X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=0e72690aa69e439df38b52b505a04662a500b007;hb=7000ea3223f2f6a390f56341ba26850d2a137ae0;hp=be2e1c063521fe55fd9a6f1a052c1dd17dc7dc3c;hpb=7abeaf76ba3913ccb95139df58b353bdde49429c;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index be2e1c0..0e72690 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -18,26 +18,27 @@
 */
 package jalview.datamodel;
 
-import java.awt.*;
 
 import java.util.*;
 
+import jalview.analysis.*;
 
 /**
- * DOCUMENT ME!
+ * 
+ * Implements the SequenceI interface for a char[] based sequence object.
  *
  * @author $author$
  * @version $Revision$
  */
-public class Sequence implements SequenceI
+public class Sequence
+    implements SequenceI
 {
   SequenceI datasetSequence;
   String name;
-  private String sequence;
+  private char [] sequence;
   String description;
   int start;
   int end;
-  Color color = Color.white;
   Vector pdbIds;
   String vamsasId;
   DBRefEntry[] dbrefs;
@@ -46,31 +47,35 @@ public class Sequence implements SequenceI
    * positions are tied to the residues of this sequence */
   Vector annotation;
 
-  /** DOCUMENT ME!! */
+  /** array of seuqence features - may not be null for a valid sequence object */
   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!
+   * @param name display name string
+   * @param sequence string to form a possibly gapped sequence out of
+   * @param start first position of non-gap residue in the sequence
+   * @param end last position of ungapped residues (nearly always only used for display purposes)
    */
   public Sequence(String name, String sequence, int start, int end)
   {
     this.name = name;
-    this.sequence = sequence;
+    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();
   }
 
@@ -97,11 +102,9 @@ public class Sequence implements SequenceI
     if (end < 1)
     {
       int endRes = 0;
-      char ch;
-      for (int j = 0; j < sequence.length(); j++)
+      for (int j = 0; j < sequence.length; j++)
       {
-        ch = sequence.charAt(j);
-        if (!jalview.util.Comparison.isGap( (ch)))
+        if (!jalview.util.Comparison.isGap( sequence[j] ))
         {
           endRes++;
         }
@@ -128,13 +131,72 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * Creates a new Sequence object.
-   *
+   * Creates a new Sequence object with new features, DBRefEntries, AlignmentAnnotations, and PDBIds
+   * but inherits any existing dataset sequence reference.
    * @param seq DOCUMENT ME!
    */
   public Sequence(SequenceI seq)
   {
-    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    this(seq, seq.getAnnotation());
+  }
+  /**
+   * Create a new sequence object with new features, DBRefEntries, and PDBIds
+   * but inherits any existing dataset sequence reference, and duplicate of
+   * any annotation that is present in the given annotation array.
+   * @param seq the sequence to be copied
+   * @param alAnnotation an array of annotation including some associated with seq 
+   */
+  public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation)
+  {
+    this(seq.getName(),
+            seq.getSequence(),
+            seq.getStart(),
+            seq.getEnd());
+    description = seq.getDescription();
+    if (seq.getSequenceFeatures()!=null) {
+      SequenceFeature[] sf = seq.getSequenceFeatures();
+      for (int i=0; i<sf.length; i++) {
+        addSequenceFeature(new SequenceFeature(sf[i]));
+      }
+    }
+    if (seq.getDBRef()!=null) {
+      DBRefEntry[] dbr = seq.getDBRef();
+      for (int i=0; i<dbr.length; i++) {
+        addDBRef(new DBRefEntry(dbr[i]));
+      }
+    }
+    setDatasetSequence(seq.getDatasetSequence());
+    if (seq.getAnnotation()!=null) {
+      AlignmentAnnotation[] sqann = seq.getAnnotation();
+      for (int i=0;i<sqann.length; i++)
+      {
+        if (sqann[i]==null)
+        {
+          continue;
+        }
+        boolean found = (alAnnotation==null);
+        if (!found)
+        {
+          for (int apos = 0; !found && apos<alAnnotation.length; apos++)
+          {
+            found = (alAnnotation[apos] == sqann[i]);
+          }
+        }
+        if (found)
+        {
+          // only copy the given annotation
+          AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
+          addAlignmentAnnotation(newann);
+        }
+      }
+    }
+    if (seq.getPDBId()!=null) {
+      Vector ids = seq.getPDBId();
+      Enumeration e = ids.elements();
+      while (e.hasMoreElements()) {
+        this.addPDBId(new PDBEntry((PDBEntry) e.nextElement()));
+      }
+    }
   }
 
