Resolved diffs from 2.8.3

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b30b28f..5ed494e 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 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.
  * 
@@ -20,6 +20,44 @@
  */
 package jalview.gui;
 
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Unmarshaller;
+
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignedCodonFrame;
@@ -83,44 +121,6 @@ import jalview.ws.params.ArgumentI;
 import jalview.ws.params.AutoCalcSetting;
 import jalview.ws.params.WsParamSetI;
 
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
-
-import org.exolab.castor.xml.Unmarshaller;
-
 /**
  * Write out the current jalview desktop state as a Jalview XML stream.
  * 
@@ -682,9 +682,9 @@ public class Jalview2XML
         }
       }
 
-      if (jdatasq.getSequenceFeatures() != null)
+      if (jds.getSequenceFeatures() != null)
       {
-        jalview.datamodel.SequenceFeature[] sf = jdatasq
+        jalview.datamodel.SequenceFeature[] sf = jds
                 .getSequenceFeatures();
         int index = 0;
         while (index < sf.length)
@@ -1056,20 +1056,14 @@ public class Jalview2XML
       view.setGatheredViews(av.isGatherViewsHere());
 
       Rectangle position = ap.av.getExplodedGeometry();
-      if (position != null)
-      {
-        view.setXpos(position.x);
-        view.setYpos(position.y);
-        view.setWidth(position.width);
-        view.setHeight(position.height);
-      }
-      else
+      if (position == null)
       {
-        view.setXpos(ap.alignFrame.getBounds().x);
-        view.setYpos(ap.alignFrame.getBounds().y);
-        view.setWidth(ap.alignFrame.getBounds().width);
-        view.setHeight(ap.alignFrame.getBounds().height);
+        position = ap.alignFrame.getBounds();
       }
+      view.setXpos(position.x);
+      view.setYpos(position.y);
+      view.setWidth(position.width);
+      view.setHeight(position.height);
 
       view.setStartRes(av.startRes);
       view.setStartSeq(av.startSeq);
@@ -1787,20 +1781,20 @@ public class Jalview2XML
       mp = new Mapping();
 
       jalview.util.MapList mlst = jmp.getMap();
-      int r[] = mlst.getFromRanges();
-      for (int s = 0; s < r.length; s += 2)
+      List<int[]> r = mlst.getFromRanges();
+      for (int[] range : r)
       {
         MapListFrom mfrom = new MapListFrom();
-        mfrom.setStart(r[s]);
-        mfrom.setEnd(r[s + 1]);
+        mfrom.setStart(range[0]);
+        mfrom.setEnd(range[1]);
         mp.addMapListFrom(mfrom);
       }
       r = mlst.getToRanges();
-      for (int s = 0; s < r.length; s += 2)
+      for (int[] range : r)
       {
         MapListTo mto = new MapListTo();
-        mto.setStart(r[s]);
-        mto.setEnd(r[s + 1]);
+        mto.setStart(range[0]);
+        mto.setEnd(range[1]);
         mp.addMapListTo(mto);
       }
       mp.setMapFromUnit(mlst.getFromRatio());
@@ -2263,17 +2257,19 @@ public class Jalview2XML
   protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
           AlignFrame proteinFrame)
   {
-    dnaFrame.setVisible(true);
-    proteinFrame.setVisible(true);
-    proteinFrame.getViewport().setCodingComplement(dnaFrame.getViewport());
-    final StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    ssm.addCommandListener(proteinFrame.getViewport());
-    ssm.addCommandListener(dnaFrame.getViewport());
-
     SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
     String title = MessageManager.getString("label.linked_view_title");
-    Desktop.addInternalFrame(splitFrame, title, -1, -1);
+    int width = (int) dnaFrame.getBounds().getWidth();
+    int height = (int) (dnaFrame.getBounds().getHeight()
+            + proteinFrame.getBounds().getHeight() + 50);
+    Desktop.addInternalFrame(splitFrame, title, width, height);
+
+    /*
+     * And compute cDNA consensus (couldn't do earlier with consensus as
+     * mappings were not yet present)
+     */
+    proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+
     return splitFrame;
   }