JAL-1620 version bump and release notes

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ac2897d..e9aa575 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -46,6 +46,70 @@ public class StructureSelectionManager
 
   StructureMapping[] mappings;
 
+  private boolean processSecondaryStructure = false,
+          secStructServices = false, addTempFacAnnot = false;
+
+  /**
+   * @return true if will try to use external services for processing secondary
+   *         structure
+   */
+  public boolean isSecStructServices()
+  {
+    return secStructServices;
+  }
+
+  /**
+   * control use of external services for processing secondary structure
+   * 
+   * @param secStructServices
+   */
+  public void setSecStructServices(boolean secStructServices)
+  {
+    this.secStructServices = secStructServices;
+  }
+
+  /**
+   * flag controlling addition of any kind of structural annotation
+   * 
+   * @return true if temperature factor annotation will be added
+   */
+  public boolean isAddTempFacAnnot()
+  {
+    return addTempFacAnnot;
+  }
+
+  /**
+   * set flag controlling addition of structural annotation
+   * 
+   * @param addTempFacAnnot
+   */
+  public void setAddTempFacAnnot(boolean addTempFacAnnot)
+  {
+    this.addTempFacAnnot = addTempFacAnnot;
+  }
+
+  /**
+   * 
+   * @return if true, the structure manager will attempt to add secondary
+   *         structure lines for unannotated sequences
+   */
+
+  public boolean isProcessSecondaryStructure()
+  {
+    return processSecondaryStructure;
+  }
+
+  /**
+   * Control whether structure manager will try to annotate mapped sequences
+   * with secondary structure from PDB data.
+   * 
+   * @param enable
+   */
+  public void setProcessSecondaryStructure(boolean enable)
+  {
+    processSecondaryStructure = enable;
+  }
+
   /**
    * debug function - write all mappings to stdout
    */
@@ -245,7 +309,7 @@ public class StructureSelectionManager
      * the tried and tested MCview pdb mapping
      */
     MCview.PDBfile pdb = null;
-    boolean parseSecStr=true;
+    boolean parseSecStr = processSecondaryStructure;
     if (isPDBFileRegistered(pdbFile))
     {
       for (SequenceI sq : sequence)
@@ -274,7 +338,8 @@ public class StructureSelectionManager
     }
     try
     {
-      pdb = new MCview.PDBfile(true, parseSecStr, pdbFile, protocol);
+      pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
+              secStructServices, pdbFile, protocol);
       if (pdb.id != null && pdb.id.trim().length() > 0
               && AppletFormatAdapter.FILE.equals(protocol))
       {
@@ -457,7 +522,6 @@ public class StructureSelectionManager
     {
       return;
     }
-    boolean removeMapping = true;
     String[] handlepdbs;
     Vector pdbs = new Vector();
     for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))