From 52c2c3879d5dc5e7b4ba7916f1ea964f83551f95 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 12 Oct 2006 13:18:40 +0000
Subject: [PATCH] HiddenSequences now array, not hashtable

---
 src/jalview/datamodel/Alignment.java       |   12 +--
 src/jalview/datamodel/AlignmentI.java      |    1 +
 src/jalview/datamodel/HiddenSequences.java |  147 +++++++++++++++++++---------
 3 files changed, 108 insertions(+), 52 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index e4bc25e..5f60530 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -146,8 +146,9 @@ public class Alignment implements AlignmentI
           getDataset().addSequence(ds);
         }
       }
-
       sequences.addElement(snew);
+
+      hiddenSequences.adjustHeightSequenceAdded();
     }
 
 
@@ -310,13 +311,7 @@ public class Alignment implements AlignmentI
      */
     public void deleteSequence(SequenceI s)
     {
-        for (int i = 0; i < getHeight(); i++)
-        {
-            if (getSequenceAt(i) == s)
-            {
-                deleteSequence(i);
-            }
-        }
+      deleteSequence(findIndex(s));
     }
 
     /**
@@ -327,6 +322,7 @@ public class Alignment implements AlignmentI
     public void deleteSequence(int i)
     {
         sequences.removeElementAt(i);
+        hiddenSequences.adjustHeightSequenceDeleted(i);
     }
 
 
diff --git a/src/jalview/datamodel/AlignmentI.java b/src/jalview/datamodel/AlignmentI.java
index aca108d..71ba3e0 100755
--- a/src/jalview/datamodel/AlignmentI.java
+++ b/src/jalview/datamodel/AlignmentI.java
@@ -107,6 +107,7 @@ public interface AlignmentI
      */
     public void deleteSequence(int i);
 
+
     /**
      * Deletes all residues in every sequence of alignment within given columns.
      *
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 0a588a2..e244dd7 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -23,7 +23,7 @@ import java.util.*;
 
 public class HiddenSequences
 {
-  Hashtable hiddenSequences;
+  public SequenceI []  hiddenSequences;
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -33,31 +33,88 @@ public class HiddenSequences
 
   public int getSize()
   {
-    return hiddenSequences == null ? 0 : hiddenSequences.size();
+    if(hiddenSequences==null)
+    {
+      System.out.println("H is null");
+      return 0;
+    }
+    int count = 0;
+    for(int i=0; i<hiddenSequences.length; i++)
+      if(hiddenSequences[i] !=null )
+        count ++;
+
+    return count;
   }
 
   public int getWidth()
   {
-    Enumeration en = hiddenSequences.elements();
     int width = 0;
-    while(en.hasMoreElements())
+    for (int i = 0; i < hiddenSequences.length; i++)
+      if (hiddenSequences[i] != null && hiddenSequences[i].getLength()>width)
+        width = hiddenSequences[i].getLength();
+
+    return width;
+  }
+
+  /**
+   * Call this method if sequences are removed from the
+   * main alignment
+   */
+  public void adjustHeightSequenceDeleted(int seqIndex)
+  {
+    if(hiddenSequences==null)
     {
-      SequenceI seq = (SequenceI)en.nextElement();
-      if(seq.getLength()>width)
-        width = seq.getLength();
+      return;
     }
-    return width;
+
+    int alHeight = alignment.getHeight();
+
+    SequenceI [] tmp = new SequenceI [alHeight + getSize()];
+    int deletionIndex = adjustForHiddenSeqs(seqIndex);
+
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (i > deletionIndex)
+        tmp[i-1] = hiddenSequences[i];
+      else
+        tmp[i] = hiddenSequences[i];
+    }
+
+   hiddenSequences = tmp;
+
   }
 
+  /**
+   * Call this method if sequences are added to or removed from the
+   * main alignment
+   */
+  public void adjustHeightSequenceAdded()
+  {
+    if(hiddenSequences==null)
+    {
+      return;
+    }
+
+    int alHeight = alignment.getHeight();
+
+    SequenceI [] tmp = new SequenceI [alHeight + getSize()];
+    System.arraycopy(hiddenSequences,0,tmp,0,hiddenSequences.length);
+    hiddenSequences = tmp;
+  }
+
+
   public void hideSequence(SequenceI sequence)
   {
     if(hiddenSequences==null)
-      hiddenSequences = new Hashtable();
+      hiddenSequences = new SequenceI[alignment.getHeight()];
 
     int alignmentIndex = alignment.findIndex(sequence);
     alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
 
-    hiddenSequences.put(new Integer(alignmentIndex), sequence);
+    if(hiddenSequences[alignmentIndex]!=null)
+    System.out.println("ERROR!!!!!!!!!!!");
+
+    hiddenSequences[alignmentIndex] = sequence;
 
     alignment.deleteSequence(sequence);
   }
@@ -65,11 +122,14 @@ public class HiddenSequences
   public Vector showAll()
   {
    Vector revealedSeqs = new Vector();
-   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
+   for(int i=0; i<hiddenSequences.length; i++)
     {
-      Vector tmp = showSequence(i);
-      for(int t=0; t<tmp.size(); t++)
-        revealedSeqs.addElement(tmp.elementAt(t));
+      if(hiddenSequences[i]!=null)
+      {
+        Vector tmp = showSequence(i);
+        for (int t = 0; t < tmp.size(); t++)
+          revealedSeqs.addElement(tmp.elementAt(t));
+      }
     }
     return revealedSeqs;
   }
@@ -89,12 +149,13 @@ public class HiddenSequences
 
     int start = adjustForHiddenSeqs(alignmentIndex-1);
     int end = adjustForHiddenSeqs(alignmentIndex);
+    if(end>=hiddenSequences.length)
+      end = hiddenSequences.length-1;
 
     for(int index = end; index > start; index--)
     {
-      SequenceI seq =  (SequenceI)hiddenSequences.remove(new Integer(
-          index));
-
+      SequenceI seq =  hiddenSequences[index];
+      hiddenSequences[index] = null;
 
       if(seq!=null)
       {
@@ -105,28 +166,27 @@ public class HiddenSequences
           repSequence.showHiddenSequence(seq);
         }
       }
+
     }
 
     return revealedSeqs;
   }
 
-  public Hashtable getHiddenSequences()
-  {
-    return hiddenSequences;
-  }
-
   public SequenceI getHiddenSequence(int alignmentIndex)
   {
-    return (SequenceI)hiddenSequences.get(new Integer(alignmentIndex));
+    return hiddenSequences[alignmentIndex];
   }
 
   public int findIndexWithoutHiddenSeqs(int alignmentIndex)
   {
     int index = 0;
     int hiddenSeqs = 0;
+    if(hiddenSequences.length<=alignmentIndex)
+      System.out.println(alignmentIndex+" "+hiddenSequences.length);
+
     while(index <= alignmentIndex)
     {
-     if(hiddenSequences.containsKey(new Integer(index)))
+     if(hiddenSequences[index]!=null)
      {
        hiddenSeqs ++;
      }
@@ -139,40 +199,35 @@ public class HiddenSequences
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     int index = 0;
-    while(index <= alignmentIndex)
+    int hSize = hiddenSequences.length;
+    while(index <= alignmentIndex && index<hSize)
     {
-     if(hiddenSequences.containsKey(new Integer(index)))
-     {
-       alignmentIndex ++;
-     }
+      if(hiddenSequences[index]!=null)
+      {
+        alignmentIndex ++;
+      }
       index ++;
     };
 
     return alignmentIndex ;
   }
 
+
   public AlignmentI getFullAlignment()
   {
-    int isize = alignment.getHeight()+hiddenSequences.size();
+    int isize = hiddenSequences.length;
     SequenceI [] seq = new Sequence[isize];
 
-    Enumeration en = hiddenSequences.keys();
-    while(en.hasMoreElements())
-    {
-      Integer key = (Integer)en.nextElement();
-      seq[key.intValue()] = (SequenceI)hiddenSequences.get(key);
-    }
-
     int index = 0;
-    for(int i=0; i<isize; i++)
+    for(int i=0; i<hiddenSequences.length; i++)
     {
-      if(seq[i]!=null)
+      if(hiddenSequences[i]!=null)
+        seq[i] = hiddenSequences[i];
+      else
       {
-        continue;
+        seq[i] = alignment.getSequenceAt(index);
+        index++;
       }
-
-      seq[i] = alignment.getSequenceAt(index);
-      index++;
     }
 
     return new Alignment(seq);
@@ -180,6 +235,10 @@ public class HiddenSequences
 
   public boolean isHidden(SequenceI seq)
   {
-    return hiddenSequences.contains(seq);
+    for(int i=0; i<hiddenSequences.length; i++)
+      if(hiddenSequences[i] !=null && hiddenSequences[i]==seq)
+        return true;
+
+    return false;
   }
 }
-- 
1.7.10.2