X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=211cff0e27a7a817e0a28324b463a3d35bc3d7e9;hb=3ef44bef1f825d26977dedd1608469712a87fe15;hp=fa33c6c678731c0fff9a9d2588d7ed5fc3b92b53;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
old mode 100755
new mode 100644
index fa33c6c..211cff0
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,35 +1,53 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package MCview;
 
-import java.io.*;
-import java.util.*;
-
+import jalview.analysis.AlignSeq;
+import jalview.appletgui.AlignmentPanel;
+import jalview.appletgui.FeatureRenderer;
+import jalview.appletgui.SequenceRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureListener;
+import jalview.structure.StructureMapping;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Event;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
 // JBPNote TODO: This class is quite noisy - needs proper log.info/log.debug
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-
-import jalview.appletgui.*;
-import jalview.structure.*;
+import java.awt.Panel;
+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;
 
 public class AppletPDBCanvas extends Panel implements MouseListener,
         MouseMotionListener, StructureListener
@@ -133,14 +151,17 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     this.pdbentry = pdbentry;
     this.sequence = seq;
 
-    ssm = StructureSelectionManager.getStructureSelectionManager();
+    ssm = StructureSelectionManager
+            .getStructureSelectionManager(ap.av.applet);
 
     try
     {
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
       if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      {
         pdbentry.setFile("INLINE" + pdb.id);
+      }
 
     } catch (Exception ex)
     {
@@ -168,17 +189,20 @@ public class AppletPDBCanvas extends Panel 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");
+      // TODO: DNa/Pep switch
+      AlignSeq as = new AlignSeq(sequence,
+              pdb.chains.elementAt(i).sequence,
+              pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
+                      : AlignSeq.PEP);
       as.calcScoreMatrix();
       as.traceAlignment();
       PrintStream ps = new PrintStream(System.out)
@@ -211,7 +235,7 @@ public class AppletPDBCanvas extends Panel 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;
@@ -270,9 +294,9 @@ public class AppletPDBCanvas extends Panel 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++)
         {
@@ -301,9 +325,9 @@ public class AppletPDBCanvas extends Panel 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++)
         {
@@ -372,9 +396,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       }
     }
 
-    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];
 
@@ -431,9 +455,9 @@ public class AppletPDBCanvas extends Panel 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();
 
@@ -465,7 +489,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       g.fillRect(0, 0, getSize().width, getSize().height);
       g.setColor(Color.black);
       g.setFont(new Font("Verdana", Font.BOLD, 14));
-      g.drawString("Error loading PDB data!!", 50, getSize().height / 2);
+      g.drawString(
+              MessageManager.getString("label.error_loading_pdb_data"), 50,
+              getSize().height / 2);
       return;
     }
 
@@ -473,7 +499,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     {
       g.setColor(Color.black);
       g.setFont(new Font("Verdana", Font.BOLD, 14));
-      g.drawString("Fetching PDB data...", 50, getSize().height / 2);
+      g.drawString(MessageManager.getString("label.fetching_pdb_data"), 50,
+              getSize().height / 2);
       return;
     }
 
@@ -540,7 +567,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (ap.av.getShowSequenceFeatures())
+    if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
       {
@@ -557,7 +584,7 @@ public class AppletPDBCanvas extends Panel 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++)
         {
@@ -769,7 +796,7 @@ public class AppletPDBCanvas extends Panel 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)
@@ -815,7 +842,7 @@ public class AppletPDBCanvas extends Panel 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);
@@ -865,18 +892,18 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
     if ((evt.getModifiers() & Event.META_MASK) != 0)
     {
-      objmat.rotatez((float) ((mx - omx)));
+      objmat.rotatez(((mx - omx)));
     }
     else
     {
-      objmat.rotatex((float) ((omy - my)));
-      objmat.rotatey((float) ((omx - mx)));
+      objmat.rotatex(((omy - my)));
+      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++)
       {
@@ -917,11 +944,11 @@ public class AppletPDBCanvas extends Panel 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++)
         {
@@ -975,13 +1002,13 @@ public class AppletPDBCanvas extends Panel 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++)
         {
@@ -1022,7 +1049,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
       if (fatom != null) // )&& chain.ds != null)
       {
-        chain = (PDBChain) pdb.chains.elementAt(foundchain);
+        chain = pdb.chains.elementAt(foundchain);
       }
     }
 
@@ -1090,7 +1117,7 @@ public class AppletPDBCanvas extends Panel 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;
@@ -1100,9 +1127,10 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String getPdbFile()
+  public String[] getPdbFile()
   {
-    return pdbentry.getFile();
+    return new String[]
+    { pdbentry.getFile() };
   }
 
   String lastMessage;
@@ -1110,7 +1138,9 @@ public class AppletPDBCanvas extends Panel 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;
   }
@@ -1119,19 +1149,40 @@ public class AppletPDBCanvas extends Panel 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();
+  }
+
+  /**
+   * @param atomIndex
+   */
+  protected void highlightAtom(int atomIndex)
+  {
     int index = -1;
     Bond tmpBond;
     for (index = 0; index < mainchain.bonds.size(); index++)
@@ -1167,9 +1218,6 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
         break;
       }
     }
-
-    redrawneeded = true;
-    repaint();
   }
 
   public Color getColour(int atomIndex, int pdbResNum, String chain,
@@ -1189,4 +1237,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }