edu.sdsc.mbt.viewers.GLViewerImpl
Class SsGeometry

java.lang.Object
  edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity
      edu.sdsc.mbt.viewers.GLViewerImpl.SsGeometry

Direct Known Subclasses:

CoilGeometry, HelixGeometry, StrandGeometry

public class SsGeometry

extends GeometryEntity

SsGeometry is the base class for the geometry of all Secondary Structure objects.

Author:

Apostol Gramada

Field Summary

static java.util.HashMap	colorCache
static java.util.HashMap	colorReference This hash is used to look up float[] values by a reference to a Color object

Constructor Summary

SsGeometry()

Method Summary

static void	drawSs(Chain c, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut, StructureMap structureMap, StructureStyles styles, boolean ribbon) Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.
static void	drawSs(Chain c, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut, StructureMap structureMap, StructureStyles styles, boolean ribbon, float helixQuality, float strandQuality, float turnQuality, float coilQuality, int helixSmoothingSteps, int strandSmoothingSteps, int turnSmoothingSteps, int coilSmoothingSteps, int helixCsType, int strandCsType, int turnCsType, int coilCsType, int helixSsShape) Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.
static void	drawSs(Chain c, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut, StructureMap structureMap, StructureStyles styles, boolean ribbon, int helixSmoothingSteps, int strandSmoothingSteps, int turnSmoothingSteps, int coilSmoothingSteps) Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.
static void	drawSs(Chain c, javax.media.opengl.GL gl, javax.media.opengl.glu.GLU glu, com.sun.opengl.util.GLUT glut, StructureMap structureMap, StructureStyles styles, boolean ribbon, int helixSmoothingSteps, int strandSmoothingSteps, int turnSmoothingSteps, int coilSmoothingSteps, int helixSsShape) Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm.
int	getClosestResidueIndex(float[] point) Returns the index of the closest residue to the given point, with the given color.
java.awt.Color[]	getColorMap() Returns the color map from a given set of float arrays.
boolean	getHighlightState()
SsGeometry	getNextSs() Returns the next Secondary Structure geometry (in a chain for instance)
Vec3f	getNextToFirstCa() First CA coord (after smoothing) may be needed outside for imposing continuity Deprecated
float[]	getNextToFirstCaCoord() First CA coord (after smoothing) may be needed outside for imposing continuity
SsGeometry	getPreviousSs() Returns the previous Secondary Structure geometry (in a chain for instance)
Vec3f	getPreviousToLastCa() Get Previous to last CA coord (after smoothing) may be needed outside for imposing continuity Deprecated
float[]	getPreviousToLastCaCoord() Previous to last CA coord (after smoothing) may be needed outside for imposing continuity
int	getPriestleSteps()
java.lang.Object	getUserData() Returns information (annotation) provided by the user
boolean[]	getVisibilityMap()
void	highlight(float[] color) Highlights the whole fragment with the given color.
void	highlightClosestResidue(float[] point, float[] color) Highlights the closest residue to the given point, with the given color.
void	highlightResidue(int index, float[] color) Hightlights the portion of SS sorounding residue at index.
void	highlightResidueRegion(int index, float[] color) Hightlights the portion of SS sorounding residue at index.
boolean	isLeftExtended() Set a flag that the fragment has been extended to the left to fill a gap
boolean	isRightExtended() Set a flag that the fragment has been extended to the right to fill a gap
void	resetColor() Resets the whole fragment to the original color map.
void	resetGeometryColor() Resets the vertex color in the geometry shape of this SsGeometry object.
void	resetRibbonColor(int index) Resets the color of the portion of SS sorounding residue at index.
void	setColorMap(java.awt.Color[] color) Sets the color map from a given set of colors Deprecated
void	setCoordinates(float[][] coord) Sets the coordinates along which to draw the spine.
void	setCoordinates(Vec3f[] coords) Sets the coordinates along which to draw the spine.
void	setCrossSectionStyle(CrossSectionStyle csStyle) Sets the cross section style
void	setCrossSectionType(int type) Sets the cross section type
void	setLeftExtended(boolean extend) Set a flag that the fragment has been extended to the left to fill a gap
void	setNextCaCoord(float[] coord) Set Next Ca atom coordinate
void	setNextCaCoord(Vec3f coord) Set Next Ca atom coordinate Deprecated
void	setNextSs(SsGeometry ss) Sets the next Secondary Structure geometry (in a chain for instance)
void	setPreviousCaCoord(float[] coord) Set Previous Ca atom coordinate.
void	setPreviousCaCoord(Vec3f coord) Set Previous Ca atom coordinate.
void	setPreviousSs(SsGeometry ss) Sets the previous Secondary Structure geometry (in a chain for instance)
void	setPriestleSteps(int i) Set the number of steps done in smoothing coordinates
void	setRightExtended(boolean extend) Set a flag that the fragment has been extended to the right to fill a gap
void	setRoundedShape(boolean round) Whether the shape should be rounded or not
void	setSegmentCount(int seg) Set number of segments to be drawn between any two consecutive CA positions.
void	setUserData(java.lang.Object info) Sets information (annotation) provided by the user
void	setVisibilityMap(boolean[] vis)

