/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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.
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
public class HiddenSequences
{
AlignmentI alignment;
+ /**
+ * Constructor given a reference to an alignment (with no hidden sequences)
+ *
+ * @param al
+ */
public HiddenSequences(AlignmentI al)
{
alignment = al;
}
+ /**
+ * Answers the number of hidden sequences
+ *
+ * @return
+ */
public int getSize()
{
if (hiddenSequences == null)
return 0;
}
int count = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
+ for (SequenceI seq : hiddenSequences)
{
- if (hiddenSequences[i] != null)
+ if (seq != null)
{
count++;
}
return count;
}
+ /**
+ * Answers the length of the longest hidden sequence
+ *
+ * @return
+ */
public int getWidth()
{
+ if (hiddenSequences == null)
+ {
+ return 0;
+ }
int width = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
+ for (SequenceI seq : hiddenSequences)
{
- if (hiddenSequences[i] != null
- && hiddenSequences[i].getLength() > width)
+ if (seq != null && seq.getLength() > width)
{
- width = hiddenSequences[i].getLength();
+ width = seq.getLength();
}
}
}
/**
- * Call this method if sequences are removed from the main alignment
+ * Call this method after a sequence is removed from the main alignment
*/
public void adjustHeightSequenceDeleted(int seqIndex)
{
}
/**
- * Call this method if sequences are added to or removed from the main
- * alignment
+ * Call this method after a sequence is added to the main alignment
*/
public void adjustHeightSequenceAdded()
{
hiddenSequences = tmp;
}
+ /**
+ * Mark the specified sequence as hidden
+ *
+ * @param sequence
+ */
public void hideSequence(SequenceI sequence)
{
if (hiddenSequences == null)
hiddenSequences = new SequenceI[alignment.getHeight()];
}
- int alignmentIndex = alignment.findIndex(sequence);
- alignmentIndex = adjustForHiddenSeqs(alignmentIndex);
+ int absAlignmentIndex = alignment.findIndex(sequence);
+ int alignmentIndex = adjustForHiddenSeqs(absAlignmentIndex);
- if (hiddenSequences[alignmentIndex] != null)
+ if (alignmentIndex < 0 || hiddenSequences[alignmentIndex] != null)
{
- System.out.println("ERROR!!!!!!!!!!!");
+ jalview.bin.Console.outPrintln("ERROR!!!!!!!!!!!");
+ return;
}
hiddenSequences[alignmentIndex] = sequence;
- alignment.deleteSequence(sequence);
+ alignment.deleteHiddenSequence(absAlignmentIndex);
}
- public Vector showAll(
+ public List<SequenceI> showAll(
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<>();
+
+ if (hiddenSequences == null)
+ {
+ return revealedSeqs;
+ }
+
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++)
+ List<SequenceI> tmp = showSequence(i, hiddenRepSequences);
+ for (SequenceI seq : tmp)
{
- revealedSeqs.addElement(tmp.elementAt(t));
+ revealedSeqs.add(seq);
}
}
}
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex,
+ /**
+ * Reveals (unhides) consecutive hidden sequences just above the given
+ * alignment index. The revealed sequences are selected (including their
+ * visible representative sequence if there was one and 'reveal' is being
+ * performed on it).
+ *
+ * @param alignmentIndex
+ * @param hiddenRepSequences
+ * a map of representative sequences to the sequences they represent
+ * @return
+ */
+ public List<SequenceI> showSequence(int alignmentIndex,
Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List<SequenceI> revealedSeqs = new ArrayList<>();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
if (repSequence != null && hiddenRepSequences != null
&& hiddenRepSequences.containsKey(repSequence))
{
hiddenRepSequences.remove(repSequence);
- revealedSeqs.addElement(repSequence);
+ revealedSeqs.add(repSequence);
}
int start = adjustForHiddenSeqs(alignmentIndex - 1);
end = hiddenSequences.length - 1;
}
- List<SequenceI> asequences;
- synchronized (asequences = alignment.getSequences())
+ List<SequenceI> asequences = alignment.getSequences();
+ synchronized (asequences)
{
for (int index = end; index > start; index--)
{
{
if (seq.getLength() > 0)
{
- revealedSeqs.addElement(seq);
+ revealedSeqs.add(seq);
asequences.add(alignmentIndex, seq);
}
else
{
- System.out.println(seq.getName()
- + " has been deleted whilst hidden");
+ jalview.bin.Console.outPrintln(
+ seq.getName() + " has been deleted whilst hidden");
}
}
-
}
}
-
return revealedSeqs;
}
public SequenceI getHiddenSequence(int alignmentIndex)
{
- return hiddenSequences[alignmentIndex];
+ return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
}
+ /**
+ * Convert absolute alignment index to visible alignment index (or -1 if
+ * before the first visible sequence)
+ *
+ * @param alignmentIndex
+ * @return
+ */
public int findIndexWithoutHiddenSeqs(int alignmentIndex)
{
+ if (hiddenSequences == null)
+ {
+ return alignmentIndex;
+ }
int index = 0;
int hiddenSeqs = 0;
+ int diff = 0;
if (hiddenSequences.length <= alignmentIndex)
{
+ // if the alignmentIndex runs past the end of hidden sequences
+ // and therefore actually past the end of the alignment
+ // store the difference to add back on at the end, so that behaviour
+ // is consistent with hidden columns behaviour (used by overview panel)
+ diff = alignmentIndex - hiddenSequences.length + 1;
alignmentIndex = hiddenSequences.length - 1;
}
}
index++;
}
- ;
- return (alignmentIndex - hiddenSeqs);
+ return (alignmentIndex - hiddenSeqs + diff);
+ }
+
+ /**
+ * Find the visible row which is a given visible number of rows above another
+ * visible row. i.e. for a startRow x, the row which is distance 1 away will
+ * be row x-1.
+ *
+ * @param visibleDistance
+ * the number of visible rows to offset by
+ * @param startRow
+ * the row to start from
+ * @return the position of the row in the visible alignment
+ */
+ public int subtractVisibleRows(int visibleDistance, int startRow)
+ {
+ // walk upwards through the alignment
+ // count all the non-null sequences until we have visibleDistance counted
+ // then return the next visible sequence
+ if (hiddenSequences == null)
+ {
+ return startRow - visibleDistance;
+ }
+
+ int index = Math.min(startRow, hiddenSequences.length - 1);
+ int count = 0;
+ while ((index > -1) && (count < visibleDistance))
+ {
+ if (hiddenSequences[index] == null)
+ {
+ // count visible sequences
+ count++;
+ }
+ index--;
+ }
+ return index;
}
+ /**
+ * Convert alignment index from visible alignment to absolute alignment
+ *
+ * @param alignmentIndex
+ * @return
+ */
public int adjustForHiddenSeqs(int alignmentIndex)
{
+ if (hiddenSequences == null)
+ {
+ return alignmentIndex;
+ }
int index = 0;
int hSize = hiddenSequences.length;
while (index <= alignmentIndex && index < hSize)
return alignmentIndex;
}
+ /**
+ * makes a copy of the alignment with hidden sequences included. Using the
+ * copy for anything other than simple output is not recommended. Note - this
+ * method DOES NOT USE THE AlignmentI COPY CONSTRUCTOR!
+ *
+ * @return
+ */
public AlignmentI getFullAlignment()
{
- int isize = hiddenSequences.length;
- SequenceI[] seq = new Sequence[isize];
-
- int index = 0;
- for (int i = 0; i < hiddenSequences.length; i++)
+ SequenceI[] seq;
+ if (hiddenSequences == null)
{
- if (hiddenSequences[i] != null)
- {
- seq[i] = hiddenSequences[i];
- }
- else
+ seq = alignment.getSequencesArray();
+ }
+ else
+ {
+ int isize = hiddenSequences.length;
+ seq = new Sequence[isize];
+
+ int index = 0;
+ for (int i = 0; i < hiddenSequences.length; i++)
{
- seq[i] = alignment.getSequenceAt(index);
- index++;
+ if (hiddenSequences[i] != null)
+ {
+ seq[i] = hiddenSequences[i];
+ }
+ else
+ {
+ seq[i] = alignment.getSequenceAt(index);
+ index++;
+ }
}
}
-
- return new Alignment(seq);
+ Alignment fAlignmt = new Alignment(seq);
+ fAlignmt.annotations = alignment.getAlignmentAnnotation();
+ fAlignmt.alignmentProperties = alignment.getProperties();
+ fAlignmt.groups = alignment.getGroups();
+ fAlignmt.hasRNAStructure = alignment.hasRNAStructure();
+ fAlignmt.setSeqrep(alignment.getSeqrep());
+
+ return fAlignmt;
}
public boolean isHidden(SequenceI seq)
{
- for (int i = 0; i < hiddenSequences.length; i++)
+ if (hiddenSequences != null)
{
- if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ for (int i = 0; i < hiddenSequences.length; i++)
{
- return true;
+ if (hiddenSequences[i] != null && hiddenSequences[i] == seq)
+ {
+ return true;
+ }
}
}
return false;
}
+
+ /**
+ * Answers if a sequence is hidden
+ *
+ * @param seq
+ * (absolute) index to test
+ * @return true if sequence at index seq is hidden
+ */
+ public boolean isHidden(int seq)
+ {
+ if (hiddenSequences != null)
+ {
+ return (hiddenSequences[seq] != null);
+ }
+ return false;
+ }
}
git://source.jalview.org / jalview.git / blobdiff