X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=afe70328877239ab9a727083384405a44644bb14;hb=1dabf099b7c77fb0a80039f72cef34669df9b2e1;hp=1312e224498b9d54115c43c5e0cecc8d0906321d;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 1312e22..afe7032 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  * 
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -25,6 +25,10 @@ import jalview.analysis.*;
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
+/**
+ * @author JimP
+ *
+ */
 public class Alignment implements AlignmentI
 {
   protected Alignment dataset;
@@ -352,6 +356,14 @@ public class Alignment implements AlignmentI
   {
     if (groups.contains(g))
     {
+      if (annotations!=null && annotations.length>0)
+      {
+        if (g.hasAnnotationRows())
+        {  // remove any annotation references. 
+          deleteAnnotation(g.getConsensus());// todo - create=false flag so we don't create another object unnecessarily
+          deleteAnnotation(g.getConservationRow());
+        }
+      }
       groups.removeElement(g);
     }
   }
@@ -442,7 +454,11 @@ public class Alignment implements AlignmentI
 
   }
 
-  /**    */
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+   */
   public int findIndex(SequenceI s)
   {
     int i = 0;
@@ -460,6 +476,26 @@ public class Alignment implements AlignmentI
     return -1;
   }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   */
+  public int findIndex(SearchResults results)
+  {
+    int i = 0;
+
+    while (i < sequences.size())
+    {
+      if (results.involvesSequence(getSequenceAt(i)))
+      {
+        return i;
+      }
+      i++;
+    }
+    return -1;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -582,14 +618,19 @@ public class Alignment implements AlignmentI
     return swap;
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param aa
-   *                DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.AlignmentAnnotation)
    */
   public void addAnnotation(AlignmentAnnotation aa)
   {
+    addAnnotation(aa, -1);
+  }
+  
+  /* (non-Javadoc)
+   * @see jalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.AlignmentAnnotation, int)
+   */
+  public void addAnnotation(AlignmentAnnotation aa, int pos)
+  {
     int aSize = 1;
     if (annotations != null)
     {
@@ -597,16 +638,24 @@ public class Alignment implements AlignmentI
     }
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
-    temp[aSize - 1] = aa;
-
     int i = 0;
-
+    if (pos==-1 || pos>=aSize) {
+      temp[aSize - 1] = aa;
+    } else {
+      temp[pos] = aa;
+    }
     if (aSize > 1)
     {
-      for (i = 0; i < (aSize - 1); i++)
+      int p=0;
+      for (i = 0; i < (aSize-1); i++,p++)
       {
-        temp[i] = annotations[i];
+        if (p==pos)
+        {
+          p++;
+        }
+        if (p<temp.length) {
+          temp[p] = annotations[i];
+        }
       }
     }
 
@@ -770,6 +819,98 @@ public class Alignment implements AlignmentI
     }
     return modified;
   }
+  /**
+   * Justify the sequences to the left or right by deleting and inserting gaps before the initial residue or after the terminal residue
+   * @param right true if alignment padded to right, false to justify to left
+   * @return true if alignment was changed
+   */
+  public boolean justify(boolean right)
+  {
+    boolean modified = false;
+
+    // Remove excess gaps from the end of alignment
+    int maxLength = -1;
+    int ends[] = new int[sequences.size()*2];
+    SequenceI current;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      // This should really be a sequence method
+      ends[i*2] = current.findIndex(current.getStart());
+      ends[i*2+1] = current.findIndex(current.getStart()+current.getLength());
+      boolean hitres=false;
+      for (int j = 0,rs=0,ssiz=current.getLength(); j<ssiz; j++)
+      {
+        if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+        {
+          if (!hitres)
+          {
+            ends[i*2] = j;
+            hitres=true;
+          } else {
+            ends[i*2+1] = j;
+            if (j-ends[i*2]>maxLength)
+            {
+              maxLength = j-ends[i*2];
+            }
+          }
+        }
+      }
+    }
+
+    maxLength++;
+    // now edit the flanking gaps to justify to either left or right
+    int cLength,extent,diff;
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      current = getSequenceAt(i);
+      
+      cLength = 1+ends[i*2+1]-ends[i*2];
+      diff = maxLength-cLength; // number of gaps to indent
+      extent = current.getLength();
+      if (right)
+      {
+        // right justify
+        if (extent>ends[i*2+1])
+        {
+          current.deleteChars(ends[i*2+1]+1, extent);
+          modified = true;
+        }
+        if (ends[i*2]>diff)
+        {
+          current.deleteChars(0, ends[i*2]-diff);
+          modified = true;
+        } else {
+          if (ends[i*2]<diff)
+          {
+            current.insertCharAt(0, diff-ends[i*2],gapCharacter);
+            modified = true;
+          }
+        }
+      } else {
+        // left justify
+        if (ends[i*2]>0)
+        {
+          current.deleteChars(0, ends[i*2]);
+          modified = true;
+          ends[i*2+1]-=ends[i*2];
+          extent-=ends[i*2];
+        }
+        if (extent>maxLength)
+        {
+          current.deleteChars(maxLength+1, extent);
+          modified = true;
+        } else {
+          if (extent<maxLength)
+          {
+            current.insertCharAt(extent, maxLength-extent,gapCharacter);
+            modified = true;
+          }
+        }
+      }
+    }
+    return modified;
+  }
 
   public HiddenSequences getHiddenSequences()
   {
@@ -904,4 +1045,110 @@ public class Alignment implements AlignmentI
     }
     return removed;
   }
+
+  public void append(AlignmentI toappend)
+  {
+    // TODO test this method for a future 2.5 release
+    // currently tested for use in jalview.gui.SequenceFetcher
+    boolean samegap = toappend.getGapCharacter()==getGapCharacter();
+    char oldc = toappend.getGapCharacter();
+    boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+    // get all sequences including any hidden ones
+    Vector sqs = (hashidden) ? toappend.getHiddenSequences().getFullAlignment().getSequences() : toappend.getSequences();
+    if (sqs != null)
+    {
+      Enumeration sq = sqs.elements();
+      while (sq.hasMoreElements())
+      {
+        SequenceI addedsq=(SequenceI) sq.nextElement();
+        if (!samegap)
+        {
+          char[] oldseq = addedsq.getSequence();
+          for (int c=0;c<oldseq.length;c++)
+          {
+            if (oldseq[c]==oldc)
+            {
+              oldseq[c] = gapCharacter;
+            }
+          }
+        }
+        addSequence(addedsq);
+      }
+    }
+    AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+    for (int a = 0; alan != null && a < alan.length; a++)
+    {
+      addAnnotation(alan[a]);
+    }
+    AlignedCodonFrame[] acod = toappend.getCodonFrames();
+    for (int a = 0; acod != null && a < acod.length; a++)
+    {
+      this.addCodonFrame(acod[a]);
+    }
+    Vector sg = toappend.getGroups();
+    if (sg != null)
+    {
+      Enumeration el = sg.elements();
+      while (el.hasMoreElements())
+      {
+        addGroup((SequenceGroup) el.nextElement());
+      }
+    }
+    if (toappend.getHiddenSequences()!=null)
+    {
+      HiddenSequences hs = toappend.getHiddenSequences();
+      if (hiddenSequences==null)
+      {
+        hiddenSequences = new HiddenSequences(this);
+      }
+      if (hs.hiddenSequences!=null)
+      {
+        for (int s=0;s<hs.hiddenSequences.length; s++)
+        {
+          // hide the newly appended sequence in the alignment
+          if (hs.hiddenSequences[s]!=null)
+          {
+            hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+          }
+        }
+      }
+    }
+    if (toappend.getProperties()!=null)
+    {
+      // we really can't do very much here - just try to concatenate strings where property collisions occur.
+      Enumeration key = toappend.getProperties().keys();
+      while (key.hasMoreElements())
+      {
+        Object k = key.nextElement();
+        Object ourval = this.getProperty(k);
+        Object toapprop = toappend.getProperty(k);
+        if (ourval!=null)
+        {
+          if (ourval.getClass().equals(toapprop.getClass()) && !ourval.equals(toapprop))
+          {
+            if (ourval instanceof String)
+            {
+              // append strings
+              this.setProperty(k, ((String) ourval)+"; "+((String) toapprop));
+            } else {
+              if (ourval instanceof Vector)
+              {
+                // append vectors
+                Enumeration theirv = ((Vector) toapprop).elements();
+                while (theirv.hasMoreElements())
+                {
+                  ((Vector)ourval).addElement(theirv);
+                }
+              }
+            }
+          }
+        } else {
+          // just add new property directly
+          setProperty(k, toapprop);
+        }
+       
+      }
+    }
+  }
+
 }