From 520cc5fe77f3f625c9a58cb6b8b83bbca68084b6 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 28 Apr 2010 10:15:51 +0000
Subject: [PATCH] group/annotation association housekeeping

---
 src/jalview/datamodel/Alignment.java           |  287 ++++++++++++++++--------
 src/jalview/datamodel/AlignmentAnnotation.java |    1 +
 2 files changed, 198 insertions(+), 90 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index afe7032..dc70c47 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -27,7 +27,7 @@ import jalview.analysis.*;
  */
 /**
  * @author JimP
- *
+ * 
  */
 public class Alignment implements AlignmentI
 {
@@ -88,7 +88,7 @@ public class Alignment implements AlignmentI
    * Make a new alignment from an array of SeqCigars
    * 
    * @param seqs
-   *                SeqCigar[]
+   *          SeqCigar[]
    */
   public Alignment(SeqCigar[] alseqs)
   {
@@ -104,7 +104,7 @@ public class Alignment implements AlignmentI
    * appropriately.
    * 
    * @param compactAlignment
-   *                CigarArray
+   *          CigarArray
    */
   public static AlignmentI createAlignment(CigarArray compactAlignment)
   {
@@ -138,7 +138,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -238,7 +238,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void deleteSequence(SequenceI s)
   {
@@ -249,7 +249,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param i
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void deleteSequence(int i)
   {
@@ -280,7 +280,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param s
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -344,10 +344,69 @@ 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();
   }
 
@@ -356,14 +415,7 @@ 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());
-        }
-      }
+      removeAnnotationForGroup(g);
       groups.removeElement(g);
     }
   }
@@ -388,7 +440,7 @@ 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)
   {
@@ -479,7 +531,8 @@ 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)
   {
@@ -530,7 +583,7 @@ public class Alignment implements AlignmentI
    * DOCUMENT ME!
    * 
    * @param gc
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setGapCharacter(char gc)
   {
@@ -577,7 +630,8 @@ 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)
   {
@@ -612,22 +666,45 @@ public class Alignment implements AlignmentI
     if (swap)
     {
       annotations = temp;
-      if (aa.sequenceRef != null)
-        aa.sequenceRef.removeAlignmentAnnotation(aa);
+      unhookAnnotation(aa);
     }
     return swap;
   }
 
-  /* (non-Javadoc)
-   * @see jalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.AlignmentAnnotation)
+  /**
+   * remove any object references associated with this annotation
+   * 
+   * @param aa
+   */
+  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)
-   * @see jalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.AlignmentAnnotation, int)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+   * AlignmentAnnotation, int)
    */
   public void addAnnotation(AlignmentAnnotation aa, int pos)
   {
@@ -639,21 +716,25 @@ public class Alignment implements AlignmentI
 
     AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
     int i = 0;
-    if (pos==-1 || pos>=aSize) {
+    if (pos == -1 || pos >= aSize)
+    {
       temp[aSize - 1] = aa;
-    } else {
+    }
+    else
+    {
       temp[pos] = aa;
     }
     if (aSize > 1)
     {
-      int p=0;
-      for (i = 0; i < (aSize-1); i++,p++)
+      int p = 0;
+      for (i = 0; i < (aSize - 1); i++, p++)
       {
-        if (p==pos)
+        if (p == pos)
         {
           p++;
         }
-        if (p<temp.length) {
+        if (p < temp.length)
+        {
           temp[p] = annotations[i];
         }
       }
@@ -819,9 +900,13 @@ 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
+   * 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)
@@ -830,28 +915,31 @@ public class Alignment implements AlignmentI
 
     // Remove excess gaps from the end of alignment
     int maxLength = -1;
-    int ends[] = new int[sequences.size()*2];
+    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++)
+      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)
+            ends[i * 2] = j;
+            hitres = true;
+          }
+          else
+          {
+            ends[i * 2 + 1] = j;
+            if (j - ends[i * 2] > maxLength)
             {
-              maxLength = j-ends[i*2];
+              maxLength = j - ends[i * 2];
             }
           }
         }
@@ -860,50 +948,56 @@ public class Alignment implements AlignmentI
 
     maxLength++;
     // now edit the flanking gaps to justify to either left or right
-    int cLength,extent,diff;
+    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
+
+      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])
+        if (extent > ends[i * 2 + 1])
         {
-          current.deleteChars(ends[i*2+1]+1, extent);
+          current.deleteChars(ends[i * 2 + 1] + 1, extent);
           modified = true;
         }
-        if (ends[i*2]>diff)
+        if (ends[i * 2] > diff)
         {
-          current.deleteChars(0, ends[i*2]-diff);
+          current.deleteChars(0, ends[i * 2] - diff);
           modified = true;
-        } else {
-          if (ends[i*2]<diff)
+        }
+        else
+        {
+          if (ends[i * 2] < diff)
           {
-            current.insertCharAt(0, diff-ends[i*2],gapCharacter);
+            current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
             modified = true;
           }
         }
-      } else {
+      }
+      else
+      {
         // left justify
-        if (ends[i*2]>0)
+        if (ends[i * 2] > 0)
         {
-          current.deleteChars(0, ends[i*2]);
+          current.deleteChars(0, ends[i * 2]);
           modified = true;
-          ends[i*2+1]-=ends[i*2];
-          extent-=ends[i*2];
+          ends[i * 2 + 1] -= ends[i * 2];
+          extent -= ends[i * 2];
         }
-        if (extent>maxLength)
+        if (extent > maxLength)
         {
-          current.deleteChars(maxLength+1, extent);
+          current.deleteChars(maxLength + 1, extent);
           modified = true;
-        } else {
-          if (extent<maxLength)
+        }
+        else
+        {
+          if (extent < maxLength)
           {
-            current.insertCharAt(extent, maxLength-extent,gapCharacter);
+            current.insertCharAt(extent, maxLength - extent, gapCharacter);
             modified = true;
           }
         }
@@ -955,7 +1049,9 @@ 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)
   {
@@ -986,7 +1082,8 @@ 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)
   {
@@ -1018,7 +1115,8 @@ 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)
   {
@@ -1050,23 +1148,25 @@ 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;
             }
@@ -1094,59 +1194,66 @@ 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);
         }
-       
+
       }
     }
   }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 22d637b..ddb420a 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -124,6 +124,7 @@ public class AlignmentAnnotation
    */
   protected void finalize() throws Throwable
   {
+    sequenceRef = null;
     groupRef = null;
     super.finalize();
   }
-- 
1.7.10.2