X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=a34e574b263dfba179cfbf0be476b62bbb1f6cc6;hb=e94c33abc7983e947f64803ab294282a236bf671;hp=6f76a25397c214875393eb0c69ccd1fd9cce8cc8;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 6f76a25..a34e574 100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -26,6 +26,9 @@ import jalview.datamodel.SequenceI;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.FeatureRenderer;
 import jalview.gui.SequenceRenderer;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -33,8 +36,7 @@ import jalview.structure.StructureSelectionManager;
 
 import java.awt.Color;
 import java.awt.Dimension;
-import java.awt.Event;
-import java.awt.Font;
+import java.awt.event.InputEvent;import java.awt.Font;
 import java.awt.Graphics;
 import java.awt.Graphics2D;
 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
@@ -52,8 +54,8 @@ import java.util.Vector;
 import javax.swing.JPanel;
 import javax.swing.ToolTipManager;
 
-public class PDBCanvas extends JPanel implements MouseListener,
-        MouseMotionListener, StructureListener
+public class PDBCanvas extends JPanel
+        implements MouseListener, MouseMotionListener, StructureListener
 {
   boolean redrawneeded = true;
 
@@ -65,7 +67,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   int my = 0;
 
-  public PDBfile pdb;
+  public StructureFile pdb;
 
   PDBEntry pdbentry;
 
@@ -123,7 +125,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   PDBChain mainchain;
 
-  Vector highlightRes;
+  Vector<String> highlightRes;
 
   boolean pdbAction = false;
 
@@ -140,7 +142,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   String errorMessage;
 
   void init(PDBEntry pdbentry, SequenceI[] seq, String[] chains,
-          AlignmentPanel ap, String protocol)
+          AlignmentPanel ap, DataSourceType protocol)
   {
     this.ap = ap;
     this.pdbentry = pdbentry;
@@ -150,11 +152,12 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     try
     {
-      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol,
+              ap.alignFrame);
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol.equals(jalview.io.DataSourceType.PASTE))
       {
-        pdbentry.setFile("INLINE" + pdb.id);
+        pdbentry.setFile("INLINE" + pdb.getId());
       }
 
     } catch (Exception ex)
@@ -168,13 +171,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
       errorMessage = "Error loading file: " + pdbentry.getId();
       return;
     }
-    pdbentry.setId(pdb.id);
+    pdbentry.setId(pdb.getId());
 
     ssm.addStructureViewerListener(this);
 
     colourBySequence();
 
-    int max = -10;
+    float max = -10;
     int maxchain = -1;
     int pdbstart = 0;
     int pdbend = 0;
@@ -184,30 +187,31 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // JUST DEAL WITH ONE SEQUENCE FOR NOW
     SequenceI sequence = seq[0];
 
-    for (int i = 0; i < pdb.chains.size(); i++)
+    for (int i = 0; i < pdb.getChains().size(); i++)
     {
 
       mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + pdb.chains.elementAt(i).sequence
+              + pdb.getChains().elementAt(i).sequence
                       .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
-              + pdb.chains.elementAt(i).residues.size()
-              + "\n\n");
+              + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 
       // Now lets compare the sequences to get
       // the start and end points.
       // Align the sequence to the pdb
       AlignSeq as = new AlignSeq(sequence,
-              pdb.chains.elementAt(i).sequence, "pep");
+              pdb.getChains().elementAt(i).sequence, "pep");
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
       {
+        @Override
         public void print(String x)
         {
           mappingDetails.append(x);
         }
 
+        @Override
         public void println()
         {
           mappingDetails.append("\n");
@@ -231,7 +235,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
     }
 
-    mainchain = pdb.chains.elementAt(maxchain);
+    mainchain = pdb.getChains().elementAt(maxchain);
 
     mainchain.pdbstart = pdbstart;
     mainchain.pdbend = pdbend;
@@ -247,6 +251,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         keyPressed(evt);
@@ -265,23 +270,21 @@ public class PDBCanvas extends JPanel implements MouseListener,
     ToolTipManager.sharedInstance().setDismissDelay(10000);
   }
 
