JAL-1780 JAL-653 Format/AppletFormat import and export pipeline regularised, uses...

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

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index 6f76a25..406d9f1 100644 (file)
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -20,17 +20,6 @@
  */
 package MCview;
 
-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;
@@ -52,6 +41,17 @@ import java.util.Vector;
 import javax.swing.JPanel;
 import javax.swing.ToolTipManager;
 
+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;
+
 public class PDBCanvas extends JPanel implements MouseListener,
         MouseMotionListener, StructureListener
 {
@@ -123,7 +123,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   PDBChain mainchain;
 
-  Vector highlightRes;
+  Vector<String> highlightRes;
 
   boolean pdbAction = false;
 
@@ -265,23 +265,21 @@ public class PDBCanvas extends JPanel implements MouseListener,
     ToolTipManager.sharedInstance().setDismissDelay(10000);
   }
 
-  Vector visiblebonds;
+  Vector<Bond> visiblebonds;
 
   void setupBonds()
   {
     seqColoursReady = false;
     // Sort the bonds by z coord
-    visiblebonds = new Vector();
+    visiblebonds = new Vector<Bond>();
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.chains)
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (chain.isVisible)
       {
-        Vector tmp = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < tmp.size(); i++)
+        for (Bond bond : chain.bonds)
         {
-          visiblebonds.addElement(tmp.elementAt(i));
+          visiblebonds.addElement(bond);
         }
       }
     }
@@ -305,16 +303,12 @@ public class PDBCanvas extends JPanel implements MouseListener,
     min[1] = (float) 1e30;
     min[2] = (float) 1e30;
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.chains)
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond tmp : chain.bonds)
         {
-          Bond tmp = (Bond) bonds.elementAt(i);
-
           if (tmp.start[0] >= max[0])
           {
             max[0] = tmp.start[0];
@@ -440,24 +434,17 @@ public class PDBCanvas extends JPanel implements MouseListener,
     int bsize = 0;
 
     // Find centre coordinate
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.chains)
     {
-      if (pdb.chains.elementAt(ii).isVisible)
+      if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
+        bsize += chain.bonds.size();
 
-        bsize += bonds.size();
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond bond : chain.bonds)
         {
-          xtot = xtot + ((Bond) bonds.elementAt(i)).start[0]
-                  + ((Bond) bonds.elementAt(i)).end[0];
-
-          ytot = ytot + ((Bond) bonds.elementAt(i)).start[1]
-                  + ((Bond) bonds.elementAt(i)).end[1];
-
-          ztot = ztot + ((Bond) bonds.elementAt(i)).start[2]
-                  + ((Bond) bonds.elementAt(i)).end[2];
+          xtot = xtot + bond.start[0] + bond.end[0];
+          ytot = ytot + bond.start[1] + bond.end[1];
+          ztot = ztot + bond.start[2] + bond.end[2];
         }
       }
     }
@@ -562,7 +549,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
         for (int i = 0; i < chain.bonds.size(); i++)
         {
-          Bond tmp = (Bond) chain.bonds.elementAt(i);
+          Bond tmp = chain.bonds.elementAt(i);
           tmp.startCol = Color.lightGray;
           tmp.endCol = Color.lightGray;
           if (chain != mainchain)
@@ -618,13 +605,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
         zsort = new Zsort();
       }
 
-      zsort.Zsort(visiblebonds);
+      zsort.sort(visiblebonds);
     }
 
     Bond tmpBond = null;
     for (int i = 0; i < visiblebonds.size(); i++)
     {
-      tmpBond = (Bond) visiblebonds.elementAt(i);
+      tmpBond = visiblebonds.elementAt(i);
 
       xstart = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
       ystart = (int) (((centre[1] - tmpBond.start[1]) * scale) + (getHeight() / 2));
@@ -779,16 +766,18 @@ public class PDBCanvas extends JPanel implements MouseListener,
           {
             if (highlightRes == null)
             {
-              highlightRes = new Vector();
+              highlightRes = new Vector<String>();
             }
 
