X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=66b3a13a4058ceff86f567bf673846a33adc8ae0;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=789667e0b2d49296053fa319b45ff933ebf0b319;hpb=0f71bfca98457c30f1051f142c31b6aaa3e23ead;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 789667e..66b3a13 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -1,162 +1,186 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
-*/
-package jalview.schemes;
-
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class AnnotationColourGradient extends ResidueColourScheme
-{
-    public static int NO_THRESHOLD = -1;
-    public static int BELOW_THRESHOLD = 0;
-    public static int ABOVE_THRESHOLD = 1;
-
-    AlignmentAnnotation annotation;
-    int aboveAnnotationThreshold = -1;
-
-    GraphLine annotationThreshold;
-
-    float r1, g1, b1, rr, gg, bb, dr, dg, db;
-    float range = 0;
-
-    ColourSchemeI colourScheme;
-
-    /**
-     * Creates a new AnnotationColourGradient object.
-     */
-    public AnnotationColourGradient(AlignmentAnnotation annotation,
-                                    ColourSchemeI originalColour,
-                                    int aboveThreshold)
-    {
-      if(originalColour instanceof AnnotationColourGradient)
-      {
-        colourScheme = ((AnnotationColourGradient)originalColour).colourScheme;
-      }
-      else
-        colourScheme = originalColour;
-
-      this.annotation = annotation;
-
-      aboveAnnotationThreshold = aboveThreshold;
-
-      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
-        annotationThreshold = annotation.threshold;
-    }
-
-    /**
-     * Creates a new AnnotationColourGradient object.
-     */
-    public AnnotationColourGradient(AlignmentAnnotation annotation,
-        Color minColour, Color maxColour, int aboveThreshold)
-    {
-      this.annotation = annotation;
-
-      aboveAnnotationThreshold = aboveThreshold;
-
-      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
-        annotationThreshold = annotation.threshold;
-
-      r1 = minColour.getRed();
-      g1 = minColour.getGreen();
-      b1 = minColour.getBlue();
-
-      rr = maxColour.getRed() - r1;
-      gg = maxColour.getGreen() - g1;
-      bb = maxColour.getBlue() - b1;
-
-      range = annotation.graphMax - annotation.graphMin;
-
-    }
-
-    public Color getMinColour()
-    {
-      return new Color( (int) r1, (int) g1, (int) b1);
-    }
-
-    public Color getMaxColour()
-    {
-      return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(String n)
-    {
-        return Color.red;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param n DOCUMENT ME!
-     * @param j DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public Color findColour(String n, int j)
-    {
-        currentColour = Color.white;
-
-        if ((threshold == 0) || aboveThreshold(n, j))
-        {
-          if( j<annotation.annotations.length
-              && annotation.annotations[j]!=null
-              && !jalview.util.Comparison.isGap(n.charAt(0)))
-          {
-            if(  aboveAnnotationThreshold==NO_THRESHOLD
-               || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
-               || (annotationThreshold!=null && aboveAnnotationThreshold==BELOW_THRESHOLD && annotation.annotations[j].value<=annotationThreshold.value))
-            {
-              if(colourScheme!=null)
-              {
-                currentColour = colourScheme.findColour(n, j);
-              }
-              else if(range!=0)
-              {
-                dr = rr *
-                    ( (annotation.annotations[j].value - annotation.graphMin) /
-                     range)
-                    + r1;
-                dg = gg *
-                    ( (annotation.annotations[j].value - annotation.graphMin) /
-                     range)
-                    + g1;
-                db = bb *
-                    ( (annotation.annotations[j].value - annotation.graphMin) /
-                     range)
-                    + b1;
-
-                currentColour = new Color( (int) dr, (int) dg, (int) db);
-              }
-            }
-          }
-        }
-
-        if(conservationColouring)
-         applyConservation(j);
-
-       return currentColour;
-    }
-}
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program 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 2
+* of the License, or (at your option) any later version.
+*
+* This program 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 this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+*/
+package jalview.schemes;
+
+import java.awt.*;
+
+import jalview.datamodel.*;
+
+public class AnnotationColourGradient extends ResidueColourScheme
+{
+    public static int NO_THRESHOLD = -1;
+    public static int BELOW_THRESHOLD = 0;
+    public static int ABOVE_THRESHOLD = 1;
+
+    AlignmentAnnotation annotation;
+    int aboveAnnotationThreshold = -1;
+
+    GraphLine annotationThreshold;
+
+    float r1, g1, b1, rr, gg, bb, dr, dg, db;
+    float range = 0;
+
+    ColourSchemeI colourScheme;
+
+    /**
+     * Creates a new AnnotationColourGradient object.
+     */
+    public AnnotationColourGradient(AlignmentAnnotation annotation,
+                                    ColourSchemeI originalColour,
+                                    int aboveThreshold)
+    {
+      if(originalColour instanceof AnnotationColourGradient)
+      {
+        colourScheme = ((AnnotationColourGradient)originalColour).colourScheme;
+      }
+      else
+        colourScheme = originalColour;
+
+      this.annotation = annotation;
+
+      aboveAnnotationThreshold = aboveThreshold;
+
+      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
+        annotationThreshold = annotation.threshold;
+    }
+
+    /**
+     * Creates a new AnnotationColourGradient object.
+     */
+    public AnnotationColourGradient(AlignmentAnnotation annotation,
+        Color minColour, Color maxColour, int aboveThreshold)
+    {
+      this.annotation = annotation;
+
+      aboveAnnotationThreshold = aboveThreshold;
+
+      if(aboveThreshold!=NO_THRESHOLD && annotation.threshold!=null)
+        annotationThreshold = annotation.threshold;
+
+      r1 = minColour.getRed();
+      g1 = minColour.getGreen();
+      b1 = minColour.getBlue();
+
+      rr = maxColour.getRed() - r1;
+      gg = maxColour.getGreen() - g1;
+      bb = maxColour.getBlue() - b1;
+
+      range = annotation.graphMax - annotation.graphMin;
+
+    }
+
+
+    public String getAnnotation()
+    {
+      return annotation.label;
+    }
+
+    public int getAboveThreshold()
+    {
+      return aboveAnnotationThreshold;
+    }
+
+    public float getAnnotationThreshold()
+    {
+      if(annotationThreshold==null)
+        return 0;
+      else
+        return annotationThreshold.value;
+    }
+
+    public ColourSchemeI getBaseColour()
+    {
+      return colourScheme;
+    }
+
+    public Color getMinColour()
+    {
+      return new Color( (int) r1, (int) g1, (int) b1);
+    }
+
+    public Color getMaxColour()
+    {
+      return new Color( (int) (r1 + rr), (int) (g1 + gg), (int) (b1 + bb));
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n)
+    {
+        return Color.red;
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param n DOCUMENT ME!
+     * @param j DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Color findColour(String n, int j)
+    {
+        currentColour = Color.white;
+
+        if ((threshold == 0) || aboveThreshold(n, j))
+        {
+          if( j<annotation.annotations.length
+              && annotation.annotations[j]!=null
+              && !jalview.util.Comparison.isGap(n.charAt(0)))
+          {
+            if(  aboveAnnotationThreshold==NO_THRESHOLD
+               || (annotationThreshold!=null && aboveAnnotationThreshold==ABOVE_THRESHOLD && annotation.annotations[j].value>=annotationThreshold.value)
+               || (annotationThreshold!=null && aboveAnnotationThreshold==BELOW_THRESHOLD && annotation.annotations[j].value<=annotationThreshold.value))
+            {
+              if(colourScheme!=null)
+              {
+                currentColour = colourScheme.findColour(n, j);
+              }
+              else if(range!=0)
+              {
+                dr = rr *
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + r1;
+                dg = gg *
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + g1;
+                db = bb *
+                    ( (annotation.annotations[j].value - annotation.graphMin) /
+                     range)
+                    + b1;
+
+                currentColour = new Color( (int) dr, (int) dg, (int) db);
+              }
+            }
+          }
+        }
+
+        if(conservationColouring)
+         applyConservation(j);
+
+       return currentColour;
+    }
+}