From 5221c772a071266446c5c959f34ec89c8e874201 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Thu, 3 Nov 2022 16:27:10 +0000
Subject: [PATCH] JAL-3855 JAL-4095 simple picking of ranges adjacent to a
 clicked region of the pAE that score less than the max pAE
 observed under the mouse

---
 src/jalview/gui/AnnotationPanel.java |   45 +++++++++++++++++++++++++++++++---
 1 file changed, 42 insertions(+), 3 deletions(-)

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 786696c..e146754 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -57,6 +57,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.ContactListI;
 import jalview.datamodel.ContactRange;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.gui.JalviewColourChooser.ColourChooserListener;
@@ -598,6 +599,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
         }
         else
         {
+          GraphLine thr = aa[graphStretch].getThreshold();
           int currentX = getColumnForXPos(evt.getX());
           ContactListI forCurrentX = av.getContactList(aa[graphStretch],
                   currentX);
@@ -610,11 +612,48 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
             int fr, to;
             fr = Math.min(cXci.cStart, cXci.cEnd);
             to = Math.max(cXci.cStart, cXci.cEnd);
-            for (int c = fr; c <= to; c++)
+            // select corresponding range in segment under mouse
             {
-              av.getColumnSelection().addElement(c);
+              for (int c = fr; c <= to; c++)
+              {
+                av.getColumnSelection().addElement(c);
+              }
+              av.getColumnSelection().addElement(currentX);
+            }
+            // and also select everything lower than the max range adjacent
+            // (kind of works)
+            {
+              int c = fr - 1;
+              ContactRange cr = forCurrentX.getRangeFor(fr, to);
+              double cval;
+              while (c > 0)
+              {
+                cval = forCurrentX.getContactAt(c);
+                if (// cr.getMin() <= cval &&
+                cval <= cr.getMax())
+                {
+                  av.getColumnSelection().addElement(c--);
+                }
+                else
+                {
+                  break;
+                }
+              }
+              c = to;
+              while (c < forCurrentX.getContactHeight())
+              {
+                cval = forCurrentX.getContactAt(c);
+                if (// cr.getMin() <= cval &&
+                cval <= cr.getMax())
+                {
+                  av.getColumnSelection().addElement(c++);
+                }
+                else
+                {
+                  break;
+                }
+              }
             }
-            av.getColumnSelection().addElement(currentX);
           }
         }
       }
-- 
1.7.10.2