X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=257f88a3009e541ce8b8489af77c9bf08f88f29f;hb=a96d51f58325f8429c5792ae554243de5628d62a;hp=aaf06f1f9d8ca2f4f018602512721886749b81de;hpb=00ac6f06b80b4a9b2b35490a7cb4033115390227;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index aaf06f1..257f88a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -24,7 +24,8 @@ import java.util.*;
 import jalview.analysis.*;
 
 /**
- * DOCUMENT ME!
+ * 
+ * Implements the SequenceI interface for a char[] based sequence object.
  *
  * @author $author$
  * @version $Revision$
@@ -46,17 +47,17 @@ public class Sequence
    * 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;
 
 
   /**
    * 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)
   {
@@ -85,6 +86,11 @@ public class Sequence
 
   void parseId()
   {
+    if (name==null)
+    {
+      System.err.println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor.");
+      name = "";
+    }
     // Does sequence have the /start-end signiature?
     if (limitrx.search(name))
     {
@@ -136,10 +142,21 @@ public class Sequence
    */
   public Sequence(SequenceI seq)
   {
+    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());
+            seq.getSequence(),
+            seq.getStart(),
+            seq.getEnd());
     description = seq.getDescription();
     if (seq.getSequenceFeatures()!=null) {
       SequenceFeature[] sf = seq.getSequenceFeatures();
@@ -158,8 +175,24 @@ public class Sequence
       AlignmentAnnotation[] sqann = seq.getAnnotation();
       for (int i=0;i<sqann.length; i++)
       {
-        AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]);
-        addAlignmentAnnotation(newann);
+        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) {
@@ -171,7 +204,6 @@ public class Sequence
     }
   }
 
-
   /**
    * DOCUMENT ME!
    *
@@ -413,6 +445,8 @@ public class Sequence
    */
   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)
     {
@@ -587,14 +621,12 @@ public class Sequence
     return map;
   }
 
-  /**
-   * DOCUMENT ME!
-   *
-   * @param i DOCUMENT ME!
-   * @param j DOCUMENT ME!
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#deleteChars(int, int)
    */
   public void deleteChars(int i, int j)
   {
+    int newstart=start,newend=end;
     if (i >= sequence.length)
     {
       return;
@@ -613,29 +645,50 @@ public class Sequence
       System.arraycopy(sequence,0,tmp,0,i);
       System.arraycopy(sequence,j,tmp,i,sequence.length-j);
     }
-
-    if (this.datasetSequence != null)
+    boolean createNewDs=false;
+    for (int s = i; s < j; s++)
     {
-      for (int s = i; s < j; s++)
+      if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
       {
-        if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23)
+        if (createNewDs)
         {
-
-          Sequence ds = new Sequence(name,
-                                     AlignSeq.extractGaps(
-                                         jalview.util.Comparison.GapChars,
-                                         this.getSequenceAsString()
-                                     ),
-                                     start,
-                                     end);
-          ds.setDescription(description);
+          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
+          }
+        }
         }
-        break;
       }
     }
-
+    // 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;
-
   }
 
 
@@ -712,8 +765,16 @@ public class Sequence
 
     for(i=0; i<iSize; i++)
     {
-      if(dbrefs[i].equals(entry))
+      if(dbrefs[i].equalRef(entry))
       {
+        if (entry.getMap()!=null)
+        {
+          if (dbrefs[i].getMap()==null)
+          {
+            // overwrite with 'superior' entry that contains a mapping.
+            dbrefs[i] = entry;
+          }
+        }
         return;
       }
     }
@@ -762,6 +823,16 @@ public class Sequence
     annotation.setSequenceRef(this);
   }
 
+  public void removeAlignmentAnnotation(AlignmentAnnotation annotation)
+  {
+    if(this.annotation!=null)
+    {
+      this.annotation.removeElement(annotation);
+      if(this.annotation.size()==0)
+        this.annotation = null;
+    }
+  }
+
 
   /**
    * test if this is a valid candidate for another
@@ -805,6 +876,7 @@ public class 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.
       }
     }
@@ -827,6 +899,41 @@ public class Sequence
     }
   }
 
+  /* (non-Javadoc)
+   * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String)
+   */
+  public AlignmentAnnotation[] getAnnotation(String label)
+  {
+    if (annotation==null || annotation.size()==0)
+    {
+      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;
+  }
+
 }