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Scrolls if dragged off the screen
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML.java
diff --git
a/src/jalview/gui/Jalview2XML.java
b/src/jalview/gui/Jalview2XML.java
index
893846c
..
5a4b03a
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML.java
+++ b/
src/jalview/gui/Jalview2XML.java
@@
-18,10
+18,11
@@
*/
\r
package jalview.gui;
\r
\r
*/
\r
package jalview.gui;
\r
\r
-import jalview.io.*;
\r
\r
import jalview.schemes.*;
\r
\r
\r
import jalview.schemes.*;
\r
\r
+import jalview.gui.*;
\r
+
\r
import java.io.*;
\r
\r
import java.net.*;
\r
import java.io.*;
\r
\r
import java.net.*;
\r
@@
-32,7
+33,11
@@
import java.util.jar.*;
\r
import javax.swing.*;
\r
\r
\r
import javax.swing.*;
\r
\r
-import jalview.binding.*;
\r
+import org.exolab.castor.xml.*;
\r
+
\r
+import jalview.schemabinding.version2.*;
\r
+
\r
+
\r
\r
\r
/**
\r
\r
\r
/**
\r
@@
-44,7
+49,7
@@
import jalview.binding.*;
public class Jalview2XML
\r
{
\r
// SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
\r
public class Jalview2XML
\r
{
\r
// SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE
\r
- public static void SaveState(File statefile)
\r
+ public void SaveState(File statefile)
\r
{
\r
long creation = System.currentTimeMillis();
\r
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
\r
{
\r
long creation = System.currentTimeMillis();
\r
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
\r
@@
-116,7
+121,7
@@
public class Jalview2XML
}
\r
\r
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
\r
}
\r
\r
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
\r
- public static void SaveAlignment(AlignFrame af, String jarFile,
\r
+ public void SaveAlignment(AlignFrame af, String jarFile,
\r
String fileName)
\r
{
\r
try
\r
String fileName)
\r
{
\r
try
\r
@@
-148,7
+153,7
@@
public class Jalview2XML
* @param jout DOCUMENT ME!
\r
* @param out DOCUMENT ME!
\r
*/
\r
* @param jout DOCUMENT ME!
\r
* @param out DOCUMENT ME!
\r
*/
\r
- public static void SaveState(AlignFrame af, long timeStamp,
\r
+ public void SaveState(AlignFrame af, long timeStamp,
\r
String fileName, JarOutputStream jout, PrintWriter out)
\r
{
\r
Vector seqids = new Vector();
\r
String fileName, JarOutputStream jout, PrintWriter out)
\r
{
\r
Vector seqids = new Vector();
\r
@@
-157,7
+162,7
@@
public class Jalview2XML
AlignViewport av = af.viewport;
\r
\r
JalviewModel object = new JalviewModel();
\r
AlignViewport av = af.viewport;
\r
\r
JalviewModel object = new JalviewModel();
\r
- object.setVamsasModel(new jalview.binding.VamsasModel());
\r
+ object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
\r
\r
object.setCreationDate(new java.util.Date(timeStamp));
\r
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
\r
\r
object.setCreationDate(new java.util.Date(timeStamp));
\r
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
\r
@@
-316,6
+321,9
@@
public class Jalview2XML
an.setGraph(true);
\r
an.setGraphType(aa[i].graph);
\r
}
\r
an.setGraph(true);
\r
an.setGraphType(aa[i].graph);
\r
}
\r
+ else
\r
+ an.setGraph(false);
\r
+
\r
an.setLabel(aa[i].label);
\r
\r
AnnotationElement ae;
\r
an.setLabel(aa[i].label);
\r
\r
AnnotationElement ae;
\r
@@
-461,7
+469,8
@@
public class Jalview2XML
\r
if(av.featuresDisplayed!=null)
\r
{
\r
\r
if(av.featuresDisplayed!=null)
\r
{
\r
- jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings();
\r
+ jalview.schemabinding.version2.FeatureSettings fs
\r
+ = new jalview.schemabinding.version2.FeatureSettings();
\r
\r
Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
\r
while (e.hasMoreElements())
\r
\r
Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
\r
while (e.hasMoreElements())
\r
@@
-508,7
+517,7
@@
public class Jalview2XML
}
\r
}
\r
\r
}
\r
}
\r
\r
- static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
