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    an array containing the sorted indexes of the peaks that are annotated
  - hasAnnotationsAt
```
public boolean hasAnnotationsAt(int index)
```
    Description copied from interface: PeakList
    
    Returns true if the spectrum has annotations at peak index
    
    Specified by:
    
    hasAnnotationsAt in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index of the peak
    
    Returns:
    true if the spectrum has annotations at peak index
  - getAnnotations
```
public List<A> getAnnotations(int index)
```
    Description copied from interface: PeakList
    
    Returns an unmodifiable list containing the annotations for the peak at index
    
    Specified by:
    
    getAnnotations in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index of the peak
    
    Returns:
    an unmodifiable list containing the annotations for the peak at index
  - getFirstAnnotation
```
public com.google.common.base.Optional<A> getFirstAnnotation(int index)
```
    Description copied from interface: PeakList
    
    Return the first annotation in the list of annotations for the peak at index. If the specified index does not have any annotations null is returned.
    
    Specified by:
    
    getFirstAnnotation in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    index - the index of the peak
    
    Returns:
    the first annotation in the list of annotations, or null if the specified index has no annotations
  - sortAnnotations
```
public void sortAnnotations(Comparator<A> comparator)
```
    Description copied from interface: PeakList
    
    Sort the annotations for each annotated peak using the comparator
    
    Specified by:
    
    sortAnnotations in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    comparator - the comparator that is to be used to sort the annotations
  - getPrecursor
```
public Peak getPrecursor()
```
    Description copied from interface: PeakList
    
    Returns the precursor peak of this peak list
    
    Specified by:
    
    getPrecursor in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the precursor peak of this peak list
  - setPrecursor
```
public void setPrecursor(Peak precursor)
```
    Description copied from interface: PeakList
    
    Set the precursor peak for this peak list
    
    Specified by:
    
    setPrecursor in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    precursor - the precursor peak
  - getMsLevel
```
public int getMsLevel()
```
    Returns the ms level that this peak list was measured at
    
    Returns:
    the ms level that this peak list was measured at
  - setMsLevel
```
public void setMsLevel(int msLevel)
```
    Set the ms level that this peak list was measured at
    
    Parameters:
    msLevel - the ms level
  - cursor
```
public PeakCursor<A> cursor()
```
    Description copied from interface: PeakList
    
    Returns a cursor over the peaks in this peak list in proper sequence.
    
    Specified by:
    
    cursor in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    a cursor over the peaks in this peak list in proper sequence
  - calcVectorLength
```
public double calcVectorLength()
```
    Description copied from interface: PeakList
    
    Calculates the vector length of this peak list
    
    Specified by:
    
    calcVectorLength in interface PeakList<A extends PeakAnnotation>
    
    Returns:
    the vector length of this peak list
  - apply
```
public void apply(PeakProcessor<A,A> peakProcessor)
```
    Description copied from interface: PeakList
    
    Apply the peakProcessor to the peaks in this PeakList
    
    Specified by:
    
    apply in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    peakProcessor - the peak processor
  - apply
```
public void apply(PeakProcessorChain<A> peakProcessorChain)
```
    Description copied from interface: PeakList
    
    Apply the peakProcessorChain to the peaks in this PeakList
    
    Specified by:
    
    apply in interface PeakList<A extends PeakAnnotation>
    
    Parameters:
    peakProcessorChain - the peak processor list
  - equals
```
public boolean equals(Object o)
```
    Overrides:
    
    equals in class Object
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class Object

Class Spectrum<A extends PeakAnnotation>

Nested Class Summary

Nested classes/interfaces inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList

Constructor Detail

Spectrum

Spectrum

Spectrum

Spectrum

Method Detail

getId

setId

addPeaks

addPeaksNoAnnotations

addPeaks

addSorted

addSorted

add

add

add

size

isEmpty

getMz

getIntensity

clear

getTotalIonCurrent

getClosestIndex

indexOf

indexOf

getMostIntenseIndex

getMostIntenseIndex

getBasePeakMz

getBasePeakIntensity

getMzs

getMzs

getMzs

getIntensities

getIntensities

getIntensities

getPrecision

setIntensityAt

trimToSize

ensureCapacity

addAnnotation

addAnnotations

removeAnnotation

clearAnnotationsAt

clearAnnotations

hasAnnotations

getAnnotationIndexes

hasAnnotationsAt

getAnnotations

getFirstAnnotation

sortAnnotations

getPrecursor

setPrecursor

getMsLevel

setMsLevel

cursor

calcVectorLength

apply

apply

equals

hashCode