From 0d326d33340305d0eaa539cbf903f778001ebeb7 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 20 Oct 2022 10:49:21 +0100
Subject: [PATCH] JAL-2349 debugged click/drag and added yellow rubber banding
 (like Alphafold)

---
 src/jalview/gui/AnnotationPanel.java |   69 ++++++++++++++++++++++++++--------
 1 file changed, 54 insertions(+), 15 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index ba02a3f..ccc086c 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -56,6 +56,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
+import jalview.datamodel.ContactRange;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
@@ -584,25 +585,35 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (graphStretch != -1)
     {
+
       if (aa[graphStretch].graph == AlignmentAnnotation.CUSTOMRENDERER)
       {
-        int currentX = getColumnForXPos(evt.getX());
-        ContactListI forCurrentX = av.getContactList(aa[graphStretch],
-                currentX);
-        if (forCurrentX != null)
+        if (evt.isAltDown() || evt.isAltGraphDown())
+        {
+          dragMode = DragMode.MatrixSelect;
+          firstDragX = mouseDragLastX;
+          firstDragY = mouseDragLastY;
+        }
+        else
         {
-          ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
-                  aa[graphStretch].graphHeight);
-          ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
-                  yOffset);
-          int fr, to;
-          fr = Math.min(cXci.cStart, cXci.cEnd);
-          to = Math.max(cXci.cStart, cXci.cEnd);
-          for (int c = fr; c <= to; c++)
+          int currentX = getColumnForXPos(evt.getX());
+          ContactListI forCurrentX = av.getContactList(aa[graphStretch],
+                  currentX);
+          if (forCurrentX != null)
           {
-            av.getColumnSelection().addElement(c);
+            ContactGeometry cXcgeom = new ContactGeometry(forCurrentX,
+                    aa[graphStretch].graphHeight);
+            ContactGeometry.contactInterval cXci = cXcgeom.mapFor(yOffset,
+                    yOffset);
+            int fr, to;
+            fr = Math.min(cXci.cStart, cXci.cEnd);
+            to = Math.max(cXci.cStart, cXci.cEnd);
+            for (int c = fr; c <= to; c++)
+            {
+              av.getColumnSelection().addElement(c);
+            }
+            av.getColumnSelection().addElement(currentX);
           }
-          av.getColumnSelection().addElement(currentX);
         }
       }
     }
@@ -676,6 +687,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     graphStretch = -1;
     mouseDragLastX = -1;
     mouseDragLastY = -1;
+    firstDragX = -1;
+    firstDragY = -1;
     mouseDragging = false;
     if (dragMode == DragMode.Resize)
     {
@@ -813,6 +826,9 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         /*
          * TODO draw a rubber band for range
          */
+        mouseDragLastX = x;
+        mouseDragLastY = y;
+        ap.paintAlignment(false, false);
       }
       else
       {
@@ -835,11 +851,23 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
      * get geometry of drag
      */
     int fromY = Math.min(firstDragY, evt.getY());
-    int deltaY = Math.abs(firstDragY - evt.getY());
     int toY = Math.max(firstDragY, evt.getY());
+    int deltaY = toY - fromY;
 
     int[] rowIndex = getRowIndexAndOffset(fromY,
             av.getAlignment().getAlignmentAnnotation());
+    int[] toRowIndex = getRowIndexAndOffset(toY,
+            av.getAlignment().getAlignmentAnnotation());
+
+    if (rowIndex == null || toRowIndex == null)
+    {
+      System.out.println("Drag out of range. needs to be clipped");
+
+    }
+    if (rowIndex[0] != toRowIndex[0])
+    {
+      System.out.println("Drag went to another row. needs to be clipped");
+    }
 
     // rectangular selection on matrix style annotation
     AlignmentAnnotation cma = av.getAlignment()
@@ -1408,6 +1436,17 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       fadedImage = oldFaded;
     }
+    if (dragMode == DragMode.MatrixSelect)
+    {
+      g.setColor(Color.yellow);
+      g.drawRect(Math.min(firstDragX, mouseDragLastX),
+              Math.min(firstDragY, mouseDragLastY),
+              Math.max(firstDragX, mouseDragLastX)
+                      - Math.min(firstDragX, mouseDragLastX),
+              Math.max(firstDragY, mouseDragLastY)
+                      - Math.min(firstDragY, mouseDragLastY));
+
+    }
   }
 
   @Override
-- 
1.7.10.2