From 51f87c0026052e327ab4eaf24f8e4dadca96a615 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 17 Mar 2009 16:58:35 +0000
Subject: [PATCH] holds shading and range parameters rendering a feature
 colour

---
 src/jalview/schemes/GraduatedColor.java |  156 +++++++++++++++++++++++++++++++
 1 file changed, 156 insertions(+)
 create mode 100644 src/jalview/schemes/GraduatedColor.java

diff --git a/src/jalview/schemes/GraduatedColor.java b/src/jalview/schemes/GraduatedColor.java
new file mode 100644
index 0000000..25681c4
--- /dev/null
+++ b/src/jalview/schemes/GraduatedColor.java
@@ -0,0 +1,156 @@
+/**
+ * 
+ */
+package jalview.schemes;
+
+import jalview.datamodel.SequenceFeature;
+
+import java.awt.Color;
+
+/**
+ * Value and/or thresholded colour scale used for colouring by annotation and feature score
+ * @author JimP
+ *
+ */
+public class GraduatedColor
+{
+  int thresholdState = AnnotationColourGradient.NO_THRESHOLD; // or ABOVE_THRESHOLD or BELOW_THRESHOLD
+  float lr,lg,lb,dr,dg,db;
+  /**
+   * linear scaling parameters, base, minimum colour threshold, range of linear scale from lower to upper
+   */
+  float base,range,thrsh;
+  /**
+   * when true, colour from u to u-d rather than u to u+d
+   */
+  boolean tolow=false;
+  /**
+   * construct a graduatedColor object from simple parameters
+   * @param low
+   * @param high
+   * @param min
+   * @param max
+   * color low->high from min->max
+   */
+  public GraduatedColor(Color low,Color high, float min,float max)
+  {
+    thrsh = Float.NaN;
+    tolow = min>=max;
+    lr = low.getRed()/255f;
+    lg = low.getGreen()/255f;
+    lb = low.getBlue()/255f;
+    dr = (high.getRed()/255f)-lr;
+    dg = (high.getGreen()/255f)-lg;
+    db = (high.getBlue()/255f)-lb;
+    if (tolow)
+    {
+      base = max;
+      range = min-max;
+    } else {
+      base = min;
+      range = max-min;
+    }
+  }
+  public GraduatedColor(GraduatedColor oldcs)
+  {
+    lr = oldcs.lr;
+    lg = oldcs.lg;
+    lb = oldcs.lb;
+    dr = oldcs.dr;
+    dg = oldcs.dg;
+    db = oldcs.db;
+    base = oldcs.base;
+    range = oldcs.range;
+    tolow = oldcs.tolow;
+    thresholdState = oldcs.thresholdState;
+    thrsh = oldcs.thrsh;
+  }
+  /**
+   * make a new gradient from an old one with a different scale range
+   * @param oldcs
+   * @param min
+   * @param max
+   */
+  public GraduatedColor(GraduatedColor oldcs, float min, float max)
+  {
+    this(oldcs);
+    if (max<min)
+    {
+      base = max;
+      range = min-max;
+      tolow=true;
+    } else {
+      base = min;
+      range = max-min;
+      tolow=false;
+    }
+  }
+  public Color getMinColor()
+  {
+    return new Color(lr,lg,lb);
+  }
+  public Color getMaxColor()
+  {
+    return new Color(lr+dr,lg+dg,lb+db);
+  }
+  public boolean getTolow()
+  {
+    return tolow;
+  }
+  public void setTolow(boolean tolower)
+  {
+    tolow = tolower;
+  }
+  public boolean isColored(SequenceFeature feature)
+  {
+    float val = feature.getScore();
+    if (val==Float.NaN)
+    {
+      return true;
+    }
+    if (this.thresholdState==AnnotationColourGradient.NO_THRESHOLD)
+    {
+      return true;
+    }
+    if (this.thrsh==Float.NaN)
+    {
+      return true;
+    }
+    boolean rtn = thresholdState==AnnotationColourGradient.ABOVE_THRESHOLD;
+    if (val<=thrsh)
+    {
+      return !rtn; //  ? !tolow : tolow;
+    } else {
+      return rtn; //  ? tolow : !tolow;
+    }
+  }
+  public Color findColor(SequenceFeature feature)
+  {     
+    if (range==0.0)
+    {
+      return getMaxColor();
+    }
+    float scr = feature.getScore();
+    if (scr==Float.NaN)
+    {
+      return getMinColor();
+    }
+    float scl = (scr-base)/range;
+    if (tolow) { scl = -scl; }
+    if (scl<0f) { scl = 0f; }
+    if (scl>1f) { scl = 1f; }
+    return new Color(lr+scl*dr,lg+scl*dg,lb+scl*db);
+  }
+  public void setThresh(float value)
+  {
+    thrsh = value;
+  }
+  public void setThreshType(int aboveThreshold)
+  {
+    thresholdState = aboveThreshold;
+  }
+  public int getThreshType()
+  {
+    return thresholdState;
+  }
+}
-- 
1.7.10.2