fr.orsay.lri.varna.views
Class VueUI
java.lang.Object
fr.orsay.lri.varna.views.VueUI
public class VueUI
- extends Object
Field Summary |
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_bpseqFilter
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_ctFilter
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_dbnFilter
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_epsFilter
|
private File |
_fileChooserDirectory
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_jpgFilter
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_pngFilter
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_svgFilter
|
private UndoableEditSupport |
_undoableEditSupport
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_varnaFilter
|
private VARNAPanel |
_vp
|
(package private) fr.orsay.lri.varna.applications.FileNameExtensionFilter |
_xfigFilter
|
Method Summary |
void |
addUndoableEditListener(UndoManager manager)
|
Hashtable<Integer,Point2D.Double> |
backupAllCoords()
|
static double |
computeAngle(Point2D.Double center,
Point2D.Double p)
|
private ArrayList<ModeleBase> |
extractMaxContiguousPortion(ArrayList<ModeleBase> m)
|
private void |
loadPath(JFileChooser jfc)
|
private double |
normalizeAngle(double angle)
|
private double |
normalizeAngle(double angle,
double base)
|
private Point2D.Double |
project(Point2D.Double O,
Point2D.Double Ox,
Point2D.Double C)
|
private void |
rotateHelix(Point2D.Double center,
int i,
int j,
double angle)
|
private Point2D.Double |
rotatePoint(Point2D.Double center,
Point2D.Double p,
double angle)
|
private void |
savePath(JFileChooser jfc)
|
void |
saveToJPEG(String filename)
|
void |
saveToPNG(String filename)
|
(package private) boolean |
shouldFlip(int index,
Point2D.Double P)
Tests if an helix needs to be flipped. |
void |
UIAbout()
|
void |
UIAddBP(int i,
int j,
ModeleBP ms)
|
void |
UIAnnotationAddFromStructure(int type,
ArrayList<Integer> listeIndex)
|
void |
UIAnnotationEditFromAnnotation(TextAnnotation textAnnotation)
|
void |
UIAnnotationEditFromStructure(int type,
ArrayList<Integer> listeIndex)
|
void |
UIAnnotationRemoveFromAnnotation(TextAnnotation textAnnotation)
|
void |
UIAnnotationRemoveFromStructure(int type,
ArrayList<Integer> listeIndex)
|
void |
UIAnnotationsAdd()
|
void |
UIAnnotationsAddBase(int x,
int y)
|
void |
UIAnnotationsAddChemProb(int x,
int y)
|
void |
UIAnnotationsAddHelix(int x,
int y)
|
void |
UIAnnotationsAddLoop(int x,
int y)
|
void |
UIAnnotationsAddPosition(int x,
int y)
|
void |
UIAnnotationsAddRegion(int x,
int y)
|
void |
UIAnnotationsEdit()
|
void |
UIAnnotationsRemove()
|
void |
UIAutoAnnotateHelices()
|
void |
UIAutoAnnotateInteriorLoops()
|
void |
UIAutoAnnotateStrandEnds()
|
void |
UIAutoAnnotateTerminalLoops()
|
void |
UIBaseAllColor()
|
void |
UIBasePairTypeColor()
|
void |
UIBaseTypeColor()
|
String |
UIChooseOutputFile(ArrayList<fr.orsay.lri.varna.applications.FileNameExtensionFilter> filtre)
Opens a save dialog with right extensions and return the absolute path |
String |
UIChooseOutputFile(fr.orsay.lri.varna.applications.FileNameExtensionFilter filtre)
|
void |
UICircular()
|
void |
UIColorBasePair()
|
void |
UICustomZoom()
|
void |
UIEditAllBasePairs()
|
void |
UIEditBasePair()
|
void |
UIExport()
|
void |
UIExportEPS()
|
void |
UIExportJPEG()
|
void |
UIExportPNG()
|
void |
UIExportSVG()
|
void |
UIExportXFIG()
|
void |
UIFile()
|
void |
UIFlipHelix(Point h)
Flip an helix around its supporting base |
void |
UIGlobalRotation()
|
void |
UIGlobalRotation(double d)
|
void |
UILine()
|
void |
UILoadColorMapValues()
|
void |
UIManualInput()
