From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 4 Feb 2005 18:29:43 +0000 (+0000)
Subject: SequenceFeature display added
X-Git-Tag: Release_2_0~701
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git

SequenceFeature display added
---

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index ce98a06..7e46b2e 100755
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -12,6 +12,15 @@ public class PDBfile extends jalview.io.FileParse {
 
   Vector lineArray = new Vector();
 
+  public PDBfile(String [] lines)
+  {
+    for(int i=0; i<lines.length; i++)
+      lineArray.add(lines[i]);
+
+    noLines = lineArray.size();
+    parse();
+  }
+
   public PDBfile(String inFile, String inType) throws IOException {
 
     super(inFile,inType);
@@ -42,8 +51,6 @@ public class PDBfile extends jalview.io.FileParse {
 
   public void parse() {
 
-    System.out.println("Parsing");
-
     for (int i = 0; i < lineArray.size(); i++) {
       StringTokenizer str = new StringTokenizer(lineArray.elementAt(i).toString());
       if (str.hasMoreTokens()) {
@@ -53,10 +60,10 @@ public class PDBfile extends jalview.io.FileParse {
           try {
             myAtom tmpatom = new myAtom(str);
             if (findChain(tmpatom.chain) != null) {
-              System.out.println("Adding to chain " + tmpatom.chain);
+           //   System.out.println("Adding to chain " + tmpatom.chain);
               findChain(tmpatom.chain).atoms.addElement(tmpatom);
             } else {
-              System.out.println("Making chain " + tmpatom.chain);
+            //  System.out.println("Making chain " + tmpatom.chain);
               PDBChain tmpchain = new PDBChain(tmpatom.chain);
               chains.addElement(tmpchain);
               tmpchain.atoms.addElement(tmpatom);
diff --git a/src/MCview/rotCanvas.java b/src/MCview/rotCanvas.java
index 4690a15..5df8d9f 100755
--- a/src/MCview/rotCanvas.java
+++ b/src/MCview/rotCanvas.java
@@ -471,7 +471,10 @@ public class rotCanvas extends JPanel implements KeyListener,
       }
     }
     if(fatom!=null)
+     {
        this.setToolTipText(fatom.resName);
+       System.out.println(fatom.resName);
+     }
      else
         this.setToolTipText(null);
   }
diff --git a/src/jalview/analysis/AlignmentUtil.java b/src/jalview/analysis/AlignmentUtil.java
index 5a773a0..1e0011a 100755
--- a/src/jalview/analysis/AlignmentUtil.java
+++ b/src/jalview/analysis/AlignmentUtil.java
@@ -226,4 +226,114 @@ public class AlignmentUtil {
          return pos;
     }
 
