-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.io.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import javax.swing.*;\r
-\r
-import java.util.*;\r
-\r
-import jalview.bin.Cache;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Preferences extends GPreferences\r
-{\r
- /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */\r
- public static Vector sequenceURLLinks;\r
- static\r
- {\r
- String string = Cache.getDefault("SEQUENCE_LINKS",\r
- "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");\r
- sequenceURLLinks = new Vector();\r
-\r
- try\r
- {\r
- StringTokenizer st = new StringTokenizer(string, "|");\r
- while (st.hasMoreElements())\r
- {\r
- sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- System.out.println(ex + "\nError parsing sequence links");\r
- }\r
- }\r
- Vector nameLinks, urlLinks;\r
-\r
- JInternalFrame frame;\r
-\r
- DasSourceBrowser dasSource;\r
-\r
-\r
- /**\r
- * Creates a new Preferences object.\r
- */\r
- public Preferences()\r
- {\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- dasSource = new DasSourceBrowser();\r
- dasPanel.add(dasSource, BorderLayout.CENTER);\r
-\r
- int width = 500, height = 420;\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
- {\r
- width = 570;\r
- height = 460;\r
- }\r
-\r
- Desktop.addInternalFrame(frame, "Preferences", width, height);\r
- frame.setMinimumSize(new Dimension(width, height));\r
-\r
- seqLimit.setSelected( Cache.getDefault("SHOW_JVSUFFIX", true));\r
- rightAlign.setSelected( Cache.getDefault("RIGHT_ALIGN_IDS", false));\r
- fullScreen.setSelected( Cache.getDefault("SHOW_FULLSCREEN", false));\r
- annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
-\r
- conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));\r
- quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
- identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));\r
-\r
- conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));\r
- quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));\r
- identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));\r
-\r
- for (int i = 0; i < 13; i++)\r
- {\r
- colour.addItem(ColourSchemeProperty.getColourName(i));\r
- }\r
-\r
- String string = Cache.getDefault("DEFAULT_COLOUR", "None");\r
-\r
- colour.setSelectedItem(string);\r
-\r
- String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()\r
- .getAvailableFontFamilyNames();\r
-\r
- for (int i = 0; i < fonts.length; i++)\r
- {\r
- fontNameCB.addItem(fonts[i]);\r
- }\r
-\r
- for (int i = 1; i < 31; i++)\r
- {\r
- fontSizeCB.addItem(i + "");\r
- }\r
-\r
- fontStyleCB.addItem("plain");\r
- fontStyleCB.addItem("bold");\r
- fontStyleCB.addItem("italic");\r
-\r
- fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));\r
- fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));\r
- fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );\r
-\r
- smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));\r
-\r
- idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));\r
-\r
- wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));\r
-\r
- gapSymbolCB.addItem("-");\r
- gapSymbolCB.addItem(".");\r
-\r
- gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));\r
-\r
- startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );\r
- startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",\r
- "http://www.jalview.org/examples/exampleFile.jar"));\r
-\r
- sortby.addItem("No sort");\r
- sortby.addItem("Id");\r
- sortby.addItem("Pairwise Identity");\r
- sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );\r
-\r
- epsRendering.addItem("Prompt each time");\r
- epsRendering.addItem("Lineart");\r
- epsRendering.addItem("Text");\r
- epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));\r
-\r
- blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );\r
- clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );\r
- fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );\r
- msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );\r
- pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );\r
- pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );\r
- pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );\r
-\r
- modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));\r
-\r
- autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));\r
- padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));\r
-\r
- /****************************************************\r
- * Set up Connections\r
- */\r
- nameLinks = new Vector();\r
- urlLinks = new Vector();\r
- for(int i=0; i<sequenceURLLinks.size(); i++)\r
- {\r
- String link = sequenceURLLinks.elementAt(i).toString();\r
- nameLinks.addElement(link.substring(0, link.indexOf("|")) );\r
- urlLinks.addElement(link.substring(link.indexOf("|")+1));\r
- }\r
-\r
- updateLinkData();\r
-\r
- useProxy.setSelected( Cache.getDefault("USE_PROXY", false));\r
- proxyServerTB.setEnabled(useProxy.isSelected());\r
- proxyPortTB.setEnabled(useProxy.isSelected());\r
- proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));\r
- proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));\r
-\r
- defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
-\r
- Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));\r
- Cache.applicationProperties.setProperty("RIGHT_ALIGN_IDS", Boolean.toString(rightAlign.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));\r
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());\r
- Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());\r
-\r
- Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());\r
- Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());\r
- Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());\r
-\r
- Cache.applicationProperties.setProperty("ID_ITALICS", Boolean.toString(idItalics.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());\r
- Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE", Boolean.toString(startupCheckbox.isSelected()));\r
-\r
- Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );\r
-\r
- if(epsRendering.getSelectedItem().equals("Prompt each time"))\r
- Cache.applicationProperties.remove("EPS_RENDERING");\r
- else\r
- Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());\r
-\r
- if(defaultBrowser.getText().trim().length()<1)\r
- Cache.applicationProperties.remove("DEFAULT_BROWSER");\r
- else\r
- Cache.applicationProperties.setProperty("DEFAULT_BROWSER",\r
- defaultBrowser.getText());\r
-\r
- jalview.util.BrowserLauncher.resetBrowser();\r
-\r
- if(nameLinks.size()>0)\r
- {\r
- StringBuffer links = new StringBuffer();\r
- sequenceURLLinks = new Vector();\r
- for (int i = 0; i < nameLinks.size(); i++)\r
- {\r
- sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));\r
- links.append(sequenceURLLinks.elementAt(i).toString());\r
- links.append("|");\r
- }\r
- // remove last "|"\r
- links.setLength( links.length()-1 );\r
- Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());\r
- }\r
- else\r
- Cache.applicationProperties.remove("SEQUENCE_LINKS");\r
-\r
-\r
- Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));\r
-\r
- if (proxyServerTB.getText().trim().length() < 1)\r
- Cache.applicationProperties.remove("PROXY_SERVER");\r
- else\r
- Cache.applicationProperties.setProperty("PROXY_SERVER",\r
- proxyServerTB.getText());\r
-\r
- if (proxyPortTB.getText().trim().length() < 1)\r
- Cache.applicationProperties.remove("PROXY_PORT");\r
- else\r
- Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());\r
-\r
- if(useProxy.isSelected())\r
- {\r
- System.setProperty("http.proxyHost", proxyServerTB.getText());\r
- System.setProperty("http.proxyPort", proxyPortTB.getText());\r
- }\r
- else\r
- {\r
- System.setProperty("http.proxyHost","");\r
- System.setProperty("http.proxyPort","");\r
- }\r
-\r
-\r
- Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );\r
- Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );\r
- Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );\r
- Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );\r
- Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );\r
- Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );\r
- Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );\r
- Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );\r
- jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();\r
-\r
- Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",\r
- Boolean.toString(autoCalculateConsCheck.isSelected()));\r
- Cache.applicationProperties.setProperty("PAD_GAPS",\r
- Boolean.toString(padGaps.isSelected()));\r
-\r
- dasSource.saveProperties(Cache.applicationProperties);\r
-\r
- Cache.saveProperties();\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void startupFileTextfield_mouseClicked()\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
- "LAST_DIRECTORY"),\r
- new String[]\r
- {\r
- "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
- "jar"\r
- },\r
- new String[]\r
- {\r
- "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
- }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Select startup file");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",\r
- chooser.getSelectedFormat());\r
