JAL-4045 - don't apply distribution dependent scale factor to the axis lines!

[jalview.git] / src / jalview / gui / StructureViewer.java

diff --git a/src/jalview/gui/StructureViewer.java b/src/jalview/gui/StructureViewer.java
index 617706a..5effa1a 100644 (file)
--- a/src/jalview/gui/StructureViewer.java
+++ b/src/jalview/gui/StructureViewer.java
@@ -29,6 +29,7 @@ import java.util.Map.Entry;
 
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.StructureViewerModel;
@@ -63,7 +64,8 @@ public class StructureViewer
    * 
    * @param structureSelectionManager
    */
-  public StructureViewer(StructureSelectionManager structureSelectionManager)
+  public StructureViewer(
+          StructureSelectionManager structureSelectionManager)
   {
     ssm = structureSelectionManager;
   }
@@ -89,7 +91,12 @@ public class StructureViewer
     }
     return "New View";
   }
-  public ViewerType getViewerType()
+
+  /**
+   * 
+   * @return ViewerType for currently configured structure viewer
+   */
+  public static ViewerType getViewerType()
   {
     String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
             ViewerType.JMOL.name());
@@ -125,10 +132,10 @@ public class StructureViewer
 
     Map<PDBEntry, SequenceI[]> seqsForPdbs = getSequencesForPdbs(pdbs,
             seqs);
-    PDBEntry[] pdbsForFile = seqsForPdbs.keySet().toArray(
-            new PDBEntry[seqsForPdbs.size()]);
-    SequenceI[][] theSeqs = seqsForPdbs.values().toArray(
-            new SequenceI[seqsForPdbs.size()][]);
+    PDBEntry[] pdbsForFile = seqsForPdbs.keySet()
+            .toArray(new PDBEntry[seqsForPdbs.size()]);
+    SequenceI[][] theSeqs = seqsForPdbs.values()
+            .toArray(new SequenceI[seqsForPdbs.size()][]);
     if (sview != null)
     {
       sview.setAlignAddedStructures(superposeAdded);
@@ -175,7 +182,7 @@ public class StructureViewer
     }
     else
     {
-      Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+      Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
     }
     return sview;
   }
@@ -323,7 +330,7 @@ public class StructureViewer
     }
     else
     {
-      Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
+      Console.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
     }
     return sview;
   }
@@ -361,7 +368,7 @@ public class StructureViewer
       viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
       break;
     default:
-      Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
+      Console.error(UNKNOWN_VIEWER_TYPE + type.toString());
     }
     return viewer;
   }