close filehandles straight after parse, without setting an error

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

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index dfe7c8f..a34e574 100644 (file)
--- 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;
 
@@ -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;
@@ -150,9 +152,10 @@ 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.getId());
       }
@@ -174,7 +177,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     colourBySequence();
 
-    int max = -10;
+    float max = -10;
     int maxchain = -1;
     int pdbstart = 0;
     int pdbend = 0;
@@ -188,7 +191,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
     {
 
       mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + pdb.getChains().elementAt(i).sequence.getSequenceAsString());
+              + pdb.getChains().elementAt(i).sequence
+                      .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
               + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 
@@ -201,11 +205,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
       {
+        @Override
         public void print(String x)
         {
           mappingDetails.append(x);
         }
 
+        @Override
         public void println()
         {
           mappingDetails.append("\n");
@@ -245,6 +251,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         keyPressed(evt);
@@ -452,6 +459,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paintComponent(Graphics g)
   {
     super.paintComponent(g);
@@ -538,6 +546,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
     PDBChain chain;
     if (bysequence && pdb != null)
     {
@@ -565,23 +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);
                 }
 
               }
@@ -611,11 +612,15 @@ public class PDBCanvas extends JPanel implements MouseListener,
     {
       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;
@@ -679,8 +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);
       }
 
@@ -745,6 +750,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -789,6 +795,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -814,8 +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
     {
@@ -824,18 +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();
@@ -846,7 +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)));
     }
@@ -885,6 +896,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -920,16 +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);
     }
@@ -955,11 +971,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
         {
           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)
             {
@@ -972,11 +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)
           {
@@ -1065,7 +1085,8 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String[] getPdbFile()
+  @Override
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }
@@ -1169,6 +1190,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();