From 9e7b5a1d3af2af268d19b2f82c964ce2c27e9c3e Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 13 Feb 2018 13:45:28 +0000
Subject: [PATCH] =?utf8?q?JAL-2781=20refactor=20possibly=20non-functional=20?=
 =?utf8?q?=E2=80=98extract=20secondary=20structure=E2=80=99=20logic=20out=20?=
 =?utf8?q?of=20computeMapping?=
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---
 .../structure/StructureSelectionManager.java       |   75 +++++++++++++-------
 1 file changed, 49 insertions(+), 26 deletions(-)

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 14cef12..8380b19 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -383,33 +383,16 @@ public class StructureSelectionManager
           IProgressIndicator progress)
   {
     long progressSessionId = System.currentTimeMillis() * 3;
+
+    /**
+     * 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
@@ -628,6 +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);
-- 
1.7.10.2