JAL-4090 JAL-1551 source license

[jalview.git] / src / jalview / renderer / ContactMapRenderer.java

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 8f38d02..9f0cc35 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -1,11 +1,27 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.renderer;
 
 import java.awt.Color;
 import java.awt.Graphics;
-import java.util.Iterator;
 
 import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
@@ -35,10 +51,12 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
      * shown when no data available from map
      */
     Color no_data;
+
     /**
      * shown for region not currently visible - should normally not see this
      */
     Color hidden;
+
     /**
      * linear shading scheme min/max
      */
@@ -49,6 +67,21 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
      */
     Color selMinColor, selMaxColor;
 
+    /**
+     * 
+     * @param no_data
+     *          - colour when no data available
+     * @param hidden
+     *          - colour if this row is hidden
+     * @param maxColor
+     *          - colour for maximum value of contact
+     * @param minColor
+     *          - colour for minimum value of contact
+     * @param selMinColor
+     *          - min colour if the contact has been selected
+     * @param selMaxColor
+     *          - max colour if contact is selected
+     */
     public Shading(Color no_data, Color hidden, Color maxColor,
             Color minColor, Color selMinColor, Color selMaxColor)
     {
@@ -79,8 +112,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
       {
         return new Shading(Color.pink, Color.red,
 
-                new Color(246, 252, 243), new Color(0, 60, 26),
-                new Color(26, 0, 60), new Color(243, 246, 252));
+                new Color(247, 252, 245), new Color(0, 68, 28),
+                new Color(28, 0, 68), new Color(245, 247, 252));
       }
     };
   }
@@ -102,22 +135,28 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
           HiddenColumns hiddenColumns, ColumnSelection columnSelection,
           AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
           int eRes, float min, float max, int y)
-  {    
+  {
     if (sRes > aa_annotations.length)
     {
       return;
     }
     eRes = Math.min(eRes, aa_annotations.length);
 
-    int x = 0, y2 = y;
+    int x = 0, topY = y;
 
-    g.setColor(shade.no_data);
+    // uncomment below to render whole area of matrix as pink
+    // g.setColor(shade.no_data);
+    // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth,
+    // _aa.graphHeight);
 
-    g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
     boolean showGroups = _aa.isShowGroupsForContactMatrix();
     int column;
     int aaMax = aa_annotations.length - 1;
     ContactMatrixI cm = viewport.getContactMatrix(_aa);
+    if (cm == null)
+    {
+      return;
+    }
     while (x < eRes - sRes)
     {
       column = sRes + x;
@@ -165,17 +204,17 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
       final ContactGeometry cgeom = new ContactGeometry(contacts,
               _aa.graphHeight);
 
-      for (int ht = y2, eht = y2
-              - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step)
+      for (int ht = 0, botY = topY
+              - _aa.height; ht < _aa.graphHeight; ht += cgeom.pixels_step)
       {
-        ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht,
-                y2 - ht + cgeom.pixels_step);
+        ContactGeometry.contactInterval ci = cgeom.mapFor(ht);
         // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
         // cend = (int) Math.min(contact_height,
         // Math.ceil(cstart + contacts_per_pixel * pixels_step));
 
         Color col;
-        boolean rowsel = false, containsHidden = false;
+        boolean rowsel = false;
+        boolean containsHidden = false;
         if (columnSelection != null)
         {
           rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
@@ -207,20 +246,20 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         if (showGroups && gpcol != null && gpcol != Color.white)
         {
           // todo - could overlay group as a transparent rectangle ?
-          col = new Color(
-                  (int) (((float) (col.getRed() + gpcol.getRed())) / 2f),
-                  (int) (((float) (col.getGreen() + gpcol.getGreen()))
-                          / 2f),
-                  (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
+          col = new Color((int) ((col.getRed() + gpcol.getRed()) / 2f),
+                  (int) ((col.getGreen() + gpcol.getGreen()) / 2f),
+                  (int) ((col.getBlue() + gpcol.getBlue()) / 2f));
         }
         g.setColor(col);
         if (cgeom.pixels_step > 1)
         {
-          g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
+          g.fillRect(x * charWidth, botY + ht, charWidth,
+                  cgeom.pixels_step);
         }
         else
         {
-          g.drawLine(x * charWidth, ht, (x + 1) * charWidth, ht);
+          g.drawLine(x * charWidth, botY + ht, (x + 1) * charWidth,
+                  botY + ht);
         }
       }
       x++;
@@ -247,7 +286,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
   {
     ContactRange cr = cl.getRangeFor(i, j);
     // average for moment - probably more interested in maxIntProj though
-    return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMean(),
+    return jalview.util.ColorUtils.getGraduatedColour((float) cr.getMin(),
             0, shade.selMinColor, max, shade.selMaxColor);
   }