merge

diff --git a/src/jalview/datamodel/SearchResults.java b/src/jalview/datamodel/SearchResults.java
index 2a33f6c..3948ba0 100755 (executable)
--- a/src/jalview/datamodel/SearchResults.java
+++ b/src/jalview/datamodel/SearchResults.java
@@ -36,6 +36,10 @@ public class SearchResults
 
   private List<Match> matches = new ArrayList<Match>();
 
+  /**
+   * One match consists of a sequence reference, start and end positions.
+   * Discontiguous ranges in a sequence require two or more Match objects.
+   */
   public class Match
   {
     SequenceI sequence;
@@ -92,13 +96,44 @@ public class SearchResults
       // convert start/end to base 0 (with bounds check)
       final int from = Math.max(start - 1, 0);
       final int to = Math.min(end, chars.length + 1);
-      return String.valueOf(Arrays.copyOfRange(chars, from, to));
+      // return String.valueOf(Arrays.copyOfRange(chars, from, to));
+      return String.valueOf(from)
+              + String.valueOf(Arrays.copyOfRange(chars, from, to));
     }
 
     public void setSequence(SequenceI seq)
     {
       this.sequence = seq;
     }
+
+    /**
+     * Hashcode is the hashcode of the matched sequence plus a hash of start and
+     * end positions. Match objects that pass the test for equals are guaranteed
+     * to have the same hashcode.
+     */
+    @Override
+    public int hashCode()
+    {
+      int hash = sequence == null ? 0 : sequence.hashCode();
+      hash += 31 * start;
+      hash += 67 * end;
+      return hash;
+    }
+
+    /**
+     * Two Match objects are equal if they are for the same sequence, start and
+     * end positions
+     */
+    @Override
+    public boolean equals(Object obj)
+    {
+      if (obj == null || !(obj instanceof Match))
+      {
+        return false;
+      }
+      Match m = (Match) obj;
+      return (this.sequence == m.sequence && this.start == m.start && this.end == m.end);
+    }
   }
 
   /**
@@ -281,4 +316,30 @@ public class SearchResults
     }
     return result.toString();
   }
+
+  /**
+   * Hashcode is has derived from the list of matches. This ensures that when
+   * two SearchResults objects satisfy the test for equals(), then they have the
+   * same hashcode.
+   */
+  @Override
+  public int hashCode()
+  {
+    return matches.hashCode();
+  }
+
+  /**
+   * Two SearchResults are considered equal if they contain the same matches in
+   * the same order.
+   */
+  @Override
+  public boolean equals(Object obj)
+  {
+    if (obj == null || !(obj instanceof SearchResults))
+    {
+      return false;
+    }
+    SearchResults sr = (SearchResults) obj;
+    return ((ArrayList<Match>) this.matches).equals(sr.matches);
+  }
 }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index b37b442..83fb7c0 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1497,6 +1497,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
       if (closeAllTabs)
       {
+        /*
+         * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+         * be called recursively, with the frame now in 'closed' state
+         */
         this.setClosed(true);
       }
     } catch (Exception ex)
@@ -2749,12 +2753,17 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
 
     /*
-     * Views share the same edits, undo and redo stacks, mappings.
+     * Views share the same edits undo and redo stacks
      */
     newap.av.setHistoryList(viewport.getHistoryList());
     newap.av.setRedoList(viewport.getRedoList());
-    newap.av.getAlignment().setCodonFrames(
-            viewport.getAlignment().getCodonFrames());
+
+    /*
+     * Views share the same mappings; need to deregister any new mappings
+     * created by copyAlignPanel, and register the new reference to the shared
+     * mappings
+     */
+    newap.av.replaceMappings(viewport.getAlignment());
 
     newap.av.viewName = getNewViewName(viewTitle);
 