-            if (highlightRes.contains(fatom.alignmentMapping + ""))
+            final String atomString = Integer
+                    .toString(fatom.alignmentMapping);
+            if (highlightRes.contains(atomString))
             {
-              highlightRes.remove(fatom.alignmentMapping + "");
+              highlightRes.remove(atomString);
             }
             else
             {
-              highlightRes.add(fatom.alignmentMapping + "");
+              highlightRes.add(atomString);
             }
           }
         }
@@ -870,14 +859,10 @@ public class PDBCanvas extends JPanel implements MouseListener,
     }
 
     // Alter the bonds
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.chains)
     {
-      Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-      for (int i = 0; i < bonds.size(); i++)
+      for (Bond tmpBond : chain.bonds)
       {
-        Bond tmpBond = (Bond) bonds.elementAt(i);
-
         // Translate the bond so the centre is 0,0,0
         tmpBond.translate(-centre[0], -centre[1], -centre[2]);
 
@@ -911,18 +896,12 @@ public class PDBCanvas extends JPanel implements MouseListener,
   void drawLabels(Graphics g)
   {
 
-    for (int ii = 0; ii < pdb.chains.size(); ii++)
+    for (PDBChain chain : pdb.chains)
     {
-      PDBChain chain = pdb.chains.elementAt(ii);
-
       if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond tmpBond : chain.bonds)
         {
-          Bond tmpBond = (Bond) bonds.elementAt(i);
-
           if (tmpBond.at1.isSelected)
           {
             labelAtom(g, tmpBond, 1);
@@ -930,7 +909,6 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
           if (tmpBond.at2.isSelected)
           {
-
             labelAtom(g, tmpBond, 2);
           }
         }
@@ -975,11 +953,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
       if (chain.isVisible)
       {
-        Vector bonds = pdb.chains.elementAt(ii).bonds;
-
-        for (int i = 0; i < bonds.size(); i++)
+        for (Bond bond : chain.bonds)
         {
-          tmpBond = (Bond) bonds.elementAt(i);
+          tmpBond = bond;
 
           truex = (int) (((tmpBond.start[0] - centre[0]) * scale) + (getWidth() / 2));
 
@@ -1015,7 +991,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
       }
 
       if (fatom != null) // )&& chain.ds != null)
-      {
+      { // dead code? value of chain is either overwritten or discarded
         chain = pdb.chains.elementAt(foundchain);
       }
     }
@@ -1041,7 +1017,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     Bond tmpBond;
     for (index = 0; index < mainchain.bonds.size(); index++)
     {
-      tmpBond = (Bond) mainchain.bonds.elementAt(index);
+      tmpBond = mainchain.bonds.elementAt(index);
       if (tmpBond.at1.alignmentMapping == ii - 1)
       {
         if (highlightBond1 != null)
@@ -1059,13 +1035,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
         if (index > 0)
         {
-          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+          highlightBond1 = mainchain.bonds.elementAt(index - 1);
           highlightBond1.at2.isSelected = true;
         }
 
         if (index != mainchain.bonds.size())
         {
-          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+          highlightBond2 = mainchain.bonds.elementAt(index);
           highlightBond2.at1.isSelected = true;
         }
 
@@ -1153,7 +1129,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
     Bond tmpBond;
     for (index = 0; index < mainchain.bonds.size(); index++)
     {
-      tmpBond = (Bond) mainchain.bonds.elementAt(index);
+      tmpBond = mainchain.bonds.elementAt(index);
       if (tmpBond.at1.atomIndex == atomIndex)
       {
         if (highlightBond1 != null)
@@ -1171,13 +1147,13 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
         if (index > 0)
         {
-          highlightBond1 = (Bond) mainchain.bonds.elementAt(index - 1);
+          highlightBond1 = mainchain.bonds.elementAt(index - 1);
           highlightBond1.at2.isSelected = true;
         }
 
         if (index != mainchain.bonds.size())
         {
-          highlightBond2 = (Bond) mainchain.bonds.elementAt(index);
+          highlightBond2 = mainchain.bonds.elementAt(index);
           highlightBond2.at1.isSelected = true;
         }
 
@@ -1210,4 +1186,19 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
   }
 
+  @Override
+  public boolean isListeningFor(SequenceI seq)
+  {
+    if (sequence != null)
+    {
+      for (SequenceI s : sequence)
+      {
+        if (s == seq)
+        {
+          return true;
+        }
+      }
+    }
+    return false;
+  }
 }