JAL-2781 refactor possibly non-functional ‘extract secondary structure’ logic out...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 2b429d7..8380b19 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -328,22 +328,20 @@ public class StructureSelectionManager
   }
 
   /**
-   * create sequence structure mappings between each sequence and the given
-   * pdbFile (retrieved via the given protocol).
+   * Import a single structure file and register sequence structure mappings for
+   * broadcasting colouring, mouseovers and selection events (convenience
+   * wrapper).
    * 
    * @param forStructureView
    *          when true, record the mapping for use in mouseOvers
-   * 
-   * @param sequenceArray
+   * @param sequence
    *          - one or more sequences to be mapped to pdbFile
-   * @param targetChainIds
+   * @param targetChains
    *          - optional chain specification for mapping each sequence to pdb
-   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
-   *          - this should be List<List<String>>, empty lists indicate no
-   *          predefined mappings
+   *          (may be nill, individual elements may be nill)
    * @param pdbFile
    *          - structure data resource
-   * @param sourceType
+   * @param protocol
    *          - how to resolve data from resource
    * @return null or the structure data parsed as a pdb file
    */
@@ -355,42 +353,46 @@ public class StructureSelectionManager
             pdbFile, sourceType, null);
   }
 
+  /**
+   * create sequence structure mappings between each sequence and the given
+   * pdbFile (retrieved via the given protocol). Either constructs a mapping
+   * using NW alignment or derives one from any available SIFTS mapping data.
+   * 
+   * @param forStructureView
+   *          when true, record the mapping for use in mouseOvers
+   * 
+   * @param sequenceArray
+   *          - one or more sequences to be mapped to pdbFile
+   * @param targetChainIds
+   *          - optional chain specification for mapping each sequence to pdb
+   *          (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+   *          - this should be List<List<String>>, empty lists indicate no
+   *          predefined mappings
+   * @param pdbFile
+   *          - structure data resource
+   * @param sourceType
+   *          - how to resolve data from resource
+   * @param IProgressIndicator
+   *          reference to UI component that maintains a progress bar for the
+   *          mapping operation
+   * @return null or the structure data parsed as a pdb file
+   */
   synchronized public StructureFile computeMapping(
           boolean forStructureView, SequenceI[] sequenceArray,
           String[] targetChainIds, String pdbFile, DataSourceType sourceType,
           IProgressIndicator progress)
   {
     long progressSessionId = System.currentTimeMillis() * 3;
-    /*
-     * There will be better ways of doing this in the future, for now we'll use
-     * the tried and tested MCview pdb mapping
+
+    /**
+     * do we extract and transfer annotation from 3D data ?
      */
-    boolean parseSecStr = processSecondaryStructure;
-    if (isPDBFileRegistered(pdbFile))
-    {
-      for (SequenceI sq : sequenceArray)
-      {
-        SequenceI ds = sq;
-        while (ds.getDatasetSequence() != null)
-        {
-          ds = ds.getDatasetSequence();
-        }
-        ;
-        if (ds.getAnnotation() != null)
-        {
-          for (AlignmentAnnotation ala : ds.getAnnotation())
-          {
-            // false if any annotation present from this structure
-            // JBPNote this fails for jmol/chimera view because the *file* is
-            // passed, not the structure data ID -
-            if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
-            {
-              parseSecStr = false;
-            }
-          }
-        }
-      }
-    }
+    // FIXME: possibly should just delete
+
+    boolean parseSecStr = processSecondaryStructure
+            ? isStructureFileProcessed(pdbFile, sequenceArray)
+            : false;
+
     StructureFile pdb = null;
     boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
     try
@@ -609,6 +611,46 @@ public class StructureSelectionManager
     return pdb;
   }
 
+  /**
+   * check if we need to extract secondary structure from given pdbFile and
+   * transfer to sequences
+   * 
+   * @param pdbFile
+   * @param sequenceArray
+   * @return
+   */
+  private boolean isStructureFileProcessed(String pdbFile,
+          SequenceI[] sequenceArray)
+  {
+    boolean parseSecStr = true;
+    if (isPDBFileRegistered(pdbFile))
+    {
+      for (SequenceI sq : sequenceArray)
+      {
+        SequenceI ds = sq;
+        while (ds.getDatasetSequence() != null)
+        {
+          ds = ds.getDatasetSequence();
+        }
+        ;
+        if (ds.getAnnotation() != null)
+        {
+          for (AlignmentAnnotation ala : ds.getAnnotation())
+          {
+            // false if any annotation present from this structure
+            // JBPNote this fails for jmol/chimera view because the *file* is
+            // passed, not the structure data ID -
+            if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile)))
+            {
+              parseSecStr = false;
+            }
+          }
+        }
+      }
+    }
+    return parseSecStr;
+  }
+
   public void addStructureMapping(StructureMapping sm)
   {
     mappings.add(sm);