From: kiramt Date: Tue, 13 Dec 2016 11:10:05 +0000 (+0000) Subject: Merge branch 'develop' into features/JAL-2316 X-Git-Tag: Release_2_10_3b1~346^2~14 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0fcc08f1f633aa9eae854ebe0c78b5fb75471898;hp=2da3a29ae39b692964b85456353985d388aa3858;p=jalview.git Merge branch 'develop' into features/JAL-2316 Conflicts (resolved): resources/lang/Messages.properties resources/lang/Messages_es.properties src/jalview/gui/Preferences.java --- diff --git a/help/html/webServices/urllinks.html b/help/html/webServices/urllinks.html index 088a539..d99633a 100644 --- a/help/html/webServices/urllinks.html +++ b/help/html/webServices/urllinks.html @@ -27,7 +27,9 @@ Opening URLs from Jalview
Both the applet and the desktop application are able to open URLs as 'popups' in your web browser.
Double-clicking on the ID of a sequence - will open the first URL that can be generated from its sequence ID. + will open the URL designated for 'popups' in the "Connections" tab of the Jalview desktop + preferences. This is by default the EMBL-EBI site, but you can easily configure your own sequence URL links.

@@ -43,14 +45,39 @@ href="../features/preferences.html">Jalview desktop preferences, or specified as applet - parameters.
By default the item "EMBL-EBI Search" is added - to this link menu. This link will show a web page in your default - browser with the selected sequence id as part of the URL.
- In the preferences dialog box, click new to add a + parameters.

+

+ By default, the list of available links in the preferences dialog box + contains the item "EMBL-EBI Search", + which is set as the URL which opens on double-clicking on a sequence ID, and as a + menu item in the Links menu. This link will show a web page in your default + browser with the selected sequence id as part of the URL. +
+ Also by default, the list of available links contains persistent URLs for many common + bioinformatics databases. These links are downloaded by Jalview from + the identifiers.org website, and the names and URLs are not user editable. +
+ The list of links is sortable, by clicking on the headers of the table. The list + can be filtered using the free text search box below the table, or the + "Custom Only" button, which displays only user-defined links. +

+

+ In the preferences dialog box, the links which appear in the Links menu + can be configured by selecting or deselecting links in the "In Menu" + column. The names of selected links will be displayed + on new menu items under the "Link" menu when you right + click on a sequence id.
+ You can configure which link is used when double-clicking on a sequence + by selecting or deselecting links in the "On Click" column. Exactly one + link must be configured for double-clicking. Since the link uses the sequence id + to construct the URL to open, the selected link must contain the + "$SEQUENCE_ID$" token (see below for details of the "$SEQUENCE_ID$" + and other tokens).

+

+ Additionally you can click new to add a new link, and edit to modify an existing link, or delete - to remove it.
You can name the link, this will be displayed - on a new menu item under the "Link" menu when you right - click on a sequence id.
The URL string must contain a + to remove it. Only URLs entered by the user (or the default EMBL-EBI link) may + be edited or deleted. When adding or editing a link, the URL string must contain a token that can be replaced with a sequence ID or DB accession ID. The simplest token is "$SEQUENCE_ID$", which will be replaced by the chosen sequence id when you click on it. diff --git a/resources/lang/Messages.properties b/resources/lang/Messages.properties index 6360dc7..7833903 100644 --- a/resources/lang/Messages.properties +++ b/resources/lang/Messages.properties @@ -139,7 +139,8 @@ action.view_flanking_regions = Show flanking regions label.view_flanking_regions = Show sequence data either side of the subsequences involved in this alignment label.structures_manager = Structures Manager label.nickname = Nickname: -label.url = URL: +label.url = URL +label.url\: = URL: label.input_file_url = Enter URL or Input File label.select_feature = Select feature label.name = Name @@ -411,7 +412,6 @@ label.couldnt_import_as_vamsas_session = Couldn't import {0} as a new vamsas ses label.vamsas_document_import_failed = Vamsas Document Import Failed label.couldnt_locate = Couldn't locate {0} label.url_not_found = URL not found -label.no_link_selected = No link selected