X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=0f23ecd9cdc0f2aff87d5d04acc12e9479a04ad0;hpb=12045b681611d64529bdaf35f05d8cb0d9a2b054;p=jalview.git
diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 0f23ecd..78a21c8 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,33 +1,57 @@
/*
- * 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 2.9)
+ * Copyright (C) 2015 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.gui;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import jalview.bin.*;
-import jalview.io.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.util.Collection;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.help.HelpSetException;
+import javax.swing.JColorChooser;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
/**
* DOCUMENT ME!
@@ -37,6 +61,35 @@ import jalview.schemes.*;
*/
public class Preferences extends GPreferences
{
+ public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+ public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+ public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+ public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+ public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+ public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+ public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+ public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+ public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+ public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+ public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+ public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+ public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+ private static final int MIN_FONT_SIZE = 1;
+
+ private static final int MAX_FONT_SIZE = 30;
/**
* Holds name and link separated with | character. Sequence ID must be
@@ -86,9 +139,10 @@ public class Preferences extends GPreferences
.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);
+ sequenceURLLinks
+ .setElementAt(
+ "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+ srsPos);
}
}
@@ -98,9 +152,6 @@ public class Preferences extends GPreferences
*/
groupURLLinks = new Vector();
- // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
- // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-
}
Vector nameLinks, urlLinks;
@@ -116,23 +167,27 @@ public class Preferences extends GPreferences
*/
public Preferences()
{
-
+ super();
frame = new JInternalFrame();
frame.setContentPane(this);
dasSource = new DasSourceBrowser();
- dasPanel.add(dasSource, BorderLayout.CENTER);
+ dasTab.add(dasSource, BorderLayout.CENTER);
wsPrefs = new WsPreferences();
- wsPanel.add(wsPrefs, BorderLayout.CENTER);
- int width = 500, height = 420;
+ wsTab.add(wsPrefs, BorderLayout.CENTER);
+ int width = 500, height = 450;
if (new jalview.util.Platform().isAMac())
{
width = 570;
- height = 460;
+ height = 480;
}
- Desktop.addInternalFrame(frame, "Preferences", width, height);
+ Desktop.addInternalFrame(frame,
+ MessageManager.getString("label.preferences"), width, height);
frame.setMinimumSize(new Dimension(width, height));
+ /*
+ * Set Visual tab defaults
+ */
seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
@@ -144,37 +199,27 @@ public class Preferences extends GPreferences
openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
showUnconserved
.setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+ showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
+ false));
+ showGroupConservation.setSelected(Cache.getDefault(
+ "SHOW_GROUP_CONSERVATION", false));
+ showConsensHistogram.setSelected(Cache.getDefault(
+ "SHOW_CONSENSUS_HISTOGRAM", true));
+ showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
+ false));
showNpTooltip.setSelected(Cache
.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));
- }
-
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
- 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();
-
for (int i = 0; i < fonts.length; i++)
{
fontNameCB.addItem(fonts[i]);
}
- for (int i = 1; i < 31; i++)
+ for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
{
fontSizeCB.addItem(i + "");
}
@@ -189,6 +234,8 @@ public class Preferences extends GPreferences
+ ""));
smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+ scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+ false));
idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
@@ -199,52 +246,75 @@ public class Preferences extends GPreferences
gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
- startupCheckbox
- .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
-
sortby.addItem("No sort");
sortby.addItem("Id");
sortby.addItem("Pairwise Identity");
sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
- epsRendering.addItem("Prompt each time");
- epsRendering.addItem("Lineart");
- 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));
- msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
- pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
- pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
- pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
-
- modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+ sortAnnBy
+ .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+ SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+ .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+ SequenceAnnotationOrder.NONE.name()));
+ sortAnnBy.setSelectedItem(savedSort.toString());
+
+ sortAutocalc.addItem("Autocalculated first");
+ sortAutocalc.addItem("Autocalculated last");
+ final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+ sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+ : sortAutocalc.getItemAt(1));
+ startupCheckbox
+ .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+ startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+ Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+ + "/examples/exampleFile_2_3.jar"));
- autoCalculateConsCheck.setSelected(Cache.getDefault(
- "AUTO_CALC_CONSENSUS", true));
- showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
- false));
- showGroupConservation.setSelected(Cache.getDefault(
- "SHOW_GROUP_CONSERVATION", false));
- showConsensHistogram.setSelected(Cache.getDefault(
- "SHOW_CONSENSUS_HISTOGRAM", true));
- showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
- false));
+ /*
+ * Set Colours tab defaults
+ */
+ for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+ {
+ protColour.addItem(ColourSchemeProperty.getColourName(i));
+ nucColour.addItem(ColourSchemeProperty.getColourName(i));
+ }
+ String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+ String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+ protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+ nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
+ minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+ Color.orange));
+ maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+ Color.red));
- padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ /*
+ * Set Structure tab defaults.
+ */
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ structFromPdb.setSelected(structSelected);
+ useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+ useRnaView.setEnabled(structSelected);
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setEnabled(structSelected);
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setEnabled(structSelected);
+ structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name()));
+ chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+ chimeraPath.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ validateChimeraPath();
+ }
+ });
- /***************************************************************************
- * Set up Connections
+ /*
+ * Set Connections tab defaults
*/
nameLinks = new Vector();
urlLinks = new Vector();
@@ -266,34 +336,64 @@ public class Preferences extends GPreferences
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ // note antisense here: default is true
questionnaire
- .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
- // antisense
- // here
- versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
- // is
- // true
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
+
+ /*
+ * Set Output tab defaults
+ */
+ epsRendering
+ .addItem(MessageManager.getString("label.prompt_each_time"));
+ epsRendering.addItem(MessageManager.getString("label.lineart"));
+ epsRendering.addItem(MessageManager.getString("action.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));
+ msfjv.setSelected(Cache.getDefault("MSF_JVSUFFIX", true));
+ pfamjv.setSelected(Cache.getDefault("PFAM_JVSUFFIX", true));
+ pileupjv.setSelected(Cache.getDefault("PILEUP_JVSUFFIX", true));
+ pirjv.setSelected(Cache.getDefault("PIR_JVSUFFIX", true));
+ modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", false));
+ embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
+ true));
+
+ /*
+ * Set Editing tab defaults
+ */
+ autoCalculateConsCheck.setSelected(Cache.getDefault(
+ "AUTO_CALC_CONSENSUS", true));
+ padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+ sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+
annotations_actionPerformed(null); // update the display of the annotation
// settings
- try
- {
- jbInit();
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
}
/**
- * DOCUMENT ME!
+ * Save user selections on the Preferences tabs to the Cache and write out to
+ * file.
*
* @param e
- * DOCUMENT ME!
*/
public void ok_actionPerformed(ActionEvent e)
{
+ if (!validateSettings())
+ {
+ return;
+ }
+ /*
+ * Save Visual settings
+ */
Cache.applicationProperties.setProperty("SHOW_JVSUFFIX",
Boolean.toString(seqLimit.isSelected()));
Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS",
@@ -311,8 +411,6 @@ public class Preferences extends GPreferences
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.toString(identity.isSelected()));
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour
- .getSelectedItem().toString());
Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
.getSelectedItem().toString());
@@ -337,6 +435,8 @@ public class Preferences extends GPreferences
Boolean.toString(showConsensLogo.isSelected()));
Cache.applicationProperties.setProperty("ANTI_ALIAS",
Boolean.toString(smoothFont.isSelected()));
+ Cache.applicationProperties.setProperty(SCALE_PROTEIN_TO_CDNA,
+ Boolean.toString(scaleProteinToCdna.isSelected()));
Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP",
Boolean.toString(showNpTooltip.isSelected()));
Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP",
@@ -353,11 +453,49 @@ public class Preferences extends GPreferences
Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
.getSelectedItem().toString());
+ // convert description of sort order to enum name for save
+ SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
+ .forDescription(sortAnnBy.getSelectedItem().toString());
+ if (annSortOrder != null)
+ {
+ Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+ annSortOrder.name());
+ }
+
