-package jalview.datamodel;\r
-\r
-import jalview.analysis.*;\r
-import java.awt.*;\r
-import java.util.StringTokenizer;\r
-import MCview.*;\r
-\r
-\r
-public class Sequence implements SequenceI\r
-{\r
- protected String name;\r
- protected String sequence;\r
- protected int start;\r
- protected int end;\r
- protected String description;\r
- protected int charHeight;\r
- protected String displayId;\r
- protected Color color = Color.white;\r
- PDBfile pdb;\r
- public int maxchain = -1;\r
-\r
- public int pdbstart;\r
- public int pdbend;\r
- public int seqstart;\r
- public int seqend;\r
- public void setPDBfile(PDBfile pdb)\r
- {\r
- this.pdb = pdb;\r
- int max = -10;\r
- maxchain = -1;\r
-\r
- for (int i=0; i < pdb.chains.size(); i++) {\r
-\r
- System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);\r
- // Now lets compare the sequences to get\r
- // the start and end points.\r
-\r
-\r
- StringTokenizer str = new StringTokenizer(sequence, ".");\r
- String newString = "";\r
-\r
- while (str.hasMoreTokens()) {\r
- newString += str.nextToken();\r
- }\r
- // Align the sequence to the pdb\r
- AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");\r
- as.calcScoreMatrix();\r
- as.traceAlignment();\r
- as.printAlignment();\r
-\r
- System.out.println("Score = " + as.maxscore);\r
- if (as.maxscore > max) {\r
- System.out.println("New max score");\r
- max = as.maxscore;\r
- maxchain = i;\r
-\r
- pdbstart = as.seq2start;\r
- pdbend = as.seq2end;\r
- seqstart = as.seq1start - 1 ;\r
- seqend = as.seq1end -1;\r
- }\r
-\r
- System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
- System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
- }\r
- }\r
-\r
- public Sequence(String name, String sequence, int start, int end)\r
- {\r
-\r
- this.name = name;\r
- this.sequence = sequence;\r
- this.start = start;\r
- this.end = end;\r
-\r
- setDisplayId();\r
-\r
- }\r
-\r
- public Sequence(String name,String sequence) {\r
- this(name,sequence,1,sequence.length());\r
- }\r
- public Sequence(SequenceI seq) {\r
- this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());\r
- }\r
- public String getDisplayId() {\r
- return displayId;\r
- }\r
- public void setDisplayId() {\r
- displayId = name + "/" + start + "-" + end;\r
- }\r
- public void setName(String name) {\r
- this.name = name;\r
- setDisplayId();\r
- }\r
- public String getName() {\r
- return this.name;\r
- }\r
- public void setStart(int start) {\r
- this.start = start;\r
- setDisplayId();\r
- }\r
- public int getStart() {\r
- return this.start;\r
- }\r
- public void setEnd(int end) {\r
- this.end = end;\r
- setDisplayId();\r
- }\r
- public int getEnd() {\r
- return this.end;\r
- }\r
- public int getLength() {\r
- return this.sequence.length();\r
- }\r
- public void setSequence(String seq) {\r
- this.sequence = seq;\r
- }\r
- public String getSequence() {\r
- return this.sequence;\r
- }\r
- public String getSequence(int start,int end) {\r
- return this.sequence.substring(start,end);\r
- }\r
-\r
- public char getCharAt(int i) {\r
- if (i < sequence.length()) {\r
- return sequence.charAt(i);\r
- } else {\r
- return ' ';\r
- }\r
- }\r
- public void setDescription(String desc) {\r
- this.description = desc;\r
- }\r
- public String getDescription() {\r
- return this.description;\r
- }\r
-\r
- public int findIndex(int pos) {\r
- // returns the alignment position for a residue\r
- int j = start;\r
- int i = 0;\r
-\r
- while (i< sequence.length() && j <= end && j <= pos) {\r
-\r
- char c = sequence.charAt(i);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
- j++;\r
-\r
- i++;\r
- }\r
- if (j == end && j < pos)\r
- return end+1;\r
- else\r
- return i;\r
-\r
- }\r
-\r
- public int findPosition(int i) {\r
- // Returns the sequence position for an alignment position\r
- int j = 0;\r
- int pos = start;\r
-\r
- while (j < i)\r
- {\r
- char c = sequence.charAt(j);\r
-\r
- if (!jalview.util.Comparison.isGap((c)))\r
- pos++;\r
-\r
- j++;\r
- }\r
- return pos;\r
- }\r
- public void deleteCharAt(int i)\r
- {\r
- StringBuffer sbuffer = new StringBuffer(sequence);\r
- sbuffer.deleteCharAt(i);\r
- sequence = sbuffer.toString();\r
- }\r
-\r
- public void insertCharAt(int i, char c)\r
- {\r
- insertCharAt(i,c,true);\r
- }\r
-\r
- public void insertCharAt(int i,char c,boolean chop) {\r
-\r
- String tmp = new String(sequence);\r
-\r
- if (i < sequence.length()) {\r
- sequence = tmp.substring(0,i) + String.valueOf(c) + tmp.substring(i);\r
- } else {\r
- sequence = tmp + String.valueOf(c);\r
- }\r
-\r
- }\r
-\r
- public void setColor(Color c) {\r
- this.color = c;\r
- }\r
-\r
- public Color getColor() {\r
- return color;\r
- }\r
-\r
-}\r
+/*
+* 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;
+ Color color = Color.white;
+ 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;
+ }
+
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceFeature [] getSequenceFeatures()
+ {
+ return sequenceFeatures;
+ }
+
+ public void addPDBId(PDBEntry entry)
+ {
+ if(pdbIds == null)
+ pdbIds = new Vector();
+
+ pdbIds.addElement(entry);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param id DOCUMENT ME!
