X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=e27c6661b03ca2c46ac29b3e522b29d40f6c35a4;hb=refs%2Fheads%2Ffeatures%2FJAL-1780_export-settings_flatfile;hp=2d59f2923d47c6e26de137919f486a8b7b3ebf99;hpb=a9315b41e948f66f4632f7d419fda643bc0b9354;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 2d59f29..e27c666 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,34 +1,43 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import jalview.api.ComplexAlignFile;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.Jalview2XML;
-
-import java.util.StringTokenizer;
-import java.util.Vector;
-
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import javax.swing.JOptionPane;
-import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
@@ -145,6 +154,7 @@ public class FileLoader implements Runnable
public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
{
this.source = source;
+
file = source.getInFile();
protocol = source.type;
this.format = format;
@@ -269,7 +279,7 @@ public class FileLoader implements Runnable
.println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
// We read the data anyway - it might make sense.
}
- alignFrame = new Jalview2XML(raiseGUI).LoadJalviewAlign(file);
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file);
}
else
{
@@ -289,7 +299,7 @@ public class FileLoader implements Runnable
// open a new source and read from it
FormatAdapter fa = new FormatAdapter();
al = fa.readFile(file, protocol, format);
- source = fa.afile; // keep reference for later if necessary.
+ source = fa.getAlignFile(); // keep reference for later if necessary.
}
} catch (java.io.IOException ex)
{
@@ -304,35 +314,69 @@ public class FileLoader implements Runnable
error = format + "\n" + error;
}
}
-
+
if ((al != null) && (al.getHeight() > 0))
{
- if (viewport != null)
+ for (SequenceI sq : al.getSequences())
{
- // TODO: create undo object for this JAL-1101
- for (int i = 0; i < al.getHeight(); i++)
+ while (sq.getDatasetSequence() != null)
{
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getPDBId() != null)
+ {
+ for (PDBEntry pdbe : sq.getPDBId())
+ {
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
-
+ }
+ if (viewport != null)
+ {
+ viewport.addAlignment(al, title);
}
else
{
- alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
-
- alignFrame.statusBar.setText("Successfully loaded file "
- + title);
-
if (!protocol.equals(AppletFormatAdapter.PASTE))
+ {
alignFrame.setFileName(file, format);
+ }
+ if (source instanceof ComplexAlignFile)
+ {
+ ColumnSelection colSel = ((ComplexAlignFile) source)
+ .getColumnSelection();
+ SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
+ .getHiddenSequences();
+ boolean showSeqFeatures = ((ComplexAlignFile) source)
+ .isShowSeqFeatures();
+ ColourSchemeI cs = ((ComplexAlignFile) source)
+ .getColourScheme();
+ alignFrame = new AlignFrame(al, hiddenSeqs, colSel,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ alignFrame.getViewport().setShowSequenceFeatures(
+ showSeqFeatures);
+ alignFrame.changeColour(cs);
+ }
+ else
+ {
+ alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ }
+
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { title }));
+
if (raiseGUI)
{
// add the window to the GUI
- // note - this actually should happen regardless of raiseGUI status in Jalview 3
- // TODO: define 'virtual desktop' for benefit of headless scripts that perform queries to find the 'current working alignment'
+ // note - this actually should happen regardless of raiseGUI
+ // 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,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
}
@@ -362,7 +406,8 @@ public class FileLoader implements Runnable
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, MessageManager.getString("label.error_loading_file"),
+ errorMessage, MessageManager
+ .getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
@@ -387,8 +432,10 @@ public class FileLoader implements Runnable
public void run()
{
javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage("label.problems_opening_file", new String[]{file}),
- MessageManager.getString("label.file_open_error"),
+ Desktop.desktop, MessageManager.formatMessage(
+ "label.problems_opening_file", new String[]
+ { file }), MessageManager
+ .getString("label.file_open_error"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
@@ -408,11 +455,8 @@ public class FileLoader implements Runnable
javax.swing.JOptionPane
.showInternalMessageDialog(
Desktop.desktop,
- "Out of memory loading file "
- + file
- + "!!"
- + "\nSee help files for increasing Java Virtual Machine memory.",
- "Out of memory",
+ MessageManager.formatMessage("warn.out_of_memory_loading_file", new String[]{file}),
+ MessageManager.getString("label.out_of_memory"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});