+ final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+ Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+ .valueOf(showAutocalcFirst).toString());
+
+ /*
+ * Save Colours settings
+ */
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
+ .getSelectedItem().toString());
Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
minColour.getBackground());
Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
maxColour.getBackground());
+ /*
+ * Save Structure settings
+ */
+ Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+ Boolean.toString(addTempFactor.isSelected()));
+ Cache.applicationProperties.setProperty(ADD_SS_ANN,
+ Boolean.toString(addSecondaryStructure.isSelected()));
+ Cache.applicationProperties.setProperty(USE_RNAVIEW,
+ Boolean.toString(useRnaView.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+ Boolean.toString(structFromPdb.isSelected()));
+ Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+ .getSelectedItem().toString());
+ Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+
+ /*
+ * Save Output settings
+ */
if (epsRendering.getSelectedItem().equals("Prompt each time"))
{
Cache.applicationProperties.remove("EPS_RENDERING");
@@ -368,15 +506,10 @@ public class Preferences extends GPreferences
.getSelectedItem().toString());
}
- if (defaultBrowser.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("DEFAULT_BROWSER");
- }
- else
- {
- Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
- defaultBrowser.getText());
- }
+ /*
+ * Save Connections settings
+ */
+ Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
jalview.util.BrowserLauncher.resetBrowser();
@@ -404,25 +537,9 @@ public class Preferences extends GPreferences
Cache.applicationProperties.setProperty("USE_PROXY",
Boolean.toString(useProxy.isSelected()));
- if (proxyServerTB.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("PROXY_SERVER");
- }
- else
- {
- Cache.applicationProperties.setProperty("PROXY_SERVER",
- proxyServerTB.getText());
- }
+ Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
- if (proxyPortTB.getText().trim().length() < 1)
- {
- Cache.applicationProperties.remove("PROXY_PORT");
- }
- else
- {
- Cache.applicationProperties.setProperty("PROXY_PORT",
- proxyPortTB.getText());
- }
+ Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
if (useProxy.isSelected())
{
@@ -452,6 +569,10 @@ public class Preferences extends GPreferences
// by just adding the given line
Cache.removeProperty("NOQUESTIONNAIRES");
}
+
+ /*
+ * Save Output settings
+ */
Cache.applicationProperties.setProperty("BLC_JVSUFFIX",
Boolean.toString(blcjv.isSelected()));
Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX",
@@ -468,6 +589,8 @@ public class Preferences extends GPreferences
Boolean.toString(pirjv.isSelected()));
Cache.applicationProperties.setProperty("PIR_MODELLER",
Boolean.toString(modellerOutput.isSelected()));
+ Cache.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+ Boolean.toString(embbedBioJSON.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
@@ -476,6 +599,9 @@ public class Preferences extends GPreferences
Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
userIdWidth.getText());
+ /*
+ * Save Editing settings
+ */
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
Cache.applicationProperties.setProperty("SORT_BY_TREE",
@@ -486,6 +612,7 @@ public class Preferences extends GPreferences
dasSource.saveProperties(Cache.applicationProperties);
wsPrefs.updateAndRefreshWsMenuConfig(false);
Cache.saveProperties();
+ Desktop.instance.doConfigureStructurePrefs();
try
{
frame.setClosed(true);
@@ -495,19 +622,42 @@ public class Preferences extends GPreferences
}
/**
+ * Do any necessary validation before saving settings. Return focus to the
+ * first tab which fails validation.
+ *
+ * @return
+ */
+ private boolean validateSettings()
+ {
+ if (!validateStructure())
+ {
+ structureTab.requestFocusInWindow();
+ return false;
+ }
+ return true;
+ }
+
+ @Override
+ protected boolean validateStructure()
+ {
+ return validateChimeraPath();
+
+ }
+
+ /**
* DOCUMENT ME!
*/
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" },
- new String[]
- { "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" },
+ 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"));
chooser.setFileView(new JalviewFileView());
- chooser.setDialogTitle("Select startup file");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_startup_file"));
int value = chooser.showOpenDialog(this);
@@ -565,8 +715,8 @@ public class Preferences extends GPreferences
while (!valid)
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
- null) == JOptionPane.OK_OPTION)
+ MessageManager.getString("label.new_sequence_url_link"),
+ JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
{
@@ -591,7 +741,8 @@ public class Preferences extends GPreferences
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;
}
@@ -604,8 +755,8 @@ public class Preferences extends GPreferences
{
if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
- "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
- null) == JOptionPane.OK_OPTION)
+ MessageManager.getString("label.new_sequence_url_link"),
+ JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
{
if (link.checkValid())
{
@@ -629,7 +780,8 @@ public class Preferences extends GPreferences
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;
}
@@ -647,7 +799,8 @@ public class Preferences extends GPreferences
public void defaultBrowser_mouseClicked(MouseEvent e)
{
JFileChooser chooser = new JFileChooser(".");
- chooser.setDialogTitle("Select default web browser");
+ chooser.setDialogTitle(MessageManager
+ .getString("label.select_default_browser"));
int value = chooser.showOpenDialog(this);
@@ -671,35 +824,35 @@ public class Preferences extends GPreferences
super.showunconserved_actionPerformed(e);
}
- private void jbInit() throws Exception
- {
- }
-
public static Collection getGroupURLLinks()
{
return groupURLLinks;
}
- public void minColour_actionPerformed()
+ @Override
+ public void minColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Minimum Value", minColour.getBackground());
+ MessageManager.getString("label.select_colour_minimum_value"),
+ minColour.getBackground());
if (col != null)
{
- minColour.setBackground(col);
+ panel.setBackground(col);
}
- minColour.repaint();
+ panel.repaint();
}
- public void maxColour_actionPerformed()
+ @Override
+ public void maxColour_actionPerformed(JPanel panel)
{
Color col = JColorChooser.showDialog(this,
- "Select Colour for Maximum Value", maxColour.getBackground());
+ MessageManager.getString("label.select_colour_maximum_value"),
+ maxColour.getBackground());
if (col != null)
{
- maxColour.setBackground(col);
+ panel.setBackground(col);
}
- maxColour.repaint();
+ panel.repaint();
}
@Override
@@ -719,12 +872,10 @@ public class Preferences extends GPreferences
}
} 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);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .getString("warn.user_defined_width_requirements"),
+ MessageManager.getString("label.invalid_id_column_width"),
+ JOptionPane.WARNING_MESSAGE);
userIdWidth.setText("");
}
}
@@ -736,4 +887,73 @@ public class Preferences extends GPreferences
userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
}
+ /**
+ * Returns true if chimera path is to a valid executable, else show an error
+ * dialog.
+ */
+ private boolean validateChimeraPath()
+ {
+ if (chimeraPath.getText().trim().length() > 0)
+ {
+ File f = new File(chimeraPath.getText());
+ if (!f.canExecute())
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.invalid_chimera_path"),
+ MessageManager.getString("label.invalid_name"),
+ JOptionPane.ERROR_MESSAGE);
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * If Chimera is selected, check it can be found on default or user-specified
+ * path, if not show a warning/help dialog.
+ */
+ @Override
+ protected void structureViewer_actionPerformed(String selectedItem)
+ {
+ if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+ {
+ return;
+ }
+ boolean found = false;
+
+ /*
+ * Try user-specified and standard paths for Chimera executable.
+ */
+ List paths = StructureManager.getChimeraPaths();
+ paths.add(0, chimeraPath.getText());
+ for (String path : paths)
+ {
+ if (new File(path.trim()).canExecute())
+ {
+ found = true;
+ break;
+ }
+ }
+ if (!found)
+ {
+ String[] options = { "OK", "Help" };
+ int showHelp = JOptionPane.showInternalOptionDialog(
+ Desktop.desktop,
+ JvSwingUtils.wrapTooltip(true,
+ MessageManager.getString("label.chimera_missing")),
+ "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+ null, options, options[0]);
+ if (showHelp == JOptionPane.NO_OPTION)
+ {
+ try
+ {
+ Help.showHelpWindow(HelpId.StructureViewer);
+ } catch (HelpSetException e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
}