JAL-2418 source formatting

[jalview.git] / src / jalview / structures / models / AAStructureBindingModel.java

diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java
index 7d57886..9f4cea0 100644 (file)
--- a/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@ -20,14 +20,12 @@
  */
 package jalview.structures.models;
 
-import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
-import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.api.StructureSelectionManagerProvider;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
@@ -55,9 +53,9 @@ import java.util.List;
  * @author gmcarstairs
  *
  */
-public abstract class AAStructureBindingModel extends
-        SequenceStructureBindingModel implements StructureListener,
-        StructureSelectionManagerProvider
+public abstract class AAStructureBindingModel
+        extends SequenceStructureBindingModel
+        implements StructureListener, StructureSelectionManagerProvider
 {
 
   private StructureSelectionManager ssm;
@@ -302,7 +300,8 @@ public abstract class AAStructureBindingModel extends
     {
       throw new Error(MessageManager.formatMessage(
               "error.implementation_error_no_pdbentry_from_index",
-              new Object[] { Integer.valueOf(pe).toString() }));
+              new Object[]
+              { Integer.valueOf(pe).toString() }));
     }
     final String nullChain = "TheNullChain";
     List<SequenceI> s = new ArrayList<SequenceI>();
@@ -534,7 +533,7 @@ public abstract class AAStructureBindingModel extends
           BitSet matched, SuperposeData[] structures)
   {
     int refStructure = -1;
-    String[] files = getPdbFile();
+    String[] files = getStructureFiles();
     if (files == null)
     {
       return -1;
@@ -640,8 +639,8 @@ public abstract class AAStructureBindingModel extends
 
     if (waiting)
     {
-      System.err
-              .println("Timed out waiting for structure viewer to load file "
+      System.err.println(
+              "Timed out waiting for structure viewer to load file "
                       + notLoaded);
       return false;
     }
@@ -659,10 +658,8 @@ public abstract class AAStructureBindingModel extends
         {
           for (SequenceI s : seqs)
           {
-            if (s == seq
-                    || (s.getDatasetSequence() != null && s
-                            .getDatasetSequence() == seq
-                            .getDatasetSequence()))
+            if (s == seq || (s.getDatasetSequence() != null
+                    && s.getDatasetSequence() == seq.getDatasetSequence()))
             {
               return true;
             }
@@ -718,24 +715,13 @@ public abstract class AAStructureBindingModel extends
    *          an array of corresponding hidden columns for each alignment
    * @return
    */
-  public abstract String superposeStructures(AlignmentI[] alignments, int[] structureIndices,
-          ColumnSelection[] hiddenCols);
+  public abstract String superposeStructures(AlignmentI[] alignments,
+          int[] structureIndices, HiddenColumns[] hiddenCols);
 
   public abstract void setBackgroundColour(Color col);
 
   protected abstract StructureMappingcommandSet[] getColourBySequenceCommands(
-          String[] files, SequenceRenderer sr, FeatureRenderer fr,
-          AlignViewportI alignViewportI);
-
-  /**
-   * returns the current featureRenderer that should be used to colour the
-   * structures
-   * 
-   * @param alignment
-   * 
-   * @return
-   */
-  public abstract FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment);
+          String[] files, SequenceRenderer sr, AlignmentViewPanel avp);
 
   /**
    * returns the current sequenceRenderer that should be used to colour the
@@ -745,7 +731,8 @@ public abstract class AAStructureBindingModel extends
    * 
    * @return
    */
-  public abstract SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment);
+  public abstract SequenceRenderer getSequenceRenderer(
+          AlignmentViewPanel alignment);
 
   protected abstract void colourBySequence(
           StructureMappingcommandSet[] colourBySequenceCommands);
@@ -769,20 +756,12 @@ public abstract class AAStructureBindingModel extends
     {
       return;
     }
-    String[] files = getPdbFile();
-  
+    String[] files = getStructureFiles();
+
     SequenceRenderer sr = getSequenceRenderer(alignmentv);
-  
-    FeatureRenderer fr = null;
-    boolean showFeatures = alignmentv.getAlignViewport()
-            .isShowSequenceFeatures();
-    if (showFeatures)
-    {
-      fr = getFeatureRenderer(alignmentv);
-    }
-  
+
     StructureMappingcommandSet[] colourBySequenceCommands = getColourBySequenceCommands(
-            files, sr, fr, alignmentv.getAlignViewport());
+            files, sr, alignmentv);
     colourBySequence(colourBySequenceCommands);
   }
 
@@ -790,4 +769,7 @@ public abstract class AAStructureBindingModel extends
   {
     return fileLoadingError != null && fileLoadingError.length() > 0;
   }
+
+  public abstract jalview.api.FeatureRenderer getFeatureRenderer(
+          AlignmentViewPanel alignment);
 }