/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
- * 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.
- *
- * 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 - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 <http://www.gnu.org/licenses/>.
*/
package jalview.datamodel;
-import jalview.analysis.*;
-
import java.util.*;
-/** Data structure to hold and manipulate a multiple sequence alignment
+import jalview.analysis.*;
+
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
+ */
+/**
+ * @author JimP
+ *
*/
public class Alignment implements AlignmentI
{
- protected Alignment dataset;
- protected Vector sequences;
- protected Vector groups = new Vector();
- protected char gapCharacter = '-';
- protected int type = NUCLEOTIDE;
- public static final int PROTEIN = 0;
- public static final int NUCLEOTIDE = 1;
+ protected Alignment dataset;
- /** DOCUMENT ME!! */
- public AlignmentAnnotation[] annotations;
+ protected Vector sequences;
- HiddenSequences hiddenSequences = new HiddenSequences(this);
+ protected Vector groups = new Vector();
- private void initAlignment(SequenceI[] seqs) {
- int i=0;
+ protected char gapCharacter = '-';
- if( jalview.util.Comparison.isNucleotide(seqs))
- type = NUCLEOTIDE;
- else
- type = PROTEIN;
+ protected int type = NUCLEOTIDE;
- sequences = new Vector();
+ public static final int PROTEIN = 0;
- for (i = 0; i < seqs.length; i++)
- {
- sequences.addElement(seqs[i]);
- }
+ public static final int NUCLEOTIDE = 1;
+
+ public boolean hasRNAStructure = false;
- }
- /** Make an alignment from an array of Sequences.
- *
- * @param sequences
- */
- public Alignment(SequenceI[] seqs)
+ /** DOCUMENT ME!! */
+ public AlignmentAnnotation[] annotations;
+
+ HiddenSequences hiddenSequences = new HiddenSequences(this);
+
+ public Hashtable alignmentProperties;
+
+ private void initAlignment(SequenceI[] seqs)
+ {
+ int i = 0;
+
+ if (jalview.util.Comparison.isNucleotide(seqs))
{
- initAlignment(seqs);
- }
- /**
- * Make a new alignment from an array of SeqCigars
- * @param seqs SeqCigar[]
- */
- public Alignment(SeqCigar[] alseqs) {
- SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, gapCharacter, new ColumnSelection(), null);
- initAlignment(seqs);
+ type = NUCLEOTIDE;
}
- /**
- * Make a new alignment from an CigarArray
- * JBPNote - can only do this when compactAlignment does not contain hidden regions.
- * JBPNote - must also check that compactAlignment resolves to a set of SeqCigars - or construct them appropriately.
- * @param compactAlignment CigarArray
- */
- public static AlignmentI createAlignment(CigarArray compactAlignment) {
- throw new Error("Alignment(CigarArray) not yet implemented");
- // this(compactAlignment.refCigars);
+ else
+ {
+ type = PROTEIN;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getSequences()
+ sequences = new Vector();
+
+ for (i = 0; i < seqs.length; i++)
{
- return sequences;
+ sequences.addElement(seqs[i]);
}
- public SequenceI [] getSequencesArray()
+ }
+
+ /**
+ * Make an alignment from an array of Sequences.
+ *
+ * @param sequences
+ */
+ public Alignment(SequenceI[] seqs)
+ {
+ initAlignment(seqs);
+ }
+
+ /**
+ * Make a new alignment from an array of SeqCigars
+ *
+ * @param seqs
+ * SeqCigar[]
+ */
+ public Alignment(SeqCigar[] alseqs)
+ {
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+ gapCharacter, new ColumnSelection(), null);
+ initAlignment(seqs);
+ }
+
+ /**
+ * Make a new alignment from an CigarArray JBPNote - can only do this when
+ * compactAlignment does not contain hidden regions. JBPNote - must also check
+ * that compactAlignment resolves to a set of SeqCigars - or construct them
+ * appropriately.
