JAL-3858 flip diagonal so matrix visualisation is top left to bottom right

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 8e04048..cf37e9e 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -1078,12 +1078,12 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       ContactGeometry lastXcgeom = new ContactGeometry(forFromX,
               cma.graphHeight);
       ContactGeometry.contactInterval lastXci = lastXcgeom
-              .mapFor(rowIndex[1], rowIndex[1] - deltaY);
+              .mapFor(rowIndex[1], rowIndex[1] + deltaY);
 
       ContactGeometry cXcgeom = new ContactGeometry(forToX,
               cma.graphHeight);
       ContactGeometry.contactInterval cXci = cXcgeom.mapFor(rowIndex[1],
-              rowIndex[1] - deltaY);
+              rowIndex[1] + deltaY);
 
       // mark rectangular region formed by drag
       jalview.bin.Console.trace("Matrix Selection from last(" + fromXc
@@ -1247,7 +1247,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       {
         row = i;
         res[0] = row;
-        res[1] = height - yPos;
+        res[1] = yPos-lheight;
         break;
       }
     }

diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index 8f38d02..0471145 100644 (file)
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -109,11 +109,12 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
     }
     eRes = Math.min(eRes, aa_annotations.length);
 
-    int x = 0, y2 = y;
+    int x = 0, topY = y;
 
-    g.setColor(shade.no_data);
-
-    g.drawLine(x, y2, (eRes - sRes) * charWidth, y2);
+    // 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;
@@ -165,11 +166,11 @@ 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,
+                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));
@@ -216,11 +217,11 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         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++;