X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d90c231aa9eeedb8c0e3f45c14b0233670a90beb;hb=37382e89e23d86a2e728c61899904dd97dd07298;hp=eceddf11607d4b5a05d8489a0a414313f7f157f5;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index eceddf1..d90c231 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,228 +1,625 @@
+/*
+* 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 jalview.analysis.*;
 import java.awt.*;
+
 import java.util.*;
-import MCview.*;
 
 
+/**
+ * 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;
-  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) {
-    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)
-    {
-      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 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;
-  }
+    SequenceI datasetSequence;
+    String name;
+    String shortName;
+    String sequence;
+    String description;
+    int start;
+    int end;
+    Color color = Color.white;
+    Vector pdbIds;
+    String vamsasId;
+    Vector dbrefs;
+
+
+    /** 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;
+      parseId();
+
+      this.sequence = sequence;
+      this.start = start;
+      this.end = end;
+
+      checkValidRange();
+    }
+
+    void parseId()
+    {
+        // Read in any DB refs first
+         StringTokenizer st = new StringTokenizer(name, "|");
+         if(st.countTokens()<1)
+         {
+           shortName = name;
+           return;
+         }
+
+         while (st.countTokens() > 1)
+         {
+           String a = st.nextToken();
+           String b = st.nextToken();
+           addDBRef(new DBRefEntry(a, "0", b));
+         }
+
+         if (st.hasMoreTokens())
+           shortName = st.nextToken();
+
+         // Remove /start-end from sequence
+         if (shortName.indexOf("/") > 0)
+         {
+           st = new StringTokenizer(shortName, "/");
+           String limits = null;
+           try
+           {
+             if (st.countTokens() == 2)
+             {
+
+               shortName = st.nextToken();
+
+               limits = st.nextToken();
+
+               st = new StringTokenizer(limits, "-");
+
+               if (st.countTokens() == 2)
+               {
+                 setStart(Integer.valueOf(st.nextToken()).intValue());
+                 setEnd(Integer.valueOf(st.nextToken()).intValue());
+               }
+             }
+
+             // If we're still in this loop, parsing of start and end was ok
+             // Therefore remove it from the sequence name
+             name = name.substring(0, name.indexOf("/"));
+           }
+           catch (NumberFormatException ex)
+           {
+             // Problem parsing sequence limits. Just add it back to the
+             // Id so we dont lose this info
+             shortName += "/" + limits;
+           }
+         }
+
+    }
+
+    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(Vector v)
+    {
+        sequenceFeatures = v;
+    }
+
+    public void addSequenceFeature(SequenceFeature sf)
+    {
+      if(sequenceFeatures==null)
+        sequenceFeatures = new Vector();
+
+      sequenceFeatures.addElement(sf);
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @return DOCUMENT ME!
+     */
+    public Vector getSequenceFeatures()
+    {
+        return sequenceFeatures;
+    }
+
+    /**
+     * 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 dbref, boolean jvsuffix)
+    {
+      StringBuffer result = new StringBuffer();
+      if (dbref && dbrefs != null)
+      {
+        for (int i = 0; i < dbrefs.size(); i++)
+        {
+          DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);
+          result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");
+        }
+      }
+
+      result.append(shortName);
+
+      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);
+    }
+
+    /**
+     * 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;
+    }
+
+    public String getVamsasId()
+    {
+      return vamsasId;
+    }
+
+    public void setVamsasId(String id)
+    {
+      vamsasId = id;
+    }
+
+    public void setDBRef(Vector dbref)
+    {
+      dbrefs = dbref;
+    }
+    public Vector getDBRef()
+    {
+      return dbrefs;
+    }
+
+    public void addDBRef(DBRefEntry entry)
+    {
+      if(dbrefs == null)
+        dbrefs = new Vector();
+
+      dbrefs.addElement(entry);
+    }
+
+    public void setDatasetSequence(SequenceI seq)
+    {
+      datasetSequence = seq;
+    }
+
+    public SequenceI getDatasetSequence()
+    {
+      return datasetSequence;
+    }
 
 }