Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index e54f471..0471145 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -25,6 +25,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 {
   /**
    * bean holding colours for shading
+   * 
    * @author jprocter
    *
    */
@@ -66,6 +67,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
   /**
    * build an EBI-AlphaFold style renderer of PAE matrices
+   * 
    * @return
    */
   public static ContactMapRenderer newPAERenderer()
@@ -100,19 +102,20 @@ 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);
@@ -146,21 +149,28 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
-      Color gpcol = (cm==null) ? Color.white: cm.getColourForGroup(cm.getGroupsFor(column));
+      // 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;
-      // TODO: pass visible column mask to the ContactGeometry object so it maps
+      // TODO: optionally pass visible column mask to the ContactGeometry object
+      // so it maps
       // only visible contacts to geometry
       // Bean holding mapping from contact list to pixels
+      // TODO: allow bracketing/limiting of range on contacts to render (like
+      // visible column mask but more flexible?)
+
+      // COntactListI provides mapping for column -> cm-groupmapping
       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,
+                ht + cgeom.pixels_step);
         // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel);
         // cend = (int) Math.min(contact_height,
         // Math.ceil(cstart + contacts_per_pixel * pixels_step));
@@ -169,29 +179,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         boolean rowsel = false, containsHidden = false;
         if (columnSelection != null)
         {
-          if (_aa.sequenceRef == null)
-          {
-            rowsel = columnSelection.intersects(ci.cStart, ci.cEnd);
-          }
-          else
-          {
-            // TODO check we have correctly mapped cstart to local sequence
-            // numbering
-            int s = _aa.sequenceRef.findIndex(ci.cStart);
-            int e = _aa.sequenceRef.findIndex(ci.cEnd);
-            if (maskHiddenCols && hasHiddenColumns)
-            {
-              // TODO: turn into function and create test !!
-              Iterator<int[]> viscont = hiddenColumns
-                      .getVisContigsIterator(s, e, false);
-              containsHidden = !viscont.hasNext();
-            }
-            if (s > 0 && s < _aa.sequenceRef.getLength())
-            {
-              rowsel = columnSelection.intersects(s, e);
-            }
-
-          }
+          rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns,
+                  maskHiddenCols);
         }
         // TODO: show selected region
         if (colsel || rowsel)
@@ -216,21 +205,23 @@ 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((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) (((float) (col.getRed() + gpcol.getRed())) / 2f),
+                  (int) (((float) (col.getGreen() + gpcol.getGreen()))
+                          / 2f),
+                  (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, 1 + 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++;
@@ -240,8 +231,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
   Color shadeFor(float min, float max, float value)
   {
-    return jalview.util.ColorUtils.getGraduatedColour(value, 0, shade.minColor,
-            max, shade.maxColor);
+    return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+            shade.minColor, max, shade.maxColor);
   }
 
   public Color getColorForRange(float min, float max, ContactListI cl,