+    class FeatureThread extends Thread
+    {
+
+    }
+
+    public static void addUniprotFeatures(AlignmentI align)
+    {
+      EBIFetchClient ebi = new EBIFetchClient();
+      int seqIndex = 0;
+      Vector sequences = align.getSequences();
+      SequenceI sequence;
+
+      while (seqIndex < sequences.size())
+      {
+        StringBuffer ids = new StringBuffer("uniprot:");
+        for (int i=0; seqIndex<sequences.size() && i<50; seqIndex++, i++)
+        {
+          sequence = (SequenceI) sequences.get(seqIndex);
+          ids.append(sequence.getName() + ";");
+        }
+
+        String[] result = ebi.fetchData(ids.toString(), "xml", null);
+        sequence = null;
+        Vector features = null;
+        String type, description, status, start, end, pdb = null;
+
+        for (int r = 0; r < result.length; r++)
+        {
+          if(sequence==null && result[r].indexOf("<name>")>-1)
+          {
+            sequence = align.findName( parseElement( result[r], "<name>" )) ;
+            features = new Vector();
+            type=""; start="0"; end="0"; description=""; status=""; pdb="";
+          }
+
+          if(sequence==null)
+            continue;
+
+           if( result[r].indexOf("<property type=\"pdb accession\"")>-1)
+           {
+             pdb = parseValue( result[r], "value=" );
+             sequence.setPDBId(pdb);
+           }
+
+           if(result[r].indexOf("feature type")>-1)
+           {
+             type = parseValue( result[r], "type=" );
+             description = parseValue( result[r], "description=" );
+             status = parseValue ( result[r], "status=");
+
+             while( result[r].indexOf("<location>")==-1)
+             {
+                 r++;  //<location>
+             }
+             r++;
+             if(result[r].indexOf("begin")>-1)
+             {
+               start = parseValue( result[r], "position=" );
+               end = parseValue( result[++r], "position=" );
+             }
+             else
+             {
+               start = parseValue( result[r], "position=" );
+               end = parseValue(   result[r], "position=" );
+             }
+             int sstart = Integer.parseInt(start);
+             int eend = Integer.parseInt(end);
+
+             if(sstart>=sequence.getStart() && eend<=sequence.getEnd())
+             {
+               SequenceFeature sf = new SequenceFeature(type,
+                   sstart,
+                   eend,
+                   description,
+                   status);
+               features.add(sf);
+             }
+           }
+
+           if(result[r].indexOf("</entry>")>-1)
+           {
+             sequence.setSequenceFeatures( features );
+             features = null;
+             sequence = null;
+           }
+        }
+      }
+    }
+
+    static String parseValue(String line, String tag)
+    {
+
+      int index = line.indexOf(tag)+tag.length()+1;
+      if(index==tag.length())
+        return "";
+
+      return line.substring( index, line.indexOf("\"", index+1) );
+    }
+
+
+    static String parseElement(String line, String tag)
+    {
+      int index = line.indexOf(tag)+tag.length();
+      return line.substring( index, line.indexOf("</") ) ;
+    }
+
+
+
+
+
 }
diff --git a/src/jalview/datamodel/FeaturePair.java b/src/jalview/datamodel/FeaturePair.java
deleted file mode 100755
index 025d2af..0000000
--- a/src/jalview/datamodel/FeaturePair.java
+++ /dev/null
@@ -1,118 +0,0 @@
-package jalview.datamodel;
-
-import java.util.*;
-
-public class FeaturePair {
-  SequenceFeature f1;
-  SequenceFeature f2;
-
-  public FeaturePair() {
-      this.f1 = new SequenceFeature();
-      this.f2 = new SequenceFeature();
-  }
-  public FeaturePair(SequenceFeature f1, SequenceFeature f2) {
-    this.f1 = f1;
-    this.f2 = f2;
-  }
-  public void        setQueryFeature(SequenceFeature feature) {
-    this.f1 = feature;
-  }
-  public SequenceFeature getQueryFeature() {
-    return f1;
-  }
-  public void        setHitFeature(SequenceFeature feature) {
-    this.f2 = feature;
-  }
-  public SequenceFeature getHitFeature() {
-    return f2;
-  }
-  public void        setStart(int start) {
-    f1.setStart(start);
-  }
-  public int        getStart() {
-    return f1.getStart();
-  }
-  public void        setEnd(int end) {
-    f1.setEnd(end);
-  }
-  public int        getEnd() {
-    return f1.getEnd();
-  }
-  public void        setStrand(int strand) {
-    f1.setStrand(strand);
-  }
-  public int         getStrand() {
-    return f1.getStrand();
-  }
-  public String      getId() {
-    return f1.getId();
-  }
-  public void setId(String id) {
-      f1.setId(id);
-  }
-  public double      getScore() {
-    return f1.getScore();
-  }
-  public void        setScore(double score) {
-    f1.setScore(score);
-      f2.setScore(score);
-  }
-
-  public String      getHitId() {
-    return f2.getId();
-  }
-  public void        setHitId(String name) {
-    f2.setId(name);
-  }
-  public int        getHstart() {
-    return f2.getStart();
-  }
-  public void        setHstart(int start) {
-    f2.setStart(start);
-  }
-  public int        getHend() {
-    return f2.getEnd();
-  }
-  public void        setHend(int end) {
-    f2.setEnd(end);
-  }
-  public void        setHstrand(int strand) {
-    f2.setStrand(strand);
-  }
-  public int         getHstrand() {
-    return f2.getStrand();
-  }
-
-  public double getPValue() {
-      return f1.getPValue();
-  }
-  public void setPValue(double value) {
-      f1.setPValue(value);
-      f2.setPValue(value);
-  }
-  public double getPercentId() {
-      return f1.getPercentId();
-  }
-  public void setPercentId(double pid) {
-      f1.setPercentId(pid);
-      f2.setPercentId(pid);
-  }
-  
-  public void invert() {
-    SequenceFeature tmp = f1;
-    f1 = f2;
-    f2 = tmp;
-  }
-
-  public String toGFFString() {
-      String tmp = f1.toGFFString();
-
-      tmp = tmp + "\t" + getHitId() + "\t" + getHstart() + "\t" + getHend() + "\t" + getPValue() + "\t" + getPercentId();
-
-      return tmp;
-  }
-  
-  public static void main(String[] args) {
-      FeaturePair fp  = new FeaturePair();
-  }
-}
\ No newline at end of file
diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index d35cbe8..eceddf1 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -2,7 +2,7 @@ package jalview.datamodel;
 
