X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenSequences.java;h=d3aa01af3aaacd2b668c9b5946e55d50f6357f6d;hb=7f4da0a2b0c10f158a03dbfce8878e67e90c4a68;hp=21dcce1aac322b23d0463c831b7739e588233ace;hpb=69cc05ae896ee0c80b55571919dec8a4ba31de6c;p=jalview.git
diff --git a/src/jalview/datamodel/HiddenSequences.java b/src/jalview/datamodel/HiddenSequences.java
index 21dcce1..d3aa01a 100755
--- a/src/jalview/datamodel/HiddenSequences.java
+++ b/src/jalview/datamodel/HiddenSequences.java
@@ -1,25 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * 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
- * as published by the Free Software Foundation; either version 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * 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
{
@@ -27,13 +30,24 @@ public class HiddenSequences
* holds a list of hidden sequences associated with an alignment.
*/
public SequenceI[] 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)
@@ -41,9 +55,9 @@ public class HiddenSequences
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++;
}
@@ -52,14 +66,23 @@ public class HiddenSequences
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();
}
}
@@ -67,8 +90,7 @@ public class HiddenSequences
}
/**
- * 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)
{
@@ -104,8 +126,7 @@ public class HiddenSequences
}
/**
- * 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()
{
@@ -121,6 +142,11 @@ public class HiddenSequences
hiddenSequences = tmp;
}
+ /**
+ * Mark the specified sequence as hidden
+ *
+ * @param sequence
+ */
public void hideSequence(SequenceI sequence)
{
if (hiddenSequences == null)
@@ -128,8 +154,8 @@ public class HiddenSequences
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)
{
@@ -138,36 +164,48 @@ public class HiddenSequences
hiddenSequences[alignmentIndex] = sequence;
- alignment.deleteSequence(sequence);
+ alignment.deleteHiddenSequence(absAlignmentIndex);
}
- public Vector showAll(Hashtable hiddenReps)
+ public List showAll(
+ Map hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List revealedSeqs = new ArrayList();
for (int i = 0; i < hiddenSequences.length; i++)
{
if (hiddenSequences[i] != null)
{
- Vector tmp = showSequence(i, hiddenReps);
- for (int t = 0; t < tmp.size(); t++)
+ List tmp = showSequence(i, hiddenRepSequences);
+ for (SequenceI seq : tmp)
{
- revealedSeqs.addElement(tmp.elementAt(t));
+ revealedSeqs.add(seq);
}
}
}
return revealedSeqs;
}
- public Vector showSequence(int alignmentIndex, Hashtable hiddenReps)
+ /**
+ * 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 showSequence(int alignmentIndex,
+ Map hiddenRepSequences)
{
- Vector revealedSeqs = new Vector();
+ List revealedSeqs = new ArrayList();
SequenceI repSequence = alignment.getSequenceAt(alignmentIndex);
- if (repSequence != null &&
- hiddenReps != null
- && hiddenReps.containsKey(repSequence))
+ if (repSequence != null && hiddenRepSequences != null
+ && hiddenRepSequences.containsKey(repSequence))
{
- hiddenReps.remove(repSequence);
- revealedSeqs.addElement(repSequence);
+ hiddenRepSequences.remove(repSequence);
+ revealedSeqs.add(repSequence);
}
int start = adjustForHiddenSeqs(alignmentIndex - 1);
@@ -177,40 +215,59 @@ public class HiddenSequences
end = hiddenSequences.length - 1;
}
- for (int index = end; index > start; index--)
+ List asequences;
+ synchronized (asequences = alignment.getSequences())
{
- SequenceI seq = hiddenSequences[index];
- hiddenSequences[index] = null;
-
- if (seq != null)
+ for (int index = end; index > start; index--)
{
- if (seq.getLength() > 0)
- {
- revealedSeqs.addElement(seq);
- alignment.getSequences().insertElementAt(seq, alignmentIndex);
- }
- else
+ SequenceI seq = hiddenSequences[index];
+ hiddenSequences[index] = null;
+
+ if (seq != null)
{
- System.out.println(seq.getName() + " has been deleted whilst hidden");
+ if (seq.getLength() > 0)
+ {
+ revealedSeqs.add(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];
+ return hiddenSequences == null ? null : hiddenSequences[alignmentIndex];
}
+ /**
+ * Convert absolute alignment index to visible alignment index
+ *
+ * @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;
}
@@ -222,13 +279,57 @@ public class HiddenSequences
}
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 findIndexNAboveRow(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 = startRow;
+ 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)
@@ -244,35 +345,59 @@ public class HiddenSequences
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;
+ }
}
}