-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.datamodel;\r
-\r
-import jalview.analysis.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.util.*;\r
-\r
-\r
-/** Data structure to hold and manipulate a multiple sequence alignment\r
- */\r
-public class Alignment implements AlignmentI\r
-{\r
- protected Alignment dataset;\r
- protected Vector sequences;\r
- protected Vector groups = new Vector();\r
- protected Vector superGroup = new Vector();\r
- protected char gapCharacter = '-';\r
- protected int type = NUCLEOTIDE;\r
- public static final int PROTEIN = 0;\r
- public static final int NUCLEOTIDE = 1;\r
-\r
- /** DOCUMENT ME!! */\r
- public AlignmentAnnotation[] annotations;\r
-\r
- /** Make an alignment from an array of Sequences.\r
- *\r
- * @param sequences\r
- */\r
- public Alignment(SequenceI[] seqs)\r
- {\r
- int i=0;\r
-\r
- if( jalview.util.Comparison.isNucleotide(seqs))\r
- type = NUCLEOTIDE;\r
- else\r
- type = PROTEIN;\r
-\r
- sequences = new Vector();\r
-\r
- for (i = 0; i < seqs.length; i++)\r
- {\r
- sequences.addElement(seqs[i]);\r
- }\r
-\r
- getWidth();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getSequences()\r
- {\r
- return sequences;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceI getSequenceAt(int i)\r
- {\r
- if (i < sequences.size())\r
- {\r
- return (SequenceI) sequences.elementAt(i);\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- *\r
- * @param snew\r
- */\r
- public void addSequence(SequenceI snew)\r
- {\r
- sequences.addElement(snew);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq DOCUMENT ME!\r
- */\r
- public void addSequence(SequenceI[] seq)\r
- {\r
- for (int i = 0; i < seq.length; i++)\r
- {\r
- addSequence(seq[i]);\r
- }\r
- }\r
-\r
- /** Adds a sequence to the alignment. Recalculates maxLength and size.\r
- *\r
- * @param snew\r
- */\r
- public void setSequenceAt(int i, SequenceI snew)\r
- {\r
- SequenceI oldseq = getSequenceAt(i);\r
- deleteSequence(oldseq);\r
-\r
- sequences.setElementAt(snew, i);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getGroups()\r
- {\r
- return groups;\r
- }\r
-\r
- /** Takes out columns consisting entirely of gaps (-,.," ")\r
- */\r
- public void removeGaps()\r
- {\r
- SequenceI current;\r
- int iSize = getWidth();\r
-\r
- for (int i = 0; i < iSize; i++)\r
- {\r
- boolean delete = true;\r
-\r
- for (int j = 0; j < getHeight(); j++)\r
- {\r
- current = getSequenceAt(j);\r
-\r
- if (current.getLength() > i)\r
- {\r
- /* MC Should move this to a method somewhere */\r
- if (!jalview.util.Comparison.isGap(current.getCharAt(i)))\r
- {\r
- delete = false;\r
- }\r
- }\r
- }\r
-\r
- if (delete)\r
- {\r
- deleteColumns(i, i);\r
- iSize--;\r
- i--;\r
- }\r
- }\r
- }\r
-\r
- /** Removes a range of columns (start to end inclusive).\r
- *\r
- * @param start Start column in the alignment\r
- * @param end End column in the alignment\r
- */\r
- public void deleteColumns(int start, int end)\r
- {\r
- deleteColumns(0, getHeight() - 1, start, end);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param seq1 DOCUMENT ME!\r
- * @param seq2 DOCUMENT ME!\r
- * @param start DOCUMENT ME!\r
- * @param end DOCUMENT ME!\r
- */\r
- public void deleteColumns(int seq1, int seq2, int start, int end)\r
- {\r
- for (int i = 0; i <= (end - start); i++)\r
- {\r
- for (int j = seq1; j <= seq2; j++)\r
- {\r
- getSequenceAt(j).deleteCharAt(start);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void trimLeft(int i)\r
- {\r
- int j, jSize = getHeight();\r
- for (j = 0; j < jSize; j++)\r
- {\r
- SequenceI s = getSequenceAt(j);\r
- int newstart = s.findPosition(i);\r
-\r
- if(i>s.getLength())\r
- {\r
- sequences.removeElement(s);\r
- j--;\r
- jSize--;\r
- }\r
- else\r
- {\r
- s.setStart(newstart);\r
- s.setSequence(s.getSequence().substring(i));\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void trimRight(int i)\r
- {\r
- for (int j = 0; j < getHeight(); j++)\r
- {\r
- SequenceI s = getSequenceAt(j);\r
- int newend = s.findPosition(i);\r
-\r
- s.setEnd(newend);\r
- if(s.getLength()>i)\r
- s.setSequence(s.getSequence().substring(0, i + 1));\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- */\r
- public void deleteSequence(SequenceI s)\r
- {\r
- for (int i = 0; i < getHeight(); i++)\r
- {\r
- if (getSequenceAt(i) == s)\r
- {\r
- deleteSequence(i);\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void deleteSequence(int i)\r
- {\r
- sequences.removeElementAt(i);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param threshold DOCUMENT ME!\r
- * @param sel DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector removeRedundancy(float threshold, Vector sel)\r
- {\r
- Vector del = new Vector();\r
-\r
- for (int i = 1; i < sel.size(); i++)\r
- {\r
- for (int j = 0; j < i; j++)\r
- {\r
- // Only do the comparison if either have not been deleted\r
- if (!del.contains((SequenceI) sel.elementAt(i)) ||\r
- !del.contains((SequenceI) sel.elementAt(j)))\r
- {\r
- // use PID instead of Comparison (which is really not pleasant)\r
- float pid = Comparison.PID((SequenceI) sel.elementAt(j),\r
- (SequenceI) sel.elementAt(i));\r
-\r
- if (pid >= threshold)\r
- {\r
- // Delete the shortest one\r
- if (((SequenceI) sel.elementAt(j)).getSequence().length() > ((SequenceI) sel\r
- .elementAt(\r
- i)).getSequence().length())\r
- {\r
- del.addElement(sel.elementAt(i));\r
- }\r
- else\r
- {\r
- del.addElement(sel.elementAt(i));\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- // Now delete the sequences\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- deleteSequence((SequenceI) del.elementAt(i));\r
- }\r
-\r
- return del;\r
- }\r
-\r
- /** */\r
- public SequenceGroup findGroup(int i)\r
- {\r
- return findGroup(getSequenceAt(i));\r
- }\r
-\r
- /** */\r
- public SequenceGroup findGroup(SequenceI s)\r
- {\r
- for (int i = 0; i < this.groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
-\r
- if (sg.sequences.contains(s))\r
- {\r
- return sg;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SequenceGroup[] findAllGroups(SequenceI s)\r
- {\r
- Vector temp = new Vector();\r
-\r
- int gSize = groups.size();\r
- for (int i = 0; i < gSize; i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if(sg==null || sg.sequences==null)\r
- {\r
- this.deleteGroup(sg);\r
- gSize--;\r
- continue;\r
- }\r
-\r
- if (sg.sequences.contains(s))\r
- {\r
- temp.addElement(sg);\r
- }\r
- }\r
-\r
- SequenceGroup[] ret = new SequenceGroup[temp.size()];\r
-\r
- for (int i = 0; i < temp.size(); i++)\r
- {\r
- ret[i] = (SequenceGroup) temp.elementAt(i);\r
- }\r
-\r
- return ret;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- */\r
- public void addSuperGroup(SuperGroup sg)\r
- {\r
- superGroup.addElement(sg);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- */\r
- public void removeSuperGroup(SuperGroup sg)\r
- {\r
- superGroup.removeElement(sg);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param sg DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public SuperGroup getSuperGroup(SequenceGroup sg)\r
- {\r
- for (int i = 0; i < this.superGroup.size(); i++)\r
- {\r
- SuperGroup temp = (SuperGroup) superGroup.elementAt(i);\r
-\r
- if (temp.sequenceGroups.contains(sg))\r
- {\r
- return temp;\r
- }\r
- }\r
-\r
- return null;\r
- }\r
-\r
- /** */\r
- public void addGroup(SequenceGroup sg)\r
- {\r
- if (!groups.contains(sg))\r
- {\r
- groups.addElement(sg);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void deleteAllGroups()\r
- {\r
- groups.removeAllElements();\r
- superGroup.removeAllElements();\r
-\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI s = getSequenceAt(i);\r
- s.setColor(java.awt.Color.white);\r
- i++;\r
- }\r
- }\r
-\r
- /** */\r
- public void deleteGroup(SequenceGroup g)\r
- {\r
- if (groups.contains(g))\r
- {\r
- groups.removeElement(g);\r
- }\r
- }\r
-\r
- /** */\r
- public SequenceI findName(String name)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- if (getSequenceAt(i).getName().equals(name))\r
- {\r
- return getSequenceAt(i);\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return null;\r
- }\r
-\r
-\r
- /** */\r
- public int findIndex(SequenceI s)\r
- {\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- if (s == getSequenceAt(i))\r
- {\r
- return i;\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return -1;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getHeight()\r
- {\r
- return sequences.size();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getWidth()\r
- {\r
- int maxLength = -1;\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- if (getSequenceAt(i).getLength() > maxLength)\r
- {\r
- maxLength = getSequenceAt(i).getLength();\r
- }\r
- }\r
-\r
- return maxLength;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getMaxIdLength()\r
- {\r
- int max = 0;\r
- int i = 0;\r
-\r
- while (i < sequences.size())\r
- {\r
- SequenceI seq = getSequenceAt(i);\r
- String tmp = seq.getName() + "/" + seq.getStart() + "-" +\r
- seq.getEnd();\r
-\r
- if (tmp.length() > max)\r
- {\r
- max = tmp.length();\r
- }\r
-\r
- i++;\r
- }\r
-\r
- return max;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param gc DOCUMENT ME!\r
- */\r
- public void setGapCharacter(char gc)\r
- {\r
- gapCharacter = gc;\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- Sequence seq = (Sequence) sequences.elementAt(i);\r
- seq.sequence = seq.sequence.replace('.', gc);\r
- seq.sequence = seq.sequence.replace('-', gc);\r
- seq.sequence = seq.sequence.replace(' ', gc);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public char getGapCharacter()\r
- {\r
- return gapCharacter;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public Vector getAAFrequency()\r
- {\r
- return AAFrequency.calculate(sequences, 0, getWidth());\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public boolean isAligned()\r
- {\r
- int width = getWidth();\r
-\r
- for (int i = 0; i < sequences.size(); i++)\r
- {\r
- if (getSequenceAt(i).getLength() != width)\r
- {\r
- return false;\r
- }\r
- }\r
-\r
- return true;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- */\r
- public void deleteAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
-\r
- if (annotations != null)\r
- {\r
- aSize = annotations.length;\r
- }\r
-\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];\r
-\r
- int tIndex = 0;\r
-\r
- for (int i = 0; i < aSize; i++)\r
- {\r
- if (annotations[i] == aa)\r
- {\r
- continue;\r
- }\r
-\r
- temp[tIndex] = annotations[i];\r
- tIndex++;\r
- }\r
-\r
- annotations = temp;\r
- }\r
-\r
-\r
- public void addAnnotation(AlignmentAnnotation aa, SequenceI seqRef, int index)\r
- {\r
- aa.refSequence = seqRef;\r
- if(seqRef!=null && index!=0)\r
- {\r
- int aSize = aa.annotations.length;\r
- int newIndex;\r
- Annotation [] temp = new Annotation[seqRef.getLength()];\r
- for(int a=0; a<aSize; a++)\r
- {\r
- newIndex = seqRef.findIndex(a + index)-1;\r
- temp[newIndex] = aa.annotations[a];\r
- }\r
-\r
- aa.annotations = temp;\r
- }\r
-\r
- addAnnotation(aa);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param aa DOCUMENT ME!\r
- */\r
- public void addAnnotation(AlignmentAnnotation aa)\r
- {\r
- int aSize = 1;\r
-\r
- if (annotations != null)\r
- {\r
- aSize = annotations.length + 1;\r
- }\r
-\r
-\r
- AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];\r
-\r
- temp[0] = aa;\r
-\r
- int i = 1;\r
-\r
- if (aSize > 1)\r
- {\r
- for (i = 1; i < (aSize); i++)\r
- {\r
- temp[i] = annotations[i-1];\r
- }\r
- }\r
-\r
- annotations = temp;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public AlignmentAnnotation[] getAlignmentAnnotation()\r
- {\r
- return annotations;\r
- }\r
-\r
- public void setNucleotide(boolean b)\r
- {\r
- if(b)\r
- type = NUCLEOTIDE;\r
- else\r
- type = PROTEIN;\r
- }\r
-\r
- public boolean isNucleotide()\r
- {\r
- if(type==NUCLEOTIDE)\r
- return true;\r
- else\r
- return false;\r
- }\r
-\r
- public void setDataset(Alignment data)\r
- {\r
- if(dataset==null && data==null)\r
- {\r
- // Create a new dataset for this alignment.\r
- // Can only be done once, if dataset is not null\r
- // This will not be performed\r
- Sequence[] seqs = new Sequence[getHeight()];\r
- for (int i = 0; i < getHeight(); i++)\r
- {\r
-\r
- seqs[i] = new Sequence(getSequenceAt(i).getName(),\r
- AlignSeq.extractGaps(\r
- jalview.util.Comparison.GapChars,\r
- getSequenceAt(i).getSequence()\r
- ),\r
- getSequenceAt(i).getStart(),\r
- getSequenceAt(i).getEnd());\r
-\r
- getSequenceAt(i).setDatasetSequence(seqs[i]);\r
- }\r
-\r
- dataset = new Alignment(seqs);\r
- }\r
- else if(dataset==null && data!=null)\r
- {\r
- dataset = data;\r
- }\r
- }\r
-\r
- public Alignment getDataset()\r
- {\r
- return dataset;\r
- }\r
-\r
- public boolean padGaps() {\r
- boolean modified=false;\r
- int Width = getWidth();\r
- SequenceI current;\r
- for (int i = 0; i < sequences.size();\r
- i++)\r
- {\r
- current = getSequenceAt(i);\r
-\r
- if (current.getLength() < Width)\r
- {\r
- current.insertCharAt(Width - 1, gapCharacter);\r
- modified=true;\r
- }\r
- }\r
- return modified;\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import jalview.analysis.AlignmentUtils;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
+import jalview.io.FastaFile;
+import jalview.util.Comparison;
+import jalview.util.LinkedIdentityHashSet;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Vector;
+
+/**
+ * Data structure to hold and manipulate a multiple sequence alignment
+ */
+/**
+ * @author JimP
+ *
+ */
+public class Alignment implements AlignmentI
+{
+ private Alignment dataset;
+
+ private List<SequenceI> sequences;
+
+ protected List<SequenceGroup> groups;
+
+ protected char gapCharacter = '-';
+
+ private boolean nucleotide = true;
+
+ private List<AlignedCodonFrame> codonFrameList;
+
+ private static final SequenceGroup[] noGroups = new SequenceGroup[0];
+
+ /*
+ * persistent object to hold result of findAllGroups(SequenceI)
+ */
+ private List<SequenceGroup> groupsForSequence = new ArrayList<>();
+
+ public boolean hasRNAStructure = false;
+
+ public AlignmentAnnotation[] annotations;
+
+ HiddenSequences hiddenSequences;
+
+ HiddenColumns hiddenCols;
+
+ public Hashtable alignmentProperties;
+
+ private void initAlignment(SequenceI[] seqs)
+ {
+ groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
+ hiddenSequences = new HiddenSequences(this);
+ hiddenCols = new HiddenColumns();
+ codonFrameList = new ArrayList<>();
+
+ nucleotide = Comparison.isNucleotide(seqs);
+
+ sequences = Collections.synchronizedList(new ArrayList<SequenceI>());
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ sequences.add(seqs[i]);
+ }
+
+ }
+
+ /**
+ * Make a 'copy' alignment - sequences have new copies of features and
+ * annotations, but share the original dataset sequences.
+ */
+ public Alignment(AlignmentI al)
+ {
+ SequenceI[] seqs = al.getSequencesArray();
+ for (int i = 0; i < seqs.length; i++)
+ {
+ seqs[i] = new Sequence(seqs[i]);
+ }
+
+ initAlignment(seqs);
+
+ /*
+ * Share the same dataset sequence mappings (if any).
+ */
+ if (dataset == null && al.getDataset() == null)
+ {
+ this.setCodonFrames(al.getCodonFrames());
+ }
+ }
+
+ /**
+ * 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 alseqs
+ */
+ public Alignment(SeqCigar[] alseqs)
+ {
+ SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
+ gapCharacter, new HiddenColumns(), 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(MessageManager
+ .getString("error.alignment_cigararray_not_implemented"));
+ // this(compactAlignment.refCigars);
+ }
+
+ @Override
+ public List<SequenceI> getSequences()
+ {
+ return sequences;
+ }
+
+ @Override
+ public List<SequenceI> getSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenReps)
+ {
+ // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to
+ // work on this.
+ return sequences;
+ }
+
+ @Override
+ public SequenceI[] getSequencesArray()
+ {
+ if (sequences == null)
+ {
+ return null;
+ }
+ synchronized (sequences)
+ {
+ return sequences.toArray(new SequenceI[sequences.size()]);
+ }
+ }
+
+ /**
+ * Returns a map of lists of sequences keyed by sequence name.
+ *
+ * @return
+ */
+ @Override
+ public Map<String, List<SequenceI>> getSequencesByName()
+ {
+ return AlignmentUtils.getSequencesByName(this);
+ }
+
+ @Override
+ public SequenceI getSequenceAt(int i)
+ {
+ synchronized (sequences)
+ {
+
+ if (i > -1 && i < sequences.size())
+ {
+ return sequences.get(i);
+ }
+ }
+
+ return null;
+ }
+
+ @Override
+ public SequenceI getSequenceAtAbsoluteIndex(int i)
+ {
+ SequenceI seq = null;
+ if (getHiddenSequences().getSize() > 0)
+ {
+ seq = getHiddenSequences().getHiddenSequence(i);
+ if (seq == null)
+ {
+ // didn't find the sequence in the hidden sequences, get it from the
+ // alignment
+ int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i);
+ seq = getSequenceAt(index);
+ }
+ }
+ else
+ {
+ seq = getSequenceAt(i);
+ }
+ return seq;
+ }
+
+ /**
+ * Adds a sequence to the alignment. Recalculates maxLength and size. Note
+ * this currently does not recalculate whether or not the alignment is
+ * nucleotide, so mixed alignments may have undefined behaviour.
