X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d35a05bb7cc6df87e94c5f7e949e11c7e6e71357;hb=9480f18113c0d16dfb157eb3fff60a1e29c33d39;hp=34c1cd917f6f0fb252de743de48435710db7bfae;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 34c1cd9..d35a05b 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -18,10 +18,6 @@
 */
 package jalview.datamodel;
 
-import MCview.*;
-
-import jalview.analysis.*;
-
 import java.awt.*;
 
 import java.util.*;
@@ -35,17 +31,23 @@ import java.util.*;
  */
 public class Sequence implements SequenceI
 {
-    protected String name;
-    protected String sequence;
-    protected String description;
-    protected int start;
-    protected int end;
-    protected String displayId;
-    protected Color color = Color.white;
-    String pdbId;
+    SequenceI datasetSequence;
+    String name;
+    String sequence;
+    String description;
+    int start;
+    int end;
+    Color color = Color.white;
+    Vector pdbIds;
+    String vamsasId;
+    Vector dbrefs;
+
+    /** This annotation is displayed below the alignment but the
+     * positions are tied to the residues of this sequence */
+    Vector annotation;
 
     /** DOCUMENT ME!! */
-    public Vector sequenceFeatures = new Vector();
+    public Vector sequenceFeatures;
 
     /**
      * Creates a new Sequence object.
@@ -57,12 +59,55 @@ public class Sequence implements SequenceI
      */
     public Sequence(String name, String sequence, int start, int end)
     {
-        this.name = name;
-        this.sequence = sequence;
-        this.start = start;
-        this.end = end;
+      this.name = name;
+      this.sequence = sequence;
+      this.start = start;
+      this.end = end;
+
+      parseId();
+
+      checkValidRange();
+    }
+
+    com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex(
+                        "[/][0-9]{1,}[-][0-9]{1,}$");
+    com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex(
+                        "[0-9]{1,}$");
+
+    void parseId()
+    {
+        // Does sequence have the /start-end signiature?
+         if(limitrx.search(name))
+         {
+            name = limitrx.left();
+            endrx.search(limitrx.stringMatched());
+            setStart( Integer.parseInt( limitrx.stringMatched().substring(1,endrx.matchedFrom()-1 )));
+            setEnd(   Integer.parseInt( endrx.stringMatched() ));
+         }
+    }
+
+    void checkValidRange()
+    {
+      if (end < 1)
+      {
+        int endRes = 0;
+        char ch;
+        for (int j = 0; j < sequence.length(); j++)
+        {
+          ch = sequence.charAt(j);
+          if (!jalview.util.Comparison.isGap( (ch)))
+          {
+            endRes++;
+          }
+        }
+        if (endRes > 0)
+        {
+          endRes += start - 1;
+        }
+
+        this.end = endRes;
+      }
 
-        setDisplayId();
     }
 
     /**
@@ -73,7 +118,7 @@ public class Sequence implements SequenceI
      */
     public Sequence(String name, String sequence)
     {
-        this(name, sequence, 1, sequence.length());
+        this(name, sequence, 1, -1);
     }
 
     /**
@@ -96,6 +141,14 @@ public class Sequence implements SequenceI
         sequenceFeatures = v;
     }
 
+    public void addSequenceFeature(SequenceFeature sf)
+    {
+      if(sequenceFeatures==null)
+        sequenceFeatures = new Vector();
+
+      sequenceFeatures.addElement(sf);
+    }
+
     /**
      * DOCUMENT ME!
      *
@@ -106,14 +159,22 @@ public class Sequence implements SequenceI
         return sequenceFeatures;
     }
 
+    public void addPDBId(PDBEntry entry)
+    {
+      if(pdbIds == null)
+        pdbIds = new Vector();
+
+      pdbIds.addElement(entry);
+    }
+
     /**
      * DOCUMENT ME!
      *
      * @param id DOCUMENT ME!
      */
-    public void setPDBId(String id)
+    public void setPDBId(Vector id)
     {
-        pdbId = id;
+        pdbIds = id;
     }
 
     /**
@@ -121,9 +182,9 @@ public class Sequence implements SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getPDBId()
+    public Vector getPDBId()
     {
-        return pdbId;
+        return pdbIds;
     }
 
     /**
@@ -131,17 +192,15 @@ public class Sequence implements SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getDisplayId()
+    public String getDisplayId(boolean jvsuffix)
     {
-        return displayId;
-    }
+      StringBuffer result = new StringBuffer(name);
+      if (jvsuffix)
+      {
+        result.append("/" + start + "-" + end);
+      }
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void setDisplayId()
-    {
-        displayId = name + "/" + start + "-" + end;
+      return result.toString();
     }
 
     /**
@@ -151,8 +210,8 @@ public class Sequence implements SequenceI
      */
     public void setName(String name)
     {
-        this.name = name;
-        setDisplayId();
+      this.name = name;
+      this.parseId();
     }
 
     /**
@@ -162,7 +221,7 @@ public class Sequence implements SequenceI
      */
     public String getName()
     {
-        return this.name;
+       return this.name;
     }
 
     /**
@@ -173,7 +232,6 @@ public class Sequence implements SequenceI
     public void setStart(int start)
     {
         this.start = start;
-        setDisplayId();
     }
 
     /**
@@ -194,7 +252,6 @@ public class Sequence implements SequenceI
     public void setEnd(int end)
     {
         this.end = end;
-        setDisplayId();
     }
 
     /**
@@ -225,6 +282,7 @@ public class Sequence implements SequenceI
     public void setSequence(String seq)
     {
         this.sequence = seq;
+        checkValidRange();
     }
 
     /**
@@ -315,9 +373,7 @@ 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++;
             }
@@ -350,9 +406,7 @@ 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++;
             }
@@ -485,4 +539,62 @@ public class Sequence implements SequenceI
     {
         return color;
     }
+
+    public String getVamsasId()
+    {
+      return vamsasId;
+    }
+
+    public void setVamsasId(String id)
+    {
+      vamsasId = id;
+    }
+
+    public void setDBRef(Vector dbref)
+    {
+      dbrefs = dbref;
+    }
+    public Vector getDBRef()
+    {
+      return dbrefs;
+    }
+
+    public void addDBRef(DBRefEntry entry)
+    {
+      if(dbrefs == null)
+        dbrefs = new Vector();
+
+      dbrefs.addElement(entry);
+    }
+
+    public void setDatasetSequence(SequenceI seq)
+    {
+      datasetSequence = seq;
+    }
+
+    public SequenceI getDatasetSequence()
+    {
+      return datasetSequence;
+    }
+
+    public AlignmentAnnotation [] getAnnotation()
+    {
+      if(annotation==null)
+        return null;
+
+      AlignmentAnnotation [] ret = new AlignmentAnnotation[annotation.size()];
+      for(int r = 0; r<ret.length; r++)
+        ret[r] = (AlignmentAnnotation)annotation.elementAt(r);
+
+      return ret;
+    }
+
+    public void addAlignmentAnnotation(AlignmentAnnotation annotation)
+    {
+      if(this.annotation==null)
+        this.annotation = new Vector();
+
+      this.annotation.addElement( annotation );
+    }
+
 }