Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews

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

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 64c1547..2f1ddc0 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -155,16 +155,16 @@ public class StructureSelectionManager
   {
     if (mappings.isEmpty())
     {
-      System.err.println("reportMapping: No PDB/Sequence mappings.");
+      jalview.bin.Console.errPrintln("reportMapping: No PDB/Sequence mappings.");
     }
     else
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "reportMapping: There are " + mappings.size() + " mappings.");
       int i = 0;
       for (StructureMapping sm : mappings)
       {
-        System.err.println("mapping " + i++ + " : " + sm.pdbfile);
+        jalview.bin.Console.errPrintln("mapping " + i++ + " : " + sm.pdbfile);
       }
     }
   }
@@ -357,6 +357,31 @@ 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,
@@ -617,12 +642,12 @@ public class StructureSelectionManager
               chain.transferResidueAnnotation(siftsMapping, null);
             } catch (SiftsException e)
             {
-              System.err.println(e.getMessage());
+              jalview.bin.Console.errPrintln(e.getMessage());
             } catch (Exception e)
             {
-              System.err.println(
+              jalview.bin.Console.errPrintln(
                       "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
-              System.err.println(e.getMessage());
+              jalview.bin.Console.errPrintln(e.getMessage());
             }
           }
           if (!foundSiftsMappings.isEmpty())
@@ -1025,7 +1050,7 @@ 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
@@ -1254,7 +1279,7 @@ public class StructureSelectionManager
      * 
      * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
      * && mappings[j].pdbfile.equals(sl.getPdbFile())) {
-     * System.out.println(pdbid+" "+mappings[j].getPdbId() +"
+     * jalview.bin.Console.outPrintln(pdbid+" "+mappings[j].getPdbId() +"
      * "+mappings[j].pdbfile);
      * 
      * java.awt.Color col; for(int index=0; index<seq.getLength(); index++) {
@@ -1351,7 +1376,7 @@ public class StructureSelectionManager
       boolean removed = seqmappings.remove(acf);
       if (removed && seqmappings.isEmpty())
       { // debug
-        System.out.println("All mappings removed");
+        jalview.bin.Console.outPrintln("All mappings removed");
       }
     }
   }