\r
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
\r
Vector userColours, JalviewModelSequence jms)
\r
{
\r
String id = null;
\r
Vector userColours, JalviewModelSequence jms)
\r
{
\r
String id = null;
\r
@@
-519,12
+528,12
@@
public class Jalview2XML
userColours.add(ucs);
\r
\r
java.awt.Color[] colours = ucs.getColours();
\r
userColours.add(ucs);
\r
\r
java.awt.Color[] colours = ucs.getColours();
\r
- jalview.binding.UserColours uc = new jalview.binding.UserColours();
\r
- jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();
\r
+ jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
\r
+ jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
\r
\r
for (int i = 0; i < colours.length; i++)
\r
{
\r
\r
for (int i = 0; i < colours.length; i++)
\r
{
\r
- jalview.binding.Colour col = new jalview.binding.Colour();
\r
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();
\r
col.setRGB(jalview.util.Format.getHexString(colours[i]));
\r
jbucs.addColour(col);
\r
}
\r
col.setRGB(jalview.util.Format.getHexString(colours[i]));
\r
jbucs.addColour(col);
\r
}
\r
@@
-538,7
+547,7
@@
public class Jalview2XML
return id;
\r
}
\r
\r
return id;
\r
}
\r
\r
- static jalview.schemes.UserColourScheme GetUserColourScheme(
\r
+ jalview.schemes.UserColourScheme GetUserColourScheme(
\r
JalviewModelSequence jms, String id)
\r
{
\r
UserColours[] uc = jms.getUserColours();
\r
JalviewModelSequence jms, String id)
\r
{
\r
UserColours[] uc = jms.getUserColours();
\r
@@
-571,9
+580,9
@@
public class Jalview2XML
*
\r
* @param file DOCUMENT ME!
\r
*/
\r
*
\r
* @param file DOCUMENT ME!
\r
*/
\r
- public static AlignFrame LoadJalviewAlign(String file)
\r
+ public AlignFrame LoadJalviewAlign(String file)
\r
{
\r
{
\r
- JalviewModel object = new JalviewModel();
\r
+
\r
jalview.gui.AlignFrame af = null;
\r
\r
try
\r
jalview.gui.AlignFrame af = null;
\r
\r
try
\r
@@
-604,12
+613,28
@@
public class Jalview2XML
for (int i = 0; i < entryCount; i++)
\r
{
\r
jarentry = jin.getNextJarEntry();
\r
for (int i = 0; i < entryCount; i++)
\r
{
\r
jarentry = jin.getNextJarEntry();
\r
- }
\r
+
\r
+ }
\r
+
\r
+
\r
+ class NoDescIDResolver implements IDResolver
\r
+ {
\r
+ public Object resolve(String idref)
\r
+ {
\r
+ System.out.println(idref+" used");
\r
+ return null;
\r
+ }
\r
+ }
\r
+
\r
\r
if (jarentry != null)
\r
{
\r
InputStreamReader in = new InputStreamReader(jin, "UTF-8");
\r
\r
if (jarentry != null)
\r
{
\r
InputStreamReader in = new InputStreamReader(jin, "UTF-8");
\r
- object = (JalviewModel) object.unmarshal(in);
\r
+ JalviewModel object = new JalviewModel();
\r
+
\r
+ Unmarshaller unmar = new Unmarshaller(object);
\r
+ object = (JalviewModel) unmar.unmarshal( in );
\r
+
\r
af = LoadFromObject(object);
\r
entryCount++;
\r
}
\r
af = LoadFromObject(object);
\r
entryCount++;
\r
}
\r
@@
-629,6
+654,14
@@
public class Jalview2XML
}
\r
catch (Exception ex)
\r
{
\r
}
\r
catch (Exception ex)
\r
{
\r
+ //Is Version 1 Jar file?
\r
+ af = new Jalview2XML_V1().LoadJalviewAlign(file);
\r
+
\r
+ if(af!=null)
\r
+ {
\r
+ System.out.println("Successfuly loaded archive file");
\r
+ return af;
\r
+ }
\r
ex.printStackTrace();
\r
System.err.println("Exception whilst loading jalview XML file : " +
\r
ex + "\n");
\r
ex.printStackTrace();
\r
System.err.println("Exception whilst loading jalview XML file : " +
\r
ex + "\n");
\r
@@
-642,7
+675,7
@@
public class Jalview2XML
return af;
\r
}
\r
\r
return af;
\r
}
\r
\r
- static AlignFrame LoadFromObject(JalviewModel object)
\r
+ AlignFrame LoadFromObject(JalviewModel object)
\r
{
\r
Vector seqids = new Vector();
\r
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
\r
{
\r
Vector seqids = new Vector();
\r
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
\r
@@
-963,3
+996,4
@@
public class Jalview2XML
return af;
\r
}
\r
}
\r
return af;
\r
}
\r
}
\r
+
\r