X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=09c9a696a7de8f5c60c8db5513666360bf1bbec0;hb=daa33859b015a7e4b1295addfff2582bf348b8bc;hp=d30003dd45822cf9d25fb79ffe09a4ddcbe272f6;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d30003d..09c9a69 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -31,17 +31,28 @@ 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 SequenceFeature [] sequenceFeatures;
+
+    /** This array holds hidden sequences
+     * of which this sequence is the representitive member of a group
+     */
+    SequenceGroup hiddenSequences;
 
     /**
      * Creates a new Sequence object.
@@ -58,6 +69,30 @@ public class Sequence implements SequenceI
       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;
@@ -78,7 +113,6 @@ public class Sequence implements SequenceI
         this.end = endRes;
       }
 
-        setDisplayId();
     }
 
     /**
@@ -89,7 +123,7 @@ public class Sequence implements SequenceI
      */
     public Sequence(String name, String sequence)
     {
-        this(name, sequence, 1, sequence.length());
+        this(name, sequence, 1, -1);
     }
 
     /**
@@ -107,29 +141,61 @@ public class Sequence implements SequenceI
      *
      * @param v DOCUMENT ME!
      */
-    public void setSequenceFeatures(Vector v)
+    public void setSequenceFeatures(SequenceFeature [] features)
     {
-        sequenceFeatures = v;
+        sequenceFeatures = features;
     }
 
+    public void addSequenceFeature(SequenceFeature sf)
+    {
+      if(sequenceFeatures==null)
+      {
+        sequenceFeatures = new SequenceFeature[0];
+      }
+
+      for(int i=0; i<sequenceFeatures.length; i++)
+      {
+        if(sequenceFeatures[i].equals(sf))
+        {
+          return;
+        }
+      }
+
+      SequenceFeature [] temp = new SequenceFeature[sequenceFeatures.length+1];
+      System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length);
+      temp[sequenceFeatures.length] = sf;
+
+
+      sequenceFeatures = temp;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
      * @return DOCUMENT ME!
      */
-    public Vector getSequenceFeatures()
+    public SequenceFeature [] getSequenceFeatures()
     {
         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;
     }
 
     /**
@@ -137,9 +203,9 @@ public class Sequence implements SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getPDBId()
+    public Vector getPDBId()
     {
-        return pdbId;
+        return pdbIds;
     }
 
     /**
@@ -147,17 +213,15 @@ 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();
     }
 
     /**
@@ -167,8 +231,8 @@ public class Sequence implements SequenceI
      */
     public void setName(String name)
     {
-        this.name = name;
-        setDisplayId();
+      this.name = name;
+      this.parseId();
     }
 
     /**
@@ -178,7 +242,7 @@ public class Sequence implements SequenceI
      */
     public String getName()
     {
-        return this.name;
+       return this.name;
     }
 
     /**
@@ -189,7 +253,6 @@ public class Sequence implements SequenceI
     public void setStart(int start)
     {
         this.start = start;
-        setDisplayId();
     }
 
     /**
@@ -210,7 +273,6 @@ public class Sequence implements SequenceI
     public void setEnd(int end)
     {
         this.end = end;
-        setDisplayId();
     }
 
     /**
@@ -241,6 +303,7 @@ public class Sequence implements SequenceI
     public void setSequence(String seq)
     {
         this.sequence = seq;
+        checkValidRange();
     }
 
     /**
@@ -331,9 +394,7 @@ 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++;
             }
@@ -366,9 +427,7 @@ 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++;
             }
@@ -443,16 +502,6 @@ public class Sequence implements SequenceI
         }
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param i DOCUMENT ME!
-     * @param c DOCUMENT ME!
-     */
-    public void insertCharAt(int i, char c)
-    {
-        insertCharAt(i, c, true);
-    }
 
     /**
      * DOCUMENT ME!
@@ -461,7 +510,7 @@ public class Sequence implements SequenceI
      * @param c DOCUMENT ME!
      * @param chop DOCUMENT ME!
      */
-    public void insertCharAt(int i, char c, boolean chop)
+    public void insertCharAt(int i, char c)
     {
         String tmp = new String(sequence);
 
@@ -501,4 +550,143 @@ 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 );
+    }
+
+    public SequenceGroup getHiddenSequences()
+    {
+      return hiddenSequences;
+    }
+
+    public void addHiddenSequence(SequenceI seq)
+    {
+      if(hiddenSequences==null)
+      {
+        hiddenSequences = new SequenceGroup();
+      }
+      hiddenSequences.addSequence(seq, false);
+    }
+
+    public void showHiddenSequence(SequenceI seq)
+    {
+      hiddenSequences.deleteSequence(seq, false);
+      if (hiddenSequences.getSize() < 1)
+      {
+        hiddenSequences = null;
+      }
+
+    }
+
+    public void changeCase(boolean toUpper, int start, int end)
+    {
+      StringBuffer newSeq = new StringBuffer();
+
+      if(end>sequence.length())
+        end = sequence.length();
+
+      if (start > 0)
+      {
+        newSeq.append(sequence.substring(0, start));
+      }
+
+      if (toUpper)
+        newSeq.append(sequence.substring(start, end).toUpperCase());
+      else
+        newSeq.append(sequence.substring(start, end).toLowerCase());
+
+      if (end < sequence.length())
+        newSeq.append(sequence.substring(end));
+
+      sequence = newSeq.toString();
+    }
+
+    public void toggleCase(int start, int end)
+    {
+      StringBuffer newSeq = new StringBuffer();
+
+     if(end>sequence.length())
+       end = sequence.length();
+
+     if (start > 0)
+     {
+       newSeq.append(sequence.substring(0, start));
+     }
+
+     char nextChar;
+     for(int c=start; c<end; c++)
+     {
+       nextChar = sequence.charAt(c);
+       if(Character.isLetter(nextChar))
+       {
+         if(Character.isUpperCase(nextChar))
+           nextChar = Character.toLowerCase(nextChar);
+         else
+           nextChar = Character.toUpperCase(nextChar);
+       }
+
+
+       newSeq.append(nextChar);
+     }
+
+     if (end < sequence.length())
+       newSeq.append(sequence.substring(end));
+
+     sequence = newSeq.toString();
+    }
+
 }