conservation removed

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index cf578c0..8928425 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -8,21 +8,14 @@ import MCview.*;
 \r
 public class Sequence implements SequenceI\r
 {\r
-  protected String   name;\r
-  protected String   sequence;\r
+  protected String name;\r
+  protected String sequence;\r
   protected String description;\r
-  protected int      start;\r
-  protected int      end;\r
-  protected String   displayId;\r
-  protected Color    color = Color.white;\r
+  protected int start;\r
+  protected int end;\r
+  protected String displayId;\r
+  protected Color color = Color.white;\r
   String pdbId;\r
-  PDBfile pdb;\r
-\r
-   public int maxchain = -1;\r
-   public int pdbstart;\r
-   public int pdbend;\r
-   public int seqstart;\r
-   public int seqend;\r
 \r
    public Vector sequenceFeatures = new Vector();\r
    public void setSequenceFeatures(Vector v)\r
@@ -42,47 +35,6 @@ public class Sequence implements SequenceI
      return pdbId;\r
    }\r
 \r
-   public void setPDBfile(PDBfile pdb)\r
-   {\r
-     this.pdb = pdb;\r
-     int max = -10;\r
-     maxchain = -1;\r
-\r
-     for (int i=0; i < pdb.chains.size(); i++) {\r
-\r
-       System.out.println("PDB sequence = " + ((PDBChain)pdb.chains.elementAt(i)).sequence);\r
-       // Now lets compare the sequences to get\r
-       // the start and end points.\r
-\r
-\r
-     StringTokenizer str = new StringTokenizer(sequence, ".");\r
-     String newString = "";\r
-\r
-     while (str.hasMoreTokens()) {\r
-         newString += str.nextToken();\r
-     }\r
-       // Align the sequence to the pdb\r
-       AlignSeq as = new AlignSeq(this,((PDBChain)pdb.chains.elementAt(i)).sequence,"pep");\r
-       as.calcScoreMatrix();\r
-       as.traceAlignment();\r
-       as.printAlignment();\r
-\r
-       System.out.println("Score = " + as.maxscore);\r
-       if (as.maxscore > max) {\r
-         System.out.println("New max score");\r
-         max = as.maxscore;\r
-         maxchain = i;\r
-\r
-         pdbstart = as.seq2start;\r
-         pdbend = as.seq2end;\r
-         seqstart = as.seq1start  - 1 ;\r
-         seqend = as.seq1end  -1;\r
-       }\r
-\r
-       System.out.println("PDB start/end " + pdbstart + " " + pdbend);\r
-       System.out.println("SEQ start/end " + seqstart + " " + seqend);\r
-     }\r
-   }\r
 \r
   public Sequence(String name, String sequence, int start, int end)\r
   {\r
@@ -139,8 +91,8 @@ public class Sequence implements SequenceI
     return this.sequence;\r
   }\r
   public String getSequence(int start,int end) {\r
-    if(end>=sequence.length())\r
-      end = sequence.length()-1;\r
+    if(end>sequence.length())\r
+      end = sequence.length();\r
     return this.sequence.substring(start,end);\r
   }\r
 \r
@@ -184,10 +136,9 @@ public class Sequence implements SequenceI
     int j   = 0;\r
     int pos = start;\r
 \r
-    while (j < i)\r
+    while (j < i && j<sequence.length())\r
     {\r
       char c = sequence.charAt(j);\r
-\r
       if (!jalview.util.Comparison.isGap((c)))\r
         pos++;\r
 \r
@@ -195,11 +146,30 @@ public class Sequence implements SequenceI
     }\r
     return pos;\r
   }\r
+\r
+  public int[] gapMap() {\r
+    // Returns an int array giving the position of each residue in the sequence in the alignment\r
+    String seq = jalview.analysis.AlignSeq.extractGaps("-. ",sequence);\r
+    int[] map = new int[seq.length()];\r
+    int j=0;\r
+    int p=0;\r
+    while (j<sequence.length()) {\r
+      if (!jalview.util.Comparison.isGap(sequence.charAt(j))) {\r
+        map[p++]=j;\r
+      }\r
+      j++;\r
+    }\r
+    return map;\r
+  }\r
+\r
   public void deleteCharAt(int i)\r
   {\r
-    StringBuffer sbuffer = new StringBuffer(sequence);\r
-    sbuffer.deleteCharAt(i);\r
-    sequence = sbuffer.toString();\r
+    sequence = sequence.substring(0,i) + sequence.substring(i+1);\r
+  }\r
+\r
+  public void deleteChars(int i, int j)\r
+  {\r
+    sequence = sequence.substring(0,i) + sequence.substring(j);\r
   }\r
 \r
   public void insertCharAt(int i, char c)\r