X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f3d17b4dcbcafc627801c13d78eb908acec69b11;hb=cd71fb9ef1a21678ad648ba13564b658b53ab834;hp=338294b77bfab6ec444146bed2d39f3242c6e1a3;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 338294b..f3d17b4 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -24,7 +24,6 @@ import jalview.util.*;
 
 import java.util.*;
 
-
 /** Data structure to hold and manipulate a multiple sequence alignment
  */
 public class Alignment implements AlignmentI
@@ -32,7 +31,6 @@ public class Alignment implements AlignmentI
     protected Alignment dataset;
     protected Vector sequences;
     protected Vector groups = new Vector();
-    protected Vector superGroup = new Vector();
     protected char gapCharacter = '-';
     protected int type = NUCLEOTIDE;
     public static final int PROTEIN = 0;
@@ -41,6 +39,9 @@ public class Alignment implements AlignmentI
     /** DOCUMENT ME!! */
     public AlignmentAnnotation[] annotations;
 
+    HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+
     /** Make an alignment from an array of Sequences.
      *
      * @param sequences
@@ -60,8 +61,6 @@ public class Alignment implements AlignmentI
         {
             sequences.addElement(seqs[i]);
         }
-
-        getWidth();
     }
 
     /**
@@ -97,22 +96,21 @@ public class Alignment implements AlignmentI
      */
     public void addSequence(SequenceI snew)
     {
-        sequences.addElement(snew);
-    }
+      if(dataset!=null)
+      {
+        Sequence ds = new Sequence(snew.getName(),
+                                   AlignSeq.extractGaps("-. ", snew.getSequence()),
+                                   snew.getStart(),
+                                   snew.getEnd());
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param seq DOCUMENT ME!
-     */
-    public void addSequence(SequenceI[] seq)
-    {
-        for (int i = 0; i < seq.length; i++)
-        {
-            addSequence(seq[i]);
-        }
+        snew.setDatasetSequence(ds);
+        getDataset().addSequence(ds);
+      }
+
+      sequences.addElement(snew);
     }
 
+
     /** Adds a sequence to the alignment.  Recalculates maxLength and size.
      *
      * @param snew
@@ -205,13 +203,23 @@ public class Alignment implements AlignmentI
      */
     public void trimLeft(int i)
     {
-        for (int j = 0; j < getHeight(); j++)
+        int j, jSize = getHeight();
+        for (j = 0; j < jSize; j++)
         {
             SequenceI s = getSequenceAt(j);
             int newstart = s.findPosition(i);
 
-            s.setStart(newstart);
-            s.setSequence(s.getSequence().substring(i));
+            if(i>s.getLength())
+            {
+              sequences.removeElement(s);
+              j--;
+              jSize--;
+            }
+            else
+            {
+              s.setStart(newstart);
+              s.setSequence(s.getSequence().substring(i));
+            }
         }
     }
 
@@ -228,7 +236,8 @@ public class Alignment implements AlignmentI
             int newend = s.findPosition(i);
 
             s.setEnd(newend);
-            s.setSequence(s.getSequence().substring(0, i + 1));
+            if(s.getLength()>i)
+              s.setSequence(s.getSequence().substring(0, i + 1));
         }
     }
 
@@ -369,47 +378,7 @@ public class Alignment implements AlignmentI
         return ret;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void addSuperGroup(SuperGroup sg)
-    {
-        superGroup.addElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     */
-    public void removeSuperGroup(SuperGroup sg)
-    {
-        superGroup.removeElement(sg);
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param sg DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public SuperGroup getSuperGroup(SequenceGroup sg)
-    {
-        for (int i = 0; i < this.superGroup.size(); i++)
-        {
-            SuperGroup temp = (SuperGroup) superGroup.elementAt(i);
-
-            if (temp.sequenceGroups.contains(sg))
-            {
-                return temp;
-            }
-        }
 
-        return null;
-    }
 
     /**    */
     public void addGroup(SequenceGroup sg)
@@ -426,7 +395,6 @@ public class Alignment implements AlignmentI
     public void deleteAllGroups()
     {
         groups.removeAllElements();
-        superGroup.removeAllElements();
 
         int i = 0;
 
@@ -631,6 +599,21 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
+
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -639,25 +622,48 @@ public class Alignment implements AlignmentI
     public void addAnnotation(AlignmentAnnotation aa)
     {
         int aSize = 1;
-
         if (annotations != null)
         {
             aSize = annotations.length + 1;
         }
 
-
         AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+        temp[aSize-1] = aa;
+
         int i = 0;
 
         if (aSize > 1)
         {
-            for (i = 0; i < (aSize - 1); i++)
+            for (i = 0; i < (aSize-1); i++)
             {
                 temp[i] = annotations[i];
             }
         }
 
-        temp[i] = aa;
+        annotations = temp;
+    }
+
+    public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+    {
+      if(aa==null || annotations==null || annotations.length-1<index)
+        return;
+
+      int aSize = annotations.length;
+      AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+      temp[index] = aa;
+
+      for (int i = 0; i < aSize; i++)
+      {
+        if(i==index)
+          continue;
+
+        if(i<index)
+          temp[i] = annotations[i];
+        else
+          temp[i] = annotations[i-1];
+      }
 
         annotations = temp;
     }
@@ -723,4 +729,50 @@ public class Alignment implements AlignmentI
       return dataset;
     }
 
+    public boolean padGaps() {
+      boolean modified=false;
+
+      //Remove excess gaps from the end of alignment
+      int maxLength = -1;
+
+      SequenceI current;
+      for (int i = 0; i < sequences.size(); i++)
+      {
+        current = getSequenceAt(i);
+        for (int j = current.getLength(); j > maxLength; j--)
+        {
+          if (j > maxLength && !jalview.util.Comparison.isGap(
+              current.getCharAt(j)))
+          {
+            maxLength = j;
+            break;
+          }
+        }
+      }
+
+      maxLength++;
+
+      for (int i = 0; i < sequences.size();
+           i++)
+      {
+        current = getSequenceAt(i);
+
+        if (current.getLength() < maxLength)
+        {
+          current.insertCharAt(maxLength - 1, gapCharacter);
+          modified=true;
+        }
+        else if(current.getLength() > maxLength)
+        {
+          current.deleteChars(maxLength, current.getLength());
+        }
+      }
+      return modified;
+    }
+
+    public HiddenSequences getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
 }