@@ -4968,10 +4977,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
               "Exception during translation. Please report this !", ex);
       final String msg = MessageManager
               .getString("label.error_when_translating_sequences_submit_bug_report");
-      final String title = MessageManager
+      final String errorTitle = MessageManager
               .getString("label.implementation_error")
               + MessageManager.getString("translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JOptionPane.ERROR_MESSAGE);
       return;
     }
@@ -4979,9 +4988,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       final String msg = MessageManager
               .getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
-      final String title = MessageManager
+      final String errorTitle = MessageManager
               .getString("label.translation_failed");
-      JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+      JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
               JOptionPane.WARNING_MESSAGE);
     }
     else
@@ -4995,8 +5004,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
       {
         final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
-        viewport.openSplitFrame(af, new Alignment(seqs),
-                al.getCodonFrames());
+        viewport.openSplitFrame(af, new Alignment(seqs));
       }
       else
       {
@@ -6088,7 +6096,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       sf.setComplementVisible(this, show);
     }
   }
-
 }
 
 class PrintThread extends Thread

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 9ed953f..aedfe12 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -45,7 +45,6 @@ import jalview.api.AlignViewportI;
 import jalview.api.ViewStyleI;
 import jalview.bin.Cache;
 import jalview.commands.CommandI;
-import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
@@ -71,7 +70,6 @@ import java.awt.Rectangle;
 import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JInternalFrame;
@@ -416,16 +414,43 @@ public class AlignViewport extends AlignmentViewport implements
    */
   public void setAlignment(AlignmentI align)
   {
-    if (alignment != null && alignment.getCodonFrames() != null)
+    replaceMappings(align);
+    this.alignment = align;
+  }
+
+  /**
+   * Replace any codon mappings for this viewport with those for the given
+   * viewport
+   * 
+   * @param align
+   */
+  public void replaceMappings(AlignmentI align)
+  {
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(Desktop.instance);
+
+    /*
+     * Deregister current mappings (if any)
+     */
+    if (alignment != null)
     {
-      StructureSelectionManager.getStructureSelectionManager(
-              Desktop.instance).removeMappings(alignment.getCodonFrames());
+      ssm.removeMappings(alignment.getCodonFrames());
     }
-    this.alignment = align;
-    if (alignment != null && alignment.getCodonFrames() != null)
+
+    /*
+     * Register new mappings (if any)
+     */
+    if (align != null)
     {
-      StructureSelectionManager.getStructureSelectionManager(
-              Desktop.instance).addMappings(alignment.getCodonFrames());
+      ssm.addMappings(align.getCodonFrames());
+    }
+
+    /*
+     * replace mappings on our alignment
+     */
+    if (alignment != null && align != null)
+    {
+      alignment.setCodonFrames(align.getCodonFrames());
     }
   }
 
@@ -884,9 +909,8 @@ public class AlignViewport extends AlignmentViewport implements
     AlignmentUtils.mapProteinToCdna(protein, cdna);
 
     /*
-     * Create the AlignFrame for the added alignment. Note this will include the
-     * cDNA consensus annotation if it is protein (because the alignment holds
-     * mappings to nucleotide)
+     * Create the AlignFrame for the added alignment. If it is protein, mappings
+     * are registered with StructureSelectionManager as a side-effect.
      */
     AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
             AlignFrame.DEFAULT_HEIGHT);
@@ -921,18 +945,9 @@ public class AlignViewport extends AlignmentViewport implements
     if (openSplitPane)
     {
       al.alignAs(thisAlignment);
-      protein = openSplitFrame(newAlignFrame, thisAlignment,
-              protein.getCodonFrames());
+      protein = openSplitFrame(newAlignFrame, thisAlignment);
     }
 
-    /*
-     * Register the mappings (held on the protein alignment) with the
-     * StructureSelectionManager (for mouseover linking).
-     */
-    final StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    ssm.addMappings(protein.getCodonFrames());
-
     return true;
   }
 