-  Vector visiblebonds;
+  Vector<Bond> visiblebonds;
 
   void setupBonds()
   {
     seqColoursReady = false;
     // Sort the bonds by z coord
-    visiblebonds = new Vector();
+    visiblebonds = new Vector<Bond>();
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.getChains())
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (chain.isVisible)
       {
-        Vector tmp = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < tmp.size(); i++)
+        for (Bond bond : chain.bonds)
         {
-          visiblebonds.addElement(tmp.elementAt(i));
+          visiblebonds.addElement(bond);
         }
       }
     }
@@ -305,16 +308,12 @@ public class PDBCanvas extends JPanel implements MouseListener,
     min[1] = (float) 1e30;
     min[2] = (float) 1e30;
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.getChains())
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond tmp : chain.bonds)
         {
-          Bond tmp = (Bond) bonds.elementAt(i);
-
           if (tmp.start[0] >= max[0])
           {
             max[0] = tmp.start[0];
@@ -440,24 +439,17 @@ public class PDBCanvas extends JPanel implements MouseListener,
     int bsize = 0;
 
     // Find centre coordinate
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.getChains())
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        bsize += bonds.size();
+        bsize += chain.bonds.size();
 
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond bond : chain.bonds)
         {
-          xtot = xtot + ((Bond) bonds.elementAt(i)).start[0]
-                  + ((Bond) bonds.elementAt(i)).end[0];
-
-          ytot = ytot + ((Bond) bonds.elementAt(i)).start[1]
-                  + ((Bond) bonds.elementAt(i)).end[1];
-
-          ztot = ztot + ((Bond) bonds.elementAt(i)).start[2]
-                  + ((Bond) bonds.elementAt(i)).end[2];
+          xtot = xtot + bond.start[0] + bond.end[0];
+          ytot = ytot + bond.start[1] + bond.end[1];
+          ztot = ztot + bond.start[2] + bond.end[2];
         }
       }
     }
@@ -467,6 +459,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paintComponent(Graphics g)
   {
     super.paintComponent(g);
@@ -553,16 +546,17 @@ public class PDBCanvas extends JPanel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
     PDBChain chain;
     if (bysequence && pdb != null)
     {
-      for (int ii = 0; ii < pdb.chains.size(); ii++)
+      for (int ii = 0; ii < pdb.getChains().size(); ii++)
       {
-        chain = pdb.chains.elementAt(ii);
+        chain = pdb.getChains().elementAt(ii);
 
         for (int i = 0; i < chain.bonds.size(); i++)
         {
-          Bond tmp = (Bond) chain.bonds.elementAt(i);
+          Bond tmp = chain.bonds.elementAt(i);
           tmp.startCol = Color.lightGray;
           tmp.endCol = Color.lightGray;
           if (chain != mainchain)
@@ -580,23 +574,15 @@ public class PDBCanvas extends JPanel implements MouseListener,
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.startCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.startCol = fr.findFeatureColour(tmp.startCol,
-                            sequence[s], pos);
-                  }
+                  tmp.startCol = sr.getResidueColour(sequence[s], pos,
+                          finder);
                 }
                 pos = mapping[m].getSeqPos(tmp.at2.resNumber) - 1;
                 if (pos > 0)
                 {
                   pos = sequence[s].findIndex(pos);
-                  tmp.endCol = sr.getResidueBoxColour(sequence[s], pos);
-                  if (showFeatures)
-                  {
-                    tmp.endCol = fr.findFeatureColour(tmp.endCol,
-                            sequence[s], pos);
-                  }
+                  tmp.endCol = sr.getResidueColour(sequence[s], pos,
+                          finder);
                 }
 
               }
@@ -618,19 +604,23 @@ public class PDBCanvas extends JPanel implements MouseListener,
         zsort = new Zsort();
       }
 
-      zsort.Zsort(visiblebonds);
+      zsort.sort(visiblebonds);
     }
 
     Bond tmpBond = null;
     for (int i = 0; i < visiblebonds.size(); i++)
     {
-      tmpBond = (Bond) visiblebonds.elementAt(i);
+      tmpBond = visiblebonds.elementAt(i);
 
-      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
-      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
+      xstart = (int) (((tmpBond.start[0] - centre[0]) * scale)
+              + (getWidth() / 2));
+      ystart = (int) (((centre[1] - tmpBond.start[1]) * scale)
+              + (getHeight() / 2));
 
-      xend = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
-      yend = (int) (((centre[1] - tmpBond.end[1]) * scale) + (getHeight() / 2));
+      xend = (int) (((tmpBond.end[0] - centre[0]) * scale)
+              + (getWidth() / 2));
+      yend = (int) (((centre[1] - tmpBond.end[1]) * scale)
+              + (getHeight() / 2));
 
       xmid = (xend + xstart) / 2;
       ymid = (yend + ystart) / 2;
@@ -694,8 +684,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
       if (highlightBond1 != null && highlightBond1 == tmpBond)
       {
-        g.setColor(tmpBond.endCol.brighter().brighter().brighter()
-                .brighter());
+        g.setColor(
+                tmpBond.endCol.brighter().brighter().brighter().brighter());
         drawLine(g, xmid, ymid, xend, yend);
       }
 
@@ -760,6 +750,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -772,23 +763,25 @@ public class PDBCanvas extends JPanel implements MouseListener,
       repaint();
       if (foundchain != -1)
       {
-        PDBChain chain = pdb.chains.elementAt(foundchain);
+        PDBChain chain = pdb.getChains().elementAt(foundchain);
         if (chain == mainchain)
         {
           if (fatom.alignmentMapping != -1)
           {
             if (highlightRes == null)
             {
-              highlightRes = new Vector();
+              highlightRes = new Vector<String>();
             }
 
-            if (highlightRes.contains(fatom.alignmentMapping + ""))
+            final String atomString = Integer
+                    .toString(fatom.alignmentMapping);
+            if (highlightRes.contains(atomString))
             {
-              highlightRes.remove(fatom.alignmentMapping + "");
+              highlightRes.remove(atomString);
             }
             else
             {
-              highlightRes.add(fatom.alignmentMapping + "");
+              highlightRes.add(atomString);
             }
           }
         }
@@ -802,6 +795,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -818,7 +812,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     PDBChain chain = null;
     if (foundchain != -1)
     {
-      chain = pdb.chains.elementAt(foundchain);
+      chain = pdb.getChains().elementAt(foundchain);
       if (chain == mainchain)
       {
         mouseOverStructure(fatom.resNumber, chain.id);
@@ -827,8 +821,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     if (fatom != null)
     {
-      this.setToolTipText(chain.id + ":" + fatom.resNumber + " "
-              + fatom.resName);
+      this.setToolTipText(
+              chain.id + ":" + fatom.resNumber + " " + fatom.resName);
     }
     else
     {
@@ -837,18 +831,22 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseClicked(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
   }
 
+  @Override
   public void mouseDragged(MouseEvent evt)
   {
     int x = evt.getX();
@@ -859,7 +857,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     MCMatrix objmat = new MCMatrix(3, 3);
     objmat.setIdentity();
 
-    if ((evt.getModifiers() & Event.META_MASK) != 0)
+    if ((evt.getModifiersEx() & InputEvent.META_DOWN_MASK) != 0)
     {
       objmat.rotatez(((mx - omx)));
     }
@@ -870,14 +868,10 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
 
     // Alter the bonds
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.getChains())
     {
-      Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-      for (int i = 0; i < bonds.size(); i++)
+      for (Bond tmpBond : chain.bonds)
       {
-        Bond tmpBond = (Bond) bonds.elementAt(i);
-
         // Translate the bond so the centre is 0,0,0
         tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 
@@ -902,6 +896,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -911,18 +906,12 @@ public class PDBCanvas extends JPanel implements MouseListener,
   void drawLabels(Graphics g)
   {
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.getChains())
     {
-      PDBChain chain = pdb.chains.elementAt(ii);
-
       if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond tmpBond : chain.bonds)
         {
-          Bond tmpBond = (Bond) bonds.elementAt(i);
-
           if (tmpBond.at1.isSelected)
           {
             labelAtom(g, tmpBond, 1);
@@ -930,7 +919,6 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
           if (tmpBond.at2.isSelected)
           {
-
             labelAtom(g, tmpBond, 2);
           }
         }
@@ -944,16 +932,20 @@ public class PDBCanvas extends JPanel implements MouseListener,
     g.setColor(Color.red);
     if (n == 1)
     {
-      int xstart = (int) (((b.start[0] - centre[0]) * scale) + (getWidth() / 2));
-      int ystart = (int) (((centre[1] - b.start[1]) * scale) + (getHeight() / 2));
+      int xstart = (int) (((b.start[0] - centre[0]) * scale)
+              + (getWidth() / 2));
+      int ystart = (int) (((centre[1] - b.start[1]) * scale)
+              + (getHeight() / 2));
 
