X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;fp=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=ec3e0a097e708ab263415159e1ed4f411597d885;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=2f1ddc07533637b08921013383d27f639ec12612;hpb=cb31e23d9138e481479623374aed7767bf8934d2;p=jalview.git

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index 2f1ddc0..ec3e0a0 100644
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -155,7 +155,8 @@ 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 +165,8 @@ 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);
       }
     }
   }
@@ -357,7 +359,6 @@ 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
@@ -377,9 +378,15 @@ public class StructureSelectionManager
    *          - 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 
+   * @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,
@@ -413,9 +420,15 @@ 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,