import java.awt.Color;
-import jalview.datamodel.annotations.AnnotationColouringI;
-
/**
* Holds all annotation values for a position in an AlignmentAnnotation row
*
public Color colour;
/**
- * link back to the AnnotationRowBuilder
- */
- private AnnotationColouringI annotationColouring = null;
-
- /**
* Creates a new Annotation object.
*
* @param displayChar
secondaryStructure = that.secondaryStructure;
value = that.value;
colour = that.colour;
- annotationColouring = that.getAnnotationColouring();
}
/**
&& (secondaryStructure == '\0' || (secondaryStructure == ' '))
&& colour == null);
}
-
- public void setAnnotationColouring(AnnotationColouringI a)
- {
- this.annotationColouring = a;
- }
-
- public AnnotationColouringI getAnnotationColouring()
- {
- return annotationColouring;
- }
}
import jalview.datamodel.Annotation;
import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.TFType;
public class AlphaFoldAnnotationRowBuilder extends AnnotationRowBuilder
{
@Override
public void processAnnotation(Annotation annotation)
{
- AnnotationColouringI ac = new AnnotationColouringPLDDT();
- annotation.setAnnotationColouring(ac);
- annotation.colour = ac.valueToColour(annotation.value);
+ if (annotation.value > 90)
+ {
+ // Very High
+ annotation.colour = new java.awt.Color(0, 83, 214);
+ }
+ if (annotation.value <= 90)
+ {
+ // High
+ annotation.colour = new java.awt.Color(101, 203, 243);
+ }
+ if (annotation.value <= 70)
+ {
+ // Confident
+ annotation.colour = new java.awt.Color(255, 219, 19);
+ }
+ if (annotation.value < 50)
+ {
+ annotation.colour = new java.awt.Color(255, 125, 69);
+ }
}
-
}
\ No newline at end of file
+++ /dev/null
-package jalview.datamodel.annotations;
-
-import java.awt.Color;
-import java.util.List;
-import java.util.Map;
-
-public abstract class AnnotationColouring implements AnnotationColouringI
-{
- @Override
- public Color valueToColour(float val)
- {
- return null;
- }
-
- @Override
- public List<Map.Entry<Float, Color>> rangeColours(float val1, float val2)
- {
- return null;
- }
-}
+++ /dev/null
-package jalview.datamodel.annotations;
-
-import java.awt.Color;
-import java.util.List;
-import java.util.Map;
-
-public interface AnnotationColouringI
-{
- /**
- * Return the colour associated with this value
- *
- * @param val
- * @return
- */
- public Color valueToColour(float val);
-
- /**
- * Given two values, val1 and val2, returns a list of (float,Color) pairs (as
- * Map.Entry objects). The float is a proportional distance (should start with
- * 0 and end with 1) and the Color is the color change from that point.
- *
- * @param val1
- * @param val2
- * @return
- */
- public List<Map.Entry<Float, Color>> rangeColours(float val1, float val2);
-}
+++ /dev/null
-package jalview.datamodel.annotations;
-
-import java.awt.Color;
-
-public class AnnotationColouringPLDDT extends AnnotationColouringRanges
- implements AnnotationColouringI
-{
- private static final Color BLUE = new Color(0, 83, 214);
-
- private static final Color CYAN = new Color(101, 203, 243);
-
- private static final Color YELLOW = new Color(255, 219, 19);
-
- private static final Color ORANGE = new Color(255, 125, 69);
-
- static
- {
- addFirstColour(ORANGE);
- addValColour(50, YELLOW);
- addValColour(70, CYAN);
- addValColour(90, BLUE);
- }
-}
+++ /dev/null
-package jalview.datamodel.annotations;
-
-import java.awt.Color;
-import java.util.AbstractMap;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-public class AnnotationColouringRanges extends AnnotationColouring
-{
- private static List<Color> colours = new ArrayList<Color>();
-
- private static List<Float> values = new ArrayList<Float>();
-
- protected static void addValColour(float v, Color c)
- {
- values.add(v);
- colours.add(c);
- }
-
- protected static void addFirstColour(Color c)
- {
- colours.add(0, c);
- }
-
- static
- {
- // e.g.
