formatting

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 271374f..c48bb7f 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,7 +24,7 @@ import java.util.*;
  */
 /**
  * @author JimP
- *
+ * 
  */
 public class Alignment implements AlignmentI
 {
@@ -77,7 +77,7 @@ public class Alignment implements AlignmentI
 
   /**
    * Make an alignment from an array of Sequences.
-   *
+   * 
    * @param sequences
    */
   public Alignment(SequenceI[] seqs)
@@ -87,7 +87,7 @@ public class Alignment implements AlignmentI
 
   /**
    * Make a new alignment from an array of SeqCigars
-   *
+   * 
    * @param seqs
    *          SeqCigar[]
    */
@@ -103,7 +103,7 @@ public class Alignment implements AlignmentI
    * compactAlignment does not contain hidden regions. JBPNote - must also check
    * that compactAlignment resolves to a set of SeqCigars - or construct them
    * appropriately.
-   *
+   * 
    * @param compactAlignment
    *          CigarArray
    */
@@ -115,7 +115,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   @Override
@@ -146,10 +146,10 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param i
    *          DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   @Override
@@ -167,7 +167,7 @@ public class Alignment implements AlignmentI
 
   /**
    * Adds a sequence to the alignment. Recalculates maxLength and size.
-   *
+   * 
    * @param snew
    */
   @Override
@@ -206,7 +206,7 @@ public class Alignment implements AlignmentI
 
   /**
    * Adds a sequence to the alignment. Recalculates maxLength and size.
-   *
+   * 
    * @param snew
    */
   @Override
@@ -222,7 +222,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   @Override
@@ -258,7 +258,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param s
    *          DOCUMENT ME!
    */
@@ -270,7 +270,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param i
    *          DOCUMENT ME!
    */
@@ -289,7 +289,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
@@ -312,7 +312,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
    */
@@ -378,7 +378,7 @@ public class Alignment implements AlignmentI
 
   /**
    * remove any annotation that references gp
-   *
+   * 
    * @param gp
    *          (if null, removes all group associated annotation)
    */
@@ -472,7 +472,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
    */
   @Override
@@ -483,7 +483,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
    * boolean)
    */
@@ -555,7 +555,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
   @Override
@@ -578,7 +578,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
@@ -600,7 +600,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   @Override
@@ -611,7 +611,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   @Override
@@ -632,7 +632,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param gc
    *          DOCUMENT ME!
    */
@@ -652,7 +652,7 @@ public class Alignment implements AlignmentI
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @return DOCUMENT ME!
    */
   @Override
@@ -663,7 +663,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#isAligned()
    */
   @Override
@@ -674,7 +674,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#isAligned(boolean)
    */
   @Override
@@ -701,7 +701,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
@@ -755,7 +755,7 @@ public class Alignment implements AlignmentI
 
   /**
    * remove any object references associated with this annotation
-   *
+   * 
    * @param aa
    */
   private void unhookAnnotation(AlignmentAnnotation aa)
@@ -773,7 +773,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
@@ -785,7 +785,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation, int)
    */
@@ -1005,7 +1005,7 @@ public class Alignment implements AlignmentI
   /**
    * Justify the sequences to the left or right by deleting and inserting gaps
    * before the initial residue or after the terminal residue
-   *
+   * 
    * @param right
    *          true if alignment padded to right, false to justify to left
    * @return true if alignment was changed
@@ -1159,7 +1159,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
    * )
@@ -1183,7 +1183,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
    */
   @Override
@@ -1194,7 +1194,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see
    * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
@@ -1218,7 +1218,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @see jalview.datamodel.AlignmentI#getCodonFrames()
    */
   @Override
@@ -1229,7 +1229,7 @@ public class Alignment implements AlignmentI
 
   /*
    * (non-Javadoc)
-   *
+   * 
    * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
    * AlignedCodonFrame)
    */
@@ -1381,14 +1381,14 @@ public class Alignment implements AlignmentI
 
   @Override
   public AlignmentAnnotation findOrCreateAnnotation(String name,
-          String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef)
+          String calcId, boolean autoCalc, SequenceI seqRef,
+          SequenceGroup groupRef)
   {
-    assert(name!=null);
+    assert (name != null);
     for (AlignmentAnnotation annot : getAlignmentAnnotation())
     {
-      if (annot.autoCalculated == autoCalc
-              && (name.equals(annot.label))
-              && (calcId==null || annot.getCalcId().equals(calcId))
+      if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+              && (calcId == null || annot.getCalcId().equals(calcId))
               && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
       {
         return annot;