X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=6a4dcbf9d53f1ba554a559cb749c88337668c4ee;hb=d423f22792e47dbc800ae220a58677f988971d06;hp=08c04f5b779f3b73c27cdba8baf081912a48d199;hpb=961b10e4c895aadb7fc9df82a641c6c53c0d5c70;p=jalview.git
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 08c04f5..6a4dcbf 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1,20 +1,19 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 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.
*
- * 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
+ * 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;
@@ -25,6 +24,10 @@ import jalview.analysis.*;
/**
* Data structure to hold and manipulate a multiple sequence alignment
*/
+/**
+ * @author JimP
+ *
+ */
public class Alignment implements AlignmentI
{
protected Alignment dataset;
@@ -84,7 +87,7 @@ public class Alignment implements AlignmentI
* Make a new alignment from an array of SeqCigars
*
* @param seqs
- * SeqCigar[]
+ * SeqCigar[]
*/
public Alignment(SeqCigar[] alseqs)
{
@@ -100,7 +103,7 @@ public class Alignment implements AlignmentI
* appropriately.
*
* @param compactAlignment
- * CigarArray
+ * CigarArray
*/
public static AlignmentI createAlignment(CigarArray compactAlignment)
{
@@ -134,7 +137,7 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -234,7 +237,7 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void deleteSequence(SequenceI s)
{
@@ -245,7 +248,7 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param i
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public void deleteSequence(int i)
{
@@ -276,7 +279,7 @@ public class Alignment implements AlignmentI
* DOCUMENT ME!
*
* @param s
- * DOCUMENT ME!
+ * DOCUMENT ME!
*
* @return DOCUMENT ME!
*/
@@ -340,10 +343,71 @@ public class Alignment implements AlignmentI
}
/**
- * DOCUMENT ME!
+ * remove any annotation that references gp
+ *
+ * @param gp
+ * (if null, removes all group associated annotation)
*/
+ private void removeAnnotationForGroup(SequenceGroup gp)
+ {
+ if (annotations == null || annotations.length == 0)
+ {
+ return;
+ }
+ // remove annotation very quickly
+ AlignmentAnnotation[] t, todelete = new AlignmentAnnotation[annotations.length], tokeep = new AlignmentAnnotation[annotations.length];
+ int i, p, k;
+ if (gp == null)
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef != null)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ else
+ {
+ for (i = 0, p = 0, k = 0; i < annotations.length; i++)
+ {
+ if (annotations[i].groupRef == gp)
+ {
+ todelete[p++] = annotations[i];
+ }
+ else
+ {
+ tokeep[k++] = annotations[i];
+ }
+ }
+ }
+ if (p > 0)
+ {
+ // clear out the group associated annotation.
+ for (i = 0; i < p; i++)
+ {
+ unhookAnnotation(todelete[i]);
+ todelete[i] = null;
+ }
+ t = new AlignmentAnnotation[k];
+ for (i = 0; i < k; i++)
+ {
+ t[i] = tokeep[i];
+ }
+ annotations = t;
+ }
+ }
+
public void deleteAllGroups()
{
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
groups.removeAllElements();
}
@@ -352,6 +416,7 @@ public class Alignment implements AlignmentI
{
if (groups.contains(g))
{
+ removeAnnotationForGroup(g);
groups.removeElement(g);
}
}
@@ -376,7 +441,7 @@ public class Alignment implements AlignmentI
* (non-Javadoc)
*
* @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
- * boolean)
+ * boolean)
*/
public SequenceI findName(SequenceI startAfter, String token, boolean b)
{
@@ -441,7 +506,10 @@ public class Alignment implements AlignmentI
return result;
}
- /* (non-Javadoc)
+
+ /*
+ * (non-Javadoc)
+ *
* @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
*/
public int findIndex(SequenceI s)
@@ -460,14 +528,18 @@ public class Alignment implements AlignmentI
return -1;
}
- /* (non-Javadoc)
- * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
*/
public int findIndex(SearchResults results)
{
- int i=0;
-
- while (i= aSize)
+ {
+ temp[aSize - 1] = aa;
+ }
+ else
+ {
+ temp[pos] = aa;
+ }
if (aSize > 1)
{
- for (i = 0; i < (aSize - 1); i++)
+ int p = 0;
+ for (i = 0; i < (aSize - 1); i++, p++)
{
- temp[i] = annotations[i];
+ if (p == pos)
+ {
+ p++;
+ }
+ if (p < temp.length)
+ {
+ temp[p] = annotations[i];
+ }
}
}
@@ -789,6 +918,111 @@ public class Alignment implements AlignmentI
return modified;
}
+ /**
+ * Justify the sequences to the left or right by deleting and inserting gaps
+ * before the initial residue or after the terminal residue
+ *
+ * @param right
+ * true if alignment padded to right, false to justify to left
+ * @return true if alignment was changed
+ */
+ public boolean justify(boolean right)
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+ int ends[] = new int[sequences.size() * 2];
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ // This should really be a sequence method
+ ends[i * 2] = current.findIndex(current.getStart());
+ ends[i * 2 + 1] = current.findIndex(current.getStart()
+ + current.getLength());
+ boolean hitres = false;