+ *
+ * @param compactAlignment
+ * CigarArray
+ */
+ public static AlignmentI createAlignment(CigarArray compactAlignment)
+ {
+ throw new Error("Alignment(CigarArray) not yet implemented");
+ // this(compactAlignment.refCigars);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getSequences()
+ {
+ return sequences;
+ }
+
+ public SequenceI[] getSequencesArray()
+ {
+ if (sequences == null)
+ return null;
+ SequenceI[] reply = new SequenceI[sequences.size()];
+ for (int i = 0; i < sequences.size(); i++)
{
- SequenceI [] reply = new SequenceI[sequences.size()];
- for(int i=0; i<sequences.size(); i++)
- {
- reply[i] = (SequenceI)sequences.elementAt(i);
- }
- return reply;
+ reply[i] = (SequenceI) sequences.elementAt(i);
}
+ return reply;
+ }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceI getSequenceAt(int i)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceI getSequenceAt(int i)
+ {
+ if (i>-1 && i < sequences.size())
{
- if (i < sequences.size())
- {
- return (SequenceI) sequences.elementAt(i);
- }
-
- return null;
+ return (SequenceI) sequences.elementAt(i);
}
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
- * @param snew
- */
- public void addSequence(SequenceI snew)
+ return null;
+ }
+
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
+ * @param snew
+ */
+ public void addSequence(SequenceI snew)
+ {
+ if (dataset != null)
{
- if(dataset!=null)
+ // maintain dataset integrity
+ if (snew.getDatasetSequence() != null)
{
- if(snew.getDatasetSequence()!=null)
- {
- getDataset().addSequence(snew.getDatasetSequence());
- }
- else
- {
- Sequence ds = new Sequence(snew.getName(),
- AlignSeq.extractGaps("-. ",
- snew.getSequenceAsString()),
- snew.getStart(),
- snew.getEnd());
-
- snew.setDatasetSequence(ds);
- getDataset().addSequence(ds);
- }
+ getDataset().addSequence(snew.getDatasetSequence());
+ }
+ else
+ {
+ // derive new sequence
+ SequenceI adding = snew.deriveSequence();
+ getDataset().addSequence(adding.getDatasetSequence());
+ snew = adding;
}
+ }
+ if (sequences == null)
+ {
+ initAlignment(new SequenceI[]
+ { snew });
+ }
+ else
+ {
sequences.addElement(snew);
-
- hiddenSequences.adjustHeightSequenceAdded();
}
+ if (hiddenSequences != null)
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size.
+ *
+ * @param snew
+ */
+ public void setSequenceAt(int i, SequenceI snew)
+ {
+ SequenceI oldseq = getSequenceAt(i);
+ deleteSequence(oldseq);
- /** Adds a sequence to the alignment. Recalculates maxLength and size.
- *
- * @param snew
- */
- public void setSequenceAt(int i, SequenceI snew)
- {
- SequenceI oldseq = getSequenceAt(i);
- deleteSequence(oldseq);
+ sequences.setElementAt(snew, i);
+ }
- sequences.setElementAt(snew, i);
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getGroups()
+ {
+ return groups;
+ }
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public Vector getGroups()
+ public void finalize()
+ {
+ if (getDataset() != null)
+ getDataset().removeAlignmentRef();
+
+ dataset = null;
+ sequences = null;
+ groups = null;
+ annotations = null;
+ hiddenSequences = null;
+ }
+
+ /**
+ * decrement the alignmentRefs counter by one and call finalize if it goes to
+ * zero.
+ */
+ private void removeAlignmentRef()
+ {
+ if (--alignmentRefs == 0)
{
- return groups;
+ finalize();
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ */
+ public void deleteSequence(SequenceI s)
+ {
+ deleteSequence(findIndex(s));
+ }
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- */
- public void deleteSequence(SequenceI s)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ */
+ public void deleteSequence(int i)
+ {
+ if (i > -1 && i < getHeight())
{
- deleteSequence(findIndex(s));
+ sequences.removeElementAt(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param i DOCUMENT ME!
