X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=b0b04cae8739551cd24ee5b045d62d5391d81b01;hb=1ed150e97b6a7df6ebe5cf92ead96cd147a58b7e;hp=2545ec1355a8d852ea3201da6ddc9048fd9addf8;hpb=7e4c4ad887a30dc26496087b0150f4ac2fe355ec;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2545ec1..b0b04ca 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
@@ -41,6 +40,9 @@ 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
@@ -59,6 +61,16 @@ public class Alignment implements AlignmentI
         for (i = 0; i < seqs.length; i++)
         {
             sequences.addElement(seqs[i]);
+
+            if(seqs[i].getDatasetSequence()!=null
+            && seqs[i].getDatasetSequence().getAnnotation()!=null)
+            {
+
+              for(int a=0; a<seqs[i].getDatasetSequence().getAnnotation().length; a++)
+              {
+                       this.addAnnotation(seqs[i].getDatasetSequence().getAnnotation()[a], seqs[i]);
+              }
+            }
         }
 
         getWidth();
@@ -380,47 +392,7 @@ 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)
@@ -642,25 +614,83 @@ public class Alignment implements AlignmentI
         annotations = temp;
     }
 
-
-    public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)
+    /**
+     *
+     * @param aa AlignmentAnnotation
+     * @param seqRef The sequence to associate this annotation with
+     * @return The adjusted AlignmentAnnotation, with dataset sequence and annotation added
+     */
+    public AlignmentAnnotation addAnnotation(AlignmentAnnotation aa, SequenceI seqRef)
     {
-      aa.refSequence = seqRef;
-      if(seqRef!=null && index!=0)
+      if(seqRef!=null)
       {
-        int aSize = aa.annotations.length;
-        int newIndex;
-        Annotation [] temp = new Annotation[seqRef.getLength()];
-        for(int a=0; a<aSize; a++)
+          //We can only add Annotations to the dataset sequences
+           if(seqRef.getDatasetSequence()==null)
+           {
+                  setDataset(null);
+            }
+
+        AlignmentAnnotation []  old = seqRef.getDatasetSequence().getAnnotation();
+
+        //First check if this is a new annotation or not. If it is new,
+        //we must add the annotation to the dataset
+        boolean newAnnotation = true;
+        if(seqRef.getDatasetSequence().getAnnotation()!=null)
         {
-          newIndex = seqRef.findIndex(a + index)-1;
-          temp[newIndex] = aa.annotations[a];
+          for(int a=0; a<old.length; a++)
+          {
+            if(old[a] == aa)
+            {
+
+              newAnnotation = false;
+              break;
+            }
+          }
         }
 
-        aa.annotations = temp;
+        if(newAnnotation)
+         {
+           seqRef.getDatasetSequence().addAlignmentAnnotation(aa);
+         }
+
+          AlignmentAnnotation copy = null;
+          if (aa.graph > 0)
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations, aa.graphMin,
+                aa.graphMax, aa.graph
+                );
+          else
+            copy = new AlignmentAnnotation(
+                aa.label, aa.description, aa.annotations
+                );
+
+         copy.datasetAnnotation = aa;
+
+         addAnnotation(copy);
+
+         copy.sequenceRef = seqRef;
+
+         return copy;
       }
+      else
+      {
+        addAnnotation(aa);
+        return aa;
+      }
+    }
 
-      addAnnotation(aa);
+    public void adjustSequenceAnnotations()
+    {
+      if(annotations!=null)
+      {
+        for (int a = 0; a < annotations.length; a++)
+        {
+          if (annotations[a].sequenceRef != null)
+          {
+            annotations[a].adjustForAlignment();
+          }
+        }
+      }
     }
 
     /**
@@ -671,30 +701,52 @@ 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[0] = aa;
+        temp[aSize-1] = aa;
 
-        int i = 1;
+        int i = 0;
 
         if (aSize > 1)
         {
-            for (i = 1; i < (aSize); i++)
+            for (i = 0; i < (aSize-1); i++)
             {
-                temp[i] = annotations[i-1];
+                temp[i] = annotations[i];
             }
         }
 
         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;
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -758,19 +810,48 @@ public class Alignment implements AlignmentI
 
     public boolean padGaps() {
       boolean modified=false;
-      int Width = getWidth();
+
+      //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() < Width)
+        if (current.getLength() < maxLength)
         {
-          current.insertCharAt(Width - 1, gapCharacter);
+          current.insertCharAt(maxLength - 1, gapCharacter);
           modified=true;
         }
+        else if(current.getLength() > maxLength)
+        {
+          current.deleteChars(maxLength, current.getLength());
+        }
       }
       return modified;
     }
+
+    public HiddenSequences getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
 }