+ for (int j = 0, rs = 0, ssiz = current.getLength(); j < ssiz; j++)
+ {
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ if (!hitres)
+ {
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
+ {
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
+ {
+ maxLength = j - ends[i * 2];
+ }
+ }
+ }
+ }
+ }
+
+ maxLength++;
+ // now edit the flanking gaps to justify to either left or right
+ int cLength, extent, diff;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+
+ cLength = 1 + ends[i * 2 + 1] - ends[i * 2];
+ diff = maxLength - cLength; // number of gaps to indent
+ extent = current.getLength();
+ if (right)
+ {
+ // right justify
+ if (extent > ends[i * 2 + 1])
+ {
+ current.deleteChars(ends[i * 2 + 1] + 1, extent);
+ modified = true;
+ }
+ if (ends[i * 2] > diff)
+ {
+ current.deleteChars(0, ends[i * 2] - diff);
+ modified = true;
+ }
+ else
+ {
+ if (ends[i * 2] < diff)
+ {
+ current.insertCharAt(0, diff - ends[i * 2], gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ else
+ {
+ // left justify
+ if (ends[i * 2] > 0)
+ {
+ current.deleteChars(0, ends[i * 2]);
+ modified = true;
+ ends[i * 2 + 1] -= ends[i * 2];
+ extent -= ends[i * 2];
+ }
+ if (extent > maxLength)
+ {
+ current.deleteChars(maxLength + 1, extent);
+ modified = true;
+ }
+ else
+ {
+ if (extent < maxLength)
+ {
+ current.insertCharAt(extent, maxLength - extent, gapCharacter);
+ modified = true;
+ }
+ }
+ }
+ }
+ return modified;
+ }
+
public HiddenSequences getHiddenSequences()
{
return hiddenSequences;
@@ -832,7 +1066,9 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
*/
public void addCodonFrame(AlignedCodonFrame codons)
{
@@ -863,7 +1099,8 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
*/
public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
{
@@ -895,7 +1132,8 @@ public class Alignment implements AlignmentI
/*
* (non-Javadoc)
*
- * @see jalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.AlignedCodonFrame)
+ * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * AlignedCodonFrame)
*/
public boolean removeCodonFrame(AlignedCodonFrame codons)
{
@@ -923,4 +1161,118 @@ public class Alignment implements AlignmentI
return removed;
}
+ public void append(AlignmentI toappend)
+ {
+ // TODO test this method for a future 2.5 release
+ // currently tested for use in jalview.gui.SequenceFetcher
+ boolean samegap = toappend.getGapCharacter() == getGapCharacter();
+ char oldc = toappend.getGapCharacter();
+ boolean hashidden = toappend.getHiddenSequences() != null
+ && toappend.getHiddenSequences().hiddenSequences != null;
+ // get all sequences including any hidden ones
+ Vector sqs = (hashidden) ? toappend.getHiddenSequences()
+ .getFullAlignment().getSequences() : toappend.getSequences();
+ if (sqs != null)
+ {
+ Enumeration sq = sqs.elements();
+ while (sq.hasMoreElements())
+ {
+ SequenceI addedsq = (SequenceI) sq.nextElement();
+ if (!samegap)
+ {
+ char[] oldseq = addedsq.getSequence();
+ for (int c = 0; c < oldseq.length; c++)
+ {
+ if (oldseq[c] == oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
+ }
+ }
+ addSequence(addedsq);
+ }
+ }
+ AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+ for (int a = 0; alan != null && a < alan.length; a++)
+ {
+ addAnnotation(alan[a]);
+ }
+ AlignedCodonFrame[] acod = toappend.getCodonFrames();
+ for (int a = 0; acod != null && a < acod.length; a++)
+ {
+ this.addCodonFrame(acod[a]);
+ }
+ Vector sg = toappend.getGroups();
+ if (sg != null)
+ {
+ Enumeration el = sg.elements();
+ while (el.hasMoreElements())
+ {
+ addGroup((SequenceGroup) el.nextElement());
+ }
+ }
+ if (toappend.getHiddenSequences() != null)
+ {
+ HiddenSequences hs = toappend.getHiddenSequences();
+ if (hiddenSequences == null)
+ {
+ hiddenSequences = new HiddenSequences(this);
+ }
+ if (hs.hiddenSequences != null)
+ {
+ for (int s = 0; s < hs.hiddenSequences.length; s++)
+ {
+ // hide the newly appended sequence in the alignment
+ if (hs.hiddenSequences[s] != null)
+ {
+ hiddenSequences.hideSequence(hs.hiddenSequences[s]);
+ }
+ }
+ }
+ }
+ if (toappend.getProperties() != null)
+ {
+ // we really can't do very much here - just try to concatenate strings
+ // where property collisions occur.
+ Enumeration key = toappend.getProperties().keys();
+ while (key.hasMoreElements())
+ {
+ Object k = key.nextElement();
+ Object ourval = this.getProperty(k);
+ Object toapprop = toappend.getProperty(k);
+ if (ourval != null)
+ {
+ if (ourval.getClass().equals(toapprop.getClass())
+ && !ourval.equals(toapprop))
+ {
+ if (ourval instanceof String)
+ {
+ // append strings
+ this.setProperty(k, ((String) ourval) + "; "
+ + ((String) toapprop));
+ }
+ else
+ {
+ if (ourval instanceof Vector)
+ {
+ // append vectors
+ Enumeration theirv = ((Vector) toapprop).elements();
+ while (theirv.hasMoreElements())
+ {
+ ((Vector) ourval).addElement(theirv);
+ }
+ }
+ }
+ }
+ }
+ else
+ {
+ // just add new property directly
+ setProperty(k, toapprop);
+ }
+
+ }
+ }
+ }
+
}