+ *
+ * @param snew
+ */
+ @Override
+ public void addSequence(SequenceI snew)
+ {
+ if (dataset != null)
+ {
+
+ // maintain dataset integrity
+ SequenceI dsseq = snew.getDatasetSequence();
+ if (dsseq == null)
+ {
+ // derive new sequence
+ SequenceI adding = snew.deriveSequence();
+ snew = adding;
+ dsseq = snew.getDatasetSequence();
+ }
+ if (getDataset().findIndex(dsseq) == -1)
+ {
+ getDataset().addSequence(dsseq);
+ }
+
+ }
+ if (sequences == null)
+ {
+ initAlignment(new SequenceI[] { snew });
+ }
+ else
+ {
+ synchronized (sequences)
+ {
+ sequences.add(snew);
+ }
+ }
+ if (hiddenSequences != null)
+ {
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ }
+
+ @Override
+ public SequenceI replaceSequenceAt(int i, SequenceI snew)
+ {
+ synchronized (sequences)
+ {
+ if (sequences.size() > i)
+ {
+ return sequences.set(i, snew);
+
+ }
+ else
+ {
+ sequences.add(snew);
+ hiddenSequences.adjustHeightSequenceAdded();
+ }
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public List<SequenceGroup> getGroups()
+ {
+ return groups;
+ }
+
+ @Override
+ public void finalize() throws Throwable
+ {
+ if (getDataset() != null)
+ {
+ getDataset().removeAlignmentRef();
+ }
+
+ nullReferences();
+ super.finalize();
+ }
+
+ /**
+ * Defensively nulls out references in case this object is not garbage
+ * collected
+ */
+ void nullReferences()
+ {
+ dataset = null;
+ sequences = null;
+ groups = null;
+ annotations = null;
+ hiddenSequences = null;
+ }
+
+ /**
+ * decrement the alignmentRefs counter by one and null references if it goes
+ * to zero.
+ *
+ * @throws Throwable
+ */
+ private void removeAlignmentRef() throws Throwable
+ {
+ if (--alignmentRefs == 0)
+ {
+ nullReferences();
+ }
+ }
+
+ @Override
+ public void deleteSequence(SequenceI s)
+ {
+ synchronized (sequences)
+ {
+ deleteSequence(findIndex(s));
+ }
+ }
+
+ @Override
+ public void deleteSequence(int i)
+ {
+ synchronized (sequences)
+ {
+ if (i > -1 && i < getHeight())
+ {
+ sequences.remove(i);
+ hiddenSequences.adjustHeightSequenceDeleted(i);
+ }
+ }
+ }
+
+ @Override
+ public void deleteHiddenSequence(int i)
+ {
+ synchronized (sequences)
+ {
+ if (i > -1 && i < getHeight())
+ {
+ sequences.remove(i);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public SequenceGroup findGroup(SequenceI seq, int position)
+ {
+ synchronized (groups)
+ {
+ for (SequenceGroup sg : groups)
+ {
+ if (sg.getSequences(null).contains(seq))
+ {
+ if (position >= sg.getStartRes() && position <= sg.getEndRes())
+ {
+ return sg;
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public SequenceGroup[] findAllGroups(SequenceI s)
+ {
+ synchronized (groups)
+ {
+ int gSize = groups.size();
+ if (gSize == 0)
+ {
+ return noGroups;
+ }
+ groupsForSequence.clear();
+ for (int i = 0; i < gSize; i++)
+ {
+ SequenceGroup sg = groups.get(i);
+ if (sg == null || sg.getSequences() == null)
+ {
+ this.deleteGroup(sg);
+ gSize--;
+ continue;
+ }
+
+ if (sg.getSequences().contains(s))
+ {
+ groupsForSequence.add(sg);
+ }
+ }
+ }
+ SequenceGroup[] ret = new SequenceGroup[groupsForSequence.size()];
+ return groupsForSequence.toArray(ret);
+ }
+
+ /** */
+ @Override
+ public void addGroup(SequenceGroup sg)
+ {
+ synchronized (groups)
+ {
+ if (!groups.contains(sg))
+ {
+ 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;
+ }
+ }
+ sg.setContext(this, true);
+ groups.add(sg);
+ }
+ }
+ }
+
+ /**
+ * 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;
+ }
+ }
+
+ @Override
+ public void deleteAllGroups()
+ {
+ synchronized (groups)
+ {
+ if (annotations != null)
+ {
+ removeAnnotationForGroup(null);
+ }
+ for (SequenceGroup sg : groups)
+ {
+ sg.setContext(null, false);
+ }
+ groups.clear();
+ }
+ }
+
+ /** */
+ @Override
+ public void deleteGroup(SequenceGroup g)
+ {
+ synchronized (groups)
+ {
+ if (groups.contains(g))
+ {
+ removeAnnotationForGroup(g);
+ groups.remove(g);
+ g.setContext(null, false);
+ }
+ }
+ }
+
+ /** */
+ @Override
+ public SequenceI findName(String name)
+ {
+ return findName(name, false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean)
+ */
+ @Override
+ public SequenceI findName(String token, boolean b)
+ {
+ return findName(null, token, b);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String,
+ * boolean)
+ */
+ @Override
+ public SequenceI findName(SequenceI startAfter, String token, boolean b)
+ {
+
+ int i = 0;
+ SequenceI sq = null;
+ String sqname = null;
+ int nseq = sequences.size();
+ if (startAfter != null)
+ {
+ // try to find the sequence in the alignment
+ boolean matched = false;
+ while (i < nseq)
+ {
+ if (getSequenceAt(i++) == startAfter)
+ {
+ matched = true;
+ break;
+ }
+ }
+ if (!matched)
+ {
+ i = 0;
+ }
+ }
+ while (i < nseq)
+ {
+ 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++;
+ }
+
+ return null;
+ }
+
+ @Override
+ public SequenceI[] findSequenceMatch(String name)
+ {
+ Vector matches = new Vector();
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (getSequenceAt(i).getName().equals(name))
+ {
+ matches.addElement(getSequenceAt(i));
+ }
+ i++;
+ }
+
+ SequenceI[] result = new SequenceI[matches.size()];
+ for (i = 0; i < result.length; i++)
+ {
+ result[i] = (SequenceI) matches.elementAt(i);
+ }
+
+ return result;
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public int findIndex(SequenceI s)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (s == getSequenceAt(i))
+ {
+ return i;
+ }
+
+ i++;
+ }
+
+ return -1;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults)
+ */
+ @Override
+ public int findIndex(SearchResultsI results)
+ {
+ int i = 0;
+
+ while (i < sequences.size())
+ {
+ if (results.involvesSequence(getSequenceAt(i)))
+ {
+ return i;
+ }
+ i++;
+ }
+ return -1;
+ }
+
+ @Override
+ public int getHeight()
+ {
+ return sequences.size();
+ }
+
+ @Override
+ public int getAbsoluteHeight()
+ {
+ return sequences.size() + getHiddenSequences().getSize();
+ }
+
+ @Override
+ public int getWidth()
+ {
+ int maxLength = -1;
+
+ for (int i = 0; i < sequences.size(); i++)
+ {
+ maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
+ }
+ return maxLength;
+ }
+
+ @Override
+ public int getVisibleWidth()
+ {
+ int w = getWidth();
+ if (hiddenCols != null)
+ {
+ w -= hiddenCols.getSize();
+ }
+ return w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gc
+ * DOCUMENT ME!
