/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
- *
+ *
* 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.ws.EnfinEnvision2OneWay;
/**
* DOCUMENT ME!
String string = Cache
.getDefault(
"SEQUENCE_LINKS",
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
sequenceURLLinks = new Vector();
try
{
System.out.println(ex + "\nError parsing sequence links");
}
+ {
+ // upgrade old SRS link
+ int srsPos = sequenceURLLinks
+ .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ if (srsPos > -1)
+ {
+ sequenceURLLinks.setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
+ }
+ }
+
/**
* TODO: reformulate groupURL encoding so two or more can be stored in the
* .properties file as '|' separated strings
.getDefault("SHOW_NPFEATS_TOOLTIP", true));
showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
true));
-
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
{
colour.addItem(ColourSchemeProperty.getColourName(i));
/**
* default min-max colours for annotation shading
*/
- minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN", Color.orange));
- maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX", Color.red));
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
String[] fonts = java.awt.GraphicsEnvironment
.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
sortby.addItem("No sort");
sortby.addItem("Id");
epsRendering.addItem("Text");
epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
"Prompt each time"));
-
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ userIdWidth.setEnabled(autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ userIdWidth.setText(wi == null ? "" : wi.toString());
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("ANNOTATIONCOLOUR_MIN", minColour.getBackground().toString());
- Cache.applicationProperties.setProperty("ANNOTATIONCOLOUR_MAX", maxColour.getBackground().toString());
-
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+ minColour.getBackground());
+ Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+ maxColour.getBackground());
+
if (epsRendering.getSelectedItem().equals("Prompt each time"))
{
Cache.applicationProperties.remove("EPS_RENDERING");
Boolean.toString(modellerOutput.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+ Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Boolean.toString(autoIdWidth.isSelected()));
+ userIdWidth_actionPerformed();
+ Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ userIdWidth.getText());
+
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
+ Cache.applicationProperties.setProperty("SORT_BY_TREE",
+ Boolean.toString(sortByTree.isSelected()));
Cache.applicationProperties.setProperty("PAD_GAPS",
Boolean.toString(padGaps.isSelected()));
try
{
wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
frame.setClosed(true);
} catch (Exception ex)
{
{
return groupURLLinks;
}
+
public void minColour_actionPerformed()
{
Color col = JColorChooser.showDialog(this,
maxColour.repaint();
}
+ @Override
+ protected void userIdWidth_actionPerformed()
+ {
+ try
+ {
+ String val = userIdWidth.getText().trim();
+ if (val.length() > 0)
+ {
+ Integer iw = Integer.parseInt(val);
+ if (iw.intValue() < 12)
+ {
+ throw new NumberFormatException();
+ }
+ userIdWidth.setText(iw.toString());
+ }
+ } catch (NumberFormatException x)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
+ "Invalid ID Column width",
+ JOptionPane.WARNING_MESSAGE);
+ userIdWidth.setText("");
+ }
+ }
+
+ @Override
+ protected void autoIdWidth_actionPerformed()
+ {
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff