X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=290cdfc10dfa46ab7ba09734be35bf2e55038b8c;hb=10ddc20a773099eaf0dc4d9d1bbb3b88b4176ed4;hp=34c1cd917f6f0fb252de743de48435710db7bfae;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 34c1cd9..290cdfc 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 +31,28 @@ 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.
@@ -57,12 +64,55 @@ 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 +123,7 @@ public class Sequence implements SequenceI
      */
     public Sequence(String name, String sequence)
     {
-        this(name, sequence, 1, sequence.length());
+        this(name, sequence, 1, -1);
     }
 
     /**
@@ -91,29 +141,68 @@ public class Sequence implements SequenceI
      *
      * @param v DOCUMENT ME!
      */
-    public void setSequenceFeatures(Vector v)
+    public void setSequenceFeatures(SequenceFeature [] features)
+    {
+        sequenceFeatures = features;
+    }
+
+    public void addSequenceFeature(SequenceFeature sf)
     {
-        sequenceFeatures = v;
+      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;
     }
 
+    SequenceFeature [] sfarray;
+
+        public SequenceFeature[] getsfarray()
+        {
+          return sfarray;
+        }
+
+
     /**
      * 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;
     }
 
     /**
@@ -121,9 +210,9 @@ public class Sequence implements SequenceI
      *
      * @return DOCUMENT ME!
      */
-    public String getPDBId()
+    public Vector getPDBId()
     {
-        return pdbId;
+        return pdbIds;
     }
 
     /**
@@ -131,17 +220,15 @@ 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 +238,8 @@ public class Sequence implements SequenceI
      */
     public void setName(String name)
     {
-        this.name = name;
-        setDisplayId();
+      this.name = name;
+      this.parseId();
     }
 
     /**
@@ -162,7 +249,7 @@ public class Sequence implements SequenceI
      */
     public String getName()
     {
-        return this.name;
+       return this.name;
     }
 
     /**
@@ -173,7 +260,6 @@ public class Sequence implements SequenceI
     public void setStart(int start)
     {
         this.start = start;
-        setDisplayId();
     }
 
     /**
@@ -194,7 +280,6 @@ public class Sequence implements SequenceI
     public void setEnd(int end)
     {
         this.end = end;
-        setDisplayId();
     }
 
     /**
@@ -225,6 +310,7 @@ public class Sequence implements SequenceI
     public void setSequence(String seq)
     {
         this.sequence = seq;
+        checkValidRange();
     }
 
     /**
@@ -315,9 +401,7 @@ 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 +434,7 @@ 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++;
             }
@@ -427,16 +509,6 @@ 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!
@@ -445,7 +517,7 @@ 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);
 
@@ -485,4 +557,143 @@ 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();
+    }
+
 }