From 457478300feb669620d4d18b8e4ce77ebbfdc4ae Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 21 Oct 2022 16:04:44 +0100
Subject: [PATCH] JAL-4033 - heuristic threshold for pAE matrix - mark any
 column where pAE values for column+8..  lie outside
 threshold - definitely better to do a watershed or other
 type of clustering

---
 src/jalview/datamodel/ColumnSelection.java |   52 +++++++++++++++++++++-------
 1 file changed, 39 insertions(+), 13 deletions(-)

diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 309aabf..db83e76 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -566,6 +566,45 @@ public class ColumnSelection
     // JBPNote - this method needs to be refactored to become independent of
     // viewmodel package
     this.clear();
+
+    if (ann_row.graph == AlignmentAnnotation.CUSTOMRENDERER && (filterParams
+            .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+            || filterParams
+                    .getThresholdType() == AnnotationFilterParameter.ThresholdType.BELOW_THRESHOLD))
+    {
+      float tVal = filterParams.getThresholdValue();
+      if (ann_row.sequenceRef != null)
+      {
+        // TODO - get ContactList from AlignmentView for non-seq-ref associatd
+        for (int column = 0; column < annotations.length; column++)
+        {
+          if (ann_row.annotations[column] == null)
+          {
+            continue;
+          }
+
+          int cpos = ann_row.sequenceRef.findPosition(column) - 1;
+          ContactListI clist = ann_row.sequenceRef
+                  .getContactListFor(ann_row, cpos);
+          for (int row = column + 8,
+                  rowEnd = clist.getContactHeight(); row < rowEnd; row++)
+          {
+            if (filterParams
+                    .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
+                            ? (clist.getContactAt(row) > tVal)
+                            : (clist.getContactAt(row) < tVal))
+            {
+              addElement(column);
+              break;
+              // int column_forrowpos = ann_row.sequenceRef.findIndex(row + 1);
+              // addElement(column_forrowpos);
+            }
+          }
+        }
+      }
+      return selection.size();
+    }
+
     int addedCount = 0;
     int column = 0;
     do
@@ -580,19 +619,6 @@ public class ColumnSelection
          * filter may have multiple conditions - 
          * these are or'd until a match is found
          */
-        if (ann_row.graph == AlignmentAnnotation.CUSTOMRENDERER)
-        {
-          if (ann_row.sequenceRef != null)
-          {
-            int cpos = ann_row.sequenceRef.findPosition(column) - 1;
-            ContactListI clist = ann_row.sequenceRef
-                    .getContactListFor(ann_row, cpos);
-            ContactRange crange = clist.getRangeFor(0,
-                    clist.getContactHeight());
-            value = (float) crange.getMean();
-          }
-        }
-
         if (filterParams
                 .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
                 && value > filterParams.getThresholdValue())
-- 
1.7.10.2