/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
* Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
* 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.
*
* 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 .
*/
package jalview.datamodel;
import java.util.*;
public class HiddenSequences
{
/**
* holds a list of hidden sequences associated with an alignment.
*/
public SequenceI[] hiddenSequences;
AlignmentI alignment;
public HiddenSequences(AlignmentI al)
{
alignment = al;
}
public int getSize()
{
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()
{
int width = 0;
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)
{
return;
}
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 SequenceI[alignment.getHeight()];
}
int alignmentIndex = alignment.findIndex(sequence);
alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
if (hiddenSequences[alignmentIndex] != null)
{
System.out.println("ERROR!!!!!!!!!!!");
}
hiddenSequences[alignmentIndex] = sequence;
alignment.deleteSequence(sequence);
}
public Vector showAll(
Map hiddenRepSequences)
{
Vector revealedSeqs = new Vector();
for (int i = 0; i < hiddenSequences.length; i++)
{
if (hiddenSequences[i] != null)
{
Vector tmp = showSequence(i, hiddenRepSequences);
for (int t = 0; t < tmp.size(); t++)
{
revealedSeqs.addElement(tmp.elementAt(t));
}
}
}
return revealedSeqs;
}
public Vector showSequence(int alignmentIndex,
Map hiddenRepSequences)
{
Vector revealedSeqs = new Vector();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
if (repSequence != null && hiddenRepSequences != null
&& hiddenRepSequences.containsKey(repSequence))
{
hiddenRepSequences.remove(repSequence);
revealedSeqs.addElement(repSequence);
}
int start = adjustForHiddenSeqs(alignmentIndex - 1);
int end = adjustForHiddenSeqs(alignmentIndex);
if (end >= hiddenSequences.length)
{
end = hiddenSequences.length - 1;
}
List asequences;
synchronized (asequences = alignment.getSequences())
{
for (int index = end; index > start; index--)
{
SequenceI seq = hiddenSequences[index];
hiddenSequences[index] = null;
if (seq != null)
{
if (seq.getLength() > 0)
{
revealedSeqs.addElement(seq);
asequences.add(alignmentIndex, seq);
}
else
{
System.out.println(seq.getName()
+ " has been deleted whilst hidden");
}
}
}
}
return revealedSeqs;
}
public SequenceI getHiddenSequence(int 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[index] != null)
{
hiddenSeqs++;
}
index++;
}
;
return (alignmentIndex - hiddenSeqs);
}
public int adjustForHiddenSeqs(int alignmentIndex)
{
int index = 0;
int hSize = hiddenSequences.length;
while (index <= alignmentIndex && index < hSize)
{
if (hiddenSequences[index] != null)
{
alignmentIndex++;
}
index++;
}
;
return alignmentIndex;
}
public AlignmentI getFullAlignment()
{
int isize = hiddenSequences.length;
SequenceI[] seq = new Sequence[isize];
int index = 0;
for (int i = 0; i < hiddenSequences.length; i++)
{
if (hiddenSequences[i] != null)
{
seq[i] = hiddenSequences[i];
}
else
{
seq[i] = alignment.getSequenceAt(index);
index++;
}
}
return new Alignment(seq);
}
public boolean isHidden(SequenceI seq)
{
for (int i = 0; i < hiddenSequences.length; i++)
{
if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
{
return true;
}
}
return false;
}
}