X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=e2fc057ed5947fefd2574623d9479554a55d33f3;hb=582d39cb05dfbb5f956f74d4a97a17d9f63b0786;hp=d30003dd45822cf9d25fb79ffe09a4ddcbe272f6;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index d30003d..e2fc057 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,504 +1,686 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -*/ -package jalview.datamodel; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class Sequence implements SequenceI -{ - protected String name; - protected String sequence; - protected String description; - protected int start; - protected int end; - protected String displayId; - protected Color color = Color.white; - String pdbId; - - /** DOCUMENT ME!! */ - public Vector sequenceFeatures = new Vector(); - - /** - * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - */ - public Sequence(String name, String sequence, int start, int end) - { - this.name = name; - this.sequence = sequence; - this.start = start; - this.end = end; - - if (end < 1) - { - int endRes = 0; - char ch; - for (int j = 0; j < sequence.length(); j++) - { - ch = sequence.charAt(j); - if (!jalview.util.Comparison.isGap( (ch))) - { - endRes++; - } - } - if (endRes > 0) - { - endRes += start - 1; - } - - this.end = endRes; - } - - setDisplayId(); - } - - /** - * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - */ - public Sequence(String name, String sequence) - { - this(name, sequence, 1, sequence.length()); - } - - /** - * Creates a new Sequence object. - * - * @param seq DOCUMENT ME! - */ - public Sequence(SequenceI seq) - { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); - } - - /** - * DOCUMENT ME! - * - * @param v DOCUMENT ME! - */ - public void setSequenceFeatures(Vector v) - { - sequenceFeatures = v; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Vector getSequenceFeatures() - { - return sequenceFeatures; - } - - /** - * DOCUMENT ME! - * - * @param id DOCUMENT ME! - */ - public void setPDBId(String id) - { - pdbId = id; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getPDBId() - { - return pdbId; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getDisplayId() - { - return displayId; - } - - /** - * DOCUMENT ME! - */ - public void setDisplayId() - { - displayId = name + "/" + start + "-" + end; - } - - /** - * DOCUMENT ME! - * - * @param name DOCUMENT ME! - */ - public void setName(String name) - { - this.name = name; - setDisplayId(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getName() - { - return this.name; - } - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - */ - public void setStart(int start) - { - this.start = start; - setDisplayId(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStart() - { - return this.start; - } - - /** - * DOCUMENT ME! - * - * @param end DOCUMENT ME! - */ - public void setEnd(int end) - { - this.end = end; - setDisplayId(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEnd() - { - return this.end; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getLength() - { - return this.sequence.length(); - } - - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setSequence(String seq) - { - this.sequence = seq; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence() - { - return this.sequence; - } - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence(int start, int end) - { - // JBPNote - left to user to pad the result here (TODO:Decide on this policy) - if (start >= sequence.length()) - { - return ""; - } - - if (end >= sequence.length()) - { - end = sequence.length(); - } - - return this.sequence.substring(start, end); - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getCharAt(int i) - { - if (i < sequence.length()) - { - return sequence.charAt(i); - } - else - { - return ' '; - } - } - - /** - * DOCUMENT ME! - * - * @param desc DOCUMENT ME! - */ - public void setDescription(String desc) - { - this.description = desc; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getDescription() - { - return this.description; - } - - /** - * DOCUMENT ME! - * - * @param pos DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findIndex(int pos) - { - // returns the alignment position for a residue - int j = start; - int i = 0; - - while ((i < sequence.length()) && (j <= end) && (j <= pos)) - { - char c = sequence.charAt(i); - - if (!jalview.util.Comparison.isGap((c))) - { - j++; - } - - i++; - } - - if ((j == end) && (j < pos)) - { - return end + 1; - } - else - { - return i; - } - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findPosition(int i) - { - // Returns the sequence position for an alignment position - int j = 0; - int pos = start; - - while ((j < i) && (j < sequence.length())) - { - char c = sequence.charAt(j); - - if (!jalview.util.Comparison.isGap((c))) - { - pos++; - } - - j++; - } - - return pos; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int[] gapMap() - { - // Returns an int array giving the position of each residue in the sequence in the alignment - String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence); - int[] map = new int[seq.length()]; - int j = 0; - int p = 0; - - while (j < sequence.length()) - { - if (!jalview.util.Comparison.isGap(sequence.charAt(j))) - { - map[p++] = j; - } - - j++; - } - - return map; - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - public void deleteCharAt(int i) - { - if (i >= sequence.length()) - { - return; - } - - sequence = sequence.substring(0, i) + sequence.substring(i + 1); - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - */ - public void deleteChars(int i, int j) - { - if (i >= sequence.length()) - { - return; - } - - if (j >= sequence.length()) - { - sequence = sequence.substring(0, i); - } - else - { - sequence = sequence.substring(0, i) + sequence.substring(j); - } - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param c DOCUMENT ME! - */ - public void insertCharAt(int i, char c) - { - insertCharAt(i, c, true); - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param c DOCUMENT ME! - * @param chop DOCUMENT ME! - */ - public void insertCharAt(int i, char c, boolean chop) - { - String tmp = new String(sequence); - - if (i < sequence.length()) - { - sequence = tmp.substring(0, i) + String.valueOf(c) + - tmp.substring(i); - } - else - { - // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet! - char[] ch = new char[(1 + i) - sequence.length()]; - - for (int j = 0, k = ch.length; j < k; j++) - ch[j] = c; - - sequence = tmp + String.valueOf(ch); - } - } - - /** - * DOCUMENT ME! - * - * @param c DOCUMENT ME! - */ - public void setColor(Color c) - { - this.color = c; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Color getColor() - { - return color; - } -} +/* +* 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 +*/ +package jalview.datamodel; + +import java.awt.*; + +import java.util.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Sequence implements SequenceI +{ + SequenceI datasetSequence; + String name; + private String sequence; + String description; + int start; + int end; + Vector pdbIds; + String vamsasId; + DBRefEntry[] dbrefs; + + /** This annotation is displayed below the alignment but the + * positions are tied to the residues of this sequence */ + Vector annotation; + + /** DOCUMENT ME!! */ + public SequenceFeature[] sequenceFeatures; + + /** This array holds hidden sequences + * of which this sequence is the representitive member of a group + */ + SequenceGroup hiddenSequences; + + /** + * Creates a new Sequence object. + * + * @param name DOCUMENT ME! + * @param sequence DOCUMENT ME! + * @param start DOCUMENT ME! + * @param end DOCUMENT ME! + */ + public Sequence(String name, String sequence, int start, int end) + { + this.name = name; + this.sequence = sequence; + this.start = start; + this.end = end; + + parseId(); + + checkValidRange(); + } + + com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex( + "[/][0-9]{1,}[-][0-9]{1,}$"); + com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex( + "[0-9]{1,}$"); + + void parseId() + { + // Does sequence have the /start-end signiature? + if (limitrx.search(name)) + { + name = limitrx.left(); + endrx.search(limitrx.stringMatched()); + setStart(Integer.parseInt(limitrx.stringMatched().substring(1, + endrx.matchedFrom() - 1))); + setEnd(Integer.parseInt(endrx.stringMatched())); + } + } + + void checkValidRange() + { + if (end < 1) + { + int endRes = 0; + char ch; + for (int j = 0; j < sequence.length(); j++) + { + ch = sequence.charAt(j); + if (!jalview.util.Comparison.isGap( (ch))) + { + endRes++; + } + } + if (endRes > 0) + { + endRes += start - 1; + } + + this.end = endRes; + } + + } + + /** + * Creates a new Sequence object. + * + * @param name DOCUMENT ME! + * @param sequence DOCUMENT ME! + */ + public Sequence(String name, String sequence) + { + this(name, sequence, 1, -1); + } + + /** + * Creates a new Sequence object. + * + * @param seq DOCUMENT ME! + */ + public Sequence(SequenceI seq) + { + this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); + } + + /** + * DOCUMENT ME! + * + * @param v DOCUMENT ME! + */ + public void setSequenceFeatures(SequenceFeature[] features) + { + sequenceFeatures = features; + } + + public synchronized void addSequenceFeature(SequenceFeature sf) + { + if (sequenceFeatures == null) + { + sequenceFeatures = new SequenceFeature[0]; + } + + for (int i = 0; i < sequenceFeatures.length; i++) + { + if (sequenceFeatures[i].equals(sf)) + { + return; + } + } + + SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1]; + System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length); + temp[sequenceFeatures.length] = sf; + + sequenceFeatures = temp; + } + + public void deleteFeature(SequenceFeature sf) + { + if(sequenceFeatures==null) + return; + + int index=0; + for (index = 0; index < sequenceFeatures.length; index++) + { + if (sequenceFeatures[index].equals(sf)) + { + break; + } + } + + + if(index==sequenceFeatures.length) + return; + + int sfLength = sequenceFeatures.length; + if(sfLength<2) + { + sequenceFeatures = null; + } + else + { + SequenceFeature[] temp = new SequenceFeature[sfLength-1]; + System.arraycopy(sequenceFeatures, 0, temp, 0, index); + + if(index= sequence.length()) + { + return ""; + } + + if (end >= sequence.length()) + { + end = sequence.length(); + } + + return this.sequence.substring(start, end); + } + + /** + * make a new Sequence