Sequence is char []

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 4237db8..b5f31bc 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -137,7 +137,7 @@ public class Alignment implements AlignmentI
         {
           Sequence ds = new Sequence(snew.getName(),
                                      AlignSeq.extractGaps("-. ",
-              snew.getSequence()),
+              snew.getSequenceAsString()),
                                      snew.getStart(),
                                      snew.getEnd());
 
@@ -259,7 +259,26 @@ public class Alignment implements AlignmentI
     {
         if (!groups.contains(sg))
         {
-            groups.addElement(sg);
+          if(hiddenSequences.getSize()>0)
+          {
+            //We're not going to make groups of
+            //Hidden sequences
+            int i, iSize = sg.getSize(false);
+            for (i = 0; i < iSize; i++)
+            {
+              if (!sequences.contains(sg.getSequenceAt(i)))
+              {
+                sg.deleteSequence(sg.getSequenceAt(i), false);
+                iSize--;
+                i--;
+              }
+            }
+
+            if (sg.getSize(true) < 1)
+              return;
+          }
+
+          groups.addElement(sg);
         }
     }
 
@@ -269,15 +288,6 @@ 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 +401,9 @@ 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) );
+            seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
+            seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
         }
     }
 
@@ -566,22 +576,25 @@ 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]);
           }