X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a0a858a8dd408f7845db84ae69ce183cd50d1b18;hb=51bbc79eee43d019f9fcb14b7aa6e0a0c2c99f76;hp=16cf4b8ecf93b462e19558eae3192e5d292e73e4;hpb=290e789d9c307fec3987c2fc2b470774b58dd874;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 16cf4b8..a0a858a 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,9 +18,9 @@
 */
 package jalview.datamodel;
 
-import java.awt.*;
 
 import java.util.*;
+import jalview.analysis.AlignSeq;
 
 
 /**
@@ -33,11 +33,10 @@ 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;
@@ -49,10 +48,6 @@ public class Sequence implements SequenceI
   /** 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.
@@ -65,12 +60,20 @@ public class Sequence implements SequenceI
   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 +100,9 @@ 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++;
         }
@@ -134,9 +135,14 @@ public class Sequence implements SequenceI
    */
   public Sequence(SequenceI seq)
   {
-    this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd());
+    this(seq.getName(),
+         seq.getSequence(),
+         seq.getStart(),
+         seq.getEnd());
+    description = seq.getDescription();
   }
 
+
   /**
    * DOCUMENT ME!
    *
@@ -169,6 +175,44 @@ 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!
    *
@@ -291,7 +335,7 @@ public class Sequence implements SequenceI
    */
   public int getLength()
   {
-    return this.sequence.length();
+    return this.sequence.length;
   }
 
   /**
@@ -301,18 +345,25 @@ 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 this.sequence;
+    return new String(getSequence(start, end));
+  }
+
+
+  public char [] getSequence()
+  {
+    return sequence;
   }
 
   /**
@@ -323,22 +374,26 @@ public class Sequence implements SequenceI
    *
    * @return DOCUMENT ME!
    */
-  public String getSequence(int start, int end)
+  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())
+    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
@@ -349,14 +404,18 @@ public class Sequence implements SequenceI
   {
     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 +428,9 @@ 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
     {
@@ -412,9 +471,9 @@ 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 +502,10 @@ 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 +524,14 @@ 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;
       }
@@ -487,40 +546,54 @@ public class Sequence implements SequenceI
    * 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())
+    if (i >= sequence.length)
     {
       return;
     }
 
-    if (j >= sequence.length())
+    char [] tmp;
+
+    if (j >= sequence.length)
     {
-      sequence = sequence.substring(0, i);
+      tmp = new char[i];
+      System.arraycopy(sequence,0,tmp,0,i);
     }
     else
     {
-      sequence = sequence.substring(0, i) + sequence.substring(j);
+      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!
    *
@@ -530,27 +603,32 @@ 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)
     {
-      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)
@@ -558,26 +636,6 @@ 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;
@@ -603,9 +661,18 @@ public class Sequence implements SequenceI
     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].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;
@@ -641,28 +708,35 @@ public class Sequence implements SequenceI
     this.annotation.addElement(annotation);
   }
 
-  public SequenceGroup getHiddenSequences()
-  {
-    return hiddenSequences;
-  }
 
-  public void addHiddenSequence(SequenceI seq)
-  {
-    if (hiddenSequences == null)
-    {
-      hiddenSequences = new SequenceGroup();
-    }
-    hiddenSequences.addSequence(seq, false);
+  /**
+   * 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;
   }
 
-  public void showHiddenSequence(SequenceI seq)
-  {
-    hiddenSequences.deleteSequence(seq, false);
-    if (hiddenSequences.getSize(false) < 1)
-    {
-      hiddenSequences = null;
-    }
-  }
 }