X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a0a858a8dd408f7845db84ae69ce183cd50d1b18;hb=bad9b1c3e957e44c2fa5ad3a0717ea2a40c1bc12;hp=99f2de2dc286be0f702046b0e0a972be60127b0d;hpb=1fea111206bcb8b84284805a3b6e233d5879084c;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 99f2de2..a0a858a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,236 +1,742 @@
-package jalview.datamodel;
-
-import jalview.analysis.*;
-import java.awt.*;
-import java.util.*;
-import MCview.*;
-
-
-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;
-  PDBfile pdb;
-
-   public int maxchain = -1;
-   public int pdbstart;
-   public int pdbend;
-   public int seqstart;
-   public int seqend;
-
-   public Vector sequenceFeatures = new Vector();
-   public void setSequenceFeatures(Vector v)
-   {
-     sequenceFeatures = v;
-   }
-
-   public Vector getSequenceFeatures()
-   {return sequenceFeatures; }
-
-   public void setPDBId(String id)
-   {
-     pdbId = id;
-   }
-   public String getPDBId()
-   {
-     return pdbId;
-   }
-
-   public void setPDBfile(PDBfile pdb)
-   {
-     this.pdb = pdb;
-     int max = -10;
-     maxchain = -1;
-
-     for (int i=0; i < pdb.chains.size(); i++) {
-
-       System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);
-       // Now lets compare the sequences to get
-       // the start and end points.
-
-
-     StringTokenizer str = new StringTokenizer(sequence, ".");
-     String newString = "";
-
-     while (str.hasMoreTokens()) {
-         newString += str.nextToken();
-     }
-       // Align the sequence to the pdb
-       AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");
-       as.calcScoreMatrix();
-       as.traceAlignment();
-       as.printAlignment();
-
-       System.out.println("Score = " + as.maxscore);
-       if (as.maxscore > max) {
-         System.out.println("New max score");
-         max = as.maxscore;
-         maxchain = i;
-
-         pdbstart = as.seq2start;
-         pdbend = as.seq2end;
-         seqstart = as.seq1start  - 1 ;
-         seqend = as.seq1end  -1;
-       }
-
-       System.out.println("PDB start/end " + pdbstart + " " + pdbend);
-       System.out.println("SEQ start/end " + seqstart + " " + seqend);
-     }
-   }
-
-  public Sequence(String name, String sequence, int start, int end)
-  {
-
-    this.name     = name;
-    this.sequence = sequence;
-    this.start    = start;
-    this.end      = end;
-
-    setDisplayId();
-
-  }
-
-  public Sequence(String name,String sequence) {
-    this(name,sequence,1,sequence.length());
-  }
-  public Sequence(SequenceI seq) {
-    this(seq.getName(),seq.getSequence(),seq.getStart(),seq.getEnd());
-  }
-  public String getDisplayId() {
-    return displayId;
-  }
-  public void setDisplayId() {
-    displayId = name + "/" + start + "-" + end;
-  }
-  public void setName(String name) {
-    this.name = name;
-    setDisplayId();
-  }
-  public String getName() {
-    return this.name;
-  }
-  public void setStart(int start) {
-    this.start = start;
-    setDisplayId();
-  }
-  public int getStart() {
-    return this.start;
-  }
-  public void setEnd(int end) {
-    this.end = end;
-    setDisplayId();
-  }
-  public int getEnd() {
-    return this.end;
-  }
-  public int getLength() {
-    return this.sequence.length();
-  }
-  public void setSequence(String seq) {
-    this.sequence = seq;
-  }
-  public String getSequence() {
-    return this.sequence;
-  }
-  public String getSequence(int start,int end) {
-    if(end>sequence.length())
-      end = sequence.length();
-    return this.sequence.substring(start,end);
-  }
-
-  public char getCharAt(int i) {
-    if (i < sequence.length()) {
-      return sequence.charAt(i);
-    } else {
-      return ' ';
-    }
-  }
-  public void setDescription(String desc) {
-    this.description = desc;
-  }
-  public String getDescription() {
-    return this.description;
-  }
-
-  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;
-
-  }
-
-  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;
-  }
-  public void deleteCharAt(int i)
-  {
-    StringBuffer sbuffer = new StringBuffer(sequence);
-    sbuffer.deleteCharAt(i);
-    sequence = sbuffer.toString();
-  }
-
-  public void deleteChars(int i, int j)
-  {
-    StringBuffer sbuffer = new StringBuffer(sequence);
-    sbuffer.delete(i,j);
-    sequence = sbuffer.toString();
-  }
-
-  public void insertCharAt(int i, char c)
-  {
-    insertCharAt(i,c,true);
-  }
-
-  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 {
-      sequence = tmp + String.valueOf(c);
-    }
-
-  }
-
-  public void        setColor(Color c) {
-    this.color = c;
-  }
-
-  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.util.*;
+import jalview.analysis.AlignSeq;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Sequence implements SequenceI
+{
+  SequenceI datasetSequence;
+  String name;
+  private char [] 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;
+
+
+  /**
+   * 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.toCharArray();
+    this.start = start;
+    this.end = end;
+    parseId();
+    checkValidRange();
+  }
+
+  public Sequence(String name, char [] 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;
+      for (int j = 0; j < sequence.length; j++)
+      {
+        if (!jalview.util.Comparison.isGap( sequence[j] ))
+        {
+          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());
+    description = seq.getDescription();
+  }
+
+
+  /**
+   * 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<sfLength)
+        System.arraycopy(sequenceFeatures,
+                         index + 1,
+                         temp,
+                         index, sequenceFeatures.length - index -1);
+
+      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.toCharArray();
+    checkValidRange();
+  }
+
+
+  public String getSequenceAsString()
+  {
+    return new String(sequence);
+  }
+
+  public String getSequenceAsString(int start, int end)
+  {
+    return new String(getSequence(start, end));
+  }
+
+
+  public char [] getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param start DOCUMENT ME!
+   * @param end DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char [] getSequence(int start, int end)
+  {
+    // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
+    if (start >= sequence.length)
+    {
+      return new char[0];
+    }
+
+    if (end >= sequence.length)
+    {
+      end = sequence.length;
+    }
+
+    char [] reply = new char[end-start];
+    System.arraycopy(sequence, start, reply, 0, end-start);
+
+    return reply;
+  }
+
+
+  /**
+   * 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;
+    char [] seq = getSequence(start, end);
+    if (seq.length == 0)
+      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);
+    if (datasetSequence!=null)
+        nseq.setDatasetSequence(datasetSequence);
+    else
+        nseq.setDatasetSequence(this);
+    return nseq;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   *
+   * @return DOCUMENT ME!
+   */
+  public char getCharAt(int i)
+  {
+    if (i < sequence.length)
+    {
+      return sequence[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[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[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, new String(sequence));
+    int[] map = new int[seq.length()];
+    int j = 0;
+    int p = 0;
+
+    while (j < sequence.length)
+    {
+      if (!jalview.util.Comparison.isGap(sequence[j]))
+      {
+        map[p++] = j;
+      }
+
+      j++;
+    }
+
+    return map;
+  }
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param j DOCUMENT ME!
+   */
+  public void deleteChars(int i, int j)
+  {
+    if (i >= sequence.length)
+    {
+      return;
+    }
+
+    char [] tmp;
+
+    if (j >= sequence.length)
+    {
+      tmp = new char[i];
+      System.arraycopy(sequence,0,tmp,0,i);
+    }
+    else
+    {
+      tmp = new char[sequence.length-j+i];
+      System.arraycopy(sequence,0,tmp,0,i);
+      System.arraycopy(sequence,j,tmp,i,sequence.length-j);
+    }
+
+    if (this.datasetSequence != null)
+    {
+      for (int s = i; s < j; s++)
+      {
+        if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+        {
+
+          Sequence ds = new Sequence(name,
+                                     AlignSeq.extractGaps(
+                                         jalview.util.Comparison.GapChars,
+                                         this.getSequenceAsString()
+                                     ),
+                                     start,
+                                     end);
+          ds.setDescription(description);
+        }
+        break;
+      }
+    }
+
+    sequence = tmp;
+
+  }
+
+
+  /**
+   * DOCUMENT ME!
+   *
+   * @param i DOCUMENT ME!
+   * @param c DOCUMENT ME!
+   * @param chop DOCUMENT ME!
+   */
+  public void insertCharAt(int i, int length, char c)
+  {
+    char [] tmp = new char[sequence.length+length];
+
+    if (i >= sequence.length)
+    {
+      System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+      i = sequence.length;
+    }
+    else
+   {
+      System.arraycopy(sequence, 0, tmp, 0, i);
+   }
+
+
+    int index = i;
+    while (length > 0)
+    {
+      tmp[ index++ ] = c;
+      length--;
+    }
+
+    if (i < sequence.length)
+    {
+      System.arraycopy(sequence, i, tmp, index, sequence.length-i );
+    }
+
+    sequence = tmp;
+  }
+
+  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];
+
+    int i, iSize = dbrefs.length;
+
+    for(i=0; i<iSize; i++)
+      if(dbrefs[i].getAccessionId().equals(entry.getAccessionId())
+      && dbrefs[i].getSource().equals(entry.getSource())
+      && dbrefs[i].getVersion().equals(entry.getVersion()))
+      {
+        return;
+      }
+
+    DBRefEntry[] temp = new DBRefEntry[iSize + 1];
+    System.arraycopy(dbrefs, 0, temp, 0, iSize);
+    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);
+  }
+
+
+  /**
+   * test if this is a valid candidate for another
+   * sequence's dataset sequence.
+   *
+   */
+  private boolean isValidDatasetSequence() {
+      if (datasetSequence!=null)
+          return false;
+      for (int i=0;i<sequence.length; i++)
+          if (jalview.util.Comparison.isGap(sequence[i]))
+              return false;
+      return true;
+  }
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#deriveSequence()
+   */
+  public SequenceI deriveSequence() {
+      SequenceI seq = new Sequence(name, sequence, start, end);
+      seq.setDescription(description);
+      if (datasetSequence!=null) {
+          seq.setDatasetSequence(datasetSequence);
+      } else {
+          if (isValidDatasetSequence())
+              seq.setDatasetSequence(this);
+      }
+      return seq;
+  }
+
+}
+
+