 import jalview.analysis.*;
 import java.awt.*;
-import java.util.StringTokenizer;
+import java.util.*;
 import MCview.*;
 
 
@@ -10,19 +10,38 @@ public class Sequence implements SequenceI
 {
   protected String   name;
   protected String   sequence;
+  protected String description;
   protected int      start;
   protected int      end;
-  protected String   description;
-  protected int      charHeight;
   protected String   displayId;
   protected Color    color = Color.white;
+  String pdbId;
   PDBfile pdb;
-   public int maxchain = -1;
 
+   public int maxchain = -1;
    public int pdbstart;
    public int pdbend;
    public int seqstart;
    public int seqend;
+
+   public Vector sequenceFeatures = new Vector();
+   public void setSequenceFeatures(Vector v)
+   {
+     sequenceFeatures = v;
+   }
+
+   public Vector getSequenceFeatures()
+   {return sequenceFeatures; }
+
+   public void setPDBId(String id)
+   {
+     pdbId = id;
+   }
+   public String getPDBId()
+   {
+     return pdbId;
+   }
+
    public void setPDBfile(PDBfile pdb)
    {
      this.pdb = pdb;
diff --git a/src/jalview/datamodel/SequenceFeature.java b/src/jalview/datamodel/SequenceFeature.java
index cba91df..a197dfd 100755
--- a/src/jalview/datamodel/SequenceFeature.java
+++ b/src/jalview/datamodel/SequenceFeature.java
@@ -1,197 +1,81 @@
 package jalview.datamodel;
 
-import jalview.util.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
 import java.awt.*;
 
 public class SequenceFeature {
-  int start;
+  int begin;
   int end;
   String type;
   String description;
-  Color color;
-  Sequence sequence;
-  String id;
-  double score;
-  int strand;
-  double pvalue;
-  double pid;
+  String status;
 
-  public SequenceFeature() {
+  public SequenceFeature()
+  {
   }
 
-  public SequenceFeature(Sequence sequence,String type, int start, int end, String description) {
-    this.sequence = sequence;
+  public SequenceFeature(String type, int start, int end, String description, String status)
+  {
     this.type = type;
-    this.start = start;
+    this.begin = start;
     this.end = end;
     this.description = description;
-
-    setColor();
-  }
-
-
-  public String toGFFString() {
-      String gff = id + "\t" + type + "\tfeature\t" + start + "\t" + end + "\t" + score + "\t" + strand + "\t.";
-      return gff;
-  }
-  public double getScore() {
-      return score;
+    this.status = status;
   }
 