@@ -944,16 +959,14 @@ public class AlignViewport extends AlignmentViewport implements
    *          containing a new alignment to be shown
    * @param complement
    *          cdna/protein complement alignment to show in the other split half
-   * @param mappings
    * @return the protein alignment in the split frame
    */
   protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
-          AlignmentI complement, Set<AlignedCodonFrame> mappings)
+          AlignmentI complement)
   {
     /*
      * Make a new frame with a copy of the alignment we are adding to. If this
-     * is protein, the new frame will have a cDNA consensus annotation row
-     * added.
+     * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
      */
     AlignFrame copyMe = new AlignFrame(complement,
             AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
@@ -964,9 +977,6 @@ public class AlignViewport extends AlignmentViewport implements
             : newAlignFrame;
     final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
             : copyMe;
-    AlignmentI protein = proteinFrame.viewport.getAlignment();
-    protein.setCodonFrames(mappings);
-
     cdnaFrame.setVisible(true);
     proteinFrame.setVisible(true);
     String linkedTitle = MessageManager
@@ -978,7 +988,7 @@ public class AlignViewport extends AlignmentViewport implements
     JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
     Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 
-    return protein;
+    return proteinFrame.viewport.getAlignment();
   }
 
   public AnnotationColumnChooser getAnnotationColumnSelectionState()

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index ad7e75c..d88e207 100644 (file)
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -362,8 +362,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
       }
       int start = r[0];
       int end = r[1];
-      // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
       // DEBUG
+//       System.err.println(this.av.viewName + " Seq : " + seqIndex
+//       + " Scroll to " + start + "," + end);
 
       /*
        * To centre results, scroll to positions half the visible width
@@ -373,7 +374,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
       {
         int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
         start = Math.max(start - offset, 0);
-        end = Math.min(end + offset, seq.getEnd() - 1);
+        end = end + offset - 1;
       }
       if (start < 0)
       {
@@ -402,6 +403,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
        */
       seqIndex = Math.max(0, seqIndex - verticalOffset);
 
+      // System.out.println("start=" + start + ", end=" + end + ", startv="
+      // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+      // + av.getStartSeq() + ", ends=" + av.getEndSeq());
       if (!av.getWrapAlignment())
       {
         if ((startv = av.getStartRes()) >= start)
@@ -668,14 +672,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
    * Adjust row/column scrollers to show a visible position in the alignment.
    * 
    * @param x
-   *          visible column to scroll to DOCUMENT ME!
+   *          visible column to scroll to
    * @param y
    *          visible row to scroll to
    * 
    */
   public void setScrollValues(int x, int y)
   {
-    // System.err.println("Scroll to "+x+","+y);
+    // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
     if (av == null || av.getAlignment() == null)
     {
       return;

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6a95363..0e1811d 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -265,10 +265,10 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       delegate.openFrame(f);
     }
 
+    @Override
     public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
             int newHeight)
     {
-      Rectangle b = desktop.getBounds();
       if (newY < 0)
       {
         newY = 0;
@@ -1301,7 +1301,17 @@ public class Desktop extends jalview.jbgui.GDesktop implements
     if (v_client != null)
     {
       // TODO clear binding to vamsas document objects on close_all
+    }
 
+    /*
+     * reset state of singleton objects as appropriate (clear down session state
+     * when all windows are closed)
+     */
+    StructureSelectionManager ssm = StructureSelectionManager
+            .getStructureSelectionManager(this);
+    if (ssm != null)
+    {
+      ssm.resetAll();
     }
   }
 
@@ -2287,6 +2297,7 @@ public class Desktop extends jalview.jbgui.GDesktop implements
       }
     }
 
+    @Override
     public void paintComponent(Graphics g)
     {
       if (showMemoryUsage && g != null && df != null)

diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index e34a864..41c3ce1 100644 (file)
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,27 +20,11 @@
  */
 package jalview.gui;
 
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.List;
-import java.util.Vector;
-
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.ToolTipManager;
-
 import jalview.api.AlignViewportI;
 import jalview.commands.EditCommand;
 import jalview.commands.EditCommand.Action;
 import jalview.commands.EditCommand.Edit;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SearchResults;
 import jalview.datamodel.SearchResults.Match;
@@ -60,6 +44,23 @@ import jalview.util.MappingUtils;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
 
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Point;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
+
 /**
  * DOCUMENT ME!
  * 
@@ -128,6 +129,8 @@ public class SeqPanel extends JPanel implements MouseListener,
 
   StructureSelectionManager ssm;
 
+  SearchResults lastSearchResults;
+
   /**
    * Creates a new SeqPanel object.
    * 
@@ -656,9 +659,20 @@ public class SeqPanel extends JPanel implements MouseListener,
     lastMessage = tmp;
   }
 
+  /**
+   * Highlight the mapped region described by the search results object (unless
+   * unchanged). This supports highlight of protein while mousing over linked
+   * cDNA and vice versa. The status bar is also updated to show the location of
+   * the start of the highlighted region.
+   */
   @Override
   public void highlightSequence(SearchResults results)
   {
+    if (results == null || results.equals(lastSearchResults)) {
+      return;
+    }
+    lastSearchResults = results;
+    
     if (av.isFollowHighlight())
     {
       /*
@@ -868,19 +882,27 @@ public class SeqPanel extends JPanel implements MouseListener,
    */
   private void setStatusMessage(SearchResults results)
   {
-    List<Match> matches = results.getResults();
-    if (!matches.isEmpty())
+    AlignmentI al = this.av.getAlignment();
+    int sequenceIndex = al.findIndex(results);
+    if (sequenceIndex == -1)
+    {
+      return;
+    }
+    SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+    for (Match m : results.getResults())
     {
-      Match m = matches.get(0);
       SequenceI seq = m.getSequence();
-      int sequenceIndex = this.av.getAlignment().findIndex(seq);
 
-      /*
-       * Convert position in sequence (base 1) to sequence character array index
-       * (base 0)
-       */
-      int start = m.getStart() - 1;
-      setStatusMessage(seq, start, sequenceIndex);
+      if (seq == ds)
+      {
+        /*
+         * Convert position in sequence (base 1) to sequence character array
+         * index (base 0)
+         */
+        int start = m.getStart() - 1;
+        setStatusMessage(seq, start, sequenceIndex);
+        return;
+      }
     }
   }
 

diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java
index ac14b52..cf60490 100644 (file)
--- a/src/jalview/structure/StructureSelectionManager.java
+++ b/src/jalview/structure/StructureSelectionManager.java
@@ -20,6 +20,22 @@
  */
 package jalview.structure;
 
+import jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
 import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -37,22 +53,6 @@ import MCview.Atom;
 import MCview.PDBChain;
 import MCview.PDBfile;
 
-import jalview.analysis.AlignSeq;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
 public class StructureSelectionManager
 {
   public final static String NEWLINE = System.lineSeparator();
@@ -76,7 +76,7 @@ public class StructureSelectionManager
    * Reference counters for the above mappings. Remove mappings when ref count
    * goes to zero.
    */
-  Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+  private Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
 
   private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
 
@@ -721,13 +721,16 @@ public class StructureSelectionManager
               {
                 results = MappingUtils.buildSearchResults(seq, index,
                         seqmappings);
-              }
+               }
               if (handlingVamsasMo)
               {
                 results.addResult(seq, index, index);
 
               }
-              seqListener.highlightSequence(results);
+              if (!results.isEmpty())
+              {
+                seqListener.highlightSequence(results);
+              }
             }
           }
         }
@@ -944,6 +947,10 @@ public class StructureSelectionManager
       {
         seqmappings.remove(acf);
         seqMappingRefCounts.remove(acf);
+        if (seqmappings.isEmpty())
+        { // debug
+          System.out.println("All mappings removed");
+        }
       }
     }
   }
@@ -985,6 +992,50 @@ public class StructureSelectionManager
     }
   }
 
+  /**
+   * Resets this object to its initial state by removing all registered
+   * listeners, codon mappings, PDB file mappings
+   */
+  public void resetAll()
+  {
+    if (mappings != null)
+    {
+      mappings.clear();
+    }
+    if (seqmappings != null)
+    {
+      seqmappings.clear();
+    }
+    if (seqMappingRefCounts != null)
+    {
+      seqMappingRefCounts.clear();
+    }
+    if (sel_listeners != null)
+    {
+      sel_listeners.clear();
+    }
+    if (listeners != null)
+    {
+      listeners.clear();
+    }
+    if (commandListeners != null)
+    {
+      commandListeners.clear();
+    }
+    if (view_listeners != null)
+    {
+      view_listeners.clear();
+    }
+    if (pdbFileNameId != null)
+    {
+      pdbFileNameId.clear();
+    }
+    if (pdbIdFileName != null)
+    {
+      pdbIdFileName.clear();
+    }
+  }
+
   public void addSelectionListener(SelectionListener selecter)
   {
     if (!sel_listeners.contains(selecter))
@@ -1136,4 +1187,20 @@ public class StructureSelectionManager
     }
     return null;
   }
+
+  /**
+   * Returns the reference count for a mapping
+   * 
+   * @param acf
+   * @return
+   */
+  protected int getMappingReferenceCount(AlignedCodonFrame acf)
+  {
+    if (seqMappingRefCounts == null)
+    {
+      return 0;
+    }
+    Integer count = seqMappingRefCounts.get(acf);
+    return (count == null ? 0 : count.intValue());
+  }
 }