+ */
+ @Override
+ public void setGapCharacter(char gc)
+ {
+ gapCharacter = gc;
+ synchronized (sequences)
+ {
+ for (SequenceI seq : sequences)
+ {
+ seq.setSequence(seq.getSequenceAsString().replace('.', gc)
+ .replace('-', gc).replace(' ', gc));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public char getGapCharacter()
+ {
+ return gapCharacter;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned()
+ */
+ @Override
+ public boolean isAligned()
+ {
+ return isAligned(false);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AlignmentI#isAligned(boolean)
+ */
+ @Override
+ 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;
+ }
+
+ @Override
+ public boolean isHidden(int alignmentIndex)
+ {
+ return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null);
+ }
+
+ /**
+ * Delete all annotations, including auto-calculated if the flag is set true.
+ * Returns true if at least one annotation was deleted, else false.
+ *
+ * @param includingAutoCalculated
+ * @return
+ */
+ @Override
+ public boolean deleteAllAnnotations(boolean includingAutoCalculated)
+ {
+ boolean result = false;
+ for (AlignmentAnnotation alan : getAlignmentAnnotation())
+ {
+ if (!alan.autoCalculated || includingAutoCalculated)
+ {
+ deleteAnnotation(alan);
+ result = true;
+ }
+ }
+ return result;
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel.
+ * AlignmentAnnotation)
+ */
+ @Override
+ public boolean deleteAnnotation(AlignmentAnnotation aa)
+ {
+ return deleteAnnotation(aa, true);
+ }
+
+ @Override
+ public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook)
+ {
+ int aSize = 1;
+
+ if (annotations != null)
+ {
+ aSize = annotations.length;
+ }
+
+ if (aSize < 1)
+ {
+ return false;
+ }
+
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize - 1];
+
+ boolean swap = false;
+ int tIndex = 0;
+
+ for (int i = 0; i < aSize; i++)
+ {
+ if (annotations[i] == aa)
+ {
+ swap = true;
+ continue;
+ }
+ if (tIndex < temp.length)
+ {
+ temp[tIndex++] = annotations[i];
+ }
+ }
+
+ if (swap)
+ {
+ annotations = temp;
+ if (unhook)
+ {
+ unhookAnnotation(aa);
+ }
+ }
+ return swap;
+ }
+
+ /**
+ * 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)
+ */
+ @Override
+ public void addAnnotation(AlignmentAnnotation aa)
+ {
+ addAnnotation(aa, -1);
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel.
+ * AlignmentAnnotation, int)
+ */
+ @Override
+ public void addAnnotation(AlignmentAnnotation aa, int pos)
+ {
+ if (aa.getRNAStruc() != null)
+ {
+ hasRNAStructure = true;
+ }
+
+ int aSize = 1;
+ if (annotations != null)
+ {
+ aSize = annotations.length + 1;
+ }
+
+ 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)
+ {
+ p++;
+ }
+ if (p < temp.length)
+ {
+ temp[p] = annotations[i];
+ }
+ }
+ }
+
+ annotations = temp;
+ }
+
+ @Override
+ public void setAnnotationIndex(AlignmentAnnotation aa, int index)
+ {
+ if (aa == null || annotations == null || annotations.length - 1 < index)
+ {
+ return;
+ }
+
+ int aSize = annotations.length;
+ AlignmentAnnotation[] temp = new AlignmentAnnotation[aSize];
+
+ temp[index] = aa;
+
+ for (int i = 0; i < aSize; i++)
+ {
+ if (i == index)
+ {
+ continue;
+ }
+
+ if (i < index)
+ {
+ temp[i] = annotations[i];
+ }
+ else
+ {
+ temp[i] = annotations[i - 1];
+ }
+ }
+
+ annotations = temp;
+ }
+
+ @Override
+ /**
+ * returns all annotation on the alignment
+ */
+ public AlignmentAnnotation[] getAlignmentAnnotation()
+ {
+ return annotations;
+ }
+
+ @Override
+ public boolean isNucleotide()
+ {
+ return nucleotide;
+ }
+
+ @Override
+ public boolean hasRNAStructure()
+ {
+ // TODO can it happen that structure is removed from alignment?
+ return hasRNAStructure;
+ }
+
+ @Override
+ public void setDataset(AlignmentI data)
+ {
+ if (dataset == null && data == null)
+ {
+ createDatasetAlignment();
+ }
+ else if (dataset == null && data != null)
+ {
+ if (data == this)
+ {
+ throw new IllegalArgumentException("Circular dataset reference");
+ }
+ if (!(data instanceof Alignment))
+ {
+ throw new Error(
+ "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference");
+ }
+ dataset = (Alignment) data;
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ SequenceI dsq = currentSeq.getDatasetSequence();
+ if (dsq == null)
+ {
+ dsq = currentSeq.createDatasetSequence();
+ dataset.addSequence(dsq);
+ }
+ else
+ {
+ while (dsq.getDatasetSequence() != null)
+ {
+ dsq = dsq.getDatasetSequence();
+ }
+ if (dataset.findIndex(dsq) == -1)
+ {
+ dataset.addSequence(dsq);
+ }
+ }
+ }
+ }
+ dataset.addAlignmentRef();
+ }
+
+ /**
+ * add dataset sequences to seq for currentSeq and any sequences it references
+ */
+ private void resolveAndAddDatasetSeq(SequenceI currentSeq,
+ Set<SequenceI> seqs, boolean createDatasetSequence)
+ {
+ SequenceI alignedSeq = currentSeq;
+ if (currentSeq.getDatasetSequence() != null)
+ {
+ currentSeq = currentSeq.getDatasetSequence();
+ }
+ else
+ {
+ if (createDatasetSequence)
+ {
+ currentSeq = currentSeq.createDatasetSequence();
+ }
+ }
+
+ List<SequenceI> toProcess = new ArrayList<>();
+ toProcess.add(currentSeq);
+ while (toProcess.size() > 0)
+ {
+ // use a queue ?
+ SequenceI curDs = toProcess.remove(0);
+
+ if (!seqs.add(curDs))
+ {
+ continue;
+ }
+ // iterate over database references, making sure we add forward referenced
+ // sequences
+ if (curDs.getDBRefs() != null)
+ {
+ for (DBRefEntry dbr : curDs.getDBRefs())
+ {
+ if (dbr.getMap() != null && dbr.getMap().getTo() != null)
+ {
+ if (dbr.getMap().getTo() == alignedSeq)
+ {
+ /*
+ * update mapping to be to the newly created dataset sequence
+ */
+ dbr.getMap().setTo(currentSeq);
+ }
+ if (dbr.getMap().getTo().getDatasetSequence() != null)
+ {
+ throw new Error("Implementation error: Map.getTo() for dbref "
+ + dbr + " from " + curDs.getName()
+ + " is not a dataset sequence.");
+ }
+ // we recurse to add all forward references to dataset sequences via
+ // DBRefs/etc
+ toProcess.add(dbr.getMap().getTo());
+ }
+ }
+ }
+ }
+ }
+
+ /**
+ * Creates a new dataset for this alignment. Can only be done once - if
+ * dataset is not null this will not be performed.
+ */
+ public void createDatasetAlignment()
+ {
+ if (dataset != null)
+ {
+ return;
+ }
+ // try to avoid using SequenceI.equals at this stage, it will be expensive
+ Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
+
+ for (int i = 0; i < getHeight(); i++)
+ {
+ SequenceI currentSeq = getSequenceAt(i);
+ resolveAndAddDatasetSeq(currentSeq, seqs, true);
+ }
+
+ // verify all mappings are in dataset
+ for (AlignedCodonFrame cf : codonFrameList)
+ {
+ for (SequenceToSequenceMapping ssm : cf.getMappings())
+ {
+ if (!seqs.contains(ssm.getFromSeq()))
+ {
+ resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false);
+ }
+ if (!seqs.contains(ssm.getMapping().getTo()))
+ {
+ resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false);
+ }
+ }
+ }
+ // finally construct dataset
+ dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()]));
+ // move mappings to the dataset alignment
+ dataset.codonFrameList = this.codonFrameList;
+ this.codonFrameList = null;
+ }
+
+ /**
+ * reference count for number of alignments referencing this one.
+ */
+ int alignmentRefs = 0;
+
+ /**
+ * increase reference count to this alignment.
+ */
+ private void addAlignmentRef()
+ {
+ alignmentRefs++;
+ }
+
+ @Override
+ public Alignment getDataset()
+ {
+ return dataset;
+ }
+
+ @Override
+ public boolean padGaps()
+ {
+ boolean modified = false;
+
+ // Remove excess gaps from the end of alignment
+ int maxLength = -1;
+
+ SequenceI current;
+ int nseq = sequences.size();
+ for (int i = 0; i < nseq; 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;
+ }
+ }
+ }
+
+ maxLength++;
+
+ int cLength;
+ for (int i = 0; i < nseq; 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
+ */
+ @Override
+ 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;
+ }
+
+ @Override
+ public HiddenSequences getHiddenSequences()
+ {
+ return hiddenSequences;
+ }
+
+ @Override
+ public HiddenColumns getHiddenColumns()
+ {
+ return hiddenCols;
+ }
+
+ @Override
+ public CigarArray getCompactAlignment()
+ {
+ synchronized (sequences)
+ {
+ SeqCigar alseqs[] = new SeqCigar[sequences.size()];
+ int i = 0;
+ for (SequenceI seq : sequences)
+ {
+ alseqs[i++] = new SeqCigar(seq);
+ }
+ CigarArray cal = new CigarArray(alseqs);
+ cal.addOperation(CigarArray.M, getWidth());
+ return cal;
+ }
+ }
+
+ @Override
+ public void setProperty(Object key, Object value)
+ {
+ if (alignmentProperties == null)
+ {
+ alignmentProperties = new Hashtable();
+ }
+
+ alignmentProperties.put(key, value);
+ }
+
+ @Override
+ public Object getProperty(Object key)
+ {
+ if (alignmentProperties != null)
+ {
+ return alignmentProperties.get(key);
+ }
+ else
+ {
+ return null;
+ }
+ }
+
+ @Override
+ public Hashtable getProperties()
+ {
+ return alignmentProperties;
+ }
+
+ /**
+ * Adds the given mapping to the stored set. Note this may be held on the
+ * dataset alignment.
+ */
+ @Override
+ public void addCodonFrame(AlignedCodonFrame codons)
+ {
+ List<AlignedCodonFrame> acfs = getCodonFrames();
+ if (codons != null && acfs != null && !acfs.contains(codons))
+ {
+ acfs.add(codons);
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI)
+ */
+ @Override
+ public List<AlignedCodonFrame> getCodonFrame(SequenceI seq)
+ {
+ if (seq == null)
+ {
+ return null;
+ }
+ List<AlignedCodonFrame> cframes = new ArrayList<>();
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.involvesSequence(seq))
+ {
+ cframes.add(acf);
+ }
+ }
+ return cframes;
+ }
+
+ /**
+ * Sets the codon frame mappings (replacing any existing mappings). Note the
+ * mappings are set on the dataset alignment instead if there is one.
+ *
+ * @see jalview.datamodel.AlignmentI#setCodonFrames()
+ */
+ @Override
+ public void setCodonFrames(List<AlignedCodonFrame> acfs)
+ {
+ if (dataset != null)
+ {
+ dataset.setCodonFrames(acfs);
+ }
+ else
+ {
+ this.codonFrameList = acfs;
+ }
+ }
+
+ /**
+ * Returns the set of codon frame mappings. Any changes to the returned set
+ * will affect the alignment. The mappings are held on (and read from) the
+ * dataset alignment if there is one.
+ *
+ * @see jalview.datamodel.AlignmentI#getCodonFrames()
+ */
+ @Override
+ public List<AlignedCodonFrame> getCodonFrames()
+ {
+ // TODO: Fix this method to fix failing AlignedCodonFrame tests
+ // this behaviour is currently incorrect. method should return codon frames
+ // for just the alignment,
+ // selected from dataset
+ return dataset != null ? dataset.getCodonFrames() : codonFrameList;
+ }
+
+ /**
+ * Removes the given mapping from the stored set. Note that the mappings are
+ * held on the dataset alignment if there is one.
+ */
+ @Override
+ public boolean removeCodonFrame(AlignedCodonFrame codons)
+ {
+ List<AlignedCodonFrame> acfs = getCodonFrames();
+ if (codons == null || acfs == null)
+ {
+ return false;
+ }
+ return acfs.remove(codons);
+ }
+
+ @Override
+ public void append(AlignmentI toappend)
+ {
+ // TODO JAL-1270 needs test coverage
+ // currently tested for use in jalview.gui.SequenceFetcher
+ char oldc = toappend.getGapCharacter();
+ boolean samegap = oldc == getGapCharacter();
+ boolean hashidden = toappend.getHiddenSequences() != null
+ && toappend.getHiddenSequences().hiddenSequences != null;
+ // get all sequences including any hidden ones
+ List<SequenceI> sqs = (hashidden)
+ ? toappend.getHiddenSequences().getFullAlignment()
+ .getSequences()
+ : toappend.getSequences();
+ if (sqs != null)
+ {
+ // avoid self append deadlock by
+ List<SequenceI> toappendsq = new ArrayList<>();
+ synchronized (sqs)
+ {
+ for (SequenceI addedsq : sqs)
+ {
+ if (!samegap)
+ {
+ addedsq.replace(oldc, gapCharacter);
+ }
+ toappendsq.add(addedsq);
+ }
+ }
+ for (SequenceI addedsq : toappendsq)
+ {
+ addSequence(addedsq);
+ }
+ }
+ AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation();
+ for (int a = 0; alan != null && a < alan.length; a++)
+ {
+ addAnnotation(alan[a]);
+ }
+
+ // use add method
+ getCodonFrames().addAll(toappend.getCodonFrames());
+
+ List<SequenceGroup> sg = toappend.getGroups();
+ if (sg != null)
+ {
+ for (SequenceGroup _sg : sg)
+ {
+ addGroup(_sg);
+ }
+ }
+ 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);
+ }
+
+ }
+ }
+ }
+
+ @Override
+ public AlignmentAnnotation findOrCreateAnnotation(String name,
+ String calcId, boolean autoCalc, SequenceI seqRef,
+ SequenceGroup groupRef)
+ {
+ if (annotations != null)
+ {
+ for (AlignmentAnnotation annot : getAlignmentAnnotation())
+ {
+ if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+ && (calcId == null || annot.getCalcId().equals(calcId))
+ && annot.sequenceRef == seqRef
+ && annot.groupRef == groupRef)
+ {
+ return annot;
+ }
+ }
+ }
+ AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
+ new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
+ annot.hasText = false;
+ if (calcId != null)
+ {
+ annot.setCalcId(new String(calcId));
+ }
+ annot.autoCalculated = autoCalc;
+ if (seqRef != null)
+ {
+ annot.setSequenceRef(seqRef);
+ }
+ annot.groupRef = groupRef;
+ addAnnotation(annot);
+
+ return annot;
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
+ {
+ AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+ if (alignmentAnnotation != null)
+ {
+ return AlignmentAnnotation.findAnnotation(
+ Arrays.asList(getAlignmentAnnotation()), calcId);
+ }
+ return Arrays.asList(new AlignmentAnnotation[] {});
+ }
+
+ @Override
+ public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
+ String calcId, String label)
+ {
+ return AlignmentAnnotation.findAnnotations(
+ Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
+ }
+
+ @Override
+ public void moveSelectedSequencesByOne(SequenceGroup sg,
+ Map<SequenceI, SequenceCollectionI> map, boolean up)
+ {
+ synchronized (sequences)
+ {
+ if (up)
+ {
+
+ for (int i = 1, iSize = sequences.size(); i < iSize; i++)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i - 1);
+ if (sg.getSequences(null).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i - 1, seq);
+ }
+ }
+ else
+ {
+ for (int i = sequences.size() - 2; i > -1; i--)
+ {
+ SequenceI seq = sequences.get(i);
+ if (!sg.getSequences(map).contains(seq))
+ {
+ continue;
+ }
+
+ SequenceI temp = sequences.get(i + 1);
+ if (sg.getSequences(map).contains(temp))
+ {
+ continue;
+ }
+
+ sequences.set(i, temp);
+ sequences.set(i + 1, seq);
+ }
+ }
+
+ }
+ }
+
+ @Override
+ public void validateAnnotation(AlignmentAnnotation alignmentAnnotation)
+ {
+ alignmentAnnotation.validateRangeAndDisplay();
+ if (isNucleotide() && alignmentAnnotation.isValidStruc())
+ {
+ hasRNAStructure = true;
+ }
+ }
+
+ private SequenceI seqrep = null;
+
+ /**
+ *
+ * @return the representative sequence for this group
+ */
+ @Override
+ public SequenceI getSeqrep()
+ {
+ return seqrep;
+ }
+
+ /**
+ * set the representative sequence for this group. Note - this affects the
+ * interpretation of the Hidereps attribute.
+ *
+ * @param seqrep
+ * the seqrep to set (null means no sequence representative)
+ */
+ @Override
+ public void setSeqrep(SequenceI seqrep)
+ {
+ this.seqrep = seqrep;
+ }
+
+ /**
+ *
+ * @return true if group has a sequence representative
+ */
+ @Override
+ public boolean hasSeqrep()
+ {
+ return seqrep != null;
+ }
+
+ @Override
+ public int getEndRes()
+ {
+ return getWidth() - 1;
+ }
+
+ @Override
+ public int getStartRes()
+ {
+ return 0;
+ }
+
+ /*
+ * In the case of AlignmentI - returns the dataset for the alignment, if set
+ * (non-Javadoc)
+ *
+ * @see jalview.datamodel.AnnotatedCollectionI#getContext()
+ */
+ @Override
+ public AnnotatedCollectionI getContext()
+ {
+ return dataset;
+ }
+
+ /**
+ * Align this alignment like the given (mapped) one.
+ */
+ @Override
+ public int alignAs(AlignmentI al)
+ {
+ /*
+ * Currently retains unmapped gaps (in introns), regaps mapped regions
+ * (exons)
+ */
+ return alignAs(al, false, true);
+ }
+
+ /**
+ * Align this alignment 'the same as' the given one. Mapped sequences only are
+ * realigned. If both of the same type (nucleotide/protein) then align both
+ * identically. If this is nucleotide and the other is protein, make 3 gaps
+ * for each gap in the protein sequences. If this is protein and the other is
+ * nucleotide, insert a gap for each 3 gaps (or part thereof) between
+ * nucleotide bases. If this is protein and the other is nucleotide, gaps
+ * protein to match the relative ordering of codons in the nucleotide.
+ *
+ * Parameters control whether gaps in exon (mapped) and intron (unmapped)
+ * regions are preserved. Gaps that connect introns to exons are treated
+ * conservatively, i.e. only preserved if both intron and exon gaps are
+ * preserved. TODO: check caveats below where the implementation fails
+ *
+ * @param al
+ * - must have same dataset, and sequences in al must have equivalent
+ * dataset sequence and start/end bounds under given mapping
+ * @param preserveMappedGaps
+ * if true, gaps within and between mapped codons are preserved
+ * @param preserveUnmappedGaps
+ * if true, gaps within and between unmapped codons are preserved
+ */
+ // @Override
+ public int alignAs(AlignmentI al, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ // TODO should this method signature be the one in the interface?
