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Merge branch 'Jalview-JS/develop' into merge_js_develop
[jalview.git]
/
src
/
jalview
/
io
/
FileLoader.java
diff --git
a/src/jalview/io/FileLoader.java
b/src/jalview/io/FileLoader.java
index
31a4deb
..
df64702
100755
(executable)
--- a/
src/jalview/io/FileLoader.java
+++ b/
src/jalview/io/FileLoader.java
@@
-20,6
+20,7
@@
*/
package jalview.io;
*/
package jalview.io;
+import java.awt.Dimension;
import java.io.File;
import java.io.IOException;
import java.util.StringTokenizer;
import java.io.File;
import java.io.IOException;
import java.util.StringTokenizer;
@@
-46,6
+47,7
@@
import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.schemes.ColourSchemeI;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.utils.UrlDownloadClient;
import java.util.ArrayList;
import jalview.ws.utils.UrlDownloadClient;
import java.util.ArrayList;
@@
-301,9
+303,9
@@
public class FileLoader implements Runnable
Runtime rt = Runtime.getRuntime();
try
{
Runtime rt = Runtime.getRuntime();
try
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
{
- Desktop.instance.startLoading(file);
+ Desktop.getInstance().startLoading(file);
}
if (format == null)
{
}
if (format == null)
{
@@
-325,12
+327,12
@@
public class FileLoader implements Runnable
if (format == null)
{
if (format == null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
+ AppletFormatAdapter.getSupportedFormats(),
@@
-341,7
+343,7
@@
public class FileLoader implements Runnable
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
System.gc();
memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
{
System.gc();
memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@
-434,7
+436,7
@@
public class FileLoader implements Runnable
// register PDB entries with desktop's structure selection
// manager
StructureSelectionManager
// register PDB entries with desktop's structure selection
// manager
StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ .getStructureSelectionManager(Desktop.getInstance())
.registerPDBEntry(pdbe);
}
}
.registerPDBEntry(pdbe);
}
}
@@
-505,8
+507,7
@@
public class FileLoader implements Runnable
// add metadata and update ui
if (!(protocol == DataSourceType.PASTE))
{
// add metadata and update ui
if (!(protocol == DataSourceType.PASTE))
{
- alignFrame.setFileName(file, format);
- alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+ alignFrame.setFile(file, selectedFile, protocol, format);
}
if (proxyColourScheme != null)
{
}
if (proxyColourScheme != null)
{
@@
-524,8
+525,12
@@
public class FileLoader implements Runnable
// status in Jalview 3
// TODO: define 'virtual desktop' for benefit of headless scripts
// that perform queries to find the 'current working alignment'
// status in Jalview 3
// TODO: define 'virtual desktop' for benefit of headless scripts
// that perform queries to find the 'current working alignment'
- Desktop.addInternalFrame(alignFrame, title,
+
+ Dimension dim = Platform.getDimIfEmbedded(alignFrame,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.setSize(dim);
+ Desktop.addInternalFrame(alignFrame, title, dim.width,
+ dim.height);
}
try
}
try
@@
-539,23
+544,23
@@
public class FileLoader implements Runnable
}
else
{
}
else
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
final String errorMessage = MessageManager.getString(
"label.couldnt_load_file") + " " + title + "\n" + error;
// TODO: refactor FileLoader to be independent of Desktop / Applet GUI
// bits ?
}
final String errorMessage = MessageManager.getString(
"label.couldnt_load_file") + " " + title + "\n" + error;
// TODO: refactor FileLoader to be independent of Desktop / Applet GUI
// bits ?
- if (raiseGUI && Desktop.desktop != null)
+ if (raiseGUI && Desktop.getDesktopPane() != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
errorMessage,
MessageManager
.getString("label.error_loading_file"),
errorMessage,
MessageManager
.getString("label.error_loading_file"),
@@
-588,7
+593,7
@@
public class FileLoader implements Runnable
@Override
public void run()
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.problems_opening_file", new String[]
{ file }),
MessageManager.formatMessage(
"label.problems_opening_file", new String[]
{ file }),
@@
-610,7
+615,7
@@
public class FileLoader implements Runnable
@Override
public void run()
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }),
MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }),
@@
-632,7
+637,7
@@
public class FileLoader implements Runnable
// memory
// after
// load
// memory
// after
// load
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
if (alignFrame != null)
{
{
if (alignFrame != null)
{
@@
-654,9
+659,9
@@
public class FileLoader implements Runnable
}
}
// remove the visual delay indicator
}
}
// remove the visual delay indicator
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
}
}
}