JAL-4290 Set structureSelectionManager settings more generically and when no desktop...

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 8968742..5865b7f 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -34,6 +34,7 @@ import java.util.Vector;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.commands.CommandI;
 import jalview.commands.EditCommand;
@@ -50,6 +51,7 @@ import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
 import jalview.gui.IProgressIndicator;
+import jalview.gui.Preferences;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.DataSourceType;
 import jalview.io.StructureFile;
@@ -155,7 +157,8 @@ public class StructureSelectionManager
   {
     if (mappings.isEmpty())
     {
-      jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
+      jalview.bin.Console
+              .errPrintln("reportMapping: No PDB/Sequence mappings.");
     }
     else
     {
@@ -164,7 +167,8 @@ public class StructureSelectionManager
       int i = 0;
       for (StructureMapping sm : mappings)
       {
-        jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
+        jalview.bin.Console
+                .errPrintln("mapping " + i++ + " : " + sm.pdbfile);
       }
     }
   }
@@ -357,6 +361,36 @@ public class StructureSelectionManager
             pdbFile, sourceType, tft, paeFilename, true);
   }
 
+  /**
+   * 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 tft
+   *          - specify how to interpret the temperature factor column in the
+   *          atom data
+   * @param paeFilename
+   *          - when not null, specifies a filename containing a matrix
+   *          formatted in JSON using one of the known PAE formats
+   * @param doXferSettings
+   *          - when true, transfer annotation to mapped sequences in
+   *          sequenceArray
+   * @return null or the structure data parsed as a pdb file
+   */
   synchronized public StructureFile setMapping(boolean forStructureView,
           SequenceI[] sequenceArray, String[] targetChainIds,
           String pdbFile, DataSourceType sourceType, TFType tft,
@@ -388,9 +422,15 @@ public class StructureSelectionManager
    * @param IProgressIndicator
    *          reference to UI component that maintains a progress bar for the
    *          mapping operation
-   * @param tft - specify how to interpret the temperature factor column in the atom data
-   * @param paeFilename - when not null, specifies a filename containing a matrix formatted in JSON using one of the known PAE formats
-   * @param doXferSettings - when true, transfer annotation to mapped sequences in sequenceArray 
+   * @param tft
+   *          - specify how to interpret the temperature factor column in the
+   *          atom data
+   * @param paeFilename
+   *          - when not null, specifies a filename containing a matrix
+   *          formatted in JSON using one of the known PAE formats
+   * @param doXferSettings
+   *          - when true, transfer annotation to mapped sequences in
+   *          sequenceArray
    * @return null or the structure data parsed as a pdb file
    */
   synchronized public StructureFile computeMapping(boolean forStructureView,
@@ -1025,7 +1065,7 @@ public class StructureSelectionManager
           int indexpos = sm.getSeqPos(atom.getPdbResNum());
           if (lastipos != indexpos || lastseq != sm.sequence)
           {
-            results.addResult(sm.sequence, indexpos, indexpos);
+            results.appendResult(sm.sequence, indexpos, indexpos);
             lastipos = indexpos;
             lastseq = sm.sequence;
             // construct highlighted sequence list
@@ -1627,4 +1667,25 @@ public class StructureSelectionManager
     return pdbIdFileName;
   }
 
+  public static void doConfigureStructurePrefs(
+          StructureSelectionManager ssm)
+  {
+    if (Cache.getDefault(Preferences.ADD_SS_ANN, true))
+    {
+      ssm.setAddTempFacAnnot(
+              Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true));
+      ssm.setProcessSecondaryStructure(
+              Cache.getDefault(Preferences.STRUCT_FROM_PDB, true));
+      // JAL-3915 - RNAView is no longer an option so this has no effect
+      ssm.setSecStructServices(
+              Cache.getDefault(Preferences.USE_RNAVIEW, false));
+    }
+    else
+    {
+      ssm.setAddTempFacAnnot(false);
+      ssm.setProcessSecondaryStructure(false);
+      ssm.setSecStructServices(false);
+    }
+  }
+
 }