From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 1 Jun 2023 12:56:53 +0000 (+0100)
Subject: JAL-4134 properly resolve positions in associated aligned sequence for matrix group... 
X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~1
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0ccaf35f7e6a5cc62d4f433b39d574d0aa4b2d26;p=jalview.git

JAL-4134 properly resolve positions in associated aligned sequence for matrix group column-wise selection actions in tree and annotation panel
---

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 9970702..8e04048 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -72,6 +72,7 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.viewmodel.ViewportListenerI;
 import jalview.viewmodel.ViewportRanges;
+import jalview.ws.datamodel.MappableContactMatrixI;
 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 /**
@@ -667,24 +668,48 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
           if (matrix.hasGroups())
           {
             SequenceI rseq = clicked.sequenceRef;
-            BitSet grp = matrix.getGroupsFor(currentX);
+            BitSet grp = new BitSet();
+            grp.or(matrix.getGroupsFor(currentX));
             // TODO: cXci needs to be mapped to real groups
             for (int c = fr; c <= to; c++)
             {
               BitSet additionalGrp = matrix.getGroupsFor(c);
               grp.or(additionalGrp);
             }
+
             HiddenColumns hc = av.getAlignment().getHiddenColumns();
-            for (int p = grp.nextSetBit(0); p >= 0; p = grp
+            ColumnSelection cs = av.getColumnSelection();
+            
+            for (int p=grp.nextSetBit(0); p >= 0; p = grp
                     .nextSetBit(p + 1))
             {
-              int offp = (rseq != null)
-                      ? rseq.findIndex(rseq.getStart() - 1 + p)
-                      : p;
-
-              if (!av.hasHiddenColumns() || hc.isVisible(offp))
+              if (matrix instanceof MappableContactMatrixI)
               {
-                av.getColumnSelection().addElement(offp);
+                // find the end of this run of set bits
+                int nextp = grp.nextClearBit(p)-1;
+                int[] pos = ((MappableContactMatrixI)matrix).getMappedPositionsFor(rseq, p,nextp);
+                p=nextp;
+                
+                if (pos!=null)
+                {
+                  for (int pos_p = pos[0];pos_p<=pos[1];pos_p++)
+                  {
+                    int col = rseq.findIndex(pos_p)-1;
+                    if (col>=0 && (!av.hasHiddenColumns() || hc.isVisible(col)))
+                    {
+                      cs.addElement(col);
+                    }
+                  }
+                }
+              } else {
+                int offp = (rseq != null)
+                        ? rseq.findIndex(rseq.getStart() - 1 + p)
+                        : p;
+  
+                if (!av.hasHiddenColumns() || hc.isVisible(offp))
+                {
+                  cs.addElement(offp);
+                }
               }
             }
           }
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 2bdfc27..55ce44a 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -1148,14 +1148,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (aa != null)
     {
       ContactMatrixI cm = av.getContactMatrix(aa);
+      // generally, we assume cm has 1:1 mapping to annotation row - probably wrong
+      // but.. if
       if (cm instanceof MappableContactMatrixI)
       {
+        int[] pos;
+          // use the mappable's mapping - always the case for PAE Matrices so good
+        // for 2.11.3
         MappableContactMatrixI mcm = (MappableContactMatrixI) cm;
-        int pos[]=mcm.getMappedPositionsFor(rseq, colm+1);
-        if (pos!=null)
+        pos = mcm.getMappedPositionsFor(rseq, colm + 1);
+        // finally, look up the position of the column
+        if (pos != null)
         {
-          offp=rseq.findIndex(pos[0]);
+          offp = rseq.findIndex(pos[0]);
         }
+      } else {
+        offp = colm;
       }
     }
     if (offp<=0)
diff --git a/src/jalview/ws/datamodel/MappableContactMatrixI.java b/src/jalview/ws/datamodel/MappableContactMatrixI.java
index b8a9779..9762428 100644
--- a/src/jalview/ws/datamodel/MappableContactMatrixI.java
+++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java
@@ -51,7 +51,7 @@ public interface MappableContactMatrixI extends ContactMatrixI
   MapList getMapFor(SequenceI sequenceRef);
 
   /**
-   * Locate a position in the mapped sequence for a column in the matrix - use
+   * Locate a position in the mapped sequence for a single column in the matrix. 
    * this to resolve positions corresponding to column clusters
    * 
    * @param localFrame
@@ -61,4 +61,16 @@ public interface MappableContactMatrixI extends ContactMatrixI
    * @return sequence position(s) corresponding to column in contact matrix
    */
   int[] getMappedPositionsFor(SequenceI localFrame, int column);
+
+  /**
+   * Locate a position in the mapped sequence for a contiguous range of columns in the matrix 
+   * use this to resolve positions corresponding to column clusters
+   * 
+   * @param localFrame
+   *          - sequence derivced from reference sequence
+   * @param column
+   *          - matrix row/column
+   * @return sequence position(s) corresponding to column in contact matrix
+   */
+  int[] getMappedPositionsFor(SequenceI localFrame, int from, int to);
 }
diff --git a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
index 0e617d7..d545741 100644
--- a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
+++ b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java
@@ -186,6 +186,7 @@ public abstract class MappableContactMatrix<T extends MappableContactMatrix<T>>
     return getMappedPositionsFor(localFrame, column, column);
   }
 
+  @Override
   public int[] getMappedPositionsFor(final SequenceI localFrame, int from,
           int to)
   {