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 899e8a7..a3b7527 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2531,7 +2531,12 @@ public abstract class AlignmentViewport implements AlignViewportI,
     int middleColumn = getStartRes() + (getEndRes() - getStartRes()) / 2;
     final HiddenSequences hiddenSequences = getAlignment()
             .getHiddenSequences();
-    for (int seqNo = getStartSeq(); seqNo < getEndSeq(); seqNo++, seqOffset++)
+    
+    /*
+     * searching to the bottom of the alignment gives smoother scrolling across all gapped visible regions
+     */
+    int lastSeq = alignment.getHeight() - 1;
+    for (int seqNo = getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))

diff --git a/test/jalview/datamodel/MatchTest.java b/test/jalview/datamodel/MatchTest.java
new file mode 100644 (file)
index 0000000..9b5e97b
--- /dev/null
+++ b/test/jalview/datamodel/MatchTest.java
@@ -0,0 +1,67 @@
+package jalview.datamodel;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.SearchResults.Match;
+
+import org.testng.annotations.Test;
+
+public class MatchTest
+{
+
+  @Test(groups = { "Functional" })
+  public void testToString()
+  {
+    SequenceI seq = new Sequence("", "abcdefghijklm");
+    Match m = new SearchResults().new Match(seq, 3, 5);
+    assertEquals("2cde", m.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    assertFalse(sr1.equals(null));
+    assertFalse(sr1.equals(seq1));
+    assertTrue(sr1.equals(sr1));
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+
+    sr1.addResult(seq1, 1, 1);
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+
+    sr2.addResult(seq1, 1, 1);
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+
+    /*
+     * same match but on different sequences - not equal
+     */
+    SearchResults sr3 = new SearchResults();
+    sr3.addResult(seq2, 1, 1);
+    assertFalse(sr1.equals(sr3));
+    assertFalse(sr3.equals(sr1));
+
+    /*
+     * same sequence but different end position - not equal
+     */
+    sr1.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 3, 5);
+    assertFalse(sr1.equals(sr2));
+
+    /*
+     * same sequence but different start position - not equal
+     */
+    sr1 = new SearchResults();
+    sr2 = new SearchResults();
+    sr1.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 2, 4);
+    assertFalse(sr1.equals(sr2));
+  }
+}

diff --git a/test/jalview/datamodel/SearchResultsTest.java b/test/jalview/datamodel/SearchResultsTest.java
index b576569..983bd34 100644 (file)
--- a/test/jalview/datamodel/SearchResultsTest.java
+++ b/test/jalview/datamodel/SearchResultsTest.java
@@ -1,6 +1,8 @@
 package jalview.datamodel;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
 
 import org.testng.annotations.Test;
 
@@ -13,12 +15,120 @@ public class SearchResultsTest
     SequenceI seq = new Sequence("", "abcdefghijklm");
     SearchResults sr = new SearchResults();
     sr.addResult(seq, 1, 1);
-    assertEquals("a", sr.toString());
+    assertEquals("0a", sr.toString());
     sr.addResult(seq, 3, 5);
-    assertEquals("acde", sr.toString());
+    assertEquals("0a2cde", sr.toString());
 
