X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=05377237f4503330d8cdba93ebef7bd47c59b703;hb=1cf86680f3af423e29529855da07896501ce9f91;hp=c74be7379ae12f601cf7ec1e3a228481561cfd0b;hpb=483c80a859264f9d743cc7ff801c65b3884d8e88;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index c74be73..0537723 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,20 +1,19 @@
 /*
- * 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 (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
  * 
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.datamodel;
 
@@ -25,6 +24,10 @@ import jalview.analysis.*;
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
+/**
+ * @author JimP
+ * 
+ */
 public class Alignment implements AlignmentI
 {
   protected Alignment dataset;
@@ -40,6 +43,8 @@ public class Alignment implements AlignmentI
   public static final int PROTEIN = 0;
 
   public static final int NUCLEOTIDE = 1;
+  
+  public boolean hasRNAStructure = false;
 
   /** DOCUMENT ME!! */
   public AlignmentAnnotation[] annotations;
@@ -84,7 +89,7 @@ public class Alignment implements AlignmentI
    * Make a new alignment from an array of SeqCigars
    * 
    * @param seqs
-   *                SeqCigar[]
+   *          SeqCigar[]
    */
   public Alignment(SeqCigar[] alseqs)
   {
@@ -100,7 +105,7 @@ public class Alignment implements AlignmentI
    * appropriately.
    * 
    * @param compactAlignment
-   *                CigarArray
+   *          CigarArray
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
@@ -134,13 +139,13 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
   public SequenceI getSequenceAt(int i)
   {
-    if (i < sequences.size())
+    if (i>-1 && i < sequences.size())
     {
       return (SequenceI) sequences.elementAt(i);
     }
@@ -234,7 +239,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s)
   {
@@ -245,7 +250,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void deleteSequence(int i)
   {
@@ -276,7 +281,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -340,10 +345,71 @@ public class Alignment implements AlignmentI
   }
 
   /**
-   * DOCUMENT ME!
+   * remove any annotation that references gp
+   * 
+   * @param gp
+   *          (if null, removes all group associated annotation)
    */
+  private void removeAnnotationForGroup(SequenceGroup gp)
+  {
+    if (annotations == null || annotations.length == 0)
+    {
+      return;
+    }
+    // remove annotation very quickly
+    AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+    int i, p, k;
+    if (gp == null)
+    {
+      for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+      {
+        if (annotations[i].groupRef != null)
+        {
+          todelete[p++] = annotations[i];
+        }
+        else
+        {
+          tokeep[k++] = annotations[i];
+        }
+      }
+    }
+    else
+    {
+      for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+      {
+        if (annotations[i].groupRef == gp)
+        {
+          todelete[p++] = annotations[i];
+        }
+        else
+        {
+          tokeep[k++] = annotations[i];
+        }
+      }
+    }
+    if (p > 0)
+    {
+      // clear out the group associated annotation.
+      for (i = 0; i < p; i++)
+      {
+        unhookAnnotation(todelete[i]);
+        todelete[i] = null;
+      }
+      t = new AlignmentAnnotation[k];
+      for (i = 0; i < k; i++)
+      {
+        t[i] = tokeep[i];
+      }
+      annotations = t;
+    }
+  }
+
   public void deleteAllGroups()
   {
+    if (annotations != null)
+    {
+      removeAnnotationForGroup(null);
+    }
     groups.removeAllElements();
   }
 
@@ -352,6 +418,7 @@ public class Alignment implements AlignmentI
   {
     if (groups.contains(g))
     {
+      removeAnnotationForGroup(g);
       groups.removeElement(g);
     }
   }
@@ -376,7 +443,7 @@ public class Alignment implements AlignmentI
    * (non-Javadoc)
    * 
    * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
-   *      boolean)
+   * boolean)
    */
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
@@ -467,7 +534,8 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+   * @see
+   * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
    */
   public int findIndex(SearchResults results)
   {
@@ -518,7 +586,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param gc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setGapCharacter(char gc)
   {
@@ -527,8 +595,8 @@ public class Alignment implements AlignmentI
     for (int i = 0; i < sequences.size(); i++)
     {
       Sequence seq = (Sequence) sequences.elementAt(i);
-      seq.setSequence(seq.getSequenceAsString().replace('.', gc).replace(
-              '-', gc).replace(' ', gc));
+      seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+              .replace('-', gc).replace(' ', gc));
     }
   }
 
@@ -542,20 +610,36 @@ public class Alignment implements AlignmentI
     return gapCharacter;
   }
 
-  /**
-   * DOCUMENT ME!
+  /*
+   * (non-Javadoc)
    * 
-   * @return DOCUMENT ME!
+   * @see jalview.datamodel.AlignmentI#isAligned()
    */
   public boolean isAligned()
   {
-    int width = getWidth();
+    return isAligned(false);
+  }
 
+  /*
+   * (non-Javadoc)
+   * 
+   * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+   */
+  public boolean isAligned(boolean includeHidden)
+  {
+    int width = getWidth();
+    if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+    {
+      includeHidden = true; // no hidden sequences to check against.
+    }
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() != width)
+      if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
       {
-        return false;
+        if (getSequenceAt(i).getLength() != width)
+        {
+          return false;
+        }
       }
     }
 
@@ -565,10 +649,16 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.AlignmentAnnotation)
+   * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
    */
   public boolean deleteAnnotation(AlignmentAnnotation aa)
   {
+    return deleteAnnotation(aa, true);
+  }
+  
+  public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+  {
     int aSize = 1;
 
     if (annotations != null)
@@ -600,20 +690,54 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      if (aa.sequenceRef != null)
-        aa.sequenceRef.removeAlignmentAnnotation(aa);
+      if (unhook) {
+        unhookAnnotation(aa);
+      }
     }
     return swap;
   }
 
   /**
-   * DOCUMENT ME!
+   * remove any object references associated with this annotation
    * 
    * @param aa
-   *                DOCUMENT ME!
+   */
+  private void unhookAnnotation(AlignmentAnnotation aa)
+  {
+    if (aa.sequenceRef != null)
+    {
+      aa.sequenceRef.removeAlignmentAnnotation(aa);
+    }
+    if (aa.groupRef != null)
+    {
+      // probably need to do more here in the future (post 2.5.0)
+      aa.groupRef = null;
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation)
    */
   public void addAnnotation(AlignmentAnnotation aa)
   {
+    addAnnotation(aa, -1);
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation, int)
+   */
+  public void addAnnotation(AlignmentAnnotation aa, int pos)
+  {
+    if(aa.getRNAStruc()!= null){
+      hasRNAStructure=true;
+    }
+    
     int aSize = 1;
     if (annotations != null)
     {
@@ -621,16 +745,28 @@ 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];
+        }
       }
     }
 
@@ -702,6 +838,11 @@ public class Alignment implements AlignmentI
       return false;
     }
   }
+  
+  public boolean hasRNAStructure(){
+    //TODO can it happen that structure is removed from alignment?
+    return hasRNAStructure;
+  }
 
   public void setDataset(Alignment data)
   {
@@ -795,6 +936,111 @@ 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()
   {
     return hiddenSequences;
@@ -838,7 +1084,9 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   * @see
+   * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+   * )
    */
   public void addCodonFrame(AlignedCodonFrame codons)
   {
@@ -869,7 +1117,8 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+   * @see
+   * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
    */
   public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
   {
@@ -901,7 +1150,8 @@ public class Alignment implements AlignmentI
   /*
    * (non-Javadoc)
    * 
-   * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+   * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+   * AlignedCodonFrame)
    */
   public boolean removeCodonFrame(AlignedCodonFrame codons)
   {
@@ -933,23 +1183,25 @@ public class Alignment implements AlignmentI
   {
     // TODO test this method for a future 2.5 release
     // currently tested for use in jalview.gui.SequenceFetcher
-    boolean samegap = toappend.getGapCharacter()==getGapCharacter();
+    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
-    boolean hashidden = toappend.getHiddenSequences()!=null && toappend.getHiddenSequences().hiddenSequences!=null;
+    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();
+    Vector sqs = (hashidden) ? toappend.getHiddenSequences()
+            .getFullAlignment().getSequences() : toappend.getSequences();
     if (sqs != null)
     {
       Enumeration sq = sqs.elements();
       while (sq.hasMoreElements())
       {
-        SequenceI addedsq=(SequenceI) sq.nextElement();
+        SequenceI addedsq = (SequenceI) sq.nextElement();
         if (!samegap)
         {
           char[] oldseq = addedsq.getSequence();
-          for (int c=0;c<oldseq.length;c++)
+          for (int c = 0; c < oldseq.length; c++)
           {
-            if (oldseq[c]==oldc)
+            if (oldseq[c] == oldc)
             {
               oldseq[c] = gapCharacter;
             }
@@ -977,59 +1229,66 @@ public class Alignment implements AlignmentI
         addGroup((SequenceGroup) el.nextElement());
       }
     }
-    if (toappend.getHiddenSequences()!=null)
+    if (toappend.getHiddenSequences() != null)
     {
       HiddenSequences hs = toappend.getHiddenSequences();
-      if (hiddenSequences==null)
+      if (hiddenSequences == null)
       {
         hiddenSequences = new HiddenSequences(this);
       }
-      if (hs.hiddenSequences!=null)
+      if (hs.hiddenSequences != null)
       {
-        for (int s=0;s<hs.hiddenSequences.length; s++)
+        for (int s = 0; s < hs.hiddenSequences.length; s++)
         {
           // hide the newly appended sequence in the alignment
-          if (hs.hiddenSequences[s]!=null)
+          if (hs.hiddenSequences[s] != null)
           {
             hiddenSequences.hideSequence(hs.hiddenSequences[s]);
           }
         }
       }
     }
-    if (toappend.getProperties()!=null)
+    if (toappend.getProperties() != null)
     {
-      // we really can't do very much here - just try to concatenate strings where property collisions occur.
+      // 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 != null)
         {
-          if (ourval.getClass().equals(toapprop.getClass()) && !ourval.equals(toapprop))
+          if (ourval.getClass().equals(toapprop.getClass())
+                  && !ourval.equals(toapprop))
           {
             if (ourval instanceof String)
             {
               // append strings
-              this.setProperty(k, ((String) ourval)+"; "+((String) toapprop));
-            } else {
+              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);
+                  ((Vector) ourval).addElement(theirv);
                 }
               }
             }
           }
-        } else {
+        }
+        else
+        {
           // just add new property directly
           setProperty(k, toapprop);
         }
-       
+
       }
     }
   }