Methods inherited from class edu.sdsc.mbt.viewers.GLViewerImpl.GeometryEntity

drawJoglGeometry, getQuality, setQuality

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

colorCache

public static java.util.HashMap colorCache

colorReference

public static java.util.HashMap colorReference

This hash is used to look up float[] values by a reference to a Color object

Constructor Detail

SsGeometry

public SsGeometry()

Method Detail

drawSs

public static void drawSs(Chain c,
                          javax.media.opengl.GL gl,
                          javax.media.opengl.glu.GLU glu,
                          com.sun.opengl.util.GLUT glut,
                          StructureMap structureMap,
                          StructureStyles styles,
                          boolean ribbon)
                   throws FragmentTooShortException

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm. **JB converted to work on a single chain...

Throws:

FragmentTooShortException

drawSs

public static void drawSs(Chain c,
                          javax.media.opengl.GL gl,
                          javax.media.opengl.glu.GLU glu,
                          com.sun.opengl.util.GLUT glut,
                          StructureMap structureMap,
                          StructureStyles styles,
                          boolean ribbon,
                          int helixSmoothingSteps,
                          int strandSmoothingSteps,
                          int turnSmoothingSteps,
                          int coilSmoothingSteps)
                   throws FragmentTooShortException

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm. **JB converted to work on a single chain...

Throws:

FragmentTooShortException

drawSs

public static void drawSs(Chain c,
                          javax.media.opengl.GL gl,
                          javax.media.opengl.glu.GLU glu,
                          com.sun.opengl.util.GLUT glut,
                          StructureMap structureMap,
                          StructureStyles styles,
                          boolean ribbon,
                          int helixSmoothingSteps,
                          int strandSmoothingSteps,
                          int turnSmoothingSteps,
                          int coilSmoothingSteps,
                          int helixSsShape)
                   throws FragmentTooShortException

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm. **JB converted to work on a single chain...

Throws:

FragmentTooShortException

drawSs

public static void drawSs(Chain c,
                          javax.media.opengl.GL gl,
                          javax.media.opengl.glu.GLU glu,
                          com.sun.opengl.util.GLUT glut,
                          StructureMap structureMap,
                          StructureStyles styles,
                          boolean ribbon,
                          float helixQuality,
                          float strandQuality,
                          float turnQuality,
                          float coilQuality,
                          int helixSmoothingSteps,
                          int strandSmoothingSteps,
                          int turnSmoothingSteps,
                          int coilSmoothingSteps,
                          int helixCsType,
                          int strandCsType,
                          int turnCsType,
                          int coilCsType,
                          int helixSsShape)
                   throws FragmentTooShortException

Builds a scene of the secondary structures, the list of SS being the one produced by the StructureMap argument based on what is explicitely available in the data source file or from the Kabsch-Sander algorithm. **JB converted to work on a single chain...

Throws:

FragmentTooShortException

setCrossSectionType

public void setCrossSectionType(int type)

Sets the cross section type

setCrossSectionStyle

public void setCrossSectionStyle(CrossSectionStyle csStyle)

Sets the cross section style

setRoundedShape

public void setRoundedShape(boolean round)

Whether the shape should be rounded or not

setSegmentCount

public void setSegmentCount(int seg)

Set number of segments to be drawn between any two consecutive CA positions.

setCoordinates

public void setCoordinates(Vec3f[] coords)

Sets the coordinates along which to draw the spine. Deprecated, use setCoordinates with an array of float[] as an argument instead.

setCoordinates

public void setCoordinates(float[][] coord)

Sets the coordinates along which to draw the spine.

setPreviousSs

public void setPreviousSs(SsGeometry ss)

Sets the previous Secondary Structure geometry (in a chain for instance)

setNextSs

public void setNextSs(SsGeometry ss)

Sets the next Secondary Structure geometry (in a chain for instance)

setLeftExtended

public void setLeftExtended(boolean extend)

Set a flag that the fragment has been extended to the left to fill a gap

setRightExtended

public void setRightExtended(boolean extend)

Set a flag that the fragment has been extended to the right to fill a gap

setPreviousCaCoord

public void setPreviousCaCoord(Vec3f coord)

Set Previous Ca atom coordinate. Deprecated.

setPreviousCaCoord

public void setPreviousCaCoord(float[] coord)

Set Previous Ca atom coordinate.

setNextCaCoord

public void setNextCaCoord(Vec3f coord)

Set Next Ca atom coordinate Deprecated

setNextCaCoord

public void setNextCaCoord(float[] coord)

Set Next Ca atom coordinate

setColorMap

public void setColorMap(java.awt.Color[] color)

Sets the color map from a given set of colors Deprecated

setVisibilityMap

public void setVisibilityMap(boolean[] vis)

setUserData

public void setUserData(java.lang.Object info)

Sets information (annotation) provided by the user

resetGeometryColor

public void resetGeometryColor()

Resets the vertex color in the geometry shape of this SsGeometry object.

getClosestResidueIndex

public int getClosestResidueIndex(float[] point)

Returns the index of the closest residue to the given point, with the given color.

highlightClosestResidue

public void highlightClosestResidue(float[] point,
                                    float[] color)

Highlights the closest residue to the given point, with the given color.

highlight

public void highlight(float[] color)

Highlights the whole fragment with the given color.

resetColor

public void resetColor()

Resets the whole fragment to the original color map.

getColorMap

public java.awt.Color[] getColorMap()

Returns the color map from a given set of float arrays.

getVisibilityMap

public boolean[] getVisibilityMap()

getPreviousSs

public SsGeometry getPreviousSs()

Returns the previous Secondary Structure geometry (in a chain for instance)

getNextSs

public SsGeometry getNextSs()

Returns the next Secondary Structure geometry (in a chain for instance)

getHighlightState

public boolean getHighlightState()

highlightResidueRegion

public void highlightResidueRegion(int index,
                                   float[] color)

Hightlights the portion of SS sorounding residue at index.

highlightResidue

public void highlightResidue(int index,
                             float[] color)

Hightlights the portion of SS sorounding residue at index.

resetRibbonColor

public void resetRibbonColor(int index)

Resets the color of the portion of SS sorounding residue at index.

getUserData

public java.lang.Object getUserData()

Returns information (annotation) provided by the user

isLeftExtended

public boolean isLeftExtended()

Set a flag that the fragment has been extended to the left to fill a gap

isRightExtended

public boolean isRightExtended()

Set a flag that the fragment has been extended to the right to fill a gap

getNextToFirstCa

public Vec3f getNextToFirstCa()

First CA coord (after smoothing) may be needed outside for imposing continuity Deprecated

getNextToFirstCaCoord

public float[] getNextToFirstCaCoord()

First CA coord (after smoothing) may be needed outside for imposing continuity

getPreviousToLastCa

public Vec3f getPreviousToLastCa()

Get Previous to last CA coord (after smoothing) may be needed outside for imposing continuity Deprecated

getPreviousToLastCaCoord

public float[] getPreviousToLastCaCoord()

Previous to last CA coord (after smoothing) may be needed outside for imposing continuity

setPriestleSteps

public void setPriestleSteps(int i)

Set the number of steps done in smoothing coordinates

getPriestleSteps

public int getPriestleSteps()