label.new_sequence_url_link = New sequence URL link label.cannot_edit_annotations_in_wrapped_view = Cannot edit annotations in wrapped view label.wrapped_view_no_edit = Wrapped view - no edit @@ -1274,4 +1274,19 @@ label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ is no longer used for DB access label.SEQUENCE_ID_for_DB_ACCESSION1 = Please review your URL links in the 'Connections' tab of the Preferences window: label.SEQUENCE_ID_for_DB_ACCESSION2 = URL links using '$SEQUENCE_ID$' for DB accessions now use '$DB_ACCESSION$'. label.do_not_display_again = Do not display this message again -label.output_seq_details = Output Sequence Details to list all database references +exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name +exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one line +label.filter = Filter text: +action.customfilter = Custom only +action.showall = Show All +label.insert = Insert: +action.seq_id = $SEQUENCE_ID$ +action.db_acc = $DB_ACCESSION$ +label.default = On Click +label.inmenu = In Menu +label.id = ID +label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option +label.edit_sequence_url_link = Edit sequence URL link +warn.name_cannot_be_duplicate = URL names must be unique and cannot be MIRIAM ids +label.invalid_name = Invalid Name ! +label.output_seq_details = Output Sequence Details to list all database references \ No newline at end of file diff --git a/resources/lang/Messages_es.properties b/resources/lang/Messages_es.properties index e5b5e27..88fb0a4 100644 --- a/resources/lang/Messages_es.properties +++ b/resources/lang/Messages_es.properties @@ -136,7 +136,8 @@ action.view_flanking_regions = Mostrar flancos label.view_flanking_regions = Mostrar los datos de la secuencia a ambos lados de las subsecuencias implicadas en este alineamiento label.structures_manager = Administrar estructuras label.nickname = Sobrenombre: -label.url = URL: +label.url\: = URL: +label.url = URL label.input_file_url = Introducir URL en el fichero de entrada label.select_feature = Seleccionar característica label.name = Nombre @@ -379,7 +380,6 @@ label.couldnt_import_as_vamsas_session = No se pudo importar {0} como una nueva label.vamsas_document_import_failed = Fallo en la importación del documento Vamsas label.couldnt_locate = No se pudo localizar {0} label.url_not_found = URL no encontrada -label.no_link_selected = Enlace no seleccionado label.new_sequence_url_link = Enlace a una nueva secuencia URL label.cannot_edit_annotations_in_wrapped_view = No se pueden editar anotaciones en vista envolvente label.wrapped_view_no_edit = Vista envolvente - no editar @@ -1275,4 +1275,19 @@ label.SEQUENCE_ID_no_longer_used = $SEQUENCE_ID$ no se utiliza m label.SEQUENCE_ID_for_DB_ACCESSION1 = Por favor, revise sus URLs en la pestaña 'Conexiones' de la ventana de Preferencias: label.SEQUENCE_ID_for_DB_ACCESSION2 = URL enlaza usando '$SEQUENCE_ID$' para accesiones DB ahora usar '$DB_ACCESSION$'. label.do_not_display_again = No mostrar este mensaje de nuevo -label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas +exception.url_cannot_have_miriam_id = {0} is a MIRIAM id and cannot be used as a custom url name +exception.url_cannot_have_duplicate_id = {0} cannot be used as a label for more than one link +label.filter = Filter text: +action.customfilter = Custom only +action.showall = Show All +label.insert = Insert: +action.seq_id = $SEQUENCE_ID$ +action.db_acc = $DB_ACCESSION$ +label.default = On Click +label.inmenu = In Menu +label.id = ID +label.urltooltip = Only one url, which must use a sequence id, can be selected for the 'On Click' option +label.edit_sequence_url_link = Edit sequence URL link +warn.name_cannot_be_duplicate = URL names must be unique and cannot be MIRIAM ids +label.invalid_name = Invalid Name ! +label.output_seq_details = Seleccionar Detalles de la secuencia para ver todas \ No newline at end of file diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java index 182f20e..4e7c9cd 100755 --- a/src/jalview/appletgui/IdPanel.java +++ b/src/jalview/appletgui/IdPanel.java @@ -20,14 +20,13 @@ */ package jalview.appletgui; -import static jalview.util.UrlConstants.EMBLEBI_STRING; -import static jalview.util.UrlConstants.SRS_STRING; - import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; -import jalview.util.UrlLink; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.applet.AppletUrlProviderFactory; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; @@ -36,6 +35,7 @@ import java.awt.event.InputEvent; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; +import java.util.HashMap; import java.util.List; import java.util.Vector; @@ -55,7 +55,7 @@ public class IdPanel extends Panel implements MouseListener, boolean mouseDragging = false; - java.util.Vector links = new java.util.Vector(); + UrlProviderI urlProvider = null; public IdPanel(AlignViewport av, AlignmentPanel parent) { @@ -69,6 +69,9 @@ public class IdPanel extends Panel implements MouseListener, String label, url; // TODO: add in group link parameter + + // make a list of label,url pairs + HashMap urlList = new HashMap(); if (av.applet != null) { for (int i = 1; i < 10; i++) @@ -76,26 +79,18 @@ public class IdPanel extends Panel implements MouseListener, label = av.applet.getParameter("linkLabel_" + i); url = av.applet.getParameter("linkURL_" + i); - if (label != null && url != null) - { - links.addElement(label + "|" + url); - } - + urlList.put(label, url); } - } - { - // upgrade old SRS link - int srsPos = links.indexOf(SRS_STRING); - if (srsPos > -1) + + if (!urlList.isEmpty()) { - links.setElementAt(EMBLEBI_STRING, srsPos); + // set default as first entry in list + String defaultUrl = av.applet.getParameter("linkLabel_1"); + UrlProviderFactoryI factory = new AppletUrlProviderFactory( + defaultUrl, urlList); + urlProvider = factory.createUrlProvider(); } } - if (links.size() < 1) - { - links = new java.util.Vector(); - links.addElement(EMBLEBI_STRING); - } } Tooltip tooltip; @@ -217,7 +212,7 @@ public class IdPanel extends Panel implements MouseListener, return; } - // DEFAULT LINK IS FIRST IN THE LINK LIST + // get the sequence details int seq = alignPanel.seqPanel.findSeq(e); SequenceI sq = av.getAlignment().getSequenceAt(seq); if (sq == null) @@ -226,53 +221,11 @@ public class IdPanel extends Panel implements MouseListener, } String id = sq.getName(); - String target = null; - String url = null; - int i = 0; - while (url == null && i < links.size()) - { - // DEFAULT LINK IS FIRST IN THE LINK LIST - // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED - url = links.elementAt(i++).toString(); - jalview.util.UrlLink urlLink = null; - try - { - urlLink = new UrlLink(url); - target = urlLink.getTarget(); - } catch (Exception foo) - { - System.err.println("Exception for URLLink '" + url + "'"); - foo.printStackTrace(); - url = null; - continue; - } - - if (urlLink.usesDBAccession()) - { - // this URL requires an accession id, not the name of a sequence - url = null; - continue; - } - - if (!urlLink.isValid()) - { - System.err.println(urlLink.getInvalidMessage()); - url = null; - continue; - } - - String urls[] = urlLink.makeUrls(id, true); - if (urls == null || urls[0] == null || urls[0].length() < 1) - { - url = null; - continue; - } - // just take first URL made from regex - url = urls[1]; - } + // get the default url with the sequence details filled in + String url = urlProvider.getDefaultUrl(id); + String target = urlProvider.getDefaultTarget(id); try { - alignPanel.alignFrame.showURL(url, target); } catch (Exception ex) { @@ -331,11 +284,8 @@ public class IdPanel extends Panel implements MouseListener, // build a new links menu based on the current links + any non-positional // features - Vector nlinks = new Vector(); - for (int l = 0, lSize = links.size(); l < lSize; l++) - { - nlinks.addElement(links.elementAt(l)); - } + Vector nlinks = urlProvider.getLinksForMenu(); + SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures(); for (int sl = 0; sf != null && sl < sf.length; sl++) { diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index 8412dab..6764430 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -22,6 +22,7 @@ package jalview.bin; import jalview.datamodel.PDBEntry; import jalview.structure.StructureImportSettings; +import jalview.urls.IdOrgSettings; import jalview.ws.dbsources.das.api.DasSourceRegistryI; import jalview.ws.dbsources.das.datamodel.DasSourceRegistry; import jalview.ws.sifts.SiftsSettings; @@ -122,6 +123,10 @@ import org.apache.log4j.SimpleLayout; *

  • SORT_ALIGNMENT (No sort|Id|Pairwise Identity)
    • *
  • SEQUENCE_LINKS list of name|URL pairs for opening a url with * $SEQUENCE_ID$
    • + *
  • STORED_LINKS list of name|url pairs which user has entered but are not + * currently used + *
  • DEFAULT_LINK name of single url to be used when user double clicks a + * sequence id (must be in SEQUENCE_LINKS or STORED_LINKS) *
  • GROUP_LINKS list of name|URL[|<separator>] tuples - see * jalview.utils.GroupURLLink for more info
    • *
  • DAS_REGISTRY_URL the registry to query
    • @@ -220,6 +225,9 @@ public class Cache public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE"; + /** + * Sifts settings + */ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System .getProperty("user.home") + File.separatorChar @@ -230,6 +238,14 @@ public class Cache private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30"; /** + * Identifiers.org download settings + */ + private static final String ID_ORG_FILE = System.getProperty("user.home") + + File.separatorChar + ".jalview_identifiers"; + + private static final String ID_ORG_URL = "http://identifiers.org/rest/collections/"; + + /** * Allowed values are PDB or mmCIF */ private final static String PDB_DOWNLOAD_FORMAT = PDBEntry.Type.MMCIF @@ -440,6 +456,9 @@ public class Cache "sifts_cache_threshold_in_days", DEFAULT_CACHE_THRESHOLD_IN_DAYS)); + IdOrgSettings.setUrl(ID_ORG_URL); + IdOrgSettings.setDownloadLocation(ID_ORG_FILE); + System.out .println("Jalview Version: " + codeVersion + codeInstallation); diff --git a/src/jalview/gui/DasSourceBrowser.java b/src/jalview/gui/DasSourceBrowser.java index 8c8f228..c5ec067 100644 --- a/src/jalview/gui/DasSourceBrowser.java +++ b/src/jalview/gui/DasSourceBrowser.java @@ -453,7 +453,7 @@ public class DasSourceBrowser extends GDasSourceBrowser implements pane12.add(nametf, BorderLayout.EAST); panel.add(pane12, BorderLayout.NORTH); pane12 = new JPanel(new BorderLayout()); - pane12.add(new JLabel(MessageManager.getString("label.url")), + pane12.add(new JLabel(MessageManager.getString("label.url:")), BorderLayout.NORTH); pane12.add(seqs, BorderLayout.SOUTH); pane12.add(urltf, BorderLayout.EAST); diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index ac957d8..b4b41a3 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -20,7 +20,6 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.EMBLEBI_STRING; import static jalview.util.UrlConstants.SEQUENCE_ID; import jalview.api.AlignViewportI; @@ -38,10 +37,13 @@ import jalview.io.JalviewFileView; import jalview.jbgui.GSplitFrame; import jalview.jbgui.GStructureViewer; import jalview.structure.StructureSelectionManager; +import jalview.urls.IdOrgSettings; import jalview.util.ImageMaker; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.UrlConstants; import jalview.viewmodel.AlignmentViewport; +import jalview.ws.UrlDownloadClient; import jalview.ws.params.ParamManager; import java.awt.BorderLayout; @@ -77,6 +79,7 @@ import java.beans.PropertyChangeListener; import java.io.BufferedInputStream; import java.io.File; import java.io.FileOutputStream; +import java.io.IOException; import java.net.URL; import java.util.ArrayList; import java.util.Hashtable; @@ -391,6 +394,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements showNews.setVisible(false); + getIdentifiersOrgData(); + checkURLLinks(); this.addWindowListener(new WindowAdapter() @@ -524,6 +529,29 @@ public class Desktop extends jalview.jbgui.GDesktop implements }); } + public void getIdentifiersOrgData() + { + // Thread off the identifiers fetcher + addDialogThread(new Runnable() + { + @Override + public void run() + { + Cache.log.debug("Downloading data from identifiers.org"); + UrlDownloadClient client = new UrlDownloadClient(); + try + { + client.download(IdOrgSettings.getUrl(), + IdOrgSettings.getDownloadLocation()); + } catch (IOException e) + { + Cache.log.debug("Exception downloading identifiers.org data" + + e.getMessage()); + } + } + }); + } + @Override protected void showNews_actionPerformed(ActionEvent e) { @@ -2288,7 +2316,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements { // check what the actual links are - if it's just the default don't // bother with the warning - Vector links = Preferences.sequenceURLLinks; + Vector links = Preferences.sequenceUrlLinks + .getLinksForMenu(); // only need to check links if there is one with a // SEQUENCE_ID which is not the default EMBL_EBI link @@ -2298,7 +2327,8 @@ public class Desktop extends jalview.jbgui.GDesktop implements while (li.hasNext()) { String link = li.next(); - if (link.contains(SEQUENCE_ID) && !link.equals(EMBLEBI_STRING)) + if (link.contains(SEQUENCE_ID) + && !link.equals(UrlConstants.DEFAULT_STRING)) { check = true; int barPos = link.indexOf("|"); diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 59d12d9..e326a7a 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -27,7 +27,6 @@ import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; import jalview.util.MessageManager; import jalview.util.Platform; -import jalview.util.UrlLink; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; @@ -199,56 +198,10 @@ public class IdPanel extends JPanel implements MouseListener, return; } - Vector links = Preferences.sequenceURLLinks; - if (links == null || links.size() < 1) - { - return; - } - int seq = alignPanel.getSeqPanel().findSeq(e); - String url = null; - int i = 0; String id = av.getAlignment().getSequenceAt(seq).getName(); - while (url == null && i < links.size()) - { - // DEFAULT LINK IS FIRST IN THE LINK LIST - // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED - url = links.elementAt(i++).toString(); - jalview.util.UrlLink urlLink = null; - try - { - urlLink = new UrlLink(url); - } catch (Exception foo) - { - jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'", - foo); - url = null; - continue; - } + String url = Preferences.sequenceUrlLinks.getDefaultUrl(id); - if (urlLink.usesDBAccession()) - { - // this URL requires an accession id, not the name of a sequence - url = null; - continue; - } - - if (!urlLink.isValid()) - { - jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); - url = null; - continue; - } - - String urls[] = urlLink.makeUrls(id, true); - if (urls == null || urls[0] == null || urls[0].length() < 4) - { - url = null; - continue; - } - // just take first URL made from regex - url = urls[1]; - } try { jalview.util.BrowserLauncher.openURL(url); @@ -375,7 +328,7 @@ public class IdPanel extends JPanel implements MouseListener, Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2); // build a new links menu based on the current links + any non-positional // features - Vector nlinks = new Vector(Preferences.sequenceURLLinks); + Vector nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures(); if (sfs != null) { diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java index 0b65c1b..00b2a38 100755 --- a/src/jalview/gui/Preferences.java +++ b/src/jalview/gui/Preferences.java @@ -20,11 +20,6 @@ */ package jalview.gui; -import static jalview.util.UrlConstants.DB_ACCESSION; -import static jalview.util.UrlConstants.EMBLEBI_STRING; -import static jalview.util.UrlConstants.SEQUENCE_ID; -import static jalview.util.UrlConstants.SRS_STRING; - import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder; import jalview.bin.Cache; import jalview.gui.Help.HelpId; @@ -35,12 +30,18 @@ import jalview.io.JalviewFileView; import jalview.jbgui.GPreferences; import jalview.jbgui.GSequenceLink; import jalview.schemes.ColourSchemeProperty; +import jalview.urls.UrlLinkTableModel; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.api.UrlProviderI; +import jalview.urls.desktop.DesktopUrlProviderFactory; import jalview.util.MessageManager; import jalview.util.Platform; +import jalview.util.UrlConstants; import jalview.ws.sifts.SiftsSettings; import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Component; import java.awt.Dimension; import java.awt.Font; import java.awt.event.ActionEvent; @@ -49,14 +50,24 @@ import java.awt.event.MouseEvent; import java.io.File; import java.util.ArrayList; 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.JPanel; +import javax.swing.ListSelectionModel; +import javax.swing.RowFilter; +import javax.swing.RowSorter; +import javax.swing.SortOrder; +import javax.swing.event.DocumentEvent; +import javax.swing.event.DocumentListener; +import javax.swing.event.ListSelectionEvent; +import javax.swing.event.ListSelectionListener; +import javax.swing.table.TableCellRenderer; +import javax.swing.table.TableColumn; +import javax.swing.table.TableModel; +import javax.swing.table.TableRowSorter; import ext.edu.ucsf.rbvi.strucviz2.StructureManager; @@ -102,7 +113,9 @@ 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; + public static UrlProviderI sequenceUrlLinks; + + public static UrlLinkTableModel dataModel; /** * Holds name and link separated with | character. Sequence IDS and Sequences @@ -115,40 +128,23 @@ public class Preferences extends GPreferences public static List groupURLLinks; static { - String string = Cache.getDefault("SEQUENCE_LINKS", EMBLEBI_STRING); - sequenceURLLinks = new Vector(); - - try + // get links selected to be in the menu (SEQUENCE_LINKS) + // and links entered by the user but not selected (STORED_LINKS) + String inMenuString = Cache.getDefault("SEQUENCE_LINKS", ""); + String notInMenuString = Cache.getDefault("STORED_LINKS", ""); + String defaultