New method for helping to quickly map different aligned versions of a

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 1875557..5db051a 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,17 +1,88 @@
 package jalview.datamodel;\r
 \r
-\r
+import jalview.analysis.*;\r
 import java.awt.*;\r
+import java.util.*;\r
+import MCview.*;\r
+\r
 \r
-public class Sequence implements SequenceI {\r
+public class Sequence implements SequenceI\r
+{\r
   protected String   name;\r
   protected String   sequence;\r
+  protected String description;\r
   protected int      start;\r
   protected int      end;\r
-  protected String   description;\r
-  protected int      charHeight;\r
   protected String   displayId;\r
-  protected Color    color = Color.black;\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
+   {\r
+     sequenceFeatures = v;\r
+   }\r
+\r
+   public Vector getSequenceFeatures()\r
+   {return sequenceFeatures; }\r
+\r
+   public void setPDBId(String id)\r
+   {\r
+     pdbId = id;\r
+   }\r
+   public String getPDBId()\r
+   {\r
+     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
@@ -68,6 +139,8 @@ 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();\r
     return this.sequence.substring(start,end);\r
   }\r
 \r
@@ -92,19 +165,18 @@ public class Sequence implements SequenceI {
 \r
     while (i< sequence.length() && j <= end && j <= pos) {\r
 \r
-      String s = sequence.substring(i,i+1);\r
+      char c = sequence.charAt(i);\r
 \r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         j++;\r
-      }\r
+\r
       i++;\r
     }\r
-    if (j == end && j < pos) {\r
+    if (j == end && j < pos)\r
       return end+1;\r
-    } else {\r
-\r
+    else\r
       return i;\r
-    }\r
+\r
   }\r
 \r
   public int findPosition(int i) {\r
@@ -112,16 +184,32 @@ public class Sequence implements SequenceI {
     int j   = 0;\r
     int pos = start;\r
 \r
-    while (j < i) {\r
-      String s = sequence.substring(j,j+1);\r
-\r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+    while (j < i && j<sequence.length())\r
+    {\r
+      char c = sequence.charAt(j);\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         pos++;\r
-      }\r
+\r
       j++;\r
     }\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
@@ -129,6 +217,13 @@ public class Sequence implements SequenceI {
     sequence = sbuffer.toString();\r
   }\r
 \r
+  public void deleteChars(int i, int j)\r
+  {\r
+    StringBuffer sbuffer = new StringBuffer(sequence);\r
+    sbuffer.delete(i,j);\r
+    sequence = sbuffer.toString();\r
+  }\r
+\r
   public void insertCharAt(int i, char c)\r
   {\r
     insertCharAt(i,c,true);\r