Merge branch 'develop' into feature/JAL-1713_overviewInProject

[jalview.git] / src / jalview / structure / StructureSelectionManager.java

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index c8a846c..24320b5 100644 (file)
--- 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;
@@ -874,6 +875,52 @@ public class StructureSelectionManager
   }
 
   /**
+   * hack to highlight a range of positions at once on any structure views
+   * 
+   * @param sequenceRef
+   * @param is
+   *          - series of int start-end ranges as positions on sequenceRef
+   * @param i
+   * @param object
+   */
+  public void highlightPositionsOn(SequenceI sequenceRef, int[][] is,
+          Object source)
+  {
+    boolean hasSequenceListeners = handlingVamsasMo
+            || !seqmappings.isEmpty();
+    SearchResultsI results = null;
+    ArrayList<Integer> listOfPositions = new ArrayList<Integer>();
+    for (int[] s_e : is)
+    {
+      for (int p = s_e[0]; p <= s_e[1]; listOfPositions.add(p++))
+        ;
+    }
+    int seqpos[] = new int[listOfPositions.size()];
+    int i = 0;
+    for (Integer p : listOfPositions)
+    {
+      seqpos[i++] = p;
+    }
+
+    for (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)
+      {
+        highlightStructure((StructureListener) listener, sequenceRef,
+                seqpos);
+      }
+
+    }
+  }
+
+  /**
    * Propagate mouseover of a single position in a structure
    * 
    * @param pdbResNum
@@ -1083,6 +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
@@ -1461,4 +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);
+      }
+    }
+  }
+
 }