-  public void setScore(double score) {
-      this.score = score;
-  }
-
-  public String getId() {
-      return this.id;
-  }
-  public void setId(String id) {
-      this.id = id;
-  }
-  public void setSequence(Sequence seq) {
-    this.sequence = seq;
-  }
-  public void setStart(int start) {
-      this.start = start;
-  }
-  public void setEnd(int end) {
-      this.end = end;
-  }
-  public int getStrand() {
-      return strand;
-  }
-  public void setStrand(int strand) {
-      this.strand = strand;
-  }
   public int getStart() {
-    return start;
+    return begin;
   }
-
   public int getEnd() {
     return end;
   }
-
   public String getType() {
     return type;
   }
-
   public String getDescription() {
     return description;
   }
-
-  public double getPValue() {
-      return pvalue;
-  }
-  public void setPValue(double value) {
-      this.pvalue = value;
-  }
-  public double getPercentId() {
-      return pid;
-  }
-  public void setPercentId(double pid) {
-      this.pid = pid;
-  }
-  public Color getColor() {
-    return color;
-  }
-
-  public void setColor() {
-    if (type.equals("CHAIN")) {
-      color = Color.white;
-    } else if (type.equals("DOMAIN")) {
-      color = Color.white;
-    } else if (type.equals("TRANSMEM")) {
-      color = Color.red.darker();
-    } else if (type.equals("SIGNAL")) {
-      color = Color.cyan;
-    } else if (type.equals("HELIX")) {
-      color = Color.magenta;
-    } else if (type.equals("TURN")) {
-      color = Color.cyan;
-    } else if (type.equals("SHEET")) {
-      color = Color.yellow;
-    } else if (type.equals("STRAND")) {
-      color = Color.yellow;
-    } else if (type.equals("CARBOHYD")) {
-      color = Color.pink;
-    } else if (type.equals("ACT_SITE")) {
-      color = Color.red;
-    } else if (type.equals("TRANSIT")) {
-      color = Color.orange;
-    } else if (type.equals("VARIANT")) {
-      color = Color.orange.darker();
-    } else if (type.equals("BINDING")) {
-      color = Color.blue;
-    } else if (type.equals("DISULFID")) {
-      color = Color.yellow.darker();
-    } else if (type.equals("NP_BIND")) {
-      color = Color.red;
-    } else if (type.indexOf("BIND") > 0) {
-      color = Color.red;
-    } else {
-      color = Color.lightGray;
-    }
-  }
-  public String print() {
-    String tmp = new Format("%15s").form(type);
-    tmp = tmp +  new Format("%6d").form(start);
-    tmp = tmp +  new Format("%6d").form(end);
-    tmp = tmp +  " " + description;
-    return tmp;
-  }
-  public void draw(Graphics g, int fstart, int fend, int x1, int y1, int width, int height) {
-    g.setColor(new Color((float)(Math.random()),(float)(Math.random()),(float)(Math.random())));
-
-    //    int xstart = sequence.findIndex(start);
-    //int xend = sequence.findIndex(end);
-    int xstart = start;
-    int xend = end;
-    long tstart = System.currentTimeMillis();
-    if (!(xend < fstart && xstart > fend)) {
-
-      if (xstart > fstart) {
-        x1 = x1 + (xstart-fstart)*width;
-        fstart = xstart;
-      }
-
-      if (xend < fend) {
-        fend = xend;
-      }
-
-      for (int i = fstart; i <= fend; i++) {
-        char c = sequence.sequence.charAt(i);
-        if (!jalview.util.Comparison.isGap((c)))
-          g.fillRect(x1+(i-fstart)*width,y1,width,height);
-        else
-          g.drawString("-",x1+(i-fstart)*width,y1+height);
-
-      }
-
-    }
-    long tend = System.currentTimeMillis();
-    System.out.println("Time = " + (tend-tstart) + "ms");
-
-  }
-
-  public static void main(String[] args) {
-      SequenceFeature sf = new SequenceFeature();
-
-      System.out.println("Feature " + sf);
-  }
-  public static int CHAIN = 0;
-  public static int DOMAIN = 1;
-  public static int TRANSMEM = 2;
-  public static int SIGNAL = 3;
-  public static int HELIX = 4;
-  public static int TURN = 5;
-  public static int SHEET = 6;
-  public static int CARBOHYD = 7;
-  public static int ACT_SITE = 8;
-  public static int TRANSIT = 9;
-  public static int VARIANT = 10;
-  public static int BINDING = 11;
+  public String getStatus()
+  {return status;}
+
+
+/*
+      <xs:enumeration value="active site" />
+<xs:enumeration value="binding site" />
+<xs:enumeration value="calcium-binding region" />
+<xs:enumeration value="chain" />
+<xs:enumeration value="cross-link" />
+<xs:enumeration value="disulfide bond" />
+<xs:enumeration value="DNA-binding region" />
+<xs:enumeration value="domain" />
+<xs:enumeration value="glycosylation site" />
+<xs:enumeration value="helix" />
+<xs:enumeration value="initiator methionine" />
+<xs:enumeration value="lipid moiety-binding region" />
+<xs:enumeration value="metal ion-binding site" />
+<xs:enumeration value="modified residue" />
+<xs:enumeration value="mutagenesis site" />
+<xs:enumeration value="non-consecutive residues" />
+<xs:enumeration value="non-terminal residue" />
+<xs:enumeration value="nucleotide phosphate-binding region" />
+<xs:enumeration value="peptide" />
+<xs:enumeration value="propeptide" />
+<xs:enumeration value="repeat" />
+<xs:enumeration value="selenocysteine" />
+<xs:enumeration value="sequence conflict" />
+<xs:enumeration value="sequence variant" />
+<xs:enumeration value="signal peptide" />
+<xs:enumeration value="similar" />
+<xs:enumeration value="site" />
+<xs:enumeration value="splice variant" />
+<xs:enumeration value="strand" />
+<xs:enumeration value="thioether bond" />
+<xs:enumeration value="thiolester bond" />
+<xs:enumeration value="transit peptide" />
+<xs:enumeration value="transmembrane region" />
+<xs:enumeration value="turn" />
+<xs:enumeration value="unsure residue" />
+<xs:enumeration value="zinc finger region" />
+*/
 
 }
 
diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 2183131..75b17eb 100755
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -36,6 +36,13 @@ public interface SequenceI {
 
   public void        setColor(Color c);
   public Color       getColor();
+
+  public Vector     getSequenceFeatures();
+  public void       setSequenceFeatures(Vector v);
+
+  public void setPDBId(String id);
+  public String getPDBId();
+
   }
 
 
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 2542216..1f6fabd 100755
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -17,7 +17,6 @@ import jalview.datamodel.*;
 import jalview.analysis.*;
 import jalview.io.*;
 import jalview.ws.*;
-import MCview.*;
 import java.awt.*;
 import java.awt.event.*;
 import java.awt.print.*;
@@ -34,14 +33,13 @@ public class AlignFrame extends GAlignFrame
   {
     super();
 
+    AlignmentUtil.addUniprotFeatures(al);
+
     viewport = new AlignViewport(al,true,true,true,false);
     alignPanel = new AlignmentPanel(this, viewport);
     getContentPane().add(alignPanel, java.awt.BorderLayout.CENTER);
     fontNameMenuItem.setText(viewport.getFont().getName());
     fontSizeMenuItem.setText(viewport.getFont().getSize()+"");
-
-    clustalColour.setSelected(true);
-    clustalColour_actionPerformed(null);
   }
 
   protected void saveAs_actionPerformed(ActionEvent e)
@@ -431,9 +429,10 @@ public class AlignFrame extends GAlignFrame
     alignPanel.RefreshPanels();
   }
 
-  public void secondaryStructure_actionPerformed(ActionEvent evt)
+  public void sequenceFeatures_actionPerformed(ActionEvent evt)
   {
-    alignPanel.setSecondaryStructureVisible(secondaryStructure.isSelected());
+    viewport.showSequenceFeatures(sequenceFeatures.isSelected());
+    alignPanel.RefreshPanels();
   }
 
   public void consensusGraphMenuItem_actionPerformed(ActionEvent e)
@@ -870,6 +869,8 @@ public class AlignFrame extends GAlignFrame
          if (alignment != null)
          {
            AlignFrame af = new AlignFrame(new Alignment(alignment));
+          af.clustalColour.setSelected(true);
+          af.clustalColour_actionPerformed(null);
            Desktop.addInternalFrame(af, getTitle().concat(" - ClustalW Alignment"),
                                     700, 500); // JBPNote - is there a new window geom. property ?
          }
@@ -895,51 +896,13 @@ public class AlignFrame extends GAlignFrame
          g.setColor(Color.black);
          g.drawString("Clustal Alignment Web Service running", 30,30);
        }
-
-
-  }
-
-
-  public void pdbTest_actionPerformed(ActionEvent e)
-  {
-   String reply =
-       JOptionPane.showInternalInputDialog(this, "Enter pdb code",
-                                           "PDB test viewer", JOptionPane.QUESTION_MESSAGE);
-
-   String url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id=1a4u";
-   if (reply.length()>1)
-     url = "http://www.ebi.ac.uk/cgi-bin/pdbfetch?id="+reply;
-
-   try
-   {
-     PDBfile pdb = new PDBfile(url,
-                               "URL");
-    Sequence seq = (Sequence)viewport.getAlignment().getSequenceAt(0);
-    seq.setPDBfile(pdb);
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).isVisible = true;
-     ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).sequence = seq;
-  // ( (PDBChain) pdb.chains.elementAt(seq.maxchain)).colourBySequence();
-
-     rotCanvas rc = new rotCanvas(pdb);
-     JInternalFrame frame = new JInternalFrame();
-     frame.setContentPane(rc);
-     Desktop.addInternalFrame(frame, url, 400,400);
-   }
-   catch (Exception ex)
-   {
-     ex.printStackTrace();
-   }
-
   }
 
 
   public void doKeyPressed(KeyEvent evt)
   {
-
-    System.out.println(evt.getKeyChar());
     if(evt.isControlDown() && evt.getKeyChar()=='f')
       findMenuItem_actionPerformed(null);
-
   }
 
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 1c6c453..7352495 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -21,6 +21,7 @@ public class AlignViewport
   boolean showBoxes=true;
   boolean wrapAlignment=false;
   boolean renderGaps = true;
+  boolean showSequenceFeatures = true;
 
   ColourSchemeI globalColourScheme = null;
   boolean conservationColourSelected = false;
@@ -89,6 +90,10 @@ public class AlignViewport
     setFont( font );
  }
 
+ public void showSequenceFeatures(boolean b)
+ {
+   showSequenceFeatures = b;
+ }
 
   public String getVisibleConsensus()
   {
diff --git a/src/jalview/gui/DrawableSequence.java b/src/jalview/gui/DrawableSequence.java
index 32e8d1c..dc6ff1e 100755
--- a/src/jalview/gui/DrawableSequence.java
+++ b/src/jalview/gui/DrawableSequence.java
@@ -3,6 +3,7 @@ package jalview.gui;
 import jalview.datamodel.*;
 import jalview.schemes.*;
 import java.awt.*;
+import java.util.*;
 
 public class DrawableSequence implements SequenceI {
   protected boolean fastDraw = true;
@@ -12,6 +13,19 @@ public class DrawableSequence implements SequenceI {
 
   ColourSchemeI cs = null;
 
+  public Vector sequenceFeatures = new Vector();
+  public void setSequenceFeatures(Vector v)
+  {   sequenceFeatures = v;  }
+  public Vector getSequenceFeatures()
+  {return sequenceFeatures; }
+
+   String pdbId;
+  public void setPDBId(String id)
+  {    pdbId = id;  }
+  public String getPDBId()
+  {    return pdbId;  }
+
+
   public DrawableSequence(SequenceI s) {
     this.sequence = s;
 
diff --git a/src/jalview/gui/FeatureRenderer.java b/src/jalview/gui/FeatureRenderer.java
new file mode 100755
index 0000000..6e38f1b
--- /dev/null
+++ b/src/jalview/gui/FeatureRenderer.java
@@ -0,0 +1,71 @@
+package jalview.gui;
+
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import java.awt.*;
+import java.util.*;
+
+public class FeatureRenderer implements RendererI
+{
+  AlignViewport av;
+
+  SequenceGroup currentSequenceGroup = null;
+  SequenceGroup [] allGroups = null;
+  Color resBoxColour;
+  Graphics graphics;
+
+  public FeatureRenderer(AlignViewport av)
+  {
+    this.av = av;
+  }
+
+
+  public void drawSequence(Graphics g,SequenceI seq,SequenceGroup [] sg, int start, int end, int x1, int y1, int width, int height, Vector pid, int seqnum)
+  {
+    Vector features = seq.getSequenceFeatures();
+    Enumeration e = features.elements();
+    while( e.hasMoreElements() )
+    {
+      SequenceFeature sf = (SequenceFeature)e.nextElement();
+      int fstart = seq.findIndex(sf.getStart())-1;
+      int fend = seq.findIndex(sf.getEnd())-1;
+
+      if(    (fstart>=start&&fstart<=end) || (fend>=start&&fend<=end))
+      {
+        if(fstart==fend)
+        {
+          g.setColor(Color.red);
+          g.fillRoundRect( (fstart - start) * width, y1, width, height, 4,4);
+          g.setColor(Color.white);
+
+          char s = seq.getSequence().charAt(fstart);
+          FontMetrics fm = g.getFontMetrics();
+          int charOffset =  (width - fm.charWidth(s))/2;
+          int pady = height/5;
+          g.drawString(String.valueOf(s), charOffset + x1 + width * (fstart - start), y1 + height - pady);
+
+        }
+        else
+        {
+          for (int i = fstart; i <= fend; i++)
+          {
+            g.setColor(Color.blue);
+            g.fillRect( (i-start) * width, y1, width, height);
+
+            g.setColor(Color.white);
+            char s = seq.getSequence().charAt(i);
+            FontMetrics fm = g.getFontMetrics();
+            int charOffset = (width - fm.charWidth(s)) / 2;
+            int pady = height / 5;
+            g.drawString(String.valueOf(s),
+                         charOffset + x1 + width * (i-start),
+                         y1 + height - pady);
+
+          }
+        }
+      }
+
+    }
+   }
+
+}
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 0e528a2..3e8af17 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -122,7 +122,7 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          av.getAlignment().getSequenceAt(seq));
+          (Sequence)av.getAlignment().getSequenceAt(seq));
       pop.show(this, e.getX(), y);
       return;
     }
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 4ad7090..2bdaf37 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -5,7 +5,8 @@ import jalview.analysis.*;
 import jalview.schemes.*;
 import javax.swing.*;
 import java.awt.event.*;
-
+import jalview.io.*;
+import MCview.*;
 