- */
- public void deleteSequence(int i)
+ /** */
+ public SequenceGroup findGroup(SequenceI s)
+ {
+ for (int i = 0; i < this.groups.size(); i++)
{
- if(i>-1 && i<getHeight())
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+
+ if (sg.getSequences(null).contains(s))
{
- sequences.removeElementAt(i);
- hiddenSequences.adjustHeightSequenceDeleted(i);
+ return sg;
}
}
+ return null;
+ }
- /** */
- public SequenceGroup findGroup(SequenceI s)
- {
- for (int i = 0; i < this.groups.size(); i++)
- {
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ /**
+ * DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceGroup[] findAllGroups(SequenceI s)
+ {
+ Vector temp = new Vector();
- if (sg.getSequences(null).contains(s))
- {
- return sg;
- }
- }
+ int gSize = groups.size();
+ for (int i = 0; i < gSize; i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if (sg == null || sg.getSequences(null) == null)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
- return null;
+ if (sg.getSequences(null).contains(s))
+ {
+ temp.addElement(sg);
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param s DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public SequenceGroup[] findAllGroups(SequenceI s)
+ SequenceGroup[] ret = new SequenceGroup[temp.size()];
+
+ for (int i = 0; i < temp.size(); i++)
{
- Vector temp = new Vector();
+ ret[i] = (SequenceGroup) temp.elementAt(i);
+ }
+
+ return ret;
+ }
- int gSize = groups.size();
- for (int i = 0; i < gSize; i++)
+ /** */
+ public void addGroup(SequenceGroup sg)
+ {
+ if (!groups.contains(sg))
+ {
+ if (hiddenSequences.getSize() > 0)
+ {
+ int i, iSize = sg.getSize();
+ for (i = 0; i < iSize; i++)
{
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
- if(sg==null || sg.getSequences(null)==null)
- {
- this.deleteGroup(sg);
- gSize--;
- continue;
- }
+ if (!sequences.contains(sg.getSequenceAt(i)))
+ {
+ sg.deleteSequence(sg.getSequenceAt(i), false);
+ iSize--;
+ i--;
+ }
+ }
- if (sg.getSequences(null).contains(s))
- {
- temp.addElement(sg);
- }
+ if (sg.getSize() < 1)
+ {
+ return;
}
+ }
- SequenceGroup[] ret = new SequenceGroup[temp.size()];
+ groups.addElement(sg);
+ }
+ }
- for (int i = 0; i < temp.size(); i++)
+ /**
+ * 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)
{
- ret[i] = (SequenceGroup) temp.elementAt(i);
+ 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();
+ }
- return ret;
+ /** */
+ public void deleteGroup(SequenceGroup g)
+ {
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.removeElement(g);
}
+ }
+ /** */
+ public SequenceI findName(String name)
+ {
+ return findName(name, false);
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ */
+ public SequenceI findName(String token, boolean b)
+ {
+ return findName(null, token, b);
+ }
- /** */
- public void addGroup(SequenceGroup sg)
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * boolean)
+ */
+ public SequenceI findName(SequenceI startAfter, String token, boolean b)
+ {
+
+ int i = 0;
+ SequenceI sq = null;
+ String sqname = null;
+ if (startAfter != null)
{
- if (!groups.contains(sg))
+ // try to find the sequence in the alignment
+ boolean matched = false;
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i++) == startAfter)
{
- if(hiddenSequences.getSize()>0)
- {
- int i, iSize = sg.getSize();
- for (i = 0; i < iSize; i++)
- {
- if (!sequences.contains(sg.getSequenceAt(i)))
- {
- sg.deleteSequence(sg.getSequenceAt(i), false);
- iSize--;
- i--;
- }
- }
-
- if (sg.getSize() < 1)
- return;
- }
-
- groups.addElement(sg);
+ matched = true;
+ break;
}
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
}
-
- /**
- * DOCUMENT ME!
