X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=1c7a1f7b00f69663158f1a26db1245c3c35bbfc8;hb=53ff9242cb709fe1e8470c5e88ecf8a8ae783b19;hp=406d9f1fa86e67d570b42910bebbc2d979ab3a27;hpb=43b415c68805f3dec44a6ddc666d52220483c120;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 406d9f1..1c7a1f7 100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -20,6 +20,18 @@
  */
 package MCview;
 
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.FeatureRenderer;
+import jalview.gui.SequenceRenderer;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+
 import java.awt.Color;
 import java.awt.Dimension;
 import java.awt.Event;
@@ -41,17 +53,6 @@ import java.util.Vector;
 import javax.swing.JPanel;
 import javax.swing.ToolTipManager;
 
-import jalview.analysis.AlignSeq;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignmentPanel;
-import jalview.gui.FeatureRenderer;
-import jalview.gui.SequenceRenderer;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureListener;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
-
 public class PDBCanvas extends JPanel implements MouseListener,
         MouseMotionListener, StructureListener
 {
@@ -65,7 +66,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   int my = 0;
 
-  public PDBfile pdb;
+  public StructureFile pdb;
 
   PDBEntry pdbentry;
 
@@ -154,7 +155,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
       if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
       {
-        pdbentry.setFile("INLINE" + pdb.id);
+        pdbentry.setFile("INLINE" + pdb.getId());
       }
 
     } catch (Exception ex)
@@ -168,7 +169,7 @@ 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);
 
@@ -184,30 +185,30 @@ 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
-                      .getSequenceAsString());
+              + 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 +232,7 @@ 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 +248,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         keyPressed(evt);
@@ -273,7 +275,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // Sort the bonds by z coord
     visiblebonds = new Vector<Bond>();
 
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       if (chain.isVisible)
       {
@@ -303,7 +305,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     min[1] = (float) 1e30;
     min[2] = (float) 1e30;
 
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       if (chain.isVisible)
       {
@@ -434,7 +436,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     int bsize = 0;
 
     // Find centre coordinate
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       if (chain.isVisible)
       {
@@ -454,6 +456,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paintComponent(Graphics g)
   {
     super.paintComponent(g);
@@ -543,9 +546,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
     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++)
         {
@@ -747,6 +750,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -759,7 +763,7 @@ 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)
@@ -791,6 +795,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -807,7 +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);
@@ -826,18 +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 +868,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
 
     // Alter the bonds
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       for (Bond tmpBond : chain.bonds)
       {
@@ -887,6 +896,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -896,7 +906,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   void drawLabels(Graphics g)
   {
 
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       if (chain.isVisible)
       {
@@ -945,9 +955,9 @@ 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;
 
@@ -992,7 +1002,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
       if (fatom != null) // )&& chain.ds != null)
       { // dead code? value of chain is either overwritten or discarded
-        chain = pdb.chains.elementAt(foundchain);
+        chain = pdb.getChains().elementAt(foundchain);
       }
     }
 
@@ -1055,9 +1065,9 @@ 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;
@@ -1067,10 +1077,10 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
+  @Override
   public String[] getPdbFile()
   {
-    return new String[]
-    { pdbentry.getFile() };
+    return new String[] { pdbentry.getFile() };
   }
 
   String lastMessage;
@@ -1172,6 +1182,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();