/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
*
* 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
import jalview.io.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.ws.EnfinEnvision2OneWay;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
height = 460;
}
- Desktop.addInternalFrame(frame, "Preferences", width, height);
+ Desktop.addInternalFrame(frame, MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
.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));
colour.setSelectedItem(string);
+ /**
+ * default min-max colours for annotation shading
+ */
+ 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));
public void ok_actionPerformed(ActionEvent e)
{
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean
- .toString(seqLimit.isSelected()));
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean
- .toString(rightAlign.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
- .toString(fullScreen.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
- .toString(openoverv.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean
- .toString(annotations.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean
- .toString(conservation.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean
- .toString(quality.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean
- .toString(identity.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
+ Boolean.toString(seqLimit.isSelected()));
+ Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
+ Boolean.toString(rightAlign.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_FULLSCREEN",
+ Boolean.toString(fullScreen.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_OVERVIEW",
+ Boolean.toString(openoverv.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.toString(annotations.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.toString(conservation.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_QUALITY",
+ Boolean.toString(quality.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_IDENTITY",
+ Boolean.toString(identity.isSelected()));
Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
.getSelectedItem().toString());
Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB
.getSelectedItem().toString());
- Cache.applicationProperties.setProperty("ID_ITALICS", Boolean
- .toString(idItalics.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean
- .toString(showUnconserved.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean
- .toString(showGroupConsensus.isSelected()));
+ Cache.applicationProperties.setProperty("ID_ITALICS",
+ Boolean.toString(idItalics.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_UNCONSERVED",
+ Boolean.toString(showUnconserved.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS",
+ Boolean.toString(showGroupConsensus.isSelected()));
Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
Boolean.toString(showGroupConservation.isSelected()));
Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
Boolean.toString(showConsensHistogram.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean
- .toString(showConsensLogo.isSelected()));
- Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
- .toString(smoothFont.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean
- .toString(showNpTooltip.isSelected()));
- Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean
- .toString(showDbRefTooltip.isSelected()));
-
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean
- .toString(wrap.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO",
+ Boolean.toString(showConsensLogo.isSelected()));
+ Cache.applicationProperties.setProperty("ANTI_ALIAS",
+ Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
+ Boolean.toString(showNpTooltip.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
+ Boolean.toString(showDbRefTooltip.isSelected()));
+
+ Cache.applicationProperties.setProperty("WRAP_ALIGNMENT",
+ Boolean.toString(wrap.isSelected()));
Cache.applicationProperties.setProperty("STARTUP_FILE",
startupFileTextfield.getText());
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean
- .toString(startupCheckbox.isSelected()));
+ Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",
+ Boolean.toString(startupCheckbox.isSelected()));
Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
.getSelectedItem().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");
}
// remove last "|"
links.setLength(links.length() - 1);
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
- .toString());
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ links.toString());
}
else
{
Cache.applicationProperties.remove("SEQUENCE_LINKS");
}
- Cache.applicationProperties.setProperty("USE_PROXY", Boolean
- .toString(useProxy.isSelected()));
+ Cache.applicationProperties.setProperty("USE_PROXY",
+ Boolean.toString(useProxy.isSelected()));
if (proxyServerTB.getText().trim().length() < 1)
{
}
else
{
- Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
- .getText());
+ Cache.applicationProperties.setProperty("PROXY_SERVER",
+ proxyServerTB.getText());
}
if (proxyPortTB.getText().trim().length() < 1)
}
else
{
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
- .getText());
+ Cache.applicationProperties.setProperty("PROXY_PORT",
+ proxyPortTB.getText());
}
if (useProxy.isSelected())
System.setProperty("http.proxyHost", "");
System.setProperty("http.proxyPort", "");
}
- Cache.setProperty("VERSION_CHECK", Boolean.toString(versioncheck
- .isSelected()));
+ Cache.setProperty("VERSION_CHECK",
+ Boolean.toString(versioncheck.isSelected()));
if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
{
// default is false - we only set this if the user has actively agreed
- Cache.setProperty("USAGESTATS", Boolean.toString(usagestats
- .isSelected()));
+ Cache.setProperty("USAGESTATS",
+ Boolean.toString(usagestats.isSelected()));
}
if (!questionnaire.isSelected())
{
// by just adding the given line
Cache.removeProperty("NOQUESTIONNAIRES");
}
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean
- .toString(blcjv.isSelected()));
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean
- .toString(clustaljv.isSelected()));
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean
- .toString(fastajv.isSelected()));
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean
- .toString(msfjv.isSelected()));
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean
- .toString(pfamjv.isSelected()));
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean
- .toString(pileupjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean
- .toString(pirjv.isSelected()));
- Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean
- .toString(modellerOutput.isSelected()));
+ Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
+ Boolean.toString(blcjv.isSelected()));
+ Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
+ Boolean.toString(clustaljv.isSelected()));
+ Cache.applicationProperties.setProperty("FASTA_JVSUFFIX",
+ Boolean.toString(fastajv.isSelected()));
+ Cache.applicationProperties.setProperty("MSF_JVSUFFIX",
+ Boolean.toString(msfjv.isSelected()));
+ Cache.applicationProperties.setProperty("PFAM_JVSUFFIX",
+ Boolean.toString(pfamjv.isSelected()));
+ Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX",
+ Boolean.toString(pileupjv.isSelected()));
+ Cache.applicationProperties.setProperty("PIR_JVSUFFIX",
+ Boolean.toString(pirjv.isSelected()));
+ Cache.applicationProperties.setProperty("PIR_MODELLER",
+ Boolean.toString(modellerOutput.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS", Boolean
- .toString(autoCalculateConsCheck.isSelected()));
- Cache.applicationProperties.setProperty("PAD_GAPS", Boolean
- .toString(padGaps.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()));
dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
*/
public void startupFileTextfield_mouseClicked()
{
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
- .getProperty("LAST_DIRECTORY"), new String[]
- { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
+ JalviewFileChooser chooser = new JalviewFileChooser(
+ jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
+ new String[]
+ { "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", "jar" },
new String[]
{ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
try
{
wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
frame.setClosed(true);
} catch (Exception ex)
{
while (!valid)
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+ MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!", "No link selected",
+ MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+ MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
if (index == -1)
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "No link selected!", "No link selected",
+ MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
JOptionPane.WARNING_MESSAGE);
return;
}
{
return groupURLLinks;
}
+
+ public void minColour_actionPerformed()
+ {
+ Color col = JColorChooser.showDialog(this,
+ "Select Colour for Minimum Value", minColour.getBackground());
+ if (col != null)
+ {
+ minColour.setBackground(col);
+ }
+ minColour.repaint();
+ }
+
+ public void maxColour_actionPerformed()
+ {
+ Color col = JColorChooser.showDialog(this,
+ "Select Colour for Maximum Value", maxColour.getBackground());
+ if (col != null)
+ {
+ maxColour.setBackground(col);
+ }
+ 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