X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f255ab5394923aa85dbdf2fae447ed95c377fd66;hb=d8412f9b4ca9533eb56dc48e1d2273ee0e45bf3f;hp=288c28a76f54e9f61be0cf3a0b7cc4d4e29b720b;hpb=fbb18baad3919cbf94fcb5159bbd5269d6af18b4;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 288c28a..f255ab5 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 +397,9 @@ 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) );
         }
     }
 
@@ -464,15 +470,53 @@ public class Alignment implements AlignmentI
     }
 
 
-    public void adjustSequenceAnnotations()
+    public void adjustSequenceAnnotations(int position,
+                                          int number,
+                                          boolean insert)
     {
       if(annotations!=null)
       {
+        int aSize, tSize;
+        Annotation [] temp;
         for (int a = 0; a < annotations.length; a++)
         {
-          if (annotations[a].sequenceRef != null)
+          if(annotations[a].autoCalculated)
+          {
+            System.out.println("ignore "+annotations[a].label);
+            continue;
+          }
+          aSize = annotations[a].annotations.length;
+          if(insert)
+            tSize = aSize + number;
+          else
+            tSize = aSize - number;
+
+          temp = new Annotation[tSize];
+
+          if(insert)
+          {
+            System.arraycopy(annotations[a].annotations,
+                0, temp, 0, position);
+
+            System.arraycopy(annotations[a].annotations,
+                position, temp, position+number, aSize - position);
+          }
+          else
           {
-            annotations[a].adjustForAlignment();
+              System.arraycopy(annotations[a].annotations,
+                               0, temp, 0, position);
+
+              System.arraycopy(annotations[a].annotations,
+                               position + number, temp, position,
+                               aSize - position - number);
+          }
+
+          annotations[a].annotations = temp;
+
+
+        //  if (annotations[a].sequenceRef != null)
+          {
+        //    annotations[a].adjustForAlignment();
           }
         }
       }
@@ -579,7 +623,7 @@ public class Alignment implements AlignmentI
             seqs[i] = new Sequence(currentSeq.getName(),
                                    AlignSeq.extractGaps(
                                        jalview.util.Comparison.GapChars,
-                                       currentSeq.getSequence()
+                                       currentSeq.getSequenceAsString()
                                    ),
                                    currentSeq.getStart(),
                                    currentSeq.getEnd());
@@ -652,34 +696,6 @@ 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()
   {