- // addFirstColour(Color.black); -infty..25 = black
- // addValColour(25,Color.darkGray); 25..50 = darkGray
- // addValColour(50,Color.gray); 50..75 = gray
- // addValColour(75,Color.lightGray); 75..100 = lightGray
- // addValColour(100,Color.white); 100..infty = white
- }
-
- @Override
- public Color valueToColour(float val)
- {
- Color col = null;
- boolean set = false;
- for (int i = 0; i < values.size(); i++)
- {
- float compareVal = values.get(i);
- if (colours.size() > i)
- {
- col = colours.get(i);
- }
- if (val < compareVal)
- {
- set = true;
- break;
- }
- }
- if (!set && colours.size() > values.size())
- {
- col = colours.get(values.size());
- }
- return col;
- }
-
- @Override
- public List<Map.Entry<Float, Color>> rangeColours(float val1, float val2)
- {
- String cacheKey = cacheKey(val1, val2);
- if (!valColorsCache.containsKey(cacheKey))
- {
- List<Map.Entry<Float, Color>> valCols = new ArrayList<>();
- float v1 = val1 <= val2 ? val1 : val2;
- float v2 = val1 <= val2 ? val2 : val1;
- boolean reversed = val1 > val2;
- Color col = null;
- boolean set1 = false;
- boolean set2 = false;
- int i = 0;
- while (i < values.size() && (!set1 || !set2))
- {
- float compareVal = values.get(i);
- if (colours.size() > i)
- {
- col = colours.get(i);
- }
-
- if (!set1 && v1 < compareVal)
- {
- // add the initial checkpoint
- valCols.add(valCol(reversed ? 1f : 0f, col));
- set1 = true;
- }
-
- if (!set2 && v2 < compareVal)
- {
- // add the final checkpoint
- valCols.add(valCol(reversed ? 0f : 1f, col));
- set2 = true;
- break;
- }
-
- if (set1) // && !set2
- {
- // add an intermediate checkpoint
- float v = (compareVal - v1) / (v2 - v1);
- valCols.add(valCol(reversed ? 1f - v : v, col));
- }
-
- i++;
- }
- if (colours.size() > i)
- {
- col = colours.get(i);
- }
- // add above the final checkpoint colour(s) if not set
- if (!set1)
- {
- valCols.add(valCol(reversed ? 1f : 0f, col));
- set1 = true;
- }
- if (!set2)
- {
- // add the final checkpoint
- valCols.add(valCol(reversed ? 0f : 1f, col));
- set2 = true;
- }
- if (reversed)
- {
- Collections.reverse(valCols);
- }
- // put in the cache
- valColorsCache.put(cacheKey, valCols);
- }
-
- return getFromCache(cacheKey);
- }
-
- private Map.Entry<Float, Color> valCol(Float v, Color c)
- {
- return new AbstractMap.SimpleEntry<Float, Color>(v, c);
- }
-
- private Map<String, List<Map.Entry<Float, Color>>> valColorsCache = new HashMap<String, List<Map.Entry<Float, Color>>>();
-
- private List<Map.Entry<Float, Color>> getFromCache(String key)
- {
- // return a copy of the list in case of element order manipulation (e.g.
- // valCols.remove(0))
- return new ArrayList<Map.Entry<Float, Color>>(valColorsCache.get(key));
- }
-
- private static String cacheKey(float f1, float f2)
- {
- return new StringBuilder().append(Float.hashCode(f1)).append(' ')
- .append(Float.hashCode(f2)).toString();
- }
-}
return tfType;
}
- /**
- * Colouring model for the annotation
- *
- * @param ac
- */
- private AnnotationColouringI annotationColouring = null;
-
- public void setAnnotationColouring(AnnotationColouringI ac)
- {
- annotationColouring = ac;
- }
-
- public AnnotationColouringI getAnnotationColouring()
- {
- return annotationColouring;
- }
-
public String getName()
{
return name;
import java.awt.geom.AffineTransform;
import java.awt.image.ImageObserver;
import java.util.BitSet;
-import java.util.Collections;
import java.util.HashMap;
import java.util.Hashtable;
-import java.util.List;
import java.util.Map;
import org.jfree.graphics2d.svg.SVGGraphics2D;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.ProfilesI;
-import jalview.datamodel.annotations.AnnotationColouringI;
