JAL-1517 source formatting

[jalview.git] / src / jalview / controller / AlignViewController.java

diff --git a/src/jalview/controller/AlignViewController.java b/src/jalview/controller/AlignViewController.java
index 74161c8..077f9cd 100644 (file)
--- a/src/jalview/controller/AlignViewController.java
+++ b/src/jalview/controller/AlignViewController.java
@@ -38,33 +38,40 @@ import jalview.datamodel.SequenceI;
 
 public class AlignViewController implements AlignViewControllerI
 {
-  AlignViewportI viewport=null;
-  AlignmentViewPanel alignPanel=null;
+  AlignViewportI viewport = null;
+
+  AlignmentViewPanel alignPanel = null;
+
   /**
    * the GUI container that is handling interactions with the user
    */
   private AlignViewControllerGuiI avcg;
+
   @Override
-  protected void finalize() throws Throwable {
+  protected void finalize() throws Throwable
+  {
     viewport = null;
     alignPanel = null;
     avcg = null;
   };
-  
-  public AlignViewController(AlignViewControllerGuiI alignFrame, AlignViewportI viewport,
-          AlignmentViewPanel alignPanel)
+
+  public AlignViewController(AlignViewControllerGuiI alignFrame,
+          AlignViewportI viewport, AlignmentViewPanel alignPanel)
   {
     this.avcg = alignFrame;
-    this.viewport=viewport;
+    this.viewport = viewport;
     this.alignPanel = alignPanel;
   }
+
   @Override
-  public void setViewportAndAlignmentPanel(AlignViewportI viewport,AlignmentViewPanel alignPanel)
+  public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+          AlignmentViewPanel alignPanel)
   {
     this.alignPanel = alignPanel;
     this.viewport = viewport;
-    
+
   }
+
   @Override
   public boolean makeGroupsFromSelection()
   {
@@ -94,53 +101,59 @@ public class AlignViewController implements AlignViewControllerI
       return true;
     }
     return false;
-}
+  }
+
   @Override
   public boolean createGroup()
   {
 
     SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg!=null)
+    if (sg != null)
     {
-        viewport.getAlignment().addGroup(sg);
-        return true;
-      } 
+      viewport.getAlignment().addGroup(sg);
+      return true;
+    }
     return false;
   }
+
   @Override
   public boolean unGroup()
   {
     SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg!=null)
+    if (sg != null)
     {
-        viewport.getAlignment().deleteGroup(sg);
-        return true;
+      viewport.getAlignment().deleteGroup(sg);
+      return true;
     }
     return false;
   }
+
   @Override
   public boolean deleteGroups()
   {
-    if (viewport.getAlignment().getGroups()!=null && viewport.getAlignment().getGroups().size()>0)
+    if (viewport.getAlignment().getGroups() != null
+            && viewport.getAlignment().getGroups().size() > 0)
     {
-    viewport.getAlignment().deleteAllGroups();
-    viewport.clearSequenceColours();
-    viewport.setSelectionGroup(null);
-    return true;
+      viewport.getAlignment().deleteAllGroups();
+      viewport.clearSequenceColours();
+      viewport.setSelectionGroup(null);
+      return true;
     }
     return false;
   }
-   
+
   @Override
-  public boolean markColumnsContainingFeatures(boolean invert, boolean extendCurrent, boolean toggle, String featureType)
+  public boolean markColumnsContainingFeatures(boolean invert,
+          boolean extendCurrent, boolean toggle, String featureType)
   {
     // JBPNote this routine could also mark rows, not just columns.
     // need a decent query structure to allow all types of feature searches
     BitSet bs = new BitSet();
-    int alw,alStart;
-    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport.getAlignment() : viewport.getSelectionGroup()); 
+    int alw, alStart;
+    SequenceCollectionI sqcol = (viewport.getSelectionGroup() == null ? viewport
+            .getAlignment() : viewport.getSelectionGroup());
     alStart = sqcol.getStartRes();
-    alw = sqcol.getEndRes()+1;
+    alw = sqcol.getEndRes() + 1;
     List<SequenceI> seqs = sqcol.getSequences();
     int nseq = 0;
     for (SequenceI sq : seqs)
@@ -159,7 +172,7 @@ public class AlignViewController implements AlignViewControllerI
         {
           int ist = sq.findIndex(sq.getStart());
           int iend = sq.findIndex(sq.getEnd());
-          if (iend < alStart || ist> alw)
+          if (iend < alStart || ist > alw)
           {
             // sequence not in region
             continue;
@@ -177,7 +190,7 @@ public class AlignViewController implements AlignViewControllerI
 
               int i = sq.findIndex(sfpos.getBegin());
               int j = sq.findIndex(sfpos.getEnd());
-              if (j<alStart || i>alw)
+              if (j < alStart || i > alw)
               {
                 // feature is outside selected region
                 continue;
@@ -186,7 +199,8 @@ public class AlignViewController implements AlignViewControllerI
               {
                 i = alStart;
               }
-              if (i< ist) {
+              if (i < ist)
+              {
                 i = ist;
               }
               if (j > alw)
@@ -213,7 +227,9 @@ public class AlignViewController implements AlignViewControllerI
       if (cs == null)
       {
         cs = new ColumnSelection();
-      } else {
+      }
+      else
+      {
         if (!extendCurrent)
         {
           cs.clear();
@@ -228,12 +244,13 @@ public class AlignViewController implements AlignViewControllerI
           if (ibs < 0 || i < ibs)
           {
             if (toggle && cs.contains(i))
-              {
-                cs.removeElement(i++);
-              } else 
-              {
-                cs.addElement(i++);
-              }
+            {
+              cs.removeElement(i++);
+            }
+            else
+            {
+              cs.addElement(i++);
+            }
           }
           else
           {
@@ -244,12 +261,14 @@ public class AlignViewController implements AlignViewControllerI
       }
       else
       {
-        for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs.nextSetBit(i + 1))
+        for (int i = bs.nextSetBit(alStart); i >= alStart; i = bs
+                .nextSetBit(i + 1))
         {
           if (toggle && cs.contains(i))
           {
             cs.removeElement(i);
-          } else 
+          }
+          else
           {
             cs.addElement(i);
           }
@@ -257,16 +276,17 @@ public class AlignViewController implements AlignViewControllerI
       }
       viewport.setColumnSelection(cs);
       alignPanel.paintAlignment(true);
-      avcg.setStatus((toggle ? "Toggled ": "Marked ")
-              + (invert ? (alw-alStart) - bs.cardinality() : bs.cardinality())
-              + " columns "+(invert ? "not " : "") + "containing features of type " + featureType
-              + " across " + nseq + " sequence(s)");
+      avcg.setStatus((toggle ? "Toggled " : "Marked ")
+              + (invert ? (alw - alStart) - bs.cardinality() : bs
+                      .cardinality()) + " columns "
+              + (invert ? "not " : "") + "containing features of type "
+              + featureType + " across " + nseq + " sequence(s)");
       return true;
     }
     else
     {
       avcg.setStatus("No features of type " + featureType + " found.");
-      if (!extendCurrent && cs!=null)
+      if (!extendCurrent && cs != null)
       {
         cs.clear();
         alignPanel.paintAlignment(true);