   /**
@@ -169,6 +231,50 @@ public class Sequence implements SequenceI
     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!
    *
@@ -182,7 +288,9 @@ public class Sequence implements SequenceI
   public void addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
+    {
       pdbIds = new Vector();
+    }
 
     pdbIds.addElement(entry);
   }
@@ -291,7 +399,7 @@ public class Sequence implements SequenceI
    */
   public int getLength()
   {
-    return this.sequence.length();
+    return this.sequence.length;
   }
 
   /**
@@ -301,18 +409,25 @@ public class Sequence implements SequenceI
    */
   public void setSequence(String seq)
   {
-    this.sequence = seq;
+    this.sequence = seq.toCharArray();
     checkValidRange();
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @return DOCUMENT ME!
-   */
-  public String getSequence()
+
+  public String getSequenceAsString()
+  {
+    return new String(sequence);
+  }
+
+  public String getSequenceAsString(int start, int end)
+  {
+    return new String(getSequence(start, end));
+  }
+
+
+  public char [] getSequence()
   {
-    return this.sequence;
+    return sequence;
   }
 
   /**
@@ -323,22 +438,28 @@ public class Sequence implements SequenceI
    *
    * @return DOCUMENT ME!
    */
-  public String getSequence(int start, int end)
+  public char [] getSequence(int start, int end)
   {
+    if (start<0)
+      start=0;
     // JBPNote - left to user to pad the result here (TODO:Decide on this policy)
-    if (start >= sequence.length())
+    if (start >= sequence.length)
     {
-      return "";
+      return new char[0];
     }
 
-    if (end >= sequence.length())
+    if (end >= sequence.length)
     {
-      end = sequence.length();
+      end = sequence.length;
     }
 
-    return this.sequence.substring(start, end);
+    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
@@ -348,15 +469,27 @@ public class Sequence implements SequenceI
   public SequenceI getSubSequence(int start, int end)
   {
     if (start < 0)
+    {
       start = 0;
-    String seq = getSequence(start, end);
-    if (seq == "")
+    }
+    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.setDatasetSequence(getDatasetSequence());
+    nseq.setDescription(description);
+    if (datasetSequence!=null)
+    {
+        nseq.setDatasetSequence(datasetSequence);
+    }
+    else
+    {
+        nseq.setDatasetSequence(this);
+    }
     return nseq;
   }
 
@@ -369,9 +502,9 @@ public class Sequence implements SequenceI
    */
   public char getCharAt(int i)
   {
-    if (i < sequence.length())
+    if (i < sequence.length)
     {
-      return sequence.charAt(i);
+      return sequence[i];
     }
     else
     {
@@ -400,11 +533,11 @@ public class Sequence implements SequenceI
   }
 
   /**
-   * DOCUMENT ME!
+   * Return the alignment position for a sequence position
    *
-   * @param pos DOCUMENT ME!
+   * @param pos lying from start to end
    *
-   * @return DOCUMENT ME!
+   * @return aligned position of residue pos
    */
   public int findIndex(int pos)
   {
@@ -412,9 +545,9 @@ public class Sequence implements SequenceI
     int j = start;
     int i = 0;
 
