JAL-2446 merged to spike branch

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

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 9cfb4ea..39111c3 100644 (file)
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -26,6 +26,9 @@ 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.renderer.seqfeatures.FeatureColourFinder;
 import jalview.structure.AtomSpec;
 import jalview.structure.StructureListener;
 import jalview.structure.StructureMapping;
@@ -67,7 +70,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   int my = 0;
 
-  public PDBfile pdb;
+  public StructureFile pdb;
 
   PDBEntry pdbentry;
 
@@ -144,7 +147,7 @@ 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;
@@ -158,9 +161,9 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     {
       pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
 
-      if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+      if (protocol == DataSourceType.PASTE)
       {
-        pdbentry.setFile("INLINE" + pdb.id);
+        pdbentry.setFile("INLINE" + pdb.getId());
       }
 
     } catch (Exception ex)
@@ -169,13 +172,13 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       return;
     }
 
-    pdbentry.setId(pdb.id);
+    pdbentry.setId(pdb.getId());
 
     ssm.addStructureViewerListener(this);
 
     colourBySequence();
 
-    int max = -10;
+    float max = -10;
     int maxchain = -1;
     int pdbstart = 0;
     int pdbend = 0;
@@ -185,30 +188,34 @@ public class AppletPDBCanvas extends Panel 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());
+      mappingDetails
+              .append("\n\nPDB Sequence is :\nSequence = "
+                      + 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
       // TODO: DNa/Pep switch
       AlignSeq as = new AlignSeq(sequence,
-              pdb.chains.elementAt(i).sequence,
-              pdb.chains.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");
@@ -232,7 +239,7 @@ public class AppletPDBCanvas extends Panel 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;
@@ -267,6 +274,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
     addKeyListener(new KeyAdapter()
     {
+      @Override
       public void keyPressed(KeyEvent evt)
       {
         doKeyPressed(evt);
@@ -289,11 +297,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     // Sort the bonds by z coord
     visiblebonds = new Vector<Bond>();
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (pdb.getChains().elementAt(ii).isVisible)
       {
-        Vector<Bond> tmp = pdb.chains.elementAt(ii).bonds;
+        Vector<Bond> tmp = pdb.getChains().elementAt(ii).bonds;
 
         for (int i = 0; i < tmp.size(); i++)
         {
@@ -320,11 +328,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     min[1] = (float) 1e30;
     min[2] = (float) 1e30;
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (pdb.getChains().elementAt(ii).isVisible)
       {
-        Vector<Bond> bonds = pdb.chains.elementAt(ii).bonds;
+        Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
 
         for (Bond tmp : bonds)
         {
@@ -448,11 +456,11 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     int bsize = 0;
 
     // Find centre coordinate
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (int ii = 0; ii < pdb.getChains().size(); ii++)
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (pdb.getChains().elementAt(ii).isVisible)
       {
-        Vector<Bond> bonds = pdb.chains.elementAt(ii).bonds;
+        Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
 
         bsize += bonds.size();
 
@@ -470,6 +478,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     centre[2] = ztot / (2 * (float) bsize);
   }
 
+  @Override
   public void paint(Graphics g)
   {
 
@@ -569,12 +578,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
       showFeatures = true;
     }
 
+    FeatureColourFinder finder = new FeatureColourFinder(fr);
+
     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++)
         {
@@ -596,25 +607,16 @@ public class AppletPDBCanvas extends Panel 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);
                 }
-
               }
             }
           }
@@ -774,6 +776,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     pdbAction = true;
@@ -786,7 +789,7 @@ public class AppletPDBCanvas extends Panel 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)
@@ -818,6 +821,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     dragging = false;
   }
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     pdbAction = true;
@@ -834,7 +838,7 @@ public class AppletPDBCanvas extends Panel 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);
@@ -860,18 +864,22 @@ 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();
@@ -893,7 +901,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     }
 
     // Alter the bonds
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       for (Bond tmpBond : chain.bonds)
       {
@@ -921,6 +929,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     repaint();
   }
 
+  @Override
   public void mouseReleased(MouseEvent evt)
   {
     dragging = false;
@@ -930,7 +939,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
   void drawLabels(Graphics g)
   {
 
-    for (PDBChain chain : pdb.chains)
+    for (PDBChain chain : pdb.getChains())
     {
       if (chain.isVisible)
       {
@@ -981,15 +990,15 @@ public class AppletPDBCanvas extends Panel 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;
 
       if (chain.isVisible)
       {
-        Vector<Bond> bonds = pdb.chains.elementAt(ii).bonds;
+        Vector<Bond> bonds = pdb.getChains().elementAt(ii).bonds;
 
         for (int i = 0; i < bonds.size(); i++)
         {
@@ -1030,13 +1039,14 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
       if (fatom != null) // )&& chain.ds != null)
       {
-        chain = pdb.chains.elementAt(foundchain);
+        chain = pdb.getChains().elementAt(foundchain);
       }
     }
 
     return fatom;
   }
 
+  @Override
   public void update(Graphics g)
   {
     paint(g);
@@ -1096,9 +1106,9 @@ public class AppletPDBCanvas extends Panel 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;
@@ -1108,7 +1118,8 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
 
   // ////////////////////////////////
   // /StructureListener
-  public String[] getPdbFile()
+  @Override
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }
@@ -1210,6 +1221,7 @@ public class AppletPDBCanvas extends Panel implements MouseListener,
     // return new Color(viewer.getAtomArgb(atomIndex));
   }
 
+  @Override
   public void updateColours(Object source)
   {
     colourBySequence();