Merge branch 'develop' into bug/JAL-4235_gradle_task_jalviewjsTranspile_does_not_fail...

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

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index edf3ca2..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
      */
@@ -51,12 +69,18 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
     /**
      * 
-     * @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
+     * @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)
@@ -89,7 +113,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         return new Shading(Color.pink, Color.red,
 
                 new Color(247, 252, 245), new Color(0, 68, 28),
-                new Color(28, 0, 68), new Color(245,247,252));
+                new Color(28, 0, 68), new Color(245, 247, 252));
       }
     };
   }
@@ -111,7 +135,7 @@ 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;
@@ -122,13 +146,14 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
     // 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.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth,
+    // _aa.graphHeight);
+
     boolean showGroups = _aa.isShowGroupsForContactMatrix();
     int column;
     int aaMax = aa_annotations.length - 1;
     ContactMatrixI cm = viewport.getContactMatrix(_aa);
-    if (cm==null)
+    if (cm == null)
     {
       return;
     }
@@ -221,20 +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, botY+ht, charWidth, cgeom.pixels_step);
+          g.fillRect(x * charWidth, botY + ht, charWidth,
+                  cgeom.pixels_step);
         }
         else
         {
-          g.drawLine(x * charWidth, botY+ht, (x + 1) * charWidth, botY+ht);
+          g.drawLine(x * charWidth, botY + ht, (x + 1) * charWidth,
+                  botY + ht);
         }
       }
       x++;