Sequence is char []

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7df3eaf..4687116 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,7 +18,6 @@
 */
 package jalview.datamodel;
 
-import java.awt.*;
 
 import java.util.*;
 
@@ -33,7 +32,7 @@ public class Sequence implements SequenceI
 {
   SequenceI datasetSequence;
   String name;
-  private String sequence;
+  private char [] sequence;
   String description;
   int start;
   int end;
@@ -64,12 +63,20 @@ 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();
   }
 
@@ -96,11 +103,9 @@ 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++;
         }
@@ -328,7 +333,7 @@ public class Sequence implements SequenceI
    */
   public int getLength()
   {
-    return this.sequence.length();
+    return this.sequence.length;
   }
 
   /**
@@ -338,18 +343,25 @@ 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;
   }
 
   /**
@@ -360,22 +372,26 @@ 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 "";
+      System.out.println("DOES THIS GET CALLED???");
     }
 
-    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
@@ -386,8 +402,8 @@ 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;
@@ -407,9 +423,9 @@ 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
     {
@@ -450,9 +466,9 @@ 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++;
       }
@@ -481,10 +497,10 @@ 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++;
       }
@@ -503,14 +519,14 @@ 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;
       }
@@ -525,38 +541,30 @@ 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);
     }
+
+    sequence = tmp;
   }
 
   /**
@@ -568,27 +576,32 @@ 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)