Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace

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

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index ef95360..edf3ca2 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -35,12 +35,10 @@ 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
      */
@@ -51,6 +49,15 @@ 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)
     {
@@ -81,8 +88,8 @@ 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));
       }
     };
   }
@@ -104,22 +111,27 @@ 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;
-
-    g.setColor(shade.no_data);
-
-    g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+    int x = 0, topY = y;
 
+    // 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);
+    
+    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;
@@ -153,7 +165,6 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
       // ContactListI from viewport can map column -> group
       Color gpcol = (cm == null) ? Color.white
               : contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column));
-
       // feature still in development - highlight or omit regions hidden in
       // the alignment - currently marks them as red rows
       boolean maskHiddenCols = false;
@@ -168,18 +179,17 @@ 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,
@@ -208,7 +218,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         {
           col = shade.hidden;
         }
-        if (gpcol != null && gpcol != Color.white)
+        if (showGroups && gpcol != null && gpcol != Color.white)
         {
           // todo - could overlay group as a transparent rectangle ?
           col = new Color(
@@ -218,14 +228,13 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
                   (int) (((float) (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++;
@@ -252,7 +261,7 @@ 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);
   }