     seq = new Sequence("", "pqrstuvwxy");
     sr.addResult(seq, 6, 7);
-    assertEquals("acdeuv", sr.toString());
+    assertEquals("0a2cde5uv", sr.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testEquals()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    assertFalse(sr1.equals(null)); // null object
+    assertFalse(sr1.equals(seq1)); // wrong type
+    assertTrue(sr1.equals(sr1)); // self
+    assertTrue(sr1.equals(sr2)); // empty
+    assertTrue(sr2.equals(sr1)); // reflexive
+
+    /*
+     * only one result is not empty
+     */
+    sr1.addResult(seq1, 1, 1);
+    assertTrue(sr1.equals(sr1));
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+
+    /*
+     * both the same
+     */
+    sr2.addResult(seq1, 1, 1);
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+
+    /*
+     * both have three matches
+     */
+    sr1.addResult(seq1, 3, 4);
+    sr1.addResult(seq1, 6, 8);
+    sr2.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 6, 8);
+    assertTrue(sr1.equals(sr1));
+    assertTrue(sr2.equals(sr2));
+    assertTrue(sr1.equals(sr2));
+    assertTrue(sr2.equals(sr1));
+  }
+
+  /**
+   * Matches that are similar but for distinct sequences are not equal
+   */
+  @Test(groups = { "Functional" })
+  public void testEquals_distinctSequences()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SequenceI seq2 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    sr1.addResult(seq1, 1, 1);
+    sr2.addResult(seq2, 1, 1);
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+  }
+
+  /**
+   * Matches that are the same except for ordering are not equal
+   */
+  @Test(groups = { "Functional" })
+  public void testEquals_orderDiffers()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    sr1.addResult(seq1, 1, 1);
+    sr1.addResult(seq1, 2, 2);
+    sr2.addResult(seq1, 2, 2);
+    sr2.addResult(seq1, 1, 1);
+    assertFalse(sr1.equals(sr2));
+    assertFalse(sr2.equals(sr1));
+  }
+
+  /**
+   * Verify that hashCode matches for equal objects
+   */
+  @Test(groups = { "Functional" })
+  public void testHashcode()
+  {
+    SequenceI seq1 = new Sequence("", "abcdefghijklm");
+    SearchResults sr1 = new SearchResults();
+    SearchResults sr2 = new SearchResults();
+
+    /*
+     * both empty
+     */
+    assertEquals(sr1.hashCode(), sr2.hashCode());
+
+    /*
+     * both one match
+     */
+    sr1.addResult(seq1, 1, 1);
+    sr2.addResult(seq1, 1, 1);
+    assertEquals(sr1.hashCode(), sr2.hashCode());
+
+    /*
+     * both three matches
+     */
+    sr1.addResult(seq1, 3, 4);
+    sr1.addResult(seq1, 6, 8);
+    sr2.addResult(seq1, 3, 4);
+    sr2.addResult(seq1, 6, 8);
+    assertEquals(sr1.hashCode(), sr2.hashCode());
   }
 }

diff --git a/test/jalview/structure/StructureSelectionManagerTest.java b/test/jalview/structure/StructureSelectionManagerTest.java
index e3612a5..0162308 100644 (file)
--- a/test/jalview/structure/StructureSelectionManagerTest.java
+++ b/test/jalview/structure/StructureSelectionManagerTest.java
@@ -33,8 +33,7 @@ public class StructureSelectionManagerTest
     ssm.addMapping(acf1);
     assertEquals(1, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
-    assertEquals(1, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+    assertEquals(1, ssm.getMappingReferenceCount(acf1));
 
     /*
      * A second mapping.
@@ -43,9 +42,8 @@ public class StructureSelectionManagerTest
     assertEquals(2, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
-    assertEquals(2, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+    assertEquals(1, ssm.getMappingReferenceCount(acf1));
+    assertEquals(1, ssm.getMappingReferenceCount(acf2));
 
     /*
      * A second reference to the first mapping.
@@ -54,9 +52,8 @@ public class StructureSelectionManagerTest
     assertEquals(2, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
-    assertEquals(2, ssm.seqMappingRefCounts.size());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+    assertEquals(2, ssm.getMappingReferenceCount(acf1));
+    assertEquals(1, ssm.getMappingReferenceCount(acf2));
   }
 