       g.drawString(b.at1.resName + "-" + b.at1.resNumber, xstart, ystart);
     }
 
     if (n == 2)
     {
-      int xstart = (int) (((b.end[0] - centre[0]) * scale) + (getWidth() / 2));
-      int ystart = (int) (((centre[1] - b.end[1]) * scale) + (getHeight() / 2));
+      int xstart = (int) (((b.end[0] - centre[0]) * scale)
+              + (getWidth() / 2));
+      int ystart = (int) (((centre[1] - b.end[1]) * scale)
+              + (getHeight() / 2));
 
       g.drawString(b.at2.resName + "-" + b.at2.resNumber, xstart, ystart);
     }
@@ -967,25 +959,25 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     foundchain = -1;
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
-      PDBChain chain = pdb.chains.elementAt(ii);
+      PDBChain chain = pdb.getChains().elementAt(ii);
       int truex;
       Bond tmpBond = null;
 
       if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond bond : chain.bonds)
         {
-          tmpBond = (Bond) bonds.elementAt(i);
+          tmpBond = bond;
 
-          truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
+          truex = (int) (((tmpBond.start[0] - centre[0]) * scale)
+                  + (getWidth() / 2));
 
           if (Math.abs(truex - x) <= 2)
           {
-            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
+            int truey = (int) (((centre[1] - tmpBond.start[1]) * scale)
+                    + (getHeight() / 2));
 
             if (Math.abs(truey - y) <= 2)
             {
@@ -998,11 +990,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
         // Still here? Maybe its the last bond
 
-        truex = (int) (((tmpBond.end[0] - centre[0]) * scale) + (getWidth() / 2));
+        truex = (int) (((tmpBond.end[0] - centre[0]) * scale)
+                + (getWidth() / 2));
 
         if (Math.abs(truex - x) <= 2)
         {
-          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale) + (getHeight() / 2));
+          int truey = (int) (((tmpBond.end[1] - centre[1]) * scale)
+                  + (getHeight() / 2));
 
           if (Math.abs(truey - y) <= 2)
           {
@@ -1015,8 +1009,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
       }
 
       if (fatom != null) // )&& chain.ds != null)
-      {
-        chain = pdb.chains.elementAt(foundchain);
+      { // dead code? value of chain is either overwritten or discarded
+        chain = pdb.getChains().elementAt(foundchain);
       }
     }
 
@@ -1041,7 +1035,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     Bond tmpBond;
     for (index = 0; index < mainchain.bonds.size(); index++)
     {
-      tmpBond = (Bond) mainchain.bonds.elementAt(index);
+      tmpBond = mainchain.bonds.elementAt(index);
       if (tmpBond.at1.alignmentMapping == ii - 1)
       {
         if (highlightBond1 != null)
@@ -1059,13 +1053,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
         if (index > 0)
         {
-          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+          highlightBond1 = mainchain.bonds.elementAt(index - 1);
           highlightBond1.at2.isSelected = true;
         }
 
         if (index != mainchain.bonds.size())
         {
-          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+          highlightBond2 = mainchain.bonds.elementAt(index);
           highlightBond2.at1.isSelected = true;
         }
 
@@ -1079,9 +1073,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   public void setAllchainsVisible(boolean b)
   {
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
-      PDBChain chain = pdb.chains.elementAt(ii);
+      PDBChain chain = pdb.getChains().elementAt(ii);
       chain.isVisible = b;
     }
     mainchain.isVisible = true;
@@ -1091,10 +1085,10 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String[] getPdbFile()
+  @Override
+  public String[] getStructureFiles()
   {
-    return new String[]
-    { pdbentry.getFile() };
+    return new String[] { pdbentry.getFile() };
   }
 
   String lastMessage;
@@ -1153,7 +1147,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     Bond tmpBond;
     for (index = 0; index < mainchain.bonds.size(); index++)
     {
-      tmpBond = (Bond) mainchain.bonds.elementAt(index);
+      tmpBond = mainchain.bonds.elementAt(index);
       if (tmpBond.at1.atomIndex == atomIndex)
       {
         if (highlightBond1 != null)
@@ -1171,13 +1165,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
         if (index > 0)
         {
-          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+          highlightBond1 = mainchain.bonds.elementAt(index - 1);
           highlightBond1.at2.isSelected = true;
         }
 
         if (index != mainchain.bonds.size())
         {
-          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+          highlightBond2 = mainchain.bonds.elementAt(index);
           highlightBond2.at1.isSelected = true;
         }
 
@@ -1196,6 +1190,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();
@@ -1210,4 +1205,19 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   }
 
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    if (sequence != null)
+    {
+      for (SequenceI s : sequence)
+      {
+        if (s == seq)
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
 }