- startupFileTextfield.setText(chooser.getSelectedFile()\r
- .getAbsolutePath());\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void cancel_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void annotations_actionPerformed(ActionEvent e)\r
- {\r
- conservation.setEnabled(annotations.isSelected());\r
- quality.setEnabled(annotations.isSelected());\r
- identity.setEnabled(annotations.isSelected());\r
- }\r
-\r
-\r
- public void newLink_actionPerformed(ActionEvent e) {\r
-\r
- GSequenceLink link = new GSequenceLink();\r
- boolean valid = false;\r
- while( !valid )\r
- {\r
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
- "New sequence URL link",\r
- JOptionPane.OK_CANCEL_OPTION\r
- ,-1, null)\r
- == JOptionPane.OK_OPTION)\r
- {\r
- if (link.checkValid())\r
- {\r
- nameLinks.addElement(link.getName());\r
- urlLinks.addElement(link.getURL());\r
- updateLinkData();\r
- valid = true;\r
- }\r
- }\r
- else\r
- break;\r
- }\r
- }\r
-\r
- public void editLink_actionPerformed(ActionEvent e) {\r
- GSequenceLink link = new GSequenceLink();\r
-\r
- int index = linkNameList.getSelectedIndex();\r
- if(index==-1)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
- ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- link.setName( nameLinks.elementAt(index).toString() );\r
- link.setURL( urlLinks.elementAt(index).toString() );\r
-\r
- boolean valid = false;\r
- while (!valid)\r
- {\r
-\r
- if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,\r
- "New sequence URL link",\r
- JOptionPane.OK_CANCEL_OPTION\r
- ,-1, null)\r
- == JOptionPane.OK_OPTION)\r
- {\r
- if (link.checkValid())\r
- {\r
- nameLinks.setElementAt(link.getName(), index);\r
- urlLinks.setElementAt(link.getURL(), index);\r
- updateLinkData();\r
- valid = true;\r
- }\r
- }\r
-\r
- else\r
- break;\r
- }\r
- }\r
-\r
- public void deleteLink_actionPerformed(ActionEvent e) {\r
- int index = linkNameList.getSelectedIndex();\r
- if(index==-1)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"\r
- ,"No link selected", JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
- nameLinks.removeElementAt(index);\r
- urlLinks.removeElementAt(index);\r
- updateLinkData();\r
- }\r
-\r
- void updateLinkData()\r
- {\r
- linkNameList.setListData(nameLinks);\r
- linkURLList.setListData(urlLinks);\r
- }\r
-\r
- public void defaultBrowser_mouseClicked(MouseEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(".");\r
- chooser.setDialogTitle("Select default web browser");\r
-\r
- int value = chooser.showOpenDialog(this);\r
-\r
- if (value == JFileChooser.APPROVE_OPTION)\r
- {\r
- defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());\r
- }\r
-\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, 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
+ * 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/>.
+ */
+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.ws.EnfinEnvision2OneWay;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+
+ /**
+ * Holds name and link separated with | character. Sequence ID must be
+ * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+ */
+ public static Vector sequenceURLLinks;
+
+ /**
+ * Holds name and link separated with | character. Sequence IDS and Sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
+ * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
+ * for first and second token specified after a pipe character at end |,|.
+ * (TODO: proper escape for using | to separate ids or sequences
+ */
+
+ public static Vector groupURLLinks;
+ static
+ {
+ String string = Cache
+ .getDefault(
+ "SEQUENCE_LINKS",
+ "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+ sequenceURLLinks = new Vector();
+
+ try
+ {
+ StringTokenizer st = new StringTokenizer(string, "|");
+ while (st.hasMoreElements())
+ {
+ String name = st.nextToken();
+ String url = st.nextToken();
+ // check for '|' within a regex
+ int rxstart = url.indexOf("$SEQUENCE_ID$");
+ while (rxstart == -1 && url.indexOf("/=$") == -1)
+ {
+ url = url + "|" + st.nextToken();
+ }
+ sequenceURLLinks.addElement(name + "|" + url);
+ }
+ } catch (Exception ex)
+ {
+ System.out.println(ex + "\nError parsing sequence links");
+ }
+ /**
+ * TODO: reformulate groupURL encoding so two or more can be stored in the
+ * .properties file as '|' separated strings
+ */
+
+ groupURLLinks = new Vector();
+ // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$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;
+
+ JInternalFrame frame;
+
+ DasSourceBrowser dasSource;
+
+ private WsPreferences wsPrefs;
+
+ /**
+ * Creates a new Preferences object.
