X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;fp=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=363ad0d54168422e4af1cae4d33f14a6f52851a3;hp=81046f14f6b65fe6401b2cdb72f7966a65d9cb0d;hb=ebadc5463ca35daa153cb20c3537db740fb5f707;hpb=6e3194d06f60246cd6ebd05ef34b1644c46f7159

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 81046f1..363ad0d 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,6 +20,11 @@
  */
 package jalview.datamodel;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.MessageManager;
+
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.HashSet;
@@ -30,10 +35,6 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.io.FastaFile;
-import jalview.util.MessageManager;
-
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
@@ -73,7 +74,7 @@ public class Alignment implements AlignmentI
   {
     int i = 0;
 
-    if (jalview.util.Comparison.isNucleotide(seqs))
+    if (Comparison.isNucleotide(seqs))
     {
       type = NUCLEOTIDE;
     }
@@ -339,7 +340,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+   * @see AlignmentI#findGroup(jalview.datamodel.SequenceI)
    */
   @Override
   public SequenceGroup findGroup(SequenceI s)
@@ -363,7 +364,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+   * AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
    */
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
@@ -527,7 +528,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+   * @see AlignmentI#findName(java.lang.String, boolean)
    */
   @Override
   public SequenceI findName(String token, boolean b)
@@ -538,7 +539,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+   * @see AlignmentI#findName(SequenceI, java.lang.String,
    * boolean)
    */
   @Override
@@ -610,7 +611,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   * @see AlignmentI#findIndex(jalview.datamodel.SequenceI)
    */
   @Override
   public int findIndex(SequenceI s)
@@ -634,7 +635,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   * AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   @Override
   public int findIndex(SearchResults results)
@@ -718,7 +719,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#isAligned()
+   * @see AlignmentI#isAligned()
    */
   @Override
   public boolean isAligned()
@@ -729,7 +730,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   * @see AlignmentI#isAligned(boolean)
    */
   @Override
   public boolean isAligned(boolean includeHidden)
@@ -778,7 +779,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+   * @seeAlignmentI#deleteAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
   @Override
@@ -852,7 +853,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * @seeAlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation)
    */
   @Override
@@ -864,7 +865,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * @seeAlignmentI#addAnnotation(jalview.datamodel.
    * AlignmentAnnotation, int)
    */
   @Override
@@ -1072,7 +1073,7 @@ public class Alignment implements AlignmentI
       for (int j = current.getLength(); j > maxLength; j--)
       {
         if (j > maxLength
-                && !jalview.util.Comparison.isGap(current.getCharAt(j)))
+                && !Comparison.isGap(current.getCharAt(j)))
         {
           maxLength = j;
           break;
@@ -1128,7 +1129,7 @@ public class Alignment implements AlignmentI
       boolean hitres = false;
       for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
       {
-        if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+        if (!Comparison.isGap(current.getCharAt(j)))
         {
           if (!hitres)
           {
@@ -1264,7 +1265,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+   * AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
    * )
    */
   @Override
@@ -1280,7 +1281,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see
-   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   * AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
   @Override
   public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
@@ -1303,7 +1304,7 @@ public class Alignment implements AlignmentI
   /**
    * Sets the codon frame mappings (replacing any existing mappings).
    * 
-   * @see jalview.datamodel.AlignmentI#setCodonFrames()
+   * @see AlignmentI#setCodonFrames()
    */
   @Override
   public void setCodonFrames(Set<AlignedCodonFrame> acfs)
@@ -1315,7 +1316,7 @@ public class Alignment implements AlignmentI
    * Returns the set of codon frame mappings. Any changes to the returned set
    * will affect the alignment.
    * 
-   * @see jalview.datamodel.AlignmentI#getCodonFrames()
+   * @see AlignmentI#getCodonFrames()
    */
   @Override
   public Set<AlignedCodonFrame> getCodonFrames()
@@ -1326,7 +1327,7 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+   * @seeAlignmentI#removeCodonFrame(jalview.datamodel.
    * AlignedCodonFrame)
    */
   @Override