JAL-3390 pull up of getShownResidues() to AAStructureBindingModel

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index d2fff3f..7a89961 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.ext.rbvi.chimera.AtomSpecModel;
 import jalview.io.DataSourceType;
 import jalview.schemes.ColourSchemeI;
 import jalview.structure.AtomSpec;
@@ -43,6 +44,8 @@ import java.awt.Color;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.BitSet;
+import java.util.Collections;
+import java.util.Iterator;
 import java.util.List;
 
 /**
@@ -954,4 +957,97 @@ public abstract class AAStructureBindingModel
     }
     return chainsToShow.contains(pdbId + ":" + chainId);
   }
+
+  @Override
+  public abstract String[] getStructureFiles();
+
+  /**
+   * Builds a model of residues mapped from sequences to show on structure, taking
+   * into account user choices of
+   * <ul>
+   * <li>which chains are shown</li>
+   * <li>whether all structure is shown, or only that mapped to the alignment</li>
+   * <li>whether hidden regions of the alignment are hidden (excluded) or grayed
+   * out (included)</li>
+   * </ul>
+   * 
+   * @param av
+   * @return
+   */
+  protected AtomSpecModel getShownResidues(AlignViewportI av)
+  {
+    AlignmentI alignment = av.getAlignment();
+    final int width = alignment.getWidth();
+  
+    String[] files = getStructureFiles();
+  
+    AtomSpecModel model = new AtomSpecModel();
+  
+    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    {
+      StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]);
+  
+      /*
+       * Find the first mapped sequence (if any) for this PDB entry which is in
+       * the alignment
+       */
+      final int seqCountForPdbFile = getSequence()[pdbfnum].length;
+      for (int s = 0; s < seqCountForPdbFile; s++)
+      {
+        for (StructureMapping mapping : mappings)
+        {
+          final SequenceI theSequence = getSequence()[pdbfnum][s];
+          if (mapping.getSequence() == theSequence
+                  && alignment.findIndex(theSequence) > -1)
+          {
+            String chainCd = mapping.getChain();
+            if (!isShowChain(mapping.getPdbId(), chainCd))
+            {
+              continue;
+            }
+            Iterator<int[]> visible;
+            if (isShowAlignmentOnly() && isHideHiddenRegions())
+            {
+              visible = alignment.getHiddenColumns()
+                    .getVisContigsIterator(0, width, true);
+            }
+            else
+            {
+              visible = Collections.singletonList(new int[] { 0, width })
+                      .iterator();
+            }
+            while (visible.hasNext())
+            {
+              int[] visibleRegion = visible.next();
+              int seqStartPos = theSequence.findPosition(visibleRegion[0]);
+              int seqEndPos = theSequence.findPosition(visibleRegion[1]);
+              List<int[]> residueRanges = mapping
+                      .getPDBResNumRanges(seqStartPos, seqEndPos);
+              if (!residueRanges.isEmpty())
+              {
+                for (int[] range : residueRanges)
+                {
+                  model.addRange(pdbfnum, range[0], range[1], chainCd);
+                }
+              }
+            }
+          }
+        }
+      }
+    }
+  
+    return model;
+  }
+
+  /**
+   * Answers a default structure model specification which is simply the string
+   * form of the model number. Override if needed to specify submodels.
+   * 
+   * @param model
+   * @return
+   */
+  public String getModelSpec(int model)
+  {
+    return String.valueOf(model);
+  }
 }