+ */
+ public Preferences()
+ {
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ dasSource = new DasSourceBrowser();
+ dasPanel.add(dasSource, BorderLayout.CENTER);
+ wsPrefs = new WsPreferences();
+ wsPanel.add(wsPrefs, BorderLayout.CENTER);
+ int width = 500, height = 420;
+ if (new jalview.util.Platform().isAMac())
+ {
+ width = 570;
+ height = 460;
+ }
+
+ Desktop.addInternalFrame(frame, "Preferences", width, height);
+ frame.setMinimumSize(new Dimension(width, height));
+
+ seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
+ rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+ fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
+ annotations.setSelected(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+ conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
+ quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
+ identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+ openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+ showUnconserved
+ .setSelected(Cache.getDefault("SHOW_UNCONSERVED", 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++)
+ {
+ fontSizeCB.addItem(i + "");
+ }
+
+ fontStyleCB.addItem("plain");
+ fontStyleCB.addItem("bold");
+ fontStyleCB.addItem("italic");
+
+ fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+ fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+ fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN
+ + ""));
+
+ smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+
+ idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+
+ wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
+ gapSymbolCB.addItem("-");
+ gapSymbolCB.addItem(".");
+
+ 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"));
+
+ 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));
+
+ 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));
+
+ padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+
+ /***************************************************************************
+ * Set up Connections
+ */
+ nameLinks = new Vector();
+ urlLinks = new Vector();
+ for (int i = 0; i < sequenceURLLinks.size(); i++)
+ {
+ String link = sequenceURLLinks.elementAt(i).toString();
+ nameLinks.addElement(link.substring(0, link.indexOf("|")));
+ urlLinks.addElement(link.substring(link.indexOf("|") + 1));
+ }
+
+ updateLinkData();
+
+ useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
+ proxyServerTB.setEnabled(useProxy.isSelected());
+ proxyPortTB.setEnabled(useProxy.isSelected());
+ proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+ proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+ defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+
+ usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+ questionnaire
+ .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
+ // antisense
+ // here
+ versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
+ // is
+ // true
+ annotations_actionPerformed(null); // update the display of the annotation
+ // settings
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ 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("DEFAULT_COLOUR", colour
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
+ .getSelectedItem().toString());
+
+ Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB
+ .getSelectedItem().toString());
+ Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB
+ .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("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("STARTUP_FILE",
+ startupFileTextfield.getText());
+ 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");
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering
+ .getSelectedItem().toString());
+ }
+
+ if (defaultBrowser.getText().trim().length() < 1)
+ {
+ Cache.applicationProperties.remove("DEFAULT_BROWSER");
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+ defaultBrowser.getText());
+ }
+
+ jalview.util.BrowserLauncher.resetBrowser();
+
+ if (nameLinks.size() > 0)
+ {
+ StringBuffer links = new StringBuffer();
+ sequenceURLLinks = new Vector();
+ for (int i = 0; i < nameLinks.size(); i++)
+ {
+ sequenceURLLinks.addElement(nameLinks.elementAt(i) + "|"
+ + urlLinks.elementAt(i));
+ links.append(sequenceURLLinks.elementAt(i).toString());
+ links.append("|");
+ }
+ // remove last "|"
+ links.setLength(links.length() - 1);
+ Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+ links.toString());
+ }
+ else
+ {
+ Cache.applicationProperties.remove("SEQUENCE_LINKS");
+ }
+
+ 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());
+ }
+
+ if (proxyPortTB.getText().trim().length() < 1)
+ {
+ Cache.applicationProperties.remove("PROXY_PORT");
+ }
+ else
+ {
