X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=af0079870b139f6d4230a701df32371c7729fc68;hb=ead72caff9aef9b7103dbb15907aeae777200832;hp=928bb47a744518dbb43466fbe708a94221320e60;hpb=8b70da73fd4073a6e28292d94c1e731878858b66;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 928bb47..af00798 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -28,7 +28,7 @@ import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SequenceI;
-import jalview.io.FormatAdapter;
+import jalview.io.AppletFormatAdapter;
 import jalview.util.MessageManager;
 
 import java.io.PrintStream;
@@ -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)
@@ -274,9 +338,10 @@ 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
-              && FormatAdapter.FILE.equals(protocol))
+              && AppletFormatAdapter.FILE.equals(protocol))
       {
         registerPDBFile(pdb.id.trim(), pdbFile);
       }
@@ -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++]))