+ */
+ public void setPDBId(Vector id)
+ {
+ pdbIds = id;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Vector getPDBId()
+ {
+ return pdbIds;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String getDisplayId(boolean jvsuffix)
+ {
+ StringBuffer result = new StringBuffer(name);
+ if (jvsuffix)
+ {
+ result.append("/" + start + "-" + end);
+ }
+
+ return result.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param name DOCUMENT ME!
+ */
+ public void setName(String name)
+ {
+ this.name = name;
+ this.parseId();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ checkValidRange();
+ }
+
+ /**
+ * 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);
+ }
+ /**
+ * 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.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;
+ }
+
+ /**
+ * 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(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, char c)
+ {
+ 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;
+ }
+
+ 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;
+ }
+ }
+
+ public void changeCase(boolean toUpper, int start, int end)
+ {
+ StringBuffer newSeq = new StringBuffer();
+
+ if(end>sequence.length())
+ end = sequence.length();
+
+ if (start > 0)
+ {
+ newSeq.append(sequence.substring(0, start));
+ }
+
+ if (toUpper)
+ newSeq.append(sequence.substring(start, end).toUpperCase());
+ else
+ newSeq.append(sequence.substring(start, end).toLowerCase());
+
+ if (end < sequence.length())
+ newSeq.append(sequence.substring(end));
+
+ sequence = newSeq.toString();
+ }
+
+ public void toggleCase(int start, int end)
+ {
+ StringBuffer newSeq = new StringBuffer();
+
+ if(end>sequence.length())
+ end = sequence.length();
+
+ if (start > 0)
+ {
+ newSeq.append(sequence.substring(0, start));
+ }
+
+ char nextChar;
+ for(int c=start; c<end; c++)
+ {
+ nextChar = sequence.charAt(c);
+ if(Character.isLetter(nextChar))
+ {
+ if(Character.isUpperCase(nextChar))
+ nextChar = Character.toLowerCase(nextChar);
+ else
+ nextChar = Character.toUpperCase(nextChar);
+ }
+
+
+ newSeq.append(nextChar);
+ }
+
+ if (end < sequence.length())
+ newSeq.append(sequence.substring(end));
+
+ sequence = newSeq.toString();
+ }
+
+ public SequenceI getSubSequence(int start)
+ {
+ int e=getLength();
+ if (start>=e)
+ return null;
+ return getSubSequence(start, getLength());
+ }
+
+ public int removeGaps() {
+ if (sequence!=null)
+ return removeGaps(0, getLength());
+ return 0;
+ }
+
+ public int removeGaps(int start, int end) {
+ int jSize = getLength();
+ int oSize=jSize;
+ if (jSize<=start)
+ return 0;
+ if (end>jSize)
+ end = jSize;
+
+ // Removing a range is much quicker than removing gaps
+ // one by one for long sequences
+ int j = start;
+ int rangeStart=-1, rangeEnd=-1;
+
+ do
+ {
+ if (jalview.util.Comparison.isGap(getCharAt(j)))
+ {
+ if(rangeStart==-1)
+ {
+ rangeStart = j;
+ rangeEnd = j+1;
+ }
+ else
+ {
+ rangeEnd++;
+ }
+ j++;
+ }
+ else
+ {
+ if(rangeStart>-1)
+ {
+ deleteChars(rangeStart, rangeEnd);
+ j-=rangeEnd-rangeStart;
+ jSize-=rangeEnd-rangeStart;
+ rangeStart = -1;
+ rangeEnd = -1;
+ }
+ else
+ j++;
+ }
+ }
+ while (j < end && j < jSize);
+ if(rangeStart>-1)
+ {
+ deleteChars(rangeStart, rangeEnd);
+ jSize-=rangeEnd-rangeStart;
+ }
+ return oSize-jSize; // number of deleted characters.
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff