JAL-2465 bugfix and rerefactor renamed getPdbFile() method to getStructureFile()

[jalview.git] / src / MCview / AppletPDBCanvas.java

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 74bec63..0f3da69 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -26,6 +26,8 @@ import jalview.appletgui.FeatureRenderer;
 import jalview.appletgui.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -67,7 +69,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   int my = 0;
 
-  public PDBfile pdb;
+  public StructureFile pdb;
 
   PDBEntry pdbentry;
 
@@ -144,7 +146,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   StructureSelectionManager ssm;
 
   public AppletPDBCanvas(PDBEntry pdbentry, SequenceI[] seq,
-          String[] chains, AlignmentPanel ap, String protocol)
+          String[] chains, AlignmentPanel ap, DataSourceType protocol)
 
   {
     this.ap = ap;
@@ -156,9 +158,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
     try
     {
-      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol, null);
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
         pdbentry.setFile("INLINE" + pdb.getId());
       }
@@ -188,8 +190,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     for (int i = 0; i < pdb.getChains().size(); i++)
     {
 
-      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+      mappingDetails
+              .append("\n\nPDB Sequence is :\nSequence = "
+                      + pdb.getChains().elementAt(i).sequence
+                              .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
               + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 
@@ -198,17 +202,19 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       // Align the sequence to the pdb
       // TODO: DNa/Pep switch
       AlignSeq as = new AlignSeq(sequence,
-              pdb.getChains().elementAt(i).sequence,
-              pdb.getChains().elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.PEP);
+              pdb.getChains().elementAt(i).sequence, pdb.getChains()
+                      .elementAt(i).isNa ? AlignSeq.DNA : AlignSeq.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");
@@ -267,6 +273,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         doKeyPressed(evt);
@@ -470,6 +477,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paint(Graphics g)
   {
 
@@ -774,6 +782,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -818,6 +827,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -860,18 +870,22 @@ public class AppletPDBCanvas extends Panel 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();
@@ -921,6 +935,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -1037,6 +1052,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     return fatom;
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
@@ -1108,7 +1124,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String[] getPdbFile()
+  @Override
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }
@@ -1210,6 +1227,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();