public class CellDesignerPathwayStaining
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
class |
CellDesignerPathwayStaining.ColorPoint |
Modifier and Type | Field and Description |
---|---|
java.util.Vector<CellDesignerPathwayStaining.ColorPoint> |
aliaspoints |
float |
gridStepX |
float |
gridStepY |
float |
height |
float |
infradius |
boolean |
normalizeColumnValues |
java.util.Vector<CellDesignerPathwayStaining.ColorPoint> |
regularpoints |
java.awt.image.BufferedImage |
staining |
SimpleTable |
table |
float |
thresholdGradient |
boolean |
useModuleDefinitionsFromCellDesignerFile |
boolean |
useProteinNameIfHUGOisntFound |
float |
width |
Constructor and Description |
---|
CellDesignerPathwayStaining() |
Modifier and Type | Method and Description |
---|---|
void |
addGroupToPoint(CellDesignerPathwayStaining.ColorPoint cp,
java.util.Vector<java.lang.String> hugos) |
void |
assignColorsToGroupsFromTable(java.lang.String numericFeature) |
void |
assignColorsToPoints(java.util.Vector<CellDesignerPathwayStaining.ColorPoint> points) |
void |
assignRandomColorsToGroups(boolean redgreen) |
void |
createPoints() |
void |
determineSizeOftheMap() |
java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> |
extractGMTFromCellDesigner(java.lang.String fn) |
java.awt.Color |
getColorFromString(java.lang.String colorString) |
java.util.Vector<java.lang.String> |
getHugosFromCellDesignerIdentity(CelldesignerSpeciesIdentity csi) |
java.util.Vector<java.lang.String> |
getSpeciesHugos(CelldesignerComplexSpeciesAlias calias) |
java.util.Vector<java.lang.String> |
getSpeciesHugos(CelldesignerSpeciesAlias alias) |
void |
loadDataTable(java.lang.String fn) |
void |
loadDataTable(java.lang.String fn,
java.lang.String keyField) |
void |
loadGroupsOfProteins(java.lang.String fn) |
void |
loadMap(java.lang.String fn) |
static void |
main(java.lang.String[] args) |
java.util.Vector<java.awt.Color> |
makeRedGreenColorFromNumbers(float[] numbers,
float threshold_zvalue) |
void |
makeRegularPoints() |
void |
paintStaining(java.lang.String fn,
java.lang.String mappng_fn) |
void |
processAnnotation(java.lang.String name,
java.lang.String notes,
java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> groups) |
void |
run(java.lang.String CellDesignerFileName,
java.lang.String PngFileName,
java.lang.String DataTableFileName,
java.lang.String ProteinGroupFileName) |
void |
writeListOfPoints(java.util.Vector<CellDesignerPathwayStaining.ColorPoint> points,
java.lang.String fncoordinates,
java.lang.String fnlabels,
java.lang.String fncolors) |
public float width
public float height
public float gridStepX
public float gridStepY
public float infradius
public float thresholdGradient
public boolean normalizeColumnValues
public boolean useModuleDefinitionsFromCellDesignerFile
public boolean useProteinNameIfHUGOisntFound
public SimpleTable table
public java.awt.image.BufferedImage staining
public java.util.Vector<CellDesignerPathwayStaining.ColorPoint> aliaspoints
public java.util.Vector<CellDesignerPathwayStaining.ColorPoint> regularpoints
public static void main(java.lang.String[] args)
public void run(java.lang.String CellDesignerFileName, java.lang.String PngFileName, java.lang.String DataTableFileName, java.lang.String ProteinGroupFileName)
public void loadMap(java.lang.String fn)
public void determineSizeOftheMap()
public void loadGroupsOfProteins(java.lang.String fn)
public void createPoints()
public void addGroupToPoint(CellDesignerPathwayStaining.ColorPoint cp, java.util.Vector<java.lang.String> hugos)
public java.util.Vector<java.lang.String> getSpeciesHugos(CelldesignerSpeciesAlias alias)
public java.util.Vector<java.lang.String> getSpeciesHugos(CelldesignerComplexSpeciesAlias calias)
public java.util.Vector<java.lang.String> getHugosFromCellDesignerIdentity(CelldesignerSpeciesIdentity csi)
public void writeListOfPoints(java.util.Vector<CellDesignerPathwayStaining.ColorPoint> points, java.lang.String fncoordinates, java.lang.String fnlabels, java.lang.String fncolors)
public void makeRegularPoints()
public void assignRandomColorsToGroups(boolean redgreen)
public java.awt.Color getColorFromString(java.lang.String colorString)
public java.util.Vector<java.awt.Color> makeRedGreenColorFromNumbers(float[] numbers, float threshold_zvalue)
public void assignColorsToPoints(java.util.Vector<CellDesignerPathwayStaining.ColorPoint> points)
public void loadDataTable(java.lang.String fn)
public void loadDataTable(java.lang.String fn, java.lang.String keyField)
public void assignColorsToGroupsFromTable(java.lang.String numericFeature)
public void paintStaining(java.lang.String fn, java.lang.String mappng_fn)
public java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> extractGMTFromCellDesigner(java.lang.String fn)
public void processAnnotation(java.lang.String name, java.lang.String notes, java.util.HashMap<java.lang.String,java.util.Vector<java.lang.String>> groups)