X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBCanvas.java;h=ab172f2cb8744b7c44b0c02f5adedce21c236557;hb=refs%2Fheads%2Ffeature%2FJAL-3180colourAnnotationMenu;hp=ae58758ff6e396ae33714923daeb28f3f3c01d8f;hpb=2888e7307e1f7c8239234941498cb86e8c65ab36;p=jalview.git

diff --git a/src/MCview/PDBCanvas.java b/src/MCview/PDBCanvas.java
index ae58758..ab172f2 100644
--- a/src/MCview/PDBCanvas.java
+++ b/src/MCview/PDBCanvas.java
@@ -55,8 +55,8 @@ 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;
 
@@ -153,7 +153,8 @@ 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.DataSourceType.PASTE))
       {
@@ -177,7 +178,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
 
     colourBySequence();
 
-    int max = -10;
+    float max = -10;
     int maxchain = -1;
     int pdbstart = 0;
     int pdbend = 0;
@@ -190,10 +191,9 @@ public class PDBCanvas extends JPanel implements MouseListener,
     for (int i = 0; i < pdb.getChains().size(); i++)
     {
 
-      mappingDetails
-              .append("\n\nPDB Sequence is :\nSequence = "
-                      + pdb.getChains().elementAt(i).sequence
-                              .getSequenceAsString());
+      mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+              + pdb.getChains().elementAt(i).sequence
+                      .getSequenceAsString());
       mappingDetails.append("\nNo of residues = "
               + pdb.getChains().elementAt(i).residues.size() + "\n\n");
 
@@ -575,23 +575,15 @@ 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 = finder.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 = finder.findFeatureColour(tmp.endCol,
-                            sequence[s], pos);
-                  }
+                  tmp.endCol = sr.getResidueColour(sequence[s], pos,
+                          finder);
                 }
 
               }
@@ -621,11 +613,15 @@ 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;
@@ -689,8 +685,8 @@ 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);
       }
 
@@ -826,8 +822,8 @@ 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
     {
@@ -937,16 +933,20 @@ 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);
     }
@@ -972,11 +972,13 @@ 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)
             {
@@ -989,11 +991,13 @@ 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)
           {
@@ -1083,7 +1087,7 @@ public class PDBCanvas extends JPanel implements MouseListener,
   // ////////////////////////////////
   // /StructureListener
   @Override
-  public String[] getPdbFile()
+  public String[] getStructureFiles()
   {
     return new String[] { pdbentry.getFile() };
   }