- */
- public void deleteAllGroups()
+ while (i < sequences.size())
{
- groups.removeAllElements();
+ sq = getSequenceAt(i);
+ sqname = sq.getName();
+ if (sqname.equals(token) // exact match
+ || (b && // allow imperfect matches - case varies
+ (sqname.equalsIgnoreCase(token))))
+ {
+ return getSequenceAt(i);
+ }
+
+ i++;
}
- /** */
- public void deleteGroup(SequenceGroup g)
+ return null;
+ }
+
+ public SequenceI[] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
+
+ while (i < sequences.size())
{
- if (groups.contains(g))
- {
- groups.removeElement(g);
- }
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
}
- /** */
- public SequenceI findName(String name)
+ SequenceI[] result = new SequenceI[matches.size()];
+ for (i = 0; i < result.length; i++)
{
- int i = 0;
+ result[i] = (SequenceI) matches.elementAt(i);
+ }
- while (i < sequences.size())
- {
- if (getSequenceAt(i).getName().equals(name))
- {
- return getSequenceAt(i);
- }
+ return result;
- i++;
- }
+ }
- return null;
- }
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
+ public int findIndex(SequenceI s)
+ {
+ int i = 0;
- public SequenceI [] findSequenceMatch(String name)
+ while (i < sequences.size())
{
- Vector matches = new Vector();
- int i = 0;
+ if (s == getSequenceAt(i))
+ {
+ return i;
+ }
- while (i < sequences.size())
+ i++;
+ }
+
+ return -1;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ public int findIndex(SearchResults results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
{
- if (getSequenceAt(i).getName().equals(name))
- {
- matches.addElement(getSequenceAt(i));
- }
- i++;
+ return i;
}
+ i++;
+ }
+ return -1;
+ }
- SequenceI [] result = new SequenceI[matches.size()];
- for(i=0; i<result.length; i++)
- result[i] = (SequenceI)matches.elementAt(i);
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getHeight()
+ {
+ return sequences.size();
+ }
- return result;
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWidth()
+ {
+ int maxLength = -1;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (getSequenceAt(i).getLength() > maxLength)
+ {
+ maxLength = getSequenceAt(i).getLength();
+ }
}
+ return maxLength;
+ }
- /** */
- public int findIndex(SequenceI s)
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
+ */
+ public void setGapCharacter(char gc)
+ {
+ gapCharacter = gc;
+
+ for (int i = 0; i < sequences.size(); i++)
{
- int i = 0;
+ Sequence seq = (Sequence) sequences.elementAt(i);
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
+ }
+ }
- while (i < sequences.size())
- {
- if (s == getSequenceAt(i))
- {
- return i;
- }
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return gapCharacter;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned()
+ */
+ public boolean isAligned()
+ {
+ return isAligned(false);
+ }
- i++;
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ public boolean isAligned(boolean includeHidden)
+ {
+ int width = getWidth();
+ if (hiddenSequences == null || hiddenSequences.getSize() == 0)
+ {
+ includeHidden = true; // no hidden sequences to check against.
+ }
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ if (includeHidden || !hiddenSequences.isHidden(getSequenceAt(i)))
+ {
+ if (getSequenceAt(i).getLength() != width)
+ {
+ return false;
}
+ }
+ }
+
+ return true;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ public boolean deleteAnnotation(AlignmentAnnotation aa)
+ {
+ return deleteAnnotation(aa, true);
+ }
+
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+ {
+ int aSize = 1;
- return -1;
+ if (annotations != null)
+ {
+ aSize = annotations.length;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getHeight()
+ if (aSize < 1)
{
- return sequences.size();
+ return false;
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public int getWidth()
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+ boolean swap = false;
+ int tIndex = 0;
+
+ for (int i = 0; i < aSize; i++)
{
- int maxLength = -1;
+ if (annotations[i] == aa)
+ {
+ swap = true;
+ continue;
+ }
+ if (tIndex < temp.length)
+ temp[tIndex++] = annotations[i];
+ }
- for (int i = 0; i < sequences.size(); i++)
- {
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
- }
+ if (swap)
+ {
+ annotations = temp;
+ if (unhook) {
+ unhookAnnotation(aa);
+ }
+ }
+ return swap;
+ }
- return maxLength;
+ /**
+ * remove any object references associated with this annotation
+ *
+ * @param aa
+ */
+ private void unhookAnnotation(AlignmentAnnotation aa)
+ {
+ if (aa.sequenceRef != null)
+ {
+ aa.sequenceRef.removeAlignmentAnnotation(aa);
}
+ if (aa.groupRef != null)
+ {
+ // probably need to do more here in the future (post 2.5.0)
+ aa.groupRef = null;
+ }
+ }
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ public void addAnnotation(AlignmentAnnotation aa)
+ {
+ addAnnotation(aa, -1);
+ }
- /**
- * DOCUMENT ME!
- *
- * @param gc DOCUMENT ME!
- */
- public void setGapCharacter(char gc)
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation, int)
+ */
+ public void addAnnotation(AlignmentAnnotation aa, int pos)
+ {
+ if(aa.getRNAStruc()!= null){
+ hasRNAStructure=true;
+ }
+
+ int aSize = 1;
+ if (annotations != null)
{
- gapCharacter = gc;
+ aSize = annotations.length + 1;
+ }
- for (int i = 0; i < sequences.size(); i++)
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+ int i = 0;
+ if (pos == -1 || pos >= aSize)
+ {
+ temp[aSize - 1] = aa;
+ }
+ else
+ {
+ temp[pos] = aa;
+ }
+ if (aSize > 1)
+ {
+ int p = 0;
+ for (i = 0; i < (aSize - 1); i++, p++)
+ {
+ if (p == pos)
{
- Sequence seq = (Sequence) sequences.elementAt(i);
- seq.setSequence( seq.getSequenceAsString().replace('.', gc) );
- seq.setSequence( seq.getSequenceAsString().replace('-', gc) );
- seq.setSequence( seq.getSequenceAsString().replace(' ', gc) );
+ p++;
}
+ if (p < temp.length)
+ {
+ temp[p] = annotations[i];
+ }
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public char getGapCharacter()
+ annotations = temp;
+ }
+
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+ {
+ if (aa == null || annotations == null || annotations.length - 1 < index)
{
- return gapCharacter;
+ return;
}
+ int aSize = annotations.length;
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public boolean isAligned()
+ temp[index] = aa;
+
+ for (int i = 0; i < aSize; i++)
{
- int width = getWidth();
+ if (i == index)
+ {
+ continue;
+ }
- for (int i = 0; i < sequences.size(); i++)
- {
- if (getSequenceAt(i).getLength() != width)
- {
- return false;
- }
- }
+ if (i < index)
+ {
+ temp[i] = annotations[i];
+ }
+ else
+ {
+ temp[i] = annotations[i - 1];
+ }
+ }
+
+ annotations = temp;
+ }
- return true;
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ return annotations;
+ }
+
+ public void setNucleotide(boolean b)
+ {
+ if (b)
+ {
+ type = NUCLEOTIDE;
+ }
+ else
+ {
+ type = PROTEIN;
}
+ }
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
- */
- public void deleteAnnotation(AlignmentAnnotation aa)
+ public boolean isNucleotide()
+ {
+ if (type == NUCLEOTIDE)
+ {
+ return true;
+ }
+ else
{
- int aSize = 1;
+ return false;
+ }
+ }
+
+ public boolean hasRNAStructure(){
+ //TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
- if (annotations != null)
+ public void setDataset(Alignment data)
+ {
+ if (dataset == null && data == null)
+ {
+ // Create a new dataset for this alignment.
+ // Can only be done once, if dataset is not null
+ // This will not be performed
+ SequenceI[] seqs = new SequenceI[getHeight()];
+ SequenceI currentSeq;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ currentSeq = getSequenceAt(i);
+ if (currentSeq.getDatasetSequence() != null)
+ {
+ seqs[i] = (Sequence) currentSeq.getDatasetSequence();
+ }
+ else
{
- aSize = annotations.length;
+ seqs[i] = currentSeq.createDatasetSequence();
}
+ }
- if(aSize<1)
- return;
+ dataset = new Alignment(seqs);
+ }
+ else if (dataset == null && data != null)
+ {
+ dataset = data;
+ }
+ dataset.addAlignmentRef();
+ }
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+ /**
+ * reference count for number of alignments referencing this one.
+ */
+ int alignmentRefs = 0;
- int tIndex = 0;
+ /**
+ * increase reference count to this alignment.
+ */
+ private void addAlignmentRef()
+ {
+ alignmentRefs++;
+ }
- for (int i = 0; i < aSize; i++)
- {
- if (annotations[i] == aa)
- {
- continue;
- }
+ public Alignment getDataset()
+ {
+ return dataset;
+ }
+
+ public boolean padGaps()
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
- temp[tIndex] = annotations[i];
- tIndex++;
+ SequenceI current;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ for (int j = current.getLength(); j > maxLength; j--)
+ {
+ if (j > maxLength
+ && !jalview.util.Comparison.isGap(current.getCharAt(j)))
+ {
+ maxLength = j;
+ break;
}
+ }
+ }
- annotations = temp;
+ maxLength++;
+
+ int cLength;
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ current = getSequenceAt(i);
+ cLength = current.getLength();
+
+ if (cLength < maxLength)
+ {
+ current.insertCharAt(cLength, maxLength - cLength, gapCharacter);
+ modified = true;
+ }
+ else if (current.getLength() > maxLength)
+ {
+ current.deleteChars(maxLength, current.getLength());
+ }
}
+ 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;
- public void adjustSequenceAnnotations()
+ // 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++)
{
- if(annotations!=null)
+ 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++)
{
- for (int a = 0; a < annotations.length; a++)
+ if (!jalview.util.Comparison.isGap(current.getCharAt(j)))
{
- if (annotations[a].sequenceRef != null)
+ if (!hitres)
+ {
+ ends[i * 2] = j;
+ hitres = true;
+ }
+ else
{
- annotations[a].adjustForAlignment();
+ ends[i * 2 + 1] = j;
+ if (j - ends[i * 2] > maxLength)
+ {
+ maxLength = j - ends[i * 2];
+ }
}
}
}
}
- /**
- * DOCUMENT ME!
- *
- * @param aa DOCUMENT ME!
- */
- public void addAnnotation(AlignmentAnnotation aa)
+ 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++)
{
- int aSize = 1;
- if (annotations != null)
+ 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])
{
- aSize = annotations.length + 1;
+ current.deleteChars(ends[i * 2 + 1] + 1, extent);
+ modified = true;
}
-
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
-
- temp[aSize-1] = aa;
-
- int i = 0;
-
- if (aSize > 1)
+ if (ends[i * 2] > diff)
{
- for (i = 0; i < (aSize-1); i++)
- {
- temp[i] = annotations[i];
- }
+ current.deleteChars(0, ends[i * 2] - diff);
+ modified = true;
}
-
- annotations = temp;
+ 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 void setAnnotationIndex(AlignmentAnnotation aa, int index)
+ public HiddenSequences getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ public CigarArray getCompactAlignment()
+ {
+ SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+ for (int i = 0; i < sequences.size(); i++)
{
- if(aa==null || annotations==null || annotations.length-1<index)
- return;
+ alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+ }
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
+ }
- int aSize = annotations.length;
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+ public void setProperty(Object key, Object value)
+ {
+ if (alignmentProperties == null)
+ alignmentProperties = new Hashtable();
- temp[index] = aa;
+ alignmentProperties.put(key, value);
+ }
- for (int i = 0; i < aSize; i++)
- {
- if(i==index)
- continue;
+ public Object getProperty(Object key)
+ {
+ if (alignmentProperties != null)
+ return alignmentProperties.get(key);
+ else
+ return null;
+ }
- if(i<index)
- temp[i] = annotations[i];
- else
- temp[i] = annotations[i-1];
- }
+ public Hashtable getProperties()
+ {
+ return alignmentProperties;
+ }
- annotations = temp;
- }
+ AlignedCodonFrame[] codonFrameList = null;
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public AlignmentAnnotation[] getAlignmentAnnotation()
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame
+ * )
+ */
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null)
+ return;
+ if (codonFrameList == null)
{
- return annotations;
+ codonFrameList = new AlignedCodonFrame[]
+ { codons };
+ return;
}
+ AlignedCodonFrame[] t = new AlignedCodonFrame[codonFrameList.length + 1];
+ System.arraycopy(codonFrameList, 0, t, 0, codonFrameList.length);
+ t[codonFrameList.length] = codons;
+ codonFrameList = t;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrame(int)
+ */
+ public AlignedCodonFrame getCodonFrame(int index)
+ {
+ return codonFrameList[index];
+ }
- public void setNucleotide(boolean b)
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ public AlignedCodonFrame[] getCodonFrame(SequenceI seq)
+ {
+ if (seq == null || codonFrameList == null)
+ return null;
+ Vector cframes = new Vector();
+ for (int f = 0; f < codonFrameList.length; f++)
{
- if(b)
- type = NUCLEOTIDE;
- else
- type = PROTEIN;
+ if (codonFrameList[f].involvesSequence(seq))
+ cframes.addElement(codonFrameList[f]);
}
+ if (cframes.size() == 0)
+ return null;
+ AlignedCodonFrame[] cfr = new AlignedCodonFrame[cframes.size()];
+ cframes.copyInto(cfr);
+ return cfr;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ public AlignedCodonFrame[] getCodonFrames()
+ {
+ return codonFrameList;
+ }
- public boolean isNucleotide()
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel.
+ * AlignedCodonFrame)
+ */
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ if (codons == null || codonFrameList == null)
+ return false;
+ boolean removed = false;
+ int i = 0, iSize = codonFrameList.length;
+ while (i < iSize)
{
- if(type==NUCLEOTIDE)
- return true;
+ if (codonFrameList[i] == codons)
+ {
+ removed = true;
+ if (i + 1 < iSize)
+ {
+ System.arraycopy(codonFrameList, i + 1, codonFrameList, i, iSize
+ - i - 1);
+ }
+ iSize--;
+ }
else
- return false;
+ {
+ i++;
+ }
}
+ return removed;
+ }
- public void setDataset(Alignment data)
+ 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)
{
- if(dataset==null && data==null)
+ Enumeration sq = sqs.elements();
+ while (sq.hasMoreElements())
{
- // Create a new dataset for this alignment.
- // Can only be done once, if dataset is not null
- // This will not be performed
- Sequence[] seqs = new Sequence[getHeight()];
- SequenceI currentSeq;
- for (int i = 0; i < getHeight(); i++)
+ SequenceI addedsq = (SequenceI) sq.nextElement();
+ if (!samegap)
{
- currentSeq = getSequenceAt(i);
- if(currentSeq.getDatasetSequence()!=null)
+ char[] oldseq = addedsq.getSequence();
+ for (int c = 0; c < oldseq.length; c++)
{
- seqs[i] = (Sequence)currentSeq.getDatasetSequence();
- }
- else
- {
- seqs[i] = new Sequence(currentSeq.getName(),
- AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- currentSeq.getSequenceAsString()
- ),
- currentSeq.getStart(),
- currentSeq.getEnd());
- seqs[i].sequenceFeatures = currentSeq.getSequenceFeatures();
- seqs[i].setDescription(currentSeq.getDescription());
- getSequenceAt(i).setSequenceFeatures(null);
- getSequenceAt(i).setDatasetSequence(seqs[i]);
+ if (oldseq[c] == oldc)
+ {
+ oldseq[c] = gapCharacter;
+ }
}
}
-
- dataset = new Alignment(seqs);
- }
- else if(dataset==null && data!=null)
- {
- dataset = data;
+ addSequence(addedsq);
}
}
-
- public Alignment getDataset()
+ AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+ for (int a = 0; alan != null && a < alan.length; a++)
{
- return dataset;
+ addAnnotation(alan[a]);
}
-
- public boolean padGaps()
+ AlignedCodonFrame[] acod = toappend.getCodonFrames();
+ for (int a = 0; acod != null && a < acod.length; a++)
{
- boolean modified=false;
-
- //Remove excess gaps from the end of alignment
- int maxLength = -1;
-
- SequenceI current;
- for (int i = 0; i < sequences.size(); i++)
+ 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)
{
- current = getSequenceAt(i);
- for (int j = current.getLength(); j > maxLength; j--)
+ for (int s = 0; s < hs.hiddenSequences.length; s++)
{
- if (j > maxLength && !jalview.util.Comparison.isGap(
- current.getCharAt(j)))
+ // hide the newly appended sequence in the alignment
+ if (hs.hiddenSequences[s] != null)
{
- maxLength = j;
- break;
+ hiddenSequences.hideSequence(hs.hiddenSequences[s]);
}
}
}
-
- maxLength++;
-
- int cLength;
- for (int i = 0; i < sequences.size();
- i++)
+ }
+ 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())
{
- current = getSequenceAt(i);
- cLength = current.getLength();
-
- if (cLength < maxLength)
+ Object k = key.nextElement();
+ Object ourval = this.getProperty(k);
+ Object toapprop = toappend.getProperty(k);
+ if (ourval != null)
{
- current.insertCharAt(cLength,
- maxLength-cLength, gapCharacter);
- modified=true;
+ 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 if(current.getLength() > maxLength)
+ else
{
- current.deleteChars(maxLength, current.getLength());
+ // just add new property directly
+ setProperty(k, toapprop);
}
- }
- return modified;
- }
- public HiddenSequences getHiddenSequences()
- {
- return hiddenSequences;
- }
-
- public CigarArray getCompactAlignment()
- {
- SeqCigar alseqs[] = new SeqCigar[sequences.size()];
- for (int i=0; i<sequences.size(); i++) {
- alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i));
+ }
}
- CigarArray cal = new CigarArray(alseqs);
- cal.addOperation(CigarArray.M, getWidth());
- return cal;
}
}
git://source.jalview.org / jalview.git / blobdiff