-    while ( (i < sequence.length()) && (j <= end) && (j <= pos))
+    while ( (i < sequence.length) && (j <= end) && (j <= pos))
     {
-      if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
+      if (!jalview.util.Comparison.isGap(sequence[i]))
       {
         j++;
       }
@@ -443,10 +576,10 @@ public class Sequence implements SequenceI
   {
     int j = 0;
     int pos = start;
-    int seqlen = sequence.length();
+    int seqlen = sequence.length;
     while ( (j < i) && (j < seqlen))
     {
-      if (!jalview.util.Comparison.isGap( (sequence.charAt(j))))
+      if (!jalview.util.Comparison.isGap( sequence[j] ))
       {
         pos++;
       }
@@ -465,14 +598,14 @@ public class Sequence implements SequenceI
   public int[] gapMap()
   {
     String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison.
-        GapChars, sequence);
+        GapChars, new String(sequence));
     int[] map = new int[seq.length()];
     int j = 0;
     int p = 0;
 
-    while (j < sequence.length())
+    while (j < sequence.length)
     {
-      if (!jalview.util.Comparison.isGap(sequence.charAt(j)))
+      if (!jalview.util.Comparison.isGap(sequence[j]))
       {
         map[p++] = j;
       }
@@ -483,44 +616,77 @@ public class Sequence implements SequenceI
     return map;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
    */
-  public void deleteCharAt(int i)
+  public void deleteChars(int i, int j)
   {
-    if (i >= sequence.length())
+    int newstart=start,newend=end;
+    if (i >= sequence.length)
     {
       return;
     }
 
-    sequence = sequence.substring(0, i) + sequence.substring(i + 1);
-  }
+    char [] tmp;
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
-   */
-  public void deleteChars(int i, int j)
-  {
-    if (i >= sequence.length())
+    if (j >= sequence.length)
     {
-      return;
+      tmp = new char[i];
+      System.arraycopy(sequence,0,tmp,0,i);
     }
-
-    if (j >= sequence.length())
+    else
     {
-      sequence = sequence.substring(0, i);
+      tmp = new char[sequence.length-j+i];
+      System.arraycopy(sequence,0,tmp,0,i);
+      System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
-    else
+    boolean createNewDs=false;
+    for (int s = i; s < j; s++)
     {
-      sequence = sequence.substring(0, i) + sequence.substring(j);
+      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+      {
+        if (createNewDs)
+        {
+          newend--;
+        } else {
+          int sindex = findIndex(start)-1;
+          if (sindex==s)
+        {
+          // delete characters including start of sequence
+          newstart = findPosition(j);
+          break; // don't need to search for any more residue characters.
+        } else {
+          // delete characters after start.
+          int eindex = findIndex(end)-1;
+          if (eindex<j)
+          {
+            // delete characters at end of sequence
+            newend = findPosition(i-1);
+            break; // don't need to search for any more residue characters.
+          } else {
+            createNewDs=true;
+            newend--; // decrease end position by one for the deleted residue and search further
+          }
+        }
+        }
+      }
+    }
+    // deletion occured in the middle of the sequence
+    if (createNewDs && this.datasetSequence != null)
+    {
+      // construct a new sequence
+      Sequence ds = new Sequence(datasetSequence);
+      // TODO: remove any non-inheritable properties ?
+      // TODO: create a sequence mapping (since there is a relation here ?)
+      ds.deleteChars(i, j);
+      datasetSequence = ds;
     }
+    start = newstart;
+    end = newend;
+    sequence = tmp;
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -530,28 +696,32 @@ public class Sequence implements SequenceI
    */
   public void insertCharAt(int i, int length, char c)
   {
-    StringBuffer tmp;
+    char [] tmp = new char[sequence.length+length];
 
-    if (i >= sequence.length())
+    if (i >= sequence.length)
     {
-      length = i - sequence.length() + 1;
-      tmp = new StringBuffer(sequence);
+      System.arraycopy(sequence, 0, tmp, 0, sequence.length);
+      i = sequence.length;
     }
     else
-      tmp = new StringBuffer(sequence.substring(0, i));
+   {
+      System.arraycopy(sequence, 0, tmp, 0, i);
+   }
+
 
+    int index = i;
     while (length > 0)
     {
-      tmp.append(c);
+      tmp[ index++ ] = c;
       length--;
     }
 
-    if (i < sequence.length())
+    if (i < sequence.length)
     {
-      tmp.append(sequence.substring(i));
+      System.arraycopy(sequence, i, tmp, index, sequence.length-i );
     }
 
-    sequence = tmp.toString();
+    sequence = tmp;
   }
 
   public void insertCharAt(int i, char c)
@@ -559,26 +729,6 @@ public class Sequence implements SequenceI
     insertCharAt(i, 1, c);
   }
 
-  /**
-   * 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;
@@ -602,11 +752,22 @@ public class Sequence implements SequenceI
   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);
+    int i, iSize = dbrefs.length;
+
+    for(i=0; i<iSize; i++)
+    {
+      if(dbrefs[i].equals(entry))
+      {
+        return;
+      }
+    }
 
+    DBRefEntry[] temp = new DBRefEntry[iSize + 1];
+    System.arraycopy(dbrefs, 0, temp, 0, iSize);
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;
@@ -625,11 +786,15 @@ public class Sequence implements SequenceI
   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;
   }
@@ -637,33 +802,125 @@ public class Sequence implements SequenceI
   public void addAlignmentAnnotation(AlignmentAnnotation annotation)
   {
     if (this.annotation == null)
+    {
       this.annotation = new Vector();
+    }
 
     this.annotation.addElement(annotation);
+    annotation.setSequenceRef(this);
   }
 
-  public SequenceGroup getHiddenSequences()
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
   {
-    return hiddenSequences;
+    if(this.annotation!=null)
+    {
+      this.annotation.removeElement(annotation);
+      if(this.annotation.size()==0)
+        this.annotation = null;
+    }
   }
 
-  public void addHiddenSequence(SequenceI seq)
+
+  /**
+   * test if this is a valid candidate for another
+   * sequence's dataset sequence.
+   *
+   */
+  private boolean isValidDatasetSequence()
   {
-    if (hiddenSequences == null)
+    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(this);
+    if (datasetSequence != null)
+    {
+      // duplicate current sequence with same dataset
+      seq.setDatasetSequence(datasetSequence);
+    }
+    else
     {
-      hiddenSequences = new SequenceGroup();
+      if (isValidDatasetSequence())
+      {
+        // Use this as dataset sequence
+        seq.setDatasetSequence(this);
+      } else {
+        // Create a new, valid dataset sequence
+        SequenceI ds = seq;
+        ds.setSequence(AlignSeq.extractGaps(jalview.util.Comparison.GapChars, new String(sequence)));
+        setDatasetSequence(ds);
+        ds.setSequenceFeatures(getSequenceFeatures());
+        seq = this; // and return this sequence as the derived sequence.
+      }
+    }
+    return seq;
+  }
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] annotations)
+   */
+  public void setAlignmentAnnotation(AlignmentAnnotation[] annotations)
+  {
+    if (annotation!=null) {
+      annotation.removeAllElements();
+    }
+    if (annotations!=null) {
+      for (int i=0; i<annotations.length; i++)
+      {
+        if (annotations[i]!=null)
+          addAlignmentAnnotation(annotations[i]);
+      }
     }
-    hiddenSequences.addSequence(seq, false);
   }
 
-  public void showHiddenSequence(SequenceI seq)
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+   */
+  public AlignmentAnnotation[] getAnnotation(String label)
   {
-    hiddenSequences.deleteSequence(seq, false);
-    if (hiddenSequences.getSize(false) < 1)
+    if (annotation==null || annotation.size()==0)
     {
-      hiddenSequences = null;
+      return null;
+    }
+    
+    Vector subset = new Vector();
+    Enumeration e = annotation.elements();
+    while (e.hasMoreElements())
+    {
+      AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement();
+      if (ann.label!=null && ann.label.equals(label))
+      {
+        subset.addElement(ann);
+      }
     }
+    if (subset.size()==0)
+    {
+      return null;
+    }
+    AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()];
+    int i=0;
+    e = subset.elements();
+    while (e.hasMoreElements())
+    {
+      anns[i++] = (AlignmentAnnotation) e.nextElement();
+    }
+    subset.removeAllElements();
+    return anns;
   }
+
 }