JAL-2418 source formatting

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 2881e81..3702cd0 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -77,8 +77,8 @@ import java.util.Map;
  * @author jimp
  * 
  */
-public abstract class AlignmentViewport implements AlignViewportI,
-        CommandListener, VamsasSource
+public abstract class AlignmentViewport
+        implements AlignViewportI, CommandListener, VamsasSource
 {
   final protected ViewportRanges ranges;
 
@@ -568,8 +568,6 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle.setSeqNameItalics(default1);
   }
 
-
-
   @Override
   public AlignmentI getAlignment()
   {
@@ -666,8 +664,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         sg.setColourScheme(cs);
         if (cs != null)
         {
-          sg.getGroupColourScheme()
-                  .alignmentChanged(sg, hiddenRepSequences);
+          sg.getGroupColourScheme().alignmentChanged(sg,
+                  hiddenRepSequences);
         }
       }
     }
@@ -676,8 +674,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public ColourSchemeI getGlobalColourScheme()
   {
-    return residueShading == null ? null : residueShading
-            .getColourScheme();
+    return residueShading == null ? null : residueShading.getColourScheme();
   }
 
   @Override
@@ -825,11 +822,11 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator
-            .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+    if (calculator.getRegisteredWorkersOfClass(
+            jalview.workers.ConservationThread.class) == null)
     {
-      calculator.registerWorker(new jalview.workers.ConservationThread(
-              this, ap));
+      calculator.registerWorker(
+              new jalview.workers.ConservationThread(this, ap));
     }
   }
 
@@ -843,7 +840,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+    if (calculator
+            .getRegisteredWorkersOfClass(ConsensusThread.class) == null)
     {
       calculator.registerWorker(new ConsensusThread(this, ap));
     }
@@ -874,8 +872,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       }
       if (doConsensus)
       {
-        if (calculator
-                .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+        if (calculator.getRegisteredWorkersOfClass(
+                ComplementConsensusThread.class) == null)
         {
           calculator
                   .registerWorker(new ComplementConsensusThread(this, ap));
@@ -899,7 +897,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       return;
     }
-    if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
+    if (calculator.getRegisteredWorkersOfClass(
+            StrucConsensusThread.class) == null)
     {
       calculator.registerWorker(new StrucConsensusThread(this, ap));
     }
@@ -1188,8 +1187,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   {
     if (sequenceSetID != null)
     {
-      System.err
-              .println("Warning - overwriting a sequenceSetId for a viewport!");
+      System.err.println(
+              "Warning - overwriting a sequenceSetId for a viewport!");
     }
     sequenceSetID = new String(newid);
   }
@@ -1406,8 +1405,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         selectionGroup = new SequenceGroup();
         selectionGroup.setEndRes(alignment.getWidth() - 1);
       }
-      List<SequenceI> tmp = alignment.getHiddenSequences().showAll(
-              hiddenRepSequences);
+      List<SequenceI> tmp = alignment.getHiddenSequences()
+              .showAll(hiddenRepSequences);
       for (SequenceI seq : tmp)
       {
         selectionGroup.addSequence(seq, false);
@@ -1430,8 +1429,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     int startSeq = ranges.getStartSeq();
     int endSeq = ranges.getEndSeq();
 
-    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(
-            index, hiddenRepSequences);
+    List<SequenceI> tmp = alignment.getHiddenSequences().showSequence(index,
+            hiddenRepSequences);
     if (tmp.size() > 0)
     {
       if (selectionGroup == null)
@@ -1511,8 +1510,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     }
 
     int gsize = selectionGroup.getSize();
-    SequenceI[] hseqs = selectionGroup.getSequences().toArray(
-            new SequenceI[gsize]);
+    SequenceI[] hseqs = selectionGroup.getSequences()
+            .toArray(new SequenceI[gsize]);
 
     hideSequence(hseqs);
     setSelectionGroup(null);
@@ -1602,8 +1601,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
    */
   public boolean isHiddenRepSequence(SequenceI seq)
   {
-    return (hiddenRepSequences != null && hiddenRepSequences
-            .containsKey(seq));
+    return (hiddenRepSequences != null
+            && hiddenRepSequences.containsKey(seq));
   }
 
   /**
@@ -1621,8 +1620,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
   @Override
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
-    return alignment.getHiddenSequences().adjustForHiddenSeqs(
-            alignmentIndex);
+    return alignment.getHiddenSequences()
+            .adjustForHiddenSeqs(alignmentIndex);
   }
 
   @Override
@@ -1692,10 +1691,10 @@ public abstract class AlignmentViewport implements AlignViewportI,
           boolean selectedOnly, boolean markGroups)
   {
     return new AlignmentView(alignment, alignment.getHiddenColumns(),
-            selectionGroup, alignment.getHiddenColumns() != null
+            selectionGroup,
+            alignment.getHiddenColumns() != null
                     && alignment.getHiddenColumns().hasHiddenColumns(),
-            selectedOnly,
-            markGroups);
+            selectedOnly, markGroups);
   }
 
   @Override
@@ -1741,8 +1740,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     if (alignment.getHiddenColumns() != null
             && alignment.getHiddenColumns().hasHiddenColumns())
     {
-      selection = alignment.getHiddenColumns().getVisibleSequenceStrings(
-              start, end, seqs);
+      selection = alignment.getHiddenColumns()
+              .getVisibleSequenceStrings(start, end, seqs);
     }
     else
     {
@@ -1811,8 +1810,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
         if (selectedOnly && selectionGroup != null)
         {
           alignment.getHiddenColumns().makeVisibleAnnotation(
-                  selectionGroup.getStartRes(),
-                  selectionGroup.getEndRes(), clone);
+                  selectionGroup.getStartRes(), selectionGroup.getEndRes(),
+                  clone);
         }
         else
         {
@@ -2001,8 +2000,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     {
       gapcounts = new AlignmentAnnotation("Occupancy",
               MessageManager.getString("label.occupancy_descr"),
-              new Annotation[1], 0f,
-              alignment.getHeight(), AlignmentAnnotation.BAR_GRAPH);
+              new Annotation[1], 0f, alignment.getHeight(),
+              AlignmentAnnotation.BAR_GRAPH);
       gapcounts.hasText = true;
       gapcounts.autoCalculated = true;
       gapcounts.scaleColLabel = true;
@@ -2020,8 +2019,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         conservation = new AlignmentAnnotation("Conservation",
                 MessageManager.formatMessage("label.conservation_descr",
-                        getConsPercGaps()), new Annotation[1],
-                0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+                        getConsPercGaps()),
+                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
         conservation.hasText = true;
         conservation.autoCalculated = true;
         alignment.addAnnotation(conservation);
@@ -2501,8 +2500,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     viewStyle = new ViewStyle(settingsForView);
     if (residueShading != null)
     {
-      residueShading.setConservationApplied(settingsForView
-              .isConservationColourSelected());
+      residueShading.setConservationApplied(
+              settingsForView.isConservationColourSelected());
     }
   }
 
@@ -2670,7 +2669,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
     return sortAnnotationsBy;
   }
 
-  public void setSortAnnotationsBy(SequenceAnnotationOrder sortAnnotationsBy)
+  public void setSortAnnotationsBy(
+          SequenceAnnotationOrder sortAnnotationsBy)
   {
     this.sortAnnotationsBy = sortAnnotationsBy;
   }
@@ -2748,8 +2748,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
       return 0;
     }
     boolean iAmProtein = !getAlignment().isNucleotide();
-    AlignmentI proteinAlignment = iAmProtein ? getAlignment() : complement
-            .getAlignment();
+    AlignmentI proteinAlignment = iAmProtein ? getAlignment()
+            : complement.getAlignment();
     if (proteinAlignment == null)
     {
       return 0;
@@ -2780,7 +2780,8 @@ public abstract class AlignmentViewport implements AlignViewportI,
      */
     int lastSeq = alignment.getHeight() - 1;
     List<AlignedCodonFrame> seqMappings = null;
-    for (int seqNo = ranges.getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
+    for (int seqNo = ranges
+            .getStartSeq(); seqNo < lastSeq; seqNo++, seqOffset++)
     {
       sequence = getAlignment().getSequenceAt(seqNo);
       if (hiddenSequences != null && hiddenSequences.isHidden(sequence))
@@ -2791,9 +2792,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         continue;
       }
-      seqMappings = MappingUtils
-              .findMappingsForSequenceAndOthers(sequence, mappings,
-                      getCodingComplement().getAlignment().getSequences());
+      seqMappings = MappingUtils.findMappingsForSequenceAndOthers(sequence,
+              mappings,
+              getCodingComplement().getAlignment().getSequences());
       if (!seqMappings.isEmpty())
       {
         break;
@@ -2928,7 +2929,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
         }
       }
     }
-  
+
     SequenceI sq = new Sequence("Consensus", seqs.toString());
     sq.setDescription("Percentage Identity Consensus "
             + ((ignoreGapsInConsensusCalculation) ? " without gaps" : ""));