 public class PopupMenu extends JPopupMenu
 {
@@ -39,10 +40,11 @@ public class PopupMenu extends JPopupMenu
   JMenu residueMenu = new JMenu();
   JMenuItem annotateResidue = new JMenuItem();
 
-  SequenceI sequence;
+  Sequence sequence;
   JMenuItem unGroupMenuItem = new JMenuItem();
+  JMenuItem pdbMenuItem = new JMenuItem();
 
-  public PopupMenu(AlignmentPanel ap, SequenceI seq)
+  public PopupMenu(AlignmentPanel ap, Sequence seq)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -189,6 +191,14 @@ public class PopupMenu extends JPopupMenu
         unGroupMenuItem_actionPerformed(e);
       }
     });
+    pdbMenuItem.setText("View PDB structure");
+    pdbMenuItem.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        pdbMenuItem_actionPerformed(e);
+      }
+    });
     add(groupMenu);
     this.add(sequenceMenu);
     this.add(residueMenu);
@@ -220,6 +230,7 @@ public class PopupMenu extends JPopupMenu
     defineMenu.add(conservationMenuItem);
 
     sequenceMenu.add(sequenceName);
+    sequenceMenu.add(pdbMenuItem);
     residueMenu.add(annotateResidue);
 
     noColourmenuItem.setText("None");
@@ -597,4 +608,33 @@ public class PopupMenu extends JPopupMenu
      ap.av.setRubberbandGroup(null);
      ap.RefreshPanels();
   }
+
+  void pdbMenuItem_actionPerformed(ActionEvent e)
+  {
+    if(sequence.getPDBId()==null)
+      return;
+
+    try
+    {
+      EBIFetchClient ebi = new EBIFetchClient();
+      String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);
+
+      PDBfile pdb = new PDBfile(result);
+      sequence.setPDBfile(pdb);
+
+      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;
+      ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;
+    //  ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();
+
+      rotCanvas rc = new rotCanvas(pdb);
+      JInternalFrame frame = new JInternalFrame();
+      frame.setContentPane(rc);
+      Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
 }
diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index 3c9bf51db..c33f3ed 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -10,6 +10,7 @@ import jalview.analysis.*;
 
 public class SeqCanvas extends JPanel
 {
+     FeatureRenderer fr;
     Image             img;
     Graphics          gg;
     int               imgWidth;
@@ -30,6 +31,7 @@ public class SeqCanvas extends JPanel
     public SeqCanvas(AlignViewport av)
     {
 	this.av         = av;
+       fr = new FeatureRenderer(av);
        setLayout(new BorderLayout());
        PaintRefresher.Register(this);
 
@@ -176,6 +178,17 @@ public class SeqCanvas extends JPanel
                  offset + AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
                  charWidth,charHeight,null, i);
 
