X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=80dfda54c35e56f521e290d007226b9b0d011e0a;hb=fbd79f8f62abc6337af57ab87ff07311eff1c74e;hp=d90c231aa9eeedb8c0e3f45c14b0233670a90beb;hpb=37382e89e23d86a2e728c61899904dd97dd07298;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d90c231..80dfda5 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -33,7 +33,6 @@ public class Sequence implements SequenceI
 {
     SequenceI datasetSequence;
     String name;
-    String shortName;
     String sequence;
     String description;
     int start;
@@ -45,7 +44,7 @@ public class Sequence implements SequenceI
 
 
     /** DOCUMENT ME!! */
-    public Vector sequenceFeatures = new Vector();
+    public Vector sequenceFeatures;
 
     /**
      * Creates a new Sequence object.
@@ -58,70 +57,30 @@ public class Sequence implements SequenceI
     public Sequence(String name, String sequence, int start, int end)
     {
       this.name = name;
-      parseId();
-
       this.sequence = sequence;
       this.start = start;
       this.end = end;
 
+      parseId();
+
       checkValidRange();
     }
 
+    static com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+                        "[/][0-9]{1,}[-][0-9]{1,}$");
+    static com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+                        "[0-9]{1,}$");
+
     void parseId()
     {
-        // Read in any DB refs first
-         StringTokenizer st = new StringTokenizer(name, "|");
-         if(st.countTokens()<1)
+        // Does sequence have the /start-end signiature?
+         if(limitrx.search(name))
          {
-           shortName = name;
-           return;
+            name = limitrx.left();
+            endrx.search(limitrx.stringMatched());
+            setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));
+            setEnd(   Integer.parseInt( endrx.stringMatched() ));
          }
-
-         while (st.countTokens() > 1)
-         {
-           String a = st.nextToken();
-           String b = st.nextToken();
-           addDBRef(new DBRefEntry(a, "0", b));
-         }
-
-         if (st.hasMoreTokens())
-           shortName = st.nextToken();
-
-         // Remove /start-end from sequence
-         if (shortName.indexOf("/") > 0)
-         {
-           st = new StringTokenizer(shortName, "/");
-           String limits = null;
-           try
-           {
-             if (st.countTokens() == 2)
-             {
-
-               shortName = st.nextToken();
-
-               limits = st.nextToken();
-
-               st = new StringTokenizer(limits, "-");
-
-               if (st.countTokens() == 2)
-               {
-                 setStart(Integer.valueOf(st.nextToken()).intValue());
-                 setEnd(Integer.valueOf(st.nextToken()).intValue());
-               }
-             }
-
-             // If we're still in this loop, parsing of start and end was ok
-             // Therefore remove it from the sequence name
-             name = name.substring(0, name.indexOf("/"));
-           }
-           catch (NumberFormatException ex)
-           {
-             // Problem parsing sequence limits. Just add it back to the
-             // Id so we dont lose this info
-             shortName += "/" + limits;
-           }
-         }
-
     }
 
     void checkValidRange()
@@ -197,6 +156,14 @@ public class Sequence implements SequenceI
         return sequenceFeatures;
     }
 
+    public void addPDBId(PDBEntry entry)
+    {
+      if(pdbIds == null)
+        pdbIds = new Vector();
+
+      pdbIds.addElement(entry);
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -222,20 +189,9 @@ public class Sequence implements SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getDisplayId(boolean dbref, boolean jvsuffix)
+    public String getDisplayId(boolean jvsuffix)
     {
-      StringBuffer result = new StringBuffer();
-      if (dbref && dbrefs != null)
-      {
-        for (int i = 0; i < dbrefs.size(); i++)
-        {
-          DBRefEntry entry = (DBRefEntry) dbrefs.elementAt(i);
-          result.append(entry.getSource() + "|" + entry.getAccessionId() + "|");
-        }
-      }
-
-      result.append(shortName);
-
+      StringBuffer result = new StringBuffer(name);
       if (jvsuffix)
       {
         result.append("/" + start + "-" + end);
@@ -414,9 +370,7 @@ public class Sequence implements SequenceI
 
         while ((i < sequence.length()) && (j <= end) && (j <= pos))
         {
-            char c = sequence.charAt(i);
-
-            if (!jalview.util.Comparison.isGap((c)))
+            if (!jalview.util.Comparison.isGap(sequence.charAt(i)))
             {
                 j++;
             }
@@ -449,9 +403,7 @@ public class Sequence implements SequenceI
 
         while ((j < i) && (j < sequence.length()))
         {
-            char c = sequence.charAt(j);
-
-            if (!jalview.util.Comparison.isGap((c)))
+            if (!jalview.util.Comparison.isGap((sequence.charAt(j))))
             {
                 pos++;
             }