From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 8 May 2018 09:57:35 +0000 (+0100)
Subject: Merge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4... 
X-Git-Tag: Release_2_10_4~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7dd97604d9087217ad6937a5b860ffb401c53094;hp=2bef55651d4b9d94148f75e3a697ec63823b218a;p=jalview.git

Merge branch 'patch/JAL-2321_addsecstrForDroppedPDBFile' into releases/Release_2_10_4_Branch
---

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index dc3d0ee..2a510a2 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -28,7 +28,6 @@ import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
-import jalview.structure.StructureImportSettings;
 import jalview.util.Format;
 import jalview.util.MessageManager;
 
@@ -60,6 +59,12 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
+  public JmolParser(boolean immediate, String inFile,
+          DataSourceType sourceType) throws IOException
+  {
+    super(immediate, inFile, sourceType);
+  }
+
   public JmolParser(String inFile, DataSourceType sourceType)
           throws IOException
   {
@@ -183,7 +188,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
         }
         lastID = tmpatom.resNumIns.trim();
       }
-      xferSettings();
+      if (isParseImmediately())
+      {
+        // configure parsing settings from the static singleton
+        xferSettings();
+      }
 
       makeResidueList();
       makeCaBondList();
@@ -200,7 +209,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           prot.add(chainseq);
         }
 
-        if (StructureImportSettings.isProcessSecondaryStructure())
+        // look at local setting for adding secondary tructure
+        if (predictSecondaryStructure)
         {
           createAnnotation(chainseq, chain, ms.at);
         }
diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 2340283..497f0a5 100755
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -72,7 +72,20 @@ public abstract class AlignFile extends FileParse
 
   long end;
 
-  private boolean parseCalled;
+  /**
+   * true if parse() has been called
+   */
+  private boolean parseCalled = false;
+
+  private boolean parseImmediately = true;
+
+  /**
+   * @return if doParse() was called at construction time
+   */
+  protected boolean isParseImmediately()
+  {
+    return parseImmediately;
+  }
 
   /**
    * Creates a new AlignFile object.
@@ -153,6 +166,11 @@ public abstract class AlignFile extends FileParse
   {
     super(source);
     initData();
+
+    // stash flag in case parse needs to know if it has to autoconfigure or was
+    // configured after construction
+    this.parseImmediately = parseImmediately;
+
     if (parseImmediately)
     {
       doParse();
diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ad259fd..cd986c0 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -398,8 +398,11 @@ public class StructureSelectionManager
     {
       // FIXME if sourceType is not null, we've lost data here
       sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
-      pdb = new JmolParser(pdbFile, sourceType);
-
+      pdb = new JmolParser(false, pdbFile, sourceType);
+      pdb.addSettings(parseSecStr && processSecondaryStructure,
+              parseSecStr && addTempFacAnnot,
+              parseSecStr && secStructServices);
+      pdb.doParse();
       if (pdb.getId() != null && pdb.getId().trim().length() > 0
               && DataSourceType.FILE == sourceType)
       {
diff --git a/test/jalview/structure/Mapping.java b/test/jalview/structure/Mapping.java
index 85aea40..4bee3f5 100644
--- a/test/jalview/structure/Mapping.java
+++ b/test/jalview/structure/Mapping.java
@@ -260,6 +260,8 @@ public class Mapping
   @Test(groups = { "Functional" })
   public void compareTransferredToRefPDBAnnot() throws Exception
   {
+    StructureImportSettings.setProcessSecondaryStructure(true);
+    StructureImportSettings.setVisibleChainAnnotation(true);
     StructureImportSettings.setShowSeqFeatures(true);
     AlignFrame ref = new FileLoader(false)
             .LoadFileWaitTillLoaded("test/jalview/ext/jmol/1QCF.pdb",