+ // JBPComment - yes - neither flag is used, so should be deleted.
+ boolean thisIsNucleotide = this.isNucleotide();
+ boolean thatIsProtein = !al.isNucleotide();
+ if (!thatIsProtein && !thisIsNucleotide)
+ {
+ return AlignmentUtils.alignProteinAsDna(this, al);
+ }
+ else if (thatIsProtein && thisIsNucleotide)
+ {
+ return AlignmentUtils.alignCdsAsProtein(this, al);
+ }
+ return AlignmentUtils.alignAs(this, al);
+ }
+
+ /**
+ * Returns the alignment in Fasta format. Behaviour of this method is not
+ * guaranteed between versions.
+ */
+ @Override
+ public String toString()
+ {
+ return new FastaFile().print(getSequencesArray(), true);
+ }
+
+ /**
+ * Returns the set of distinct sequence names. No ordering is guaranteed.
+ */
+ @Override
+ public Set<String> getSequenceNames()
+ {
+ Set<String> names = new HashSet<>();
+ for (SequenceI seq : getSequences())
+ {
+ names.add(seq.getName());
+ }
+ return names;
+ }
+
+ @Override
+ public boolean hasValidSequence()
+ {
+ boolean hasValidSeq = false;
+ for (SequenceI seq : getSequences())
+ {
+ if ((seq.getEnd() - seq.getStart()) > 0)
+ {
+ hasValidSeq = true;
+ break;
+ }
+ }
+ return hasValidSeq;
+ }
+
+ /**
+ * Update any mappings to 'virtual' sequences to compatible real ones, if
+ * present in the added sequences. Returns a count of mappings updated.
+ *
+ * @param seqs
+ * @return
+ */
+ @Override
+ public int realiseMappings(List<SequenceI> seqs)
+ {
+ int count = 0;
+ for (SequenceI seq : seqs)
+ {
+ for (AlignedCodonFrame mapping : getCodonFrames())
+ {
+ count += mapping.realiseWith(seq);
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Returns the first AlignedCodonFrame that has a mapping between the given
+ * dataset sequences
+ *
+ * @param mapFrom
+ * @param mapTo
+ * @return
+ */
+ @Override
+ public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo)
+ {
+ for (AlignedCodonFrame acf : getCodonFrames())
+ {
+ if (acf.getAaForDnaSeq(mapFrom) == mapTo)
+ {
+ return acf;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public boolean setHiddenColumns(HiddenColumns cols)
+ {
+ boolean changed = cols == null ? hiddenCols != null
+ : !cols.equals(hiddenCols);
+ hiddenCols = cols;
+ return changed;
+ }
+
+ @Override
+ public void setupJPredAlignment()
+ {
+ SequenceI repseq = getSequenceAt(0);
+ setSeqrep(repseq);
+ HiddenColumns cs = new HiddenColumns();
+ cs.hideList(repseq.getInsertions());
+ setHiddenColumns(cs);
+ }
+
+ @Override
+ public HiddenColumns propagateInsertions(SequenceI profileseq,
+ AlignmentView input)
+ {
+ int profsqpos = 0;
+
+ char gc = getGapCharacter();
+ Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+ HiddenColumns nview = (HiddenColumns) alandhidden[1];
+ SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+ return propagateInsertions(profileseq, origseq, nview);
+ }
+
+ /**
+ *
+ * @param profileseq
+ * sequence in al which corresponds to origseq
+ * @param al
+ * alignment which is to have gaps inserted into it
+ * @param origseq
+ * sequence corresponding to profileseq which defines gap map for
+ * modifying al
+ */
+ private HiddenColumns propagateInsertions(SequenceI profileseq,
+ SequenceI origseq, HiddenColumns hc)
+ {
+ // take the set of hidden columns, and the set of gaps in origseq,
+ // and remove all the hidden gaps from hiddenColumns
+
+ // first get the gaps as a Bitset
+ // then calculate hidden ^ not(gap)
+ BitSet gaps = origseq.gapBitset();
+ hc.andNot(gaps);
+
+ // for each sequence in the alignment, except the profile sequence,
+ // insert gaps corresponding to each hidden region but where each hidden
+ // column region is shifted backwards by the number of preceding visible
+ // gaps update hidden columns at the same time
+ HiddenColumns newhidden = new HiddenColumns();
+
+ int numGapsBefore = 0;
+ int gapPosition = 0;
+ Iterator<int[]> it = hc.iterator();
+ while (it.hasNext())
+ {
+ int[] region = it.next();
+
+ // get region coordinates accounting for gaps
+ // we can rely on gaps not being *in* hidden regions because we already
+ // removed those
+ while (gapPosition < region[0])
+ {
+ gapPosition++;
+ if (gaps.get(gapPosition))
+ {
+ numGapsBefore++;
+ }
+ }
+
+ int left = region[0] - numGapsBefore;
+ int right = region[1] - numGapsBefore;
+
+ newhidden.hideColumns(left, right);
+ padGaps(left, right, profileseq);
+ }
+ return newhidden;
+ }
+
+ /**
+ * Pad gaps in all sequences in alignment except profileseq
+ *
+ * @param left
+ * position of first gap to insert
+ * @param right
+ * position of last gap to insert
+ * @param profileseq
+ * sequence not to pad
+ */
+ private void padGaps(int left, int right, SequenceI profileseq)
+ {
+ char gc = getGapCharacter();
+
+ // make a string with number of gaps = length of hidden region
+ StringBuilder sb = new StringBuilder();
+ for (int g = 0; g < right - left + 1; g++)
+ {
+ sb.append(gc);
+ }
+
+ // loop over the sequences and pad with gaps where required
+ for (int s = 0, ns = getHeight(); s < ns; s++)
+ {
+ SequenceI sqobj = getSequenceAt(s);
+ if ((sqobj != profileseq) && (sqobj.getLength() >= left))
+ {
+ String sq = sqobj.getSequenceAsString();
+ sqobj.setSequence(
+ sq.substring(0, left) + sb.toString() + sq.substring(left));
+ }
+ }
+ }
+
+ @Override
+ public void resetColors()
+ {
+ for (int i = getHeight(); --i >= 0;)
+ {
+ sequences.get(i).resetColors();
+ }
+ // if (dataset != null)
+ // {
+ // dataset.resetColors();
+ // }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff