From: Jim Procter <j.procter@dundee.ac.uk>
Date: Fri, 28 Oct 2022 12:21:41 +0000 (+0100)
Subject: Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into bug/JAL-4083_excepti... 
X-Git-Tag: Release_2_11_3_0~23^2~18^2~4
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ac3fe94f6d237a0a2032474844217d542040776c;hp=768df7afff3cb5ecb636cf324f5965f0aeb1b9a4;p=jalview.git

Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into bug/JAL-4083_exceptions_for_multiple_residue_highlights_in_jmol
---

diff --git a/src/jalview/gui/ScalePanel.java b/src/jalview/gui/ScalePanel.java
index ca3faf8..4e4a274 100755
--- a/src/jalview/gui/ScalePanel.java
+++ b/src/jalview/gui/ScalePanel.java
@@ -20,16 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.HiddenColumns;
-import jalview.datamodel.SequenceGroup;
-import jalview.renderer.ScaleRenderer;
-import jalview.renderer.ScaleRenderer.ScaleMark;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.viewmodel.ViewportListenerI;
-import jalview.viewmodel.ViewportRanges;
-
 import java.awt.Color;
 import java.awt.FontMetrics;
 import java.awt.Graphics;
@@ -50,6 +40,16 @@ import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.ToolTipManager;
 
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceGroup;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
 /**
  * The panel containing the sequence ruler (when not in wrapped mode), and
  * supports a range of mouse operations to select, hide or reveal columns.
@@ -409,6 +409,9 @@ public class ScalePanel extends JPanel
     reveal = null;
     if (!av.hasHiddenColumns())
     {
+      int res = (evt.getX() / av.getCharWidth())
+              + av.getRanges().getStartRes();
+      highlightAllStructPos(res);
       return;
     }
 
@@ -419,13 +422,21 @@ public class ScalePanel extends JPanel
             .getRegionWithEdgeAtRes(res);
 
     res = av.getAlignment().getHiddenColumns().visibleToAbsoluteColumn(res);
-
+    highlightAllStructPos(res);
     ToolTipManager.sharedInstance().registerComponent(this);
     this.setToolTipText(
             MessageManager.getString("label.reveal_hidden_columns"));
     repaint();
   }
 
+  public void highlightAllStructPos(int col)
+  {
+    ap.getStructureSelectionManager().highlightPositionsOnMany(
+            ap.av.getAlignment().getSequencesArray(), new int[]
+            { col, col }, ap);
+
+  }
+
   /**
    * DOCUMENT ME!
    * 
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ba3ef71..24320b5 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -42,6 +42,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
@@ -1129,6 +1130,62 @@ public class StructureSelectionManager
     sl.highlightAtoms(atoms);
   }
 
+  public void highlightStructureRegionsFor(StructureListener sl,
+          SequenceI[] seqs, int... columns)
+  {
+    List<SequenceI> to_highlight = new ArrayList<SequenceI>();
+    for (SequenceI seq : seqs)
+    {
+      if (sl.isListeningFor(seq))
+      {
+        to_highlight.add(seq);
+      }
+    }
+    if (to_highlight.size() == 0)
+    {
+      return;
+    }
+    List<AtomSpec> atoms = new ArrayList<>();
+    for (SequenceI seq : to_highlight)
+    {
+      int atomNo;
+      for (StructureMapping sm : mappings)
+      {
+        if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
+                || (sm.sequence.getDatasetSequence() != null && sm.sequence
+                        .getDatasetSequence() == seq.getDatasetSequence()))
+        {
+
+          for (int i = 0; i < columns.length; i += 2)
+          {
+            ContiguousI positions = seq.findPositions(columns[i] + 1,
+                    columns[i + 1] + 1);
+            if (positions == null)
+            {
+              continue;
+            }
+            for (int index = positions.getBegin(); index <= positions
+                    .getEnd(); index++)
+            {
+
+              atomNo = sm.getAtomNum(index);
+
+              if (atomNo > 0)
+              {
+                atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+                        sm.getPDBResNum(index), atomNo));
+              }
+            }
+          }
+        }
+      }
+      if (atoms.size() > 0)
+      {
+        sl.highlightAtoms(atoms);
+      }
+    }
+  }
+
   /**
    * true if a mouse over event from an external (ie Vamsas) source is being
    * handled
@@ -1507,4 +1564,34 @@ public class StructureSelectionManager
     return seqmappings;
   }
 
+  /**
+   * quick and dirty route to just highlight all structure positions for a range
+   * of columns
+   * 
+   * @param sequencesArray
+   * @param is
+   *          start-end columns on sequencesArray
+   * @param source
+   *          origin parent AlignmentPanel
+   */
+  public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is,
+          Object source)
+  {
+    for (int i = 0; i < listeners.size(); i++)
+    {
+      Object listener = listeners.elementAt(i);
+      if (listener == source)
+      {
+        // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+        // Temporary fudge with SequenceListener.getVamsasSource()
+        continue;
+      }
+      if (listener instanceof StructureListener)
+      {
+        highlightStructureRegionsFor((StructureListener) listener,
+                sequencesArray, is);
+      }
+    }
+  }
+
 }