X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=0514fb89013eca8926704c7c48ca36181edf61fa;hb=f01d9453eff16cb42d6dd5780b528d3ae10247ef;hp=31eda50520f39cb1b451f6258f8d26bdf23cf34c;hpb=5cf622544aaa7453e5e1710186b53734334783d6;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 31eda50..0514fb8 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) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
 {
-  public SequenceI []  hiddenSequences;
+  public SequenceI[] hiddenSequences;
   AlignmentI alignment;
 
   public HiddenSequences(AlignmentI al)
@@ -33,14 +33,18 @@ public class HiddenSequences
 
   public int getSize()
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
     {
       return 0;
     }
     int count = 0;
-    for(int i=0; i<hiddenSequences.length; i++)
-      if(hiddenSequences[i] !=null )
-        count ++;
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null)
+      {
+        count++;
+      }
+    }
 
     return count;
   }
@@ -49,8 +53,12 @@ public class HiddenSequences
   {
     int width = 0;
     for (int i = 0; i < hiddenSequences.length; i++)
-      if (hiddenSequences[i] != null && hiddenSequences[i].getLength()>width)
+    {
+      if (hiddenSequences[i] != null && hiddenSequences[i].getLength() > width)
+      {
         width = hiddenSequences[i].getLength();
+      }
+    }
 
     return width;
   }
@@ -61,28 +69,34 @@ public class HiddenSequences
    */
   public void adjustHeightSequenceDeleted(int seqIndex)
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
     {
       return;
     }
 
     int alHeight = alignment.getHeight();
 
-    SequenceI [] tmp = new SequenceI [alHeight + getSize()];
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
     int deletionIndex = adjustForHiddenSeqs(seqIndex);
 
     for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if(hiddenSequences[i]==null)
+      if (hiddenSequences[i] == null)
+      {
         continue;
+      }
 
       if (i > deletionIndex)
-        tmp[i-1] = hiddenSequences[i];
+      {
+        tmp[i - 1] = hiddenSequences[i];
+      }
       else
-       tmp[i] = hiddenSequences[i];
+      {
+        tmp[i] = hiddenSequences[i];
+      }
     }
 
-   hiddenSequences = tmp;
+    hiddenSequences = tmp;
 
   }
 
@@ -92,86 +106,90 @@ public class HiddenSequences
    */
   public void adjustHeightSequenceAdded()
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
     {
       return;
     }
 
     int alHeight = alignment.getHeight();
 
-    SequenceI [] tmp = new SequenceI [alHeight + getSize()];
-    System.arraycopy(hiddenSequences,0,tmp,0,hiddenSequences.length);
+    SequenceI[] tmp = new SequenceI[alHeight + getSize()];
+    System.arraycopy(hiddenSequences, 0, tmp, 0, hiddenSequences.length);
     hiddenSequences = tmp;
   }
 
-
   public void hideSequence(SequenceI sequence)
   {
-    if(hiddenSequences==null)
+    if (hiddenSequences == null)
+    {
       hiddenSequences = new SequenceI[alignment.getHeight()];
+    }
 
     int alignmentIndex = alignment.findIndex(sequence);
     alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
 
-    if(hiddenSequences[alignmentIndex]!=null)
+    if (hiddenSequences[alignmentIndex] != null)
+    {
       System.out.println("ERROR!!!!!!!!!!!");
+    }
 
     hiddenSequences[alignmentIndex] = sequence;
 
     alignment.deleteSequence(sequence);
   }
 
-  public Vector showAll()
+  public Vector showAll(Hashtable hiddenReps)
   {
-   Vector revealedSeqs = new Vector();
-   for(int i=0; i<hiddenSequences.length; i++)
+    Vector revealedSeqs = new Vector();
+    for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if(hiddenSequences[i]!=null)
+      if (hiddenSequences[i] != null)
       {
-        Vector tmp = showSequence(i);
+        Vector tmp = showSequence(i, hiddenReps);
         for (int t = 0; t < tmp.size(); t++)
+        {
           revealedSeqs.addElement(tmp.elementAt(t));
+        }
       }
     }
     return revealedSeqs;
   }
 
-  public Vector showSequence(int alignmentIndex)
+  public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
   {
     Vector revealedSeqs = new Vector();
     SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
-    if(repSequence!=null
-       && repSequence.getHiddenSequences()==null
-       && alignmentIndex>0)
-      repSequence = alignment.getSequenceAt(alignmentIndex-1);
-
-    if(repSequence!=null
-       && repSequence.getHiddenSequences()==null)
-      repSequence = null;
+    if (repSequence != null &&
+        hiddenReps != null
+        && hiddenReps.containsKey(repSequence))
+    {
+      hiddenReps.remove(repSequence);
+      revealedSeqs.addElement(repSequence);
+    }
 
-    int start = adjustForHiddenSeqs(alignmentIndex-1);
+    int start = adjustForHiddenSeqs(alignmentIndex - 1);
     int end = adjustForHiddenSeqs(alignmentIndex);
-    if(end>=hiddenSequences.length)
-      end = hiddenSequences.length-1;
+    if (end >= hiddenSequences.length)
+    {
+      end = hiddenSequences.length - 1;
+    }
 
-    for(int index = end; index > start; index--)
+    for (int index = end; index > start; index--)
     {
-      SequenceI seq =  hiddenSequences[index];
+      SequenceI seq = hiddenSequences[index];
       hiddenSequences[index] = null;
 
-      if(seq!=null)
+      if (seq != null)
       {
-        if(seq.getLength()>0)
-         {
-           revealedSeqs.addElement(seq);
-           alignment.getSequences().insertElementAt(seq, alignmentIndex);
-         }
-         else
-           System.out.println(seq.getName()+" has been deleted");
-         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");
+        }
       }
 
     }
@@ -188,48 +206,53 @@ public class HiddenSequences
   {
     int index = 0;
     int hiddenSeqs = 0;
-    if(hiddenSequences.length<=alignmentIndex)
-      alignmentIndex = hiddenSequences.length-1;
+    if (hiddenSequences.length <= alignmentIndex)
+    {
+      alignmentIndex = hiddenSequences.length - 1;
+    }
 
-    while(index <= alignmentIndex)
+    while (index <= alignmentIndex)
     {
-     if(hiddenSequences[index]!=null)
-     {
-       hiddenSeqs ++;
-     }
-      index ++;
-    };
+      if (hiddenSequences[index] != null)
+      {
+        hiddenSeqs++;
+      }
+      index++;
+    }
+    ;
 
-    return (alignmentIndex - hiddenSeqs) ;
+    return (alignmentIndex - hiddenSeqs);
   }
 
   public int adjustForHiddenSeqs(int alignmentIndex)
   {
     int index = 0;
     int hSize = hiddenSequences.length;
-    while(index <= alignmentIndex && index<hSize)
+    while (index <= alignmentIndex && index < hSize)
     {
-      if(hiddenSequences[index]!=null)
+      if (hiddenSequences[index] != null)
       {
-        alignmentIndex ++;
+        alignmentIndex++;
       }
-      index ++;
-    };
+      index++;
+    }
+    ;
 
-    return alignmentIndex ;
+    return alignmentIndex;
   }
 
-
   public AlignmentI getFullAlignment()
   {
     int isize = hiddenSequences.length;
-    SequenceI [] seq = new Sequence[isize];
+    SequenceI[] seq = new Sequence[isize];
 
     int index = 0;
-    for(int i=0; i<hiddenSequences.length; i++)
+    for (int i = 0; i < hiddenSequences.length; i++)
     {
-      if(hiddenSequences[i]!=null)
+      if (hiddenSequences[i] != null)
+      {
         seq[i] = hiddenSequences[i];
+      }
       else
       {
         seq[i] = alignment.getSequenceAt(index);
@@ -242,9 +265,13 @@ public class HiddenSequences
 
   public boolean isHidden(SequenceI seq)
   {
-    for(int i=0; i<hiddenSequences.length; i++)
-      if(hiddenSequences[i] !=null && hiddenSequences[i]==seq)
+    for (int i = 0; i < hiddenSequences.length; i++)
+    {
+      if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+      {
         return true;
+      }
+    }
 
     return false;
   }