import jalview.renderer.api.AnnotationRendererFactoryI;
import jalview.renderer.api.AnnotationRowRendererI;
import jalview.schemes.ColourSchemeI;
continue;
}
- boolean individualColour = false;
if (aa_annotations[column].colour == null)
{
g.setColor(Color.black);
else
{
g.setColor(aa_annotations[column].colour);
- individualColour = true;
}
boolean value1Exists = column > 0
&& aa_annotations[column - 1] != null;
float value1 = 0f;
- Color color1 = null;
if (value1Exists)
{
value1 = aa_annotations[column - 1].value;
- color1 = aa_annotations[column - 1].colour;
}
float value2 = aa_annotations[column].value;
boolean nextValueExists = aa_annotations.length > column + 1
y1 = y - yValueToPixelHeight(value1, min, range, graphHeight);
y2 = y - yValueToPixelHeight(value2, min, range, graphHeight);
- float v1 = value1;
- float v2 = value2;
int a1 = (x - 1) * charWidth + charWidth / 2;
int b1 = y1;
int a2 = x * charWidth + charWidth / 2;
// only draw an initial half-line
a1 = x * charWidth;
b1 = y1 + (y2 - y1) / 2;
- v1 = value1 + (value2 - value1) / 2;
}
else if (x == eRes - sRes)
{
// line
a2 = x * charWidth - 1;
b2 = y1 + (y2 - y1) / 2;
- v2 = value1 + (value2 - value1) / 2;
}
else
{
}
- AnnotationColouringI ac = aa_annotations[column]
- .getAnnotationColouring();
- List<Map.Entry<Float, Color>> valCols = ac == null ? null
- : ac.rangeColours(v1, v2);
- if (valCols != null)
- {
- drawSegmentedLine(g, valCols, a1, b1, a2, b2);
- }
- else
- {
- drawLine(g, a1, b1, a2, b2);
- }
+ drawLine(g, a1, b1, a2, b2);
x++;
}
return dashedLineLookup.get(charWidth);
}
- private void drawSegmentedLine(Graphics g,
- List<Map.Entry<Float, Color>> valCols, int x1, int y1, int x2,
- int y2)
- {
- if (valCols == null || valCols.size() == 0)
- {
- return;
- }
- // let's only go forwards+up|down -- try and avoid providing right to left
- // x values
- if (x2 < x1)
- {
- int tmp = y2;
- y2 = y1;
- y1 = tmp;
- tmp = x2;
- x2 = x1;
- x1 = tmp;
- Collections.reverse(valCols);
- }
- Graphics2D g2d = (Graphics2D) g.create();
- float yd = y2 - y1;
- boolean reverse = yd > 0; // reverse => line going DOWN (y increasing)
- Map.Entry<Float, Color> firstValCol = valCols.remove(0);
- float firstVal = firstValCol.getKey();
- Color firstCol = firstValCol.getValue();
- int yy1 = 0;
- yy1 = reverse ? (int) Math.ceil(y1 + firstVal * yd)
- : (int) Math.floor(y1 + firstVal * yd);
- Color thisCol = firstCol;
- for (int i = 0; i < valCols.size(); i++)
- {
- Map.Entry<Float, Color> valCol = valCols.get(i);
- float val = valCol.getKey();
- Color col = valCol.getValue();
- int clipX = x1 - 1;
- int clipW = x2 - x1 + 2;
- int clipY = 0;
- int clipH = 0;
- int yy2 = 0;
- if (reverse) // line going down
- {
- yy2 = (int) Math.ceil(y1 + val * yd);
- g2d.setColor(thisCol);
- clipY = yy1 - 1;
- clipH = yy2 - yy1;
- if (i == 0)
- {
- // highest segment, don't clip at the top
- clipY -= 2;
- clipH += 2;
- }
- if (i == valCols.size() - 1)
- {
- // lowest segment, don't clip at the bottom
- clipH += 2;
- }
- }
- else // line going up (or level)
- {
- yy2 = (int) Math.floor(y1 + val * yd);
- // g2d.setColor(Color.cyan); g2d.drawRect(x1 - 1, yy1, x2 - x1 + 1, yy2
- // -
- // yy1 + 1);
- g2d.setColor(col);
- clipY = yy2;
- clipH = yy1 - yy2;
- if (i == 0)
- {
- // lowest segment, don't clip at the bottom
- clipH += 2;
- }
- if (i == valCols.size() - 1)
- {
- // highest segment, don't clip at the top
- clipY -= 2;
- clipH += 2;
- }
- }
- g2d.setClip(clipX, clipY, clipW, clipH);
- drawLine(g2d, x1, y1, x2, y2);
- yy1 = yy2;
- thisCol = col;
- }
- g2d.dispose();
- }
-
private static int yValueToPixelHeight(float value, float min,
float range, int graphHeight)
{
git://source.jalview.org / jalview.git / commitdiff