X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FGraduatedColor.java;h=665a78b77ab5227843ff1d87239c3ba7b2b650a7;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=25681c4e83fefddbe619c3a570433b0b9851a8f1;hpb=51f87c0026052e327ab4eaf24f8e4dadca96a615;p=jalview.git

diff --git a/src/jalview/schemes/GraduatedColor.java b/src/jalview/schemes/GraduatedColor.java
index 25681c4..665a78b 100644
--- a/src/jalview/schemes/GraduatedColor.java
+++ b/src/jalview/schemes/GraduatedColor.java
@@ -1,5 +1,20 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
@@ -8,49 +23,69 @@ import jalview.datamodel.SequenceFeature;
 import java.awt.Color;
 
 /**
- * Value and/or thresholded colour scale used for colouring by annotation and feature score
+ * 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;
+  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
+   * linear scaling parameters, base, minimum colour threshold, range of linear
+   * scale from lower to upper
    */
-  float base,range,thrsh;
+  float base, range, thrsh;
+
   /**
    * when true, colour from u to u-d rather than u to u+d
    */
-  boolean tolow=false;
+  boolean tolow = false;
+
+  /**
+   * when false, min/max range has been manually set so should not be
+   * dynamically adjusted.
+   */
+  boolean autoScale = true;
+
   /**
    * construct a graduatedColor object from simple parameters
+   * 
    * @param low
    * @param high
    * @param min
    * @param max
-   * color low->high from min->max
+   *          color low->high from min->max
    */
-  public GraduatedColor(Color low,Color high, float min,float 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;
+    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 {
+      range = min - max;
+    }
+    else
+    {
       base = min;
-      range = max-min;
+      range = max - min;
     }
   }
+
   public GraduatedColor(GraduatedColor oldcs)
   {
     lr = oldcs.lr;
@@ -64,9 +99,13 @@ public class GraduatedColor
     tolow = oldcs.tolow;
     thresholdState = oldcs.thresholdState;
     thrsh = oldcs.thrsh;
+    autoScale = oldcs.autoScale;
+    colourByLabel = oldcs.colourByLabel;
   }
+
   /**
    * make a new gradient from an old one with a different scale range
+   * 
    * @param oldcs
    * @param min
    * @param max
@@ -74,83 +113,184 @@ public class GraduatedColor
   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;
-    }
+    updateBounds(min, max);
   }
+
   public Color getMinColor()
   {
-    return new Color(lr,lg,lb);
+    return new Color(lr, lg, lb);
   }
+
   public Color getMaxColor()
   {
-    return new Color(lr+dr,lg+dg,lb+db);
+    return new Color(lr + dr, lg + dg, lb + db);
   }
+
+  /**
+   * 
+   * @return true if original min/max scale was from high to low
+   */
   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)
+    if (val == Float.NaN)
     {
       return true;
     }
-    if (this.thresholdState==AnnotationColourGradient.NO_THRESHOLD)
+    if (this.thresholdState == AnnotationColourGradient.NO_THRESHOLD)
     {
       return true;
     }
-    if (this.thrsh==Float.NaN)
+    if (this.thrsh == Float.NaN)
     {
       return true;
     }
-    boolean rtn = thresholdState==AnnotationColourGradient.ABOVE_THRESHOLD;
-    if (val<=thrsh)
+    boolean rtn = thresholdState == AnnotationColourGradient.ABOVE_THRESHOLD;
+    if (val <= thrsh)
     {
-      return !rtn; //  ? !tolow : tolow;
-    } else {
-      return rtn; //  ? tolow : !tolow;
+      return !rtn; // ? !tolow : tolow;
+    }
+    else
+    {
+      return rtn; // ? tolow : !tolow;
     }
   }
+
+  /**
+   * default implementor of a getColourFromString method. TODO: abstract an
+   * interface enabling pluggable colour from string
+   */
+  private UserColourScheme ucs = null;
+
+  private boolean colourByLabel = false;
+
+  /**
+   * 
+   * @return true if colourByLabel style is set
+   */
+  public boolean isColourByLabel()
+  {
+    return colourByLabel;
+  }
+
+  /**
+   * @param colourByLabel
+   *          the colourByLabel to set
+   */
+  public void setColourByLabel(boolean colourByLabel)
+  {
+    this.colourByLabel = colourByLabel;
+  }
+
   public Color findColor(SequenceFeature feature)
-  {     
-    if (range==0.0)
+  {
+    if (colourByLabel)
+    {
+      // TODO: allow user defined feature label colourschemes. Colour space is
+      // {type,regex,%anytype%}x{description string, regex, keyword}
+      if (ucs == null)
+      {
+        ucs = new UserColourScheme();
+      }
+      return ucs.createColourFromName(feature.getDescription());
+    }
+    if (range == 0.0)
     {
       return getMaxColor();
     }
     float scr = feature.getScore();
-    if (scr==Float.NaN)
+    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);
+    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 float getThresh()
+  {
+    return thrsh;
+  }
+
   public void setThreshType(int aboveThreshold)
   {
     thresholdState = aboveThreshold;
   }
+
   public int getThreshType()
   {
     return thresholdState;
   }
+
+  public float getMax()
+  {
+    // regenerate the original values passed in to the constructor
+    return (tolow) ? base : (base + range);
+  }
+
+  public float getMin()
+  {
+    // regenerate the original value passed in to the constructor
+    return (tolow) ? (base + range) : base;
+  }
+
+  public boolean isAutoScale()
+  {
+    return autoScale;
+  }
+
+  public void setAutoScaled(boolean autoscale)
+  {
+    autoScale = autoscale;
+  }
+
+  /**
+   * update the base and range appropriatly for the given minmax range
+   * 
+   * @param a
+   *          float[] {min,max} array containing minmax range for the associated
+   *          score values
+   */
+  public void updateBounds(float min, float max)
+  {
+    if (max < min)
+    {
+      base = max;
+      range = min - max;
+      tolow = true;
+    }
+    else
+    {
+      base = min;
+      range = max - min;
+      tolow = false;
+    }
+  }
 }