+ Cache.applicationProperties.setProperty("PROXY_PORT",
+ proxyPortTB.getText());
+ }
+
+ if (useProxy.isSelected())
+ {
+ System.setProperty("http.proxyHost", proxyServerTB.getText());
+ System.setProperty("http.proxyPort", proxyPortTB.getText());
+ }
+ else
+ {
+ System.setProperty("http.proxyHost", "");
+ System.setProperty("http.proxyPort", "");
+ }
+ 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()));
+ }
+ if (!questionnaire.isSelected())
+ {
+ Cache.setProperty("NOQUESTIONNAIRES", "true");
+ }
+ else
+ {
+ // special - made easy to edit a property file to disable questionnaires
+ // 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()));
+ jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+ 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);
+ Cache.saveProperties();
+ try
+ {
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * 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("DEFAULT_FILE_FORMAT"));
+ chooser.setFileView(new JalviewFileView());
+ chooser.setDialogTitle("Select startup file");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JalviewFileChooser.APPROVE_OPTION)
+ {
+ jalview.bin.Cache.applicationProperties.setProperty(
+ "DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
+ startupFileTextfield.setText(chooser.getSelectedFile()
+ .getAbsolutePath());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void cancel_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ wsPrefs.updateWsMenuConfig(true);
+ wsPrefs.refreshWs_actionPerformed(e);
+ frame.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void annotations_actionPerformed(ActionEvent e)
+ {
+ conservation.setEnabled(annotations.isSelected());
+ quality.setEnabled(annotations.isSelected());
+ identity.setEnabled(annotations.isSelected());
+ showGroupConsensus.setEnabled(annotations.isSelected());
+ showGroupConservation.setEnabled(annotations.isSelected());
+ showConsensHistogram.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ showConsensLogo.setEnabled(annotations.isSelected()
+ && (identity.isSelected() || showGroupConsensus.isSelected()));
+ }
+
+ public void newLink_actionPerformed(ActionEvent e)
+ {
+
+ GSequenceLink link = new GSequenceLink();
+ boolean valid = false;
+ while (!valid)
+ {
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JOptionPane.OK_OPTION)
+ {
+ if (link.checkValid())
+ {
+ nameLinks.addElement(link.getName());
+ urlLinks.addElement(link.getURL());
+ updateLinkData();
+ valid = true;
+ }
+ }
+ else
+ {
+ break;
+ }
+ }
+ }
+
+ public void editLink_actionPerformed(ActionEvent e)
+ {
+ GSequenceLink link = new GSequenceLink();
+
+ int index = linkNameList.getSelectedIndex();
+ if (index == -1)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "No link selected!", "No link selected",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ link.setName(nameLinks.elementAt(index).toString());
+ link.setURL(urlLinks.elementAt(index).toString());
+
+ boolean valid = false;
+ while (!valid)
+ {
+
+ if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+ "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+ null) == JOptionPane.OK_OPTION)
+ {
+ if (link.checkValid())
+ {
+ nameLinks.setElementAt(link.getName(), index);
+ urlLinks.setElementAt(link.getURL(), index);
+ updateLinkData();
+ valid = true;
+ }
+ }
+
+ else
+ {
+ break;
+ }
+ }
+ }
+
+ public void deleteLink_actionPerformed(ActionEvent e)
+ {
+ int index = linkNameList.getSelectedIndex();
+ if (index == -1)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "No link selected!", "No link selected",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+ nameLinks.removeElementAt(index);
+ urlLinks.removeElementAt(index);
+ updateLinkData();
+ }
+
+ void updateLinkData()
+ {
+ linkNameList.setListData(nameLinks);
+ linkURLList.setListData(urlLinks);
+ }
+
+ public void defaultBrowser_mouseClicked(MouseEvent e)
+ {
+ JFileChooser chooser = new JFileChooser(".");
+ chooser.setDialogTitle("Select default web browser");
+
+ int value = chooser.showOpenDialog(this);
+
+ if (value == JFileChooser.APPROVE_OPTION)
+ {
+ defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+ }
+
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see
+ * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
+ * .ActionEvent)
+ */
+ protected void showunconserved_actionPerformed(ActionEvent e)
+ {
+ // TODO Auto-generated method stub
+ super.showunconserved_actionPerformed(e);
+ }
+
+ private void jbInit() throws Exception
+ {
+ }
+
+ public static Collection getGroupURLLinks()
+ {
+ 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();
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff