X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=9d9fa81609aa1112b652cc45afa6d812e6ddae2b;hb=a2aa22698dd5bbcfb8578fb39c8a4e8025ac243b;hp=36c64989e80d9c9d85c6cb72bf10af213eac988c;hpb=32c056ffe34e60a1fde83bf4061af6e82d41f958;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 36c6498..9d9fa81 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 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
@@ -23,7 +23,7 @@ import java.util.*;
 
 public class HiddenSequences
 {
-  Hashtable hiddenSequences;
+  public SequenceI []  hiddenSequences;
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -33,43 +33,112 @@ public class HiddenSequences
 
   public int getSize()
   {
-    return hiddenSequences == null ? 0 : hiddenSequences.size();
+    if(hiddenSequences==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(hiddenSequences[i]==null)
+        continue;
+
+      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);
   }
 
-  public void showAll()
+  public Vector showAll()
   {
-   for(int i=0; i<alignment.getHeight()+hiddenSequences.size(); i++)
-     showSequence(i);
+   Vector revealedSeqs = new Vector();
+   for(int i=0; i<hiddenSequences.length; i++)
+    {
+      if(hiddenSequences[i]!=null)
+      {
+        Vector tmp = showSequence(i);
+        for (int t = 0; t < tmp.size(); t++)
+          revealedSeqs.addElement(tmp.elementAt(t));
+      }
+    }
+    return revealedSeqs;
   }
 
-  public void showSequence(int alignmentIndex)
+  public Vector showSequence(int alignmentIndex)
   {
+    Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
     if(repSequence!=null
        && repSequence.getHiddenSequences()==null
@@ -82,40 +151,50 @@ 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)
       {
-        alignment.getSequences().insertElementAt(seq, alignmentIndex);
-        if(repSequence!=null)
-        {
-          repSequence.showHiddenSequence(seq);
-        }
+        if(seq.getLength()>0)
+         {
+           revealedSeqs.addElement(seq);
+           alignment.getSequences().insertElementAt(seq, alignmentIndex);
+         }
+         else
+           System.out.println(seq.getName()+" has been deleted whilst hidden");
+
+         if (repSequence != null)
+         {
+           repSequence.showHiddenSequence(seq);
+         }
       }
+
     }
-  }
 
-  public Hashtable getHiddenSequences()
-  {
-    return hiddenSequences;
+    return revealedSeqs;
   }
 
   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)
+      alignmentIndex = hiddenSequences.length-1;
+
     while(index <= alignmentIndex)
     {
-     if(hiddenSequences.containsKey(new Integer(index)))
+     if(hiddenSequences[index]!=null)
      {
        hiddenSeqs ++;
      }
@@ -128,40 +207,35 @@ 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);
@@ -169,6 +243,10 @@ 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;
   }
 }