|
void |
UIMOTIFView()
|
void |
UIMoveHelixAtom(int index,
Point2D.Double newPos)
Move a helix of the rna |
void |
UIMoveSingleBase(int index,
double nx,
double ny)
|
void |
UIMoveSingleBase(int index,
Point2D.Double dv)
|
void |
UINAView()
|
void |
UIPickGapsBasesColor()
|
void |
UIPickSpecialBasesColor()
|
void |
UIPrint()
|
void |
UIRadiate()
|
void |
UIRedo()
|
void |
UIRemoveBP(ModeleBP ms)
|
void |
UIReset()
|
void |
UIRotateEverything(double delta,
double base,
double pLimL,
double pLimR,
Point h,
Point ml)
|
void |
UIRotateHelixAtom(int index,
Point2D.Double newPos)
|
void |
UISaveAs()
|
void |
UISaveAsBPSEQ()
|
void |
UISaveAsCT()
|
void |
UISaveAsDBN()
|
void |
UISetBackboneColor()
|
void |
UISetBackground()
|
void |
UISetBaseCenter(int index,
double x,
double y)
|
void |
UISetBaseCenter(int index,
Point2D.Double p)
|
void |
UISetBaseCharacter()
|
void |
UISetBorder()
|
void |
UISetBPHeightIncrement()
|
void |
UISetBPStyle()
|
void |
UISetColorMapCaption()
|
void |
UISetColorMapStyle()
|
void |
UISetColorMapValues()
|
void |
UISetNumPeriod()
|
void |
UISetSpaceBetweenBases()
|
void |
UISetTitle()
|
void |
UISetTitleColor()
|
void |
UISetTitleFont()
|
void |
UIShiftBaseCoord(ArrayList<Integer> indices,
double dx,
double dy)
|
void |
UIShiftBaseCoord(ArrayList<Integer> indices,
Point2D.Double dv)
|
void |
UIThicknessBasePair()
|
void |
UIToggleColorGapsBases()
|
void |
UIToggleColorMap()
|
void |
UIToggleColorSpecialBases()
|
void |
UIToggleFlatExteriorLoop()
|
void |
UIToggleGaspinMode()
|
void |
UIToggleModifiable()
|
void |
UIToggleShowNCBP()
|
void |
UIToggleShowNonPlanar()
|
void |
UIToggleShowWarnings()
|
void |
UIUndo()
|
void |
UIVARNAView()
|
void |
UIZoomIn()
|
void |
UIZoomOut()
|
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
_vp
private VARNAPanel _vp
_fileChooserDirectory
private File _fileChooserDirectory
_undoableEditSupport
private UndoableEditSupport _undoableEditSupport
_varnaFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _varnaFilter
_bpseqFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _bpseqFilter
_ctFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _ctFilter
_dbnFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _dbnFilter
_jpgFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _jpgFilter
_pngFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _pngFilter
_epsFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _epsFilter
_svgFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _svgFilter
_xfigFilter
fr.orsay.lri.varna.applications.FileNameExtensionFilter _xfigFilter
VueUI
public VueUI(VARNAPanel vp)
addUndoableEditListener
public void addUndoableEditListener(UndoManager manager)
UIToggleColorMap
public void UIToggleColorMap()
backupAllCoords
public Hashtable<Integer,Point2D.Double> backupAllCoords()
UIToggleFlatExteriorLoop
public void UIToggleFlatExteriorLoop()
UIRadiate
public void UIRadiate()
UIMOTIFView
public void UIMOTIFView()
UILine
public void UILine()
UICircular
public void UICircular()
UINAView
public void UINAView()
UIVARNAView
public void UIVARNAView()
UIReset
public void UIReset()
savePath
private void savePath(JFileChooser jfc)
loadPath
private void loadPath(JFileChooser jfc)
UIFile
public void UIFile()
throws fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
UISetColorMapStyle
public void UISetColorMapStyle()
UILoadColorMapValues
public void UILoadColorMapValues()
UISetColorMapValues
public void UISetColorMapValues()
UIManualInput
public void UIManualInput()
throws ParseException,
fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
