X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=8b159a63de117095db79ad5bbb7d6c22e784d88c;hb=51bbc79eee43d019f9fcb14b7aa6e0a0c2c99f76;hp=713cb0d04c918103753e01b5ae73f43f83d0d16a;hpb=52f42d57f0f08942ce54e3a739f1c9936cc5f293;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 713cb0d..8b159a6 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,8 +20,6 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 
-import jalview.util.*;
-
 import java.util.*;
 
 /** Data structure to hold and manipulate a multiple sequence alignment
@@ -137,7 +135,7 @@ public class Alignment implements AlignmentI
         {
           Sequence ds = new Sequence(snew.getName(),
                                      AlignSeq.extractGaps("-. ",
-              snew.getSequence()),
+              snew.getSequenceAsString()),
                                      snew.getStart(),
                                      snew.getEnd());
 
@@ -205,7 +203,7 @@ public class Alignment implements AlignmentI
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
 
-            if (sg.getSequences(false).contains(s))
+            if (sg.getSequences(null).contains(s))
             {
                 return sg;
             }
@@ -229,14 +227,14 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < gSize; i++)
         {
             SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
-            if(sg==null || sg.getSequences(false)==null)
+            if(sg==null || sg.getSequences(null)==null)
             {
               this.deleteGroup(sg);
               gSize--;
               continue;
             }
 
-            if (sg.getSequences(false).contains(s))
+            if (sg.getSequences(null).contains(s))
             {
                 temp.addElement(sg);
             }
@@ -259,7 +257,24 @@ public class Alignment implements AlignmentI
     {
         if (!groups.contains(sg))
         {
-            groups.addElement(sg);
+          if(hiddenSequences.getSize()>0)
+          {
+            int i, iSize = sg.getSize();
+            for (i = 0; i < iSize; i++)
+            {
+              if (!sequences.contains(sg.getSequenceAt(i)))
+              {
+                sg.deleteSequence(sg.getSequenceAt(i), false);
+                iSize--;
+                i--;
+              }
+            }
+
+            if (sg.getSize() < 1)
+              return;
+          }
+
+          groups.addElement(sg);
         }
     }
 
@@ -269,15 +284,6 @@ public class Alignment implements AlignmentI
     public void deleteAllGroups()
     {
         groups.removeAllElements();
-
-        int i = 0;
-
-        while (i < sequences.size())
-        {
-            SequenceI s = getSequenceAt(i);
-            s.setColor(java.awt.Color.white);
-            i++;
-        }
     }
 
     /**    */
@@ -391,9 +397,11 @@ public class Alignment implements AlignmentI
         for (int i = 0; i < sequences.size(); i++)
         {
             Sequence seq = (Sequence) sequences.elementAt(i);
-            seq.setSequence( seq.getSequence().replace('.', gc) );
-            seq.setSequence( seq.getSequence().replace('-', gc) );
-            seq.setSequence( seq.getSequence().replace(' ', gc) );
+            seq.setSequence(seq.getSequenceAsString()
+                            .replace('.', gc)
+                            .replace('-', gc)
+                            .replace(' ', gc)
+                );
         }
     }
 
@@ -442,6 +450,9 @@ public class Alignment implements AlignmentI
             aSize = annotations.length;
         }
 
+        if(aSize<1)
+          return;
+
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
 
         int tIndex = 0;
@@ -461,20 +472,6 @@ public class Alignment implements AlignmentI
     }
 
 
-    public void adjustSequenceAnnotations()
-    {
-      if(annotations!=null)
-      {
-        for (int a = 0; a < annotations.length; a++)
-        {
-          if (annotations[a].sequenceRef != null)
-          {
-            annotations[a].adjustForAlignment();
-          }
-        }
-      }
-    }
-
     /**
      * DOCUMENT ME!
      *
@@ -563,22 +560,25 @@ public class Alignment implements AlignmentI
         // Can only be done once, if dataset is not null
         // This will not be performed
         Sequence[] seqs = new Sequence[getHeight()];
+        SequenceI currentSeq;
         for (int i = 0; i < getHeight(); i++)
         {
-          if(getSequenceAt(i).getDatasetSequence()!=null)
+          currentSeq = getSequenceAt(i);
+          if(currentSeq.getDatasetSequence()!=null)
           {
-            seqs[i] = (Sequence)getSequenceAt(i).getDatasetSequence();
+            seqs[i] = (Sequence)currentSeq.getDatasetSequence();
           }
           else
           {
-            seqs[i] = new Sequence(getSequenceAt(i).getName(),
+            seqs[i] = new Sequence(currentSeq.getName(),
                                    AlignSeq.extractGaps(
                                        jalview.util.Comparison.GapChars,
-                                       getSequenceAt(i).getSequence()
+                                       currentSeq.getSequenceAsString()
                                    ),
-                                   getSequenceAt(i).getStart(),
-                                   getSequenceAt(i).getEnd());
-            seqs[i].sequenceFeatures = getSequenceAt(i).getSequenceFeatures();
+                                   currentSeq.getStart(),
+                                   currentSeq.getEnd());
+            seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
+            seqs[i].setDescription(currentSeq.getDescription());
             getSequenceAt(i).setSequenceFeatures(null);
             getSequenceAt(i).setDatasetSequence(seqs[i]);
           }
@@ -646,34 +646,6 @@ public class Alignment implements AlignmentI
     {
       return hiddenSequences;
     }
-    SequenceI [] getVisibleAndRepresentedSeqs()
-    {
-      if(hiddenSequences==null || hiddenSequences.getSize()<1)
-        return getSequencesArray();
-
-      Vector seqs = new Vector();
-      SequenceI seq;
-      SequenceGroup hidden;
-      for (int i = 0; i < sequences.size(); i++)
-      {
-        seq = (SequenceI) sequences.elementAt(i);
-        seqs.addElement(seq);
-        hidden = seq.getHiddenSequences();
-        if(hidden!=null)
-        {
-          for(int j=0; j<hidden.getSize(false); j++)
-          {
-            seqs.addElement(hidden.getSequenceAt(j));
-          }
-        }
-      }
-      SequenceI [] result = new SequenceI[seqs.size()];
-      for(int i=0; i<seqs.size(); i++)
-        result[i] = (SequenceI)seqs.elementAt(i);
-
-      return result;
-
-    }
 
   public CigarArray getCompactAlignment()
   {