X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FAppletPDBCanvas.java;h=d0c7da86f0a4993d0edac204655fead035f2ace0;hb=a581135c768ce6c60c38bbd47003477f8c557eea;hp=0c7320d7104f6bf1071b984f3f05fd8180c141e4;hpb=05ecc2de6c739e536b7fe198a4cd2402491cc66f;p=jalview.git

diff --git a/src/MCview/AppletPDBCanvas.java b/src/MCview/AppletPDBCanvas.java
index 0c7320d..d0c7da8 100755
--- a/src/MCview/AppletPDBCanvas.java
+++ b/src/MCview/AppletPDBCanvas.java
@@ -1,17 +1,17 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
  * 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 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.
- *
+ * 
  * 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
@@ -83,6 +83,7 @@ public class AppletPDBCanvas
 
   public AppletPDBCanvas(PDBEntry pdbentry,
                          SequenceI[] seq,
+                         String [] chains,
                          AlignmentPanel ap,
                          String protocol)
 
@@ -94,9 +95,11 @@ public class AppletPDBCanvas
     ssm = StructureSelectionManager.getStructureSelectionManager();
 
     try{
-      pdb = ssm.setMapping(seq, pdbentry.getFile(), protocol);
-      //if (fr!=null)
-      //  fr.featuresAdded();
+      pdb = ssm.setMapping(seq, chains, pdbentry.getFile(), protocol);
+
+      if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
+       pdbentry.setFile("INLINE"+pdb.id);
+
     }catch(Exception ex)
     {
       ex.printStackTrace();
@@ -107,9 +110,7 @@ public class AppletPDBCanvas
 
     ssm.addStructureViewerListener(this);
 
-    colourBySequence(ap.getSequenceRenderer(),
-                     ap.av.getShowSequenceFeatures() ?
-                     ap.getFeatureRenderer() : null);
+    colourBySequence();
 
     int max = -10;
     int maxchain = -1;
@@ -117,7 +118,6 @@ public class AppletPDBCanvas
     int pdbend = 0;
     int seqstart = 0;
     int seqend = 0;
-    AlignSeq maxAlignseq = null;
 
     //JUST DEAL WITH ONE SEQUENCE FOR NOW
     SequenceI sequence = seq[0];
@@ -164,8 +164,7 @@ public class AppletPDBCanvas
         pdbend = as.seq2end;
         seqstart = as.seq1start + sequence.getStart() - 1;
         seqend = as.seq1end + sequence.getEnd() - 1;
-        maxAlignseq = as;
-      }
+       }
 
       mappingDetails.append("\nPDB start/end " + pdbstart + " " + pdbend);
       mappingDetails.append("\nSEQ start/end " + seqstart + " " + seqend);
@@ -240,9 +239,7 @@ public class AppletPDBCanvas
       }
     }
     seqColoursReady = true;
-    colourBySequence(ap.getSequenceRenderer(),
-                               ap.av.getShowSequenceFeatures() ?
-                               ap.getFeatureRenderer() : null);
+    colourBySequence();
     redrawneeded = true;
     repaint();
   }
@@ -497,18 +494,22 @@ public class AppletPDBCanvas
 
   // This method has been taken out of PDBChain to allow
   // Applet and Application specific sequence renderers to be used
-  void colourBySequence(SequenceRenderer sr, FeatureRenderer fr)
+  void colourBySequence()
   {
+    SequenceRenderer sr = new SequenceRenderer(ap.av);
+
     StructureMapping[] mapping = ssm.getMapping(pdbentry.getFile());
 
     boolean showFeatures = false;
-    if (fr!=null)
+    if (ap.av.getShowSequenceFeatures())
     {
       if (fr == null)
       {
         fr = new jalview.appletgui.FeatureRenderer(ap.av);
       }
-      fr.transferSettings(fr);
+
+      fr.transferSettings(ap.getFeatureRenderer());
+
       showFeatures = true;
     }
 
@@ -588,12 +589,12 @@ public class AppletPDBCanvas
 
       xstart = (int) ( ( (tmpBond.start[0] - centre[0]) * scale) +
                       (getSize().width / 2));
-      ystart = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+      ystart = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
                       (getSize().height / 2));
 
       xend = (int) ( ( (tmpBond.end[0] - centre[0]) * scale) +
                     (getSize().width / 2));
-      yend = (int) ( ( (tmpBond.end[1] - centre[1]) * scale) +
+      yend = (int) ( ( (centre[1] - tmpBond.end[1] ) * scale) +
                     (getSize().height / 2));
 
       xmid = (xend + xstart) / 2;
@@ -833,7 +834,7 @@ public class AppletPDBCanvas
     }
     else
     {
-      objmat.rotatex( (float) ( (my - omy)));
+      objmat.rotatex( (float) ( (omy - my)));
       objmat.rotatey( (float) ( (omx - mx)));
     }
 
@@ -914,7 +915,7 @@ public class AppletPDBCanvas
     {
       int xstart = (int) ( ( (b.start[0] - centre[0]) * scale) +
                           (getSize().width / 2));
-      int ystart = (int) ( ( (b.start[1] - centre[1]) * scale) +
+      int ystart = (int) ( ( (centre[1] - b.start[1]) * scale) +
                           (getSize().height / 2));
 
       g.setColor(Color.red);
@@ -925,7 +926,7 @@ public class AppletPDBCanvas
     {
       int xstart = (int) ( ( (b.end[0] - centre[0]) * scale) +
                           (getSize().width / 2));
-      int ystart = (int) ( ( (b.end[1] - centre[1]) * scale) +
+      int ystart = (int) ( ( (centre[1] - b.end[1]) * scale) +
                           (getSize().height / 2));
 
       g.setColor(Color.red);
@@ -959,7 +960,7 @@ public class AppletPDBCanvas
 
           if (Math.abs(truex - x) <= 2)
           {
-            int truey = (int) ( ( (tmpBond.start[1] - centre[1]) * scale) +
+            int truey = (int) ( ( (centre[1] - tmpBond.start[1] ) * scale) +
                                (getSize().height / 2));
 
             if (Math.abs(truey - y) <= 2)
@@ -1075,7 +1076,7 @@ public class AppletPDBCanvas
   ///StructureListener
   public String getPdbFile()
   {
-    return "???";
+    return pdbentry.getFile();
   }
 
 
@@ -1144,12 +1145,19 @@ public class AppletPDBCanvas
     repaint();
   }
 
+
+  public Color getColour(int atomIndex, int pdbResNum, String chain, String pdbfile)
+  {
+    return Color.white;
+   // if (!pdbfile.equals(pdbentry.getFile()))
+   //   return null;
+
+    //return new Color(viewer.getAtomArgb(atomIndex));
+  }
+
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.getSequenceRenderer(),
-                     ap.av.getShowSequenceFeatures() ?
-                     ap.getFeatureRenderer() : null);
+    colourBySequence();
     redrawneeded = true;
     repaint();
   }