- Throws:
ParseException
fr.orsay.lri.varna.exceptions.ExceptionNonEqualLength
UISetTitle
public void UISetTitle()
UISetColorMapCaption
public void UISetColorMapCaption()
UISetBaseCharacter
public void UISetBaseCharacter()
UIExport
public void UIExport()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied,
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden,
fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding
UIExportJPEG
public void UIExportJPEG()
throws fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding,
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
UIPrint
public void UIPrint()
UIExportPNG
public void UIExportPNG()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
UIExportXFIG
public void UIExportXFIG()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
UIExportEPS
public void UIExportEPS()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
UIExportSVG
public void UIExportSVG()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionWritingForbidden
UISaveAsDBN
public void UISaveAsDBN()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
UISaveAsCT
public void UISaveAsCT()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
UISaveAsBPSEQ
public void UISaveAsBPSEQ()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
UISaveAs
public void UISaveAs()
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed,
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied
UIChooseOutputFile
public String UIChooseOutputFile(fr.orsay.lri.varna.applications.FileNameExtensionFilter filtre)
UIChooseOutputFile
public String UIChooseOutputFile(ArrayList<fr.orsay.lri.varna.applications.FileNameExtensionFilter> filtre)
- Opens a save dialog with right extensions and return the absolute path
- Parameters:
filtre
- Allowed extensions
- Returns:
null
if the user doesn't approve the save dialog,
absolutePath
if the user approve the save dialog
UISetBorder
public void UISetBorder()
UISetBackground
public void UISetBackground()
UIZoomIn
public void UIZoomIn()
UIZoomOut
public void UIZoomOut()
UICustomZoom
public void UICustomZoom()
UIGlobalRotation
public void UIGlobalRotation()
UIGlobalRotation
public void UIGlobalRotation(double d)
UISetBPStyle
public void UISetBPStyle()
UISetTitleColor
public void UISetTitleColor()
UISetBackboneColor
public void UISetBackboneColor()
UISetTitleFont
public void UISetTitleFont()
UISetSpaceBetweenBases
public void UISetSpaceBetweenBases()
UISetBPHeightIncrement
public void UISetBPHeightIncrement()
UISetNumPeriod
public void UISetNumPeriod()
UIEditBasePair
public void UIEditBasePair()
UIColorBasePair
public void UIColorBasePair()
UIThicknessBasePair
public void UIThicknessBasePair()
saveToPNG
public void saveToPNG(String filename)
throws fr.orsay.lri.varna.exceptions.ExceptionExportFailed
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
saveToJPEG
public void saveToJPEG(String filename)
throws fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding,
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
- Throws:
fr.orsay.lri.varna.exceptions.ExceptionJPEGEncoding
fr.orsay.lri.varna.exceptions.ExceptionExportFailed
UIToggleShowNCBP
public void UIToggleShowNCBP()
UIToggleColorSpecialBases
public void UIToggleColorSpecialBases()
UIToggleColorGapsBases
public void UIToggleColorGapsBases()
UIToggleShowNonPlanar
public void UIToggleShowNonPlanar()
UIToggleShowWarnings
public void UIToggleShowWarnings()
UIPickSpecialBasesColor
public void UIPickSpecialBasesColor()
UIPickGapsBasesColor
public void UIPickGapsBasesColor()
UIBaseTypeColor
public void UIBaseTypeColor()
UIToggleModifiable
public void UIToggleModifiable()
UIBasePairTypeColor
public void UIBasePairTypeColor()
UIBaseAllColor
public void UIBaseAllColor()
UIAbout
public void UIAbout()
UIAutoAnnotateHelices
public void UIAutoAnnotateHelices()
UIAutoAnnotateStrandEnds
public void UIAutoAnnotateStrandEnds()
UIAutoAnnotateInteriorLoops
public void UIAutoAnnotateInteriorLoops()
UIAutoAnnotateTerminalLoops
public void UIAutoAnnotateTerminalLoops()
UIAnnotationRemoveFromAnnotation
public void UIAnnotationRemoveFromAnnotation(TextAnnotation textAnnotation)
UIAnnotationEditFromAnnotation
public void UIAnnotationEditFromAnnotation(TextAnnotation textAnnotation)
UIAnnotationAddFromStructure
public void UIAnnotationAddFromStructure(int type,
ArrayList<Integer> listeIndex)
throws Exception
- Throws:
Exception
UIAnnotationEditFromStructure
public void UIAnnotationEditFromStructure(int type,
ArrayList<Integer> listeIndex)
UIAnnotationRemoveFromStructure
public void UIAnnotationRemoveFromStructure(int type,
ArrayList<Integer> listeIndex)
UIAnnotationsAddPosition
public void UIAnnotationsAddPosition(int x,
int y)
UIAnnotationsAddBase
public void UIAnnotationsAddBase(int x,
int y)
UIAnnotationsAddLoop
public void UIAnnotationsAddLoop(int x,
int y)
extractMaxContiguousPortion
private ArrayList<ModeleBase> extractMaxContiguousPortion(ArrayList<ModeleBase> m)
UIAnnotationsAddRegion
public void UIAnnotationsAddRegion(int x,
int y)
UIAnnotationsAddChemProb
public void UIAnnotationsAddChemProb(int x,
int y)
UIAnnotationsAddHelix
public void UIAnnotationsAddHelix(int x,
int y)
UIToggleGaspinMode
public void UIToggleGaspinMode()
UIAnnotationsAdd
public void UIAnnotationsAdd()
UIEditAllBasePairs
public void UIEditAllBasePairs()
UIAnnotationsRemove
public void UIAnnotationsRemove()
UIAnnotationsEdit
public void UIAnnotationsEdit()
UIAddBP
public void UIAddBP(int i,
int j,
ModeleBP ms)
UIRemoveBP
public void UIRemoveBP(ModeleBP ms)
UIShiftBaseCoord
public void UIShiftBaseCoord(ArrayList<Integer> indices,
double dx,
double dy)
UIShiftBaseCoord
public void UIShiftBaseCoord(ArrayList<Integer> indices,
Point2D.Double dv)
UIMoveSingleBase
public void UIMoveSingleBase(int index,
double nx,
double ny)
UIMoveSingleBase
public void UIMoveSingleBase(int index,
Point2D.Double dv)
UISetBaseCenter
public void UISetBaseCenter(int index,
double x,
double y)
UISetBaseCenter
public void UISetBaseCenter(int index,
Point2D.Double p)
UIUndo
public void UIUndo()
UIRedo
public void UIRedo()
UIMoveHelixAtom
public void UIMoveHelixAtom(int index,
Point2D.Double newPos)
- Move a helix of the rna
- Parameters:
index
- :the index of the selected basenewPos
- :the new xy coordinate, within the logical system of coordinates
project
private Point2D.Double project(Point2D.Double O,
Point2D.Double Ox,
Point2D.Double C)
UIFlipHelix
public void UIFlipHelix(Point h)
- Flip an helix around its supporting base
shouldFlip
boolean shouldFlip(int index,
Point2D.Double P)
- Tests if an helix needs to be flipped.
UIRotateHelixAtom
public void UIRotateHelixAtom(int index,
Point2D.Double newPos)
UIRotateEverything
public void UIRotateEverything(double delta,
double base,
double pLimL,
double pLimR,
Point h,
Point ml)
normalizeAngle
private double normalizeAngle(double angle)
normalizeAngle
private double normalizeAngle(double angle,
double base)
computeAngle
public static double computeAngle(Point2D.Double center,
Point2D.Double p)
rotateHelix
private void rotateHelix(Point2D.Double center,
int i,
int j,
double angle)
rotatePoint
private Point2D.Double rotatePoint(Point2D.Double center,
Point2D.Double p,
double angle)