From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 14 Nov 2005 18:36:10 +0000 (+0000)
Subject: Modifications for Applet PDB viewer
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=58d59957854fee335ca28d804297e0e0890bfa8a;p=jalview.git

Modifications for Applet PDB viewer
---

diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java
index 0d1dad3..0435d25 100755
--- a/src/jalview/appletgui/APopupMenu.java
+++ b/src/jalview/appletgui/APopupMenu.java
@@ -54,7 +54,7 @@ public class APopupMenu
   CheckboxMenuItem showText = new CheckboxMenuItem();
   CheckboxMenuItem showColourText = new CheckboxMenuItem();
 
-  public APopupMenu(AlignmentPanel apanel, Sequence seq, Vector links)
+  public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
   {
     ///////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -111,9 +111,32 @@ public class APopupMenu
           linkMenu.add(item);
       }
       add(linkMenu);
+
+      item = new MenuItem("Show PDB Structure");
+      item.addActionListener(new java.awt.event.ActionListener()
+           {
+               public void actionPerformed(ActionEvent e)
+               {
+                  addPDB(seq);
+               }
+           });
+
+      add(item);
+
+
     }
   }
 
+  void addPDB(Sequence seq)
+  {
+    CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);
+    cap.setText("Paste your PDB file here.");
+    cap.setPDBImport(seq, ap.seqPanel.seqCanvas);
+    Frame frame = new Frame();
+    frame.add(cap);
+    jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
+  }
+
   private void jbInit()
       throws Exception
   {
@@ -467,26 +490,6 @@ public class APopupMenu
     refresh();
   }
 
-  protected void analyze_actionPerformed(ActionEvent e)
-  {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
-    SequenceGroup sg = getGroup();
-    StringBuffer sb = new StringBuffer();
-
-    for (int i = 0; i < sg.sequences.size(); i++)
-    {
-      Sequence tmp = (Sequence) sg.sequences.elementAt(i);
-      sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
-      sb.append("\n");
-    }
-
-    sb.append("Something amazing will happen soon");
-    cap.setText(sb.toString());
-
-  }
 
   SequenceGroup getGroup()
   {
diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 7c3ab49..692c2fd 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -35,7 +35,7 @@ public class AlignFrame
     extends GAlignFrame
 {
   final AlignmentPanel alignPanel;
-  final AlignViewport viewport;
+  public final AlignViewport viewport;
   int NEW_WINDOW_WIDTH = 700;
   int NEW_WINDOW_HEIGHT = 500;
   jalview.bin.JalviewLite applet;
@@ -249,7 +249,6 @@ public class AlignFrame
   public void closeMenuItem_actionPerformed(ActionEvent e)
   {
     PaintRefresher.components.remove(viewport.alignment);
-    dispose();
     if(PaintRefresher.components.size()==0 && applet==null)
       System.exit(0);
   }
diff --git a/src/jalview/appletgui/CutAndPasteTransfer.java b/src/jalview/appletgui/CutAndPasteTransfer.java
index 6627e88..43ec65e 100755
--- a/src/jalview/appletgui/CutAndPasteTransfer.java
+++ b/src/jalview/appletgui/CutAndPasteTransfer.java
@@ -30,6 +30,11 @@ public class CutAndPasteTransfer
     extends GCutAndPasteTransfer
 {
   jalview.bin.JalviewLite applet;
+
+  boolean pdbImport = false;
+  Sequence seq;
+  SeqCanvas seqcanvas;
+
   public CutAndPasteTransfer(boolean forImport, jalview.bin.JalviewLite mainApplet)
   {
     super();
@@ -41,6 +46,14 @@ public class CutAndPasteTransfer
     }
   }
 
+  public void setPDBImport(Sequence seq, SeqCanvas seqcanvas)
+  {
+    this.seq = seq;
+    this.seqcanvas = seqcanvas;
+    pdbImport = true;
+  }
+
+
   public String getText()
   {
     return textarea.getText();
@@ -71,18 +84,24 @@ public class CutAndPasteTransfer
       return;
     }
 
-    SequenceI[] sequences = null;
-
-    String format = IdentifyFile.Identify(text, "Paste");
-    sequences = new AppletFormatAdapter().readFile(text, "Paste", format);
-
-    if (sequences != null)
+    if(pdbImport)
     {
-      AlignFrame af = new AlignFrame(new Alignment(sequences), applet,
-                                     "Cut & Paste input - " + format);
-      af.statusBar.setText("Successfully pasted alignment file");
+      new MCview.AppletPDBViewer(text, seq, seqcanvas);
     }
+    else
+    {
+      SequenceI[] sequences = null;
 
+      String format = IdentifyFile.Identify(text, "Paste");
+      sequences = new AppletFormatAdapter().readFile(text, "Paste", format);
+
+      if (sequences != null)
+      {
+        AlignFrame af = new AlignFrame(new Alignment(sequences), applet,
+                                       "Cut & Paste input - " + format);
+        af.statusBar.setText("Successfully pasted alignment file");
+      }
+    }
     Frame frame = (Frame)this.getParent();
     frame.setVisible(false);
   }
diff --git a/src/jalview/appletgui/MyGraphics.java b/src/jalview/appletgui/MyGraphics.java
index 835aff2..bcad0fb 100755
--- a/src/jalview/appletgui/MyGraphics.java
+++ b/src/jalview/appletgui/MyGraphics.java
@@ -5,17 +5,17 @@ public class MyGraphics
 {
   public static void AntiAlias(Graphics g)
   {
-    Graphics2D g2 = (Graphics2D)g;
-    g2.setRenderingHint( RenderingHints.KEY_ANTIALIASING,
-            RenderingHints.VALUE_ANTIALIAS_ON);
+  //  Graphics2D g2 = (Graphics2D)g;
+   // g2.setRenderingHint( RenderingHints.KEY_ANTIALIASING,
+   //         RenderingHints.VALUE_ANTIALIAS_ON);
   }
 
 
   public static void SetTransparency(Graphics g, float transparency)
     {
-      Graphics2D g2 = (Graphics2D) g;
-      g2.setComposite(
-          AlphaComposite.getInstance(
-              AlphaComposite.SRC_OVER, transparency));
+    //  Graphics2D g2 = (Graphics2D) g;
+     // g2.setComposite(
+      //    AlphaComposite.getInstance(
+      //        AlphaComposite.SRC_OVER, transparency));
     }
 }
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index ddc32e8..8984d62 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -51,7 +51,11 @@ public class SeqCanvas
     fr = new FeatureRenderer(av);
     sr = new SequenceRenderer(av);
     PaintRefresher.Register(this, av.alignment);
+  }
 
+  public AlignViewport getViewport()
+  {
+    return av;
   }
 
   public FeatureRenderer getFeatureRenderer()
@@ -59,6 +63,18 @@ public class SeqCanvas
     return fr;
   }
 
+  MCview.AppletPDBCanvas pdbViewer;
+  public SequenceRenderer getSequenceRenderer()
+  {
+    return sr;
+  }
+
+  public void setPDBViewer(MCview.AppletPDBCanvas pc)
+  {
+    pdbViewer = pc;
+  }
+
+
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)
   {
     int scalestartx = startx - startx % 10 + 10;
@@ -263,6 +279,10 @@ public class SeqCanvas
 
     g.drawImage(img, 0, 0, this);
 
+    if (pdbViewer != null)
+    {
+      pdbViewer.updateSeqColours();
+    }
   }
 
   int LABEL_WEST, LABEL_EAST;
diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index c413588..d546634 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -62,6 +62,12 @@ public class SequenceRenderer
     }
   }
 
+  public Color findSequenceColour(SequenceI seq, int i)
+  {
+    drawBoxes(seq, i,i, 0, 0, 1,1);
+    return resBoxColour;
+  }
+
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,
                            int start, int end, int x1, int y1, int width,
                            int height)