+     if(av.showSequenceFeatures)
+     {
+       fr.drawSequence(g, nextSeq, groups, x1, x2,
+                       (x1 - startx) * charWidth,
+                       offset +
+                       AlignmentUtil.getPixelHeight(starty, i, av.getCharHeight()),
+                       charWidth, charHeight, null, i);
+     }
+
+
+
 
      if( group!=null )
      {
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index aa4a456..cc16a26 100755
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -4,6 +4,7 @@ import java.awt.*;
 import java.awt.event.*;
 import jalview.datamodel.*;
 import javax.swing.*;
+import java.util.*;
 import jalview.schemes.*;
 import jalview.analysis.*;
 
@@ -168,17 +169,40 @@ public class SeqPanel extends JPanel
     if(seq>=av.getAlignment().getHeight())
       return;
 
-    Object obj = ResidueProperties.aa2Triplet.get( av.getAlignment().getSequenceAt(seq).getCharAt(res)+"" ) ;
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+    Object obj = ResidueProperties.aa2Triplet.get( sequence.getCharAt(res)+"" ) ;
     String aa = "";
     if(obj!=null)
          aa = obj.toString();
 
-    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+av.getAlignment().getSequenceAt(seq).getName());
+    StringBuffer text = new StringBuffer("Sequence " +(seq+1)+" ID: "+sequence.getName());
     if(aa!="")
       text.append("  Residue: "+aa+" ("+  av.getAlignment().getSequenceAt(seq).findPosition(res)+")");
 
     ap.alignFrame.statusBar.setText(text.toString());
 
+    if(av.showSequenceFeatures)
+    {
+      Vector features = sequence.getSequenceFeatures();
+      Enumeration e = features.elements();
+      StringBuffer sbuffer = new StringBuffer();
+
+      this.setToolTipText(null);
+      while (e.hasMoreElements())
+      {
+        SequenceFeature sf = (SequenceFeature) e.nextElement();
+        if (sf.getStart() <= sequence.findPosition(res) &&
+            sf.getEnd() >= sequence.findPosition(res))
+        {
+          sbuffer.append(sf.getType() + " " + sf.getDescription());
+          ToolTipManager.sharedInstance().registerComponent(this);
+          this.setToolTipText(sbuffer.toString());
+        }
+
+      }
+    }
+
+
   }
 
   public void doMouseDragged(MouseEvent evt) {
diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index ab133fe..764f5cf 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -80,7 +80,7 @@ public class GAlignFrame extends JInternalFrame
   JMenuItem findMenuItem = new JMenuItem();
   JMenu searchMenu = new JMenu();
   protected JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
-  protected JCheckBoxMenuItem secondaryStructure = new JCheckBoxMenuItem();
+  protected JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
   JMenuItem deleteGroups = new JMenuItem();
   public GAlignFrame()
@@ -593,14 +593,13 @@ public class GAlignFrame extends JInternalFrame
         abovePIDThreshold_actionPerformed(e);
       }
     });
-    secondaryStructure.setEnabled(false);
-    secondaryStructure.setSelected(true);
-    secondaryStructure.setText("Secondary Structure");
-    secondaryStructure.addActionListener(new ActionListener()
+    sequenceFeatures.setSelected(true);
+    sequenceFeatures.setText("Sequence Features");
+    sequenceFeatures.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent actionEvent)
       {
-        secondaryStructure_actionPerformed(actionEvent);
+        sequenceFeatures_actionPerformed(actionEvent);
       }
     });
     nucleotideColour.setText("Nucleotide colours");
@@ -661,7 +660,7 @@ public class GAlignFrame extends JInternalFrame
     viewMenu.add(renderGapsMenuItem);
     viewMenu.add(consensusGraphMenuItem);
     viewMenu.add(overviewMenuItem);
-    viewMenu.add(secondaryStructure);
+    viewMenu.add(sequenceFeatures);
     colourMenu.add(noColourmenuItem);
     colourMenu.add(clustalColour);
     colourMenu.add(zappoColour);
@@ -993,7 +992,7 @@ public class GAlignFrame extends JInternalFrame
 
   }
 
-  public void secondaryStructure_actionPerformed(ActionEvent actionEvent)
+  public void sequenceFeatures_actionPerformed(ActionEvent actionEvent)
   {
 
   }