returns color.white if the underlying colourscheme is null

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 1875557..d35cbe8 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1,9 +1,13 @@
 package jalview.datamodel;\r
 \r
-\r
+import jalview.analysis.*;\r
 import java.awt.*;\r
+import java.util.StringTokenizer;\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 int      start;\r
@@ -11,7 +15,55 @@ public class Sequence implements SequenceI {
   protected String   description;\r
   protected int      charHeight;\r
   protected String   displayId;\r
-  protected Color    color = Color.black;\r
+  protected Color    color = Color.white;\r
+  PDBfile pdb;\r
+   public int maxchain = -1;\r
+\r
+   public int pdbstart;\r
+   public int pdbend;\r
+   public int seqstart;\r
+   public int seqend;\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
@@ -92,19 +144,18 @@ 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
@@ -112,12 +163,13 @@ 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
+    while (j < i)\r
+    {\r
+      char c = sequence.charAt(j);\r
 \r
-      if (!(s.equals(".") || s.equals("-") || s.equals(" "))) {\r
+      if (!jalview.util.Comparison.isGap((c)))\r
         pos++;\r
-      }\r
+\r
       j++;\r
     }\r
     return pos;\r