   @Test(groups ={ "Functional" })
@@ -83,10 +80,9 @@ public class StructureSelectionManagerTest
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
     assertTrue(ssm.seqmappings.contains(acf3));
-    assertEquals(3, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf2).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+    assertEquals(1, ssm.getMappingReferenceCount(acf1));
+    assertEquals(2, ssm.getMappingReferenceCount(acf2));
+    assertEquals(1, ssm.getMappingReferenceCount(acf3));
   }
 
   @Test(groups ={ "Functional" })
@@ -94,15 +90,16 @@ public class StructureSelectionManagerTest
   {
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
     AlignedCodonFrame acf2 = new AlignedCodonFrame();
-    ssm.addMapping(acf1);
 
     /*
      * Add one and remove it.
      */
+    ssm.addMapping(acf1);
     ssm.removeMapping(acf1);
     ssm.removeMapping(acf2);
     assertEquals(0, ssm.seqmappings.size());
-    assertEquals(0, ssm.seqMappingRefCounts.size());
+    assertEquals(0, ssm.getMappingReferenceCount(acf1));
+    assertEquals(0, ssm.getMappingReferenceCount(acf2));
 
     /*
      * Add one twice and remove it once.
@@ -114,9 +111,8 @@ public class StructureSelectionManagerTest
     assertEquals(2, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
-    assertEquals(2, ssm.seqMappingRefCounts.size());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+    assertEquals(1, ssm.getMappingReferenceCount(acf1));
+    assertEquals(1, ssm.getMappingReferenceCount(acf2));
 
     /*
      * Remove both once more to clear the set.
@@ -124,7 +120,8 @@ public class StructureSelectionManagerTest
     ssm.removeMapping(acf1);
     ssm.removeMapping(acf2);
     assertEquals(0, ssm.seqmappings.size());
-    assertEquals(0, ssm.seqMappingRefCounts.size());
+    assertEquals(0, ssm.getMappingReferenceCount(acf1));
+    assertEquals(0, ssm.getMappingReferenceCount(acf2));
   }
 
   @Test(groups ={ "Functional" })
@@ -159,10 +156,9 @@ public class StructureSelectionManagerTest
     assertTrue(ssm.seqmappings.contains(acf1));
     assertTrue(ssm.seqmappings.contains(acf2));
     assertTrue(ssm.seqmappings.contains(acf3));
-    assertEquals(3, ssm.seqMappingRefCounts.size());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
-    assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+    assertEquals(2, ssm.getMappingReferenceCount(acf1));
+    assertEquals(1, ssm.getMappingReferenceCount(acf2));
+    assertEquals(1, ssm.getMappingReferenceCount(acf3));
 
     /*
      * Remove one ref each to acf2, acf3 - they are removed
@@ -170,7 +166,6 @@ public class StructureSelectionManagerTest
     ssm.removeMappings(set2);
     assertEquals(1, ssm.seqmappings.size());
     assertTrue(ssm.seqmappings.contains(acf1));
-    assertEquals(1, ssm.seqMappingRefCounts.size());
-    assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+    assertEquals(2, ssm.getMappingReferenceCount(acf1));
   }
 }

diff --git a/utils/eclipse/JalviewCodeStyle.xml b/utils/eclipse/JalviewCodeStyle.xml
index afd6402..9923e8e 100644 (file)
--- a/utils/eclipse/JalviewCodeStyle.xml
+++ b/utils/eclipse/JalviewCodeStyle.xml
@@ -17,271 +17,289 @@
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
-<profiles version="11">
-<profile kind="CodeFormatterProfile" name="Jalview" version="11">
-<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_annotation" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_comma_in_type_parameters" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_type_declaration" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_comma_in_type_arguments" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration" value="next_line"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_colon_in_case" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_brace_in_array_initializer" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_new_line_in_empty_annotation_declaration" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_closing_brace_in_array_initializer" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_annotation" value="do not insert"/>
+<profiles version="12">
+<profile kind="CodeFormatterProfile" name="Jalview" version="12">
+<setting id="org.eclipse.jdt.core.compiler.codegen.inlineJsrBytecode" value="enabled"/>
+<setting id="org.eclipse.jdt.core.compiler.codegen.targetPlatform" value="1.5"/>
+<setting id="org.eclipse.jdt.core.compiler.compliance" value="1.5"/>
+<setting id="org.eclipse.jdt.core.compiler.problem.assertIdentifier" value="error"/>
+<setting id="org.eclipse.jdt.core.compiler.problem.enumIdentifier" value="error"/>
+<setting id="org.eclipse.jdt.core.compiler.source" value="1.5"/>
+<setting id="org.eclipse.jdt.core.formatter.align_type_members_on_columns" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_allocation_expression" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_annotation" value="52"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_enum_constant" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_explicit_constructor_call" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_method_invocation" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_arguments_in_qualified_allocation_expression" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_assignment" value="0"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_binary_expression" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_compact_if" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_enum_constants" value="0"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_method_declaration" value="0"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_constructor_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_parameters_in_method_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_superclass_in_type_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_enum_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_superinterfaces_in_type_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_constructor_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.alignment_for_throws_clause_in_method_declaration" value="16"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_imports" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_after_package" value="1"/>
 <setting id="org.eclipse.jdt.core.formatter.blank_lines_before_field" value="1"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_opening_paren_in_while" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_annotation_type_member_declaration" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_else_in_if_statement" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_prefix_operator" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.keep_else_statement_on_same_line" value="false"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_ellipsis" value="insert"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_first_class_body_declaration" value="0"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_imports" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_member_type" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_method" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_new_chunk" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_before_package" value="0"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_between_import_groups" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.blank_lines_between_type_declarations" value="1"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_annotation_type_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_anonymous_type_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_array_initializer" value="next_line_on_wrap"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block_in_case" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_block" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_constructor_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_constant" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_enum_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_method_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_switch" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.brace_position_for_type_declaration" value="next_line"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_block_comment" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.clear_blank_lines_in_javadoc_comment" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_block_comments" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_header" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_html" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_javadoc_comments" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_line_comments" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.format_source_code" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.indent_parameter_description" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.indent_root_tags" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_before_root_tags" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.comment.insert_new_line_for_parameter" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_brace_in_annotation_type_declaration" value="insert"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.line_length" value="80"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_block_boundaries" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.new_lines_at_javadoc_boundaries" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.comment.preserve_white_space_between_code_and_line_comments" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.compact_else_if" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.continuation_indentation_for_array_initializer" value="2"/>
+<setting id="org.eclipse.jdt.core.formatter.continuation_indentation" value="4"/>
+<setting id="org.eclipse.jdt.core.formatter.disabling_tag" value="@formatter\:off"/>
+<setting id="org.eclipse.jdt.core.formatter.enabling_tag" value="@formatter\:on"/>
+<setting id="org.eclipse.jdt.core.formatter.format_guardian_clause_on_one_line" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.format_line_comment_starting_on_first_column" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_annotation_declaration_header" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_constant_header" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_enum_declaration_header" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_body_declarations_compare_to_type_header" value="true"/>
 <setting id="org.eclipse.jdt.core.formatter.indent_breaks_compare_to_cases" value="true"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_at_in_annotation" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.alignment_for_multiple_fields" value="16"/>
-<setting id="org.eclipse.jdt.core.formatter.alignment_for_expressions_in_array_initializer" value="16"/>
-<setting id="org.eclipse.jdt.core.formatter.alignment_for_conditional_expression" value="80"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_opening_paren_in_for" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_after_binary_operator" value="insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_before_question_in_wildcard" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.brace_position_for_array_initializer" value="next_line"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_space_between_empty_parens_in_enum_constant" value="do not insert"/>
-<setting id="org.eclipse.jdt.core.formatter.insert_new_line_before_finally_in_try_statement" value="do not insert"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_empty_lines" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_block" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_statements_compare_to_body" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_cases" value="true"/>
+<setting id="org.eclipse.jdt.core.formatter.indent_switchstatements_compare_to_switch" value="false"/>
+<setting id="org.eclipse.jdt.core.formatter.indentation.size" value="8"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_field" value="insert"/>
 <setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_local_variable" value="insert"/>
+<setting id="org.eclipse.jdt.core.formatter.insert_new_line_after_annotation_on_method" value="insert"/>
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 <setting id="org.eclipse.jdt.core.formatter.keep_then_statement_on_same_line" value="false"/>
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 </profiles>