object from start to end (including gaps) over this seqeunce + * @param start int + * @param end int + * @return SequenceI + */ + public SequenceI getSubSequence(int start, int end) + { + if (start < 0) + start = 0; + String seq = getSequence(start, end); + if (seq == "") + return null; + int nstart = findPosition(start); + int nend = findPosition(end) - 1; + // JBPNote - this is an incomplete copy. + SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend); + nseq.setDescription(description); + nseq.setDatasetSequence(getDatasetSequence()); + return nseq; + } + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getCharAt(int i) + { + if (i < sequence.length()) + { + return sequence.charAt(i); + } + else + { + return ' '; + } + } + + /** + * DOCUMENT ME! + * + * @param desc DOCUMENT ME! + */ + public void setDescription(String desc) + { + this.description = desc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getDescription() + { + return this.description; + } + + /** + * DOCUMENT ME! + * + * @param pos DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public int findIndex(int pos) + { + // returns the alignment position for a residue + int j = start; + int i = 0; + + while ( (i < sequence.length()) && (j <= end) && (j <= pos)) + { + if (!jalview.util.Comparison.isGap(sequence.charAt(i))) + { + j++; + } + + i++; + } + + if ( (j == end) && (j < pos)) + { + return end + 1; + } + else + { + return i; + } + } + + /** + * Returns the sequence position for an alignment position + * + * @param i column index in alignment (from 1) + * + * @return residue number for residue (left of and) nearest ith column + */ + public int findPosition(int i) + { + int j = 0; + int pos = start; + int seqlen = sequence.length(); + while ( (j < i) && (j < seqlen)) + { + if (!jalview.util.Comparison.isGap( (sequence.charAt(j)))) + { + pos++; + } + + j++; + } + + return pos; + } + + /** + * Returns an int array where indices correspond to each residue in the sequence and the element value gives its position in the alignment + * + * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no residues in SequenceI object + */ + public int[] gapMap() + { + String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison. + GapChars, sequence); + int[] map = new int[seq.length()]; + int j = 0; + int p = 0; + + while (j < sequence.length()) + { + if (!jalview.util.Comparison.isGap(sequence.charAt(j))) + { + map[p++] = j; + } + + j++; + } + + return map; + } + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + */ + public void deleteCharAt(int i) + { + if (i >= sequence.length()) + { + return; + } + + sequence = sequence.substring(0, i) + sequence.substring(i + 1); + } + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param j DOCUMENT ME! + */ + public void deleteChars(int i, int j) + { + if (i >= sequence.length()) + { + return; + } + + if (j >= sequence.length()) + { + sequence = sequence.substring(0, i); + } + else + { + sequence = sequence.substring(0, i) + sequence.substring(j); + } + } + + /** + * DOCUMENT ME! + * + * @param i DOCUMENT ME! + * @param c DOCUMENT ME! + * @param chop DOCUMENT ME! + */ + public void insertCharAt(int i, int length, char c) + { + StringBuffer tmp; + + if (i >= sequence.length()) + { + tmp = new StringBuffer(sequence); + } + else + tmp = new StringBuffer(sequence.substring(0, i)); + + while (length > 0) + { + tmp.append(c); + length--; + } + + if (i < sequence.length()) + { + tmp.append(sequence.substring(i)); + } + + sequence = tmp.toString(); + } + + public void insertCharAt(int i, char c) + { + insertCharAt(i, 1, c); + } + + public String getVamsasId() + { + return vamsasId; + } + + public void setVamsasId(String id) + { + vamsasId = id; + } + + public void setDBRef(DBRefEntry[] dbref) + { + dbrefs = dbref; + } + + public DBRefEntry[] getDBRef() + { + return dbrefs; + } + + public void addDBRef(DBRefEntry entry) + { + if (dbrefs == null) + dbrefs = new DBRefEntry[0]; + + DBRefEntry[] temp = new DBRefEntry[dbrefs.length + 1]; + System.arraycopy(dbrefs, 0, temp, 0, dbrefs.length); + + temp[temp.length - 1] = entry; + + dbrefs = temp; + } + + public void setDatasetSequence(SequenceI seq) + { + datasetSequence = seq; + } + + public SequenceI getDatasetSequence() + { + return datasetSequence; + } + + public AlignmentAnnotation[] getAnnotation() + { + if (annotation == null) + return null; + + AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()]; + for (int r = 0; r < ret.length; r++) + ret[r] = (AlignmentAnnotation) annotation.elementAt(r); + + return ret; + } + + public void addAlignmentAnnotation(AlignmentAnnotation annotation) + { + if (this.annotation == null) + this.annotation = new Vector(); + + this.annotation.addElement(annotation); + } + + public SequenceGroup getHiddenSequences() + { + return hiddenSequences; + } + + public void addHiddenSequence(SequenceI seq) + { + if (hiddenSequences == null) + { + hiddenSequences = new SequenceGroup(); + } + hiddenSequences.addSequence(seq, false); + } + + public void showHiddenSequence(SequenceI seq) + { + hiddenSequences.deleteSequence(seq, false); + if (hiddenSequences.getSize(false) < 1) + { + hiddenSequences = null; + } + } +} + +