Merge develop to Release_2_8_3_Branch

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

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index f6e6427..6f76a25 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -20,18 +20,37 @@
  */
 package MCview;
 
-import java.io.*;
-import java.util.*;
-
+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;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Event;
+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
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.structure.*;
+import java.awt.Image;
+import java.awt.RenderingHints;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.io.PrintStream;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JPanel;
+import javax.swing.ToolTipManager;
 
 public class PDBCanvas extends JPanel implements MouseListener,
         MouseMotionListener, StructureListener
@@ -134,7 +153,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
       if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      {
         pdbentry.setFile("INLINE" + pdb.id);
+      }
 
     } catch (Exception ex)
     {
@@ -167,17 +188,17 @@ public class PDBCanvas extends JPanel implements MouseListener,
     {
 
       mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
-              + ((PDBChain) pdb.chains.elementAt(i)).sequence
+              + pdb.chains.elementAt(i).sequence
                       .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
-              + ((PDBChain) pdb.chains.elementAt(i)).residues.size()
+              + pdb.chains.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,
-              ((PDBChain) pdb.chains.elementAt(i)).sequence, "pep");
+              pdb.chains.elementAt(i).sequence, "pep");
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -210,7 +231,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
     }
 
-    mainchain = (PDBChain) pdb.chains.elementAt(maxchain);
+    mainchain = pdb.chains.elementAt(maxchain);
 
     mainchain.pdbstart = pdbstart;
     mainchain.pdbend = pdbend;
@@ -254,9 +275,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (pdb.chains.elementAt(ii).isVisible)
       {
-        Vector tmp = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector tmp = pdb.chains.elementAt(ii).bonds;
 
         for (int i = 0; i < tmp.size(); i++)
         {
@@ -286,9 +307,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (pdb.chains.elementAt(ii).isVisible)
       {
-        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = pdb.chains.elementAt(ii).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -362,9 +383,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
      * System.out.println("zmax " + max[2] + " min " + min[2]);
      */
 
-    width[0] = (float) Math.abs(max[0] - min[0]);
-    width[1] = (float) Math.abs(max[1] - min[1]);
-    width[2] = (float) Math.abs(max[2] - min[2]);
+    width[0] = Math.abs(max[0] - min[0]);
+    width[1] = Math.abs(max[1] - min[1]);
+    width[2] = Math.abs(max[2] - min[2]);
 
     maxwidth = width[0];
 
@@ -421,9 +442,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
     // Find centre coordinate
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      if (((PDBChain) pdb.chains.elementAt(ii)).isVisible)
+      if (pdb.chains.elementAt(ii).isVisible)
       {
-        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = pdb.chains.elementAt(ii).bonds;
 
         bsize += bonds.size();
 
@@ -537,7 +558,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     {
       for (int ii = 0; ii < pdb.chains.size(); ii++)
       {
-        chain = (PDBChain) pdb.chains.elementAt(ii);
+        chain = pdb.chains.elementAt(ii);
 
         for (int i = 0; i < chain.bonds.size(); i++)
         {
@@ -751,7 +772,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       repaint();
       if (foundchain != -1)
       {
-        PDBChain chain = (PDBChain) pdb.chains.elementAt(foundchain);
+        PDBChain chain = pdb.chains.elementAt(foundchain);
         if (chain == mainchain)
         {
           if (fatom.alignmentMapping != -1)
@@ -797,7 +818,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     PDBChain chain = null;
     if (foundchain != -1)
     {
-      chain = (PDBChain) pdb.chains.elementAt(foundchain);
+      chain = pdb.chains.elementAt(foundchain);
       if (chain == mainchain)
       {
         mouseOverStructure(fatom.resNumber, chain.id);
@@ -840,18 +861,18 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     if ((evt.getModifiers() & Event.META_MASK) != 0)
     {
-      objmat.rotatez((float) ((mx - omx)));
+      objmat.rotatez(((mx - omx)));
     }
     else
     {
-      objmat.rotatex((float) ((my - omy)));
-      objmat.rotatey((float) ((omx - mx)));
+      objmat.rotatex(((my - omy)));
+      objmat.rotatey(((omx - mx)));
     }
 
     // Alter the bonds
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+      Vector bonds = pdb.chains.elementAt(ii).bonds;
 
       for (int i = 0; i < bonds.size(); i++)
       {
@@ -892,11 +913,11 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+      PDBChain chain = pdb.chains.elementAt(ii);
 
       if (chain.isVisible)
       {
-        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = pdb.chains.elementAt(ii).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -948,13 +969,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+      PDBChain chain = pdb.chains.elementAt(ii);
       int truex;
       Bond tmpBond = null;
 
       if (chain.isVisible)
       {
-        Vector bonds = ((PDBChain) pdb.chains.elementAt(ii)).bonds;
+        Vector bonds = pdb.chains.elementAt(ii).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -995,7 +1016,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
       if (fatom != null) // )&& chain.ds != null)
       {
-        chain = (PDBChain) pdb.chains.elementAt(foundchain);
+        chain = pdb.chains.elementAt(foundchain);
       }
     }
 
@@ -1060,7 +1081,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   {
     for (int ii = 0; ii < pdb.chains.size(); ii++)
     {
-      PDBChain chain = (PDBChain) pdb.chains.elementAt(ii);
+      PDBChain chain = pdb.chains.elementAt(ii);
       chain.isVisible = b;
     }
     mainchain.isVisible = true;
@@ -1081,7 +1102,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
   public void mouseOverStructure(int pdbResNum, String chain)
   {
     if (lastMessage == null || !lastMessage.equals(pdbResNum + chain))
+    {
       ssm.mouseOverStructure(pdbResNum, chain, pdbentry.getFile());
+    }
 
     lastMessage = pdbResNum + chain;
   }
@@ -1090,19 +1113,42 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   StringBuffer eval = new StringBuffer();
 
-  public void highlightAtom(int atomIndex, int pdbResNum, String chain,
-          String pdbfile)
+  /**
+   * Highlight the specified atoms in the structure.
+   * 
+   * @param atoms
+   */
+  @Override
+  public void highlightAtoms(List<AtomSpec> atoms)
   {
     if (!seqColoursReady)
     {
       return;
     }
 
-    if (highlightRes != null && highlightRes.contains((atomIndex - 1) + ""))
+    for (AtomSpec atom : atoms)
     {
-      return;
+      int atomIndex = atom.getAtomIndex();
+      if (highlightRes != null
+              && highlightRes.contains((atomIndex - 1) + ""))
+      {
+        continue;
+      }
+
+      highlightAtom(atomIndex);
     }
 
+    redrawneeded = true;
+    repaint();
+  }
+
+  /**
+   * Highlight the atom at the specified index.
+   * 
+   * @param atomIndex
+   */
+  protected void highlightAtom(int atomIndex)
+  {
     int index = -1;
     Bond tmpBond;
     for (index = 0; index < mainchain.bonds.size(); index++)
@@ -1138,9 +1184,6 @@ public class PDBCanvas extends JPanel implements MouseListener,
         break;
       }
     }
-
-    redrawneeded = true;
-    repaint();
   }
 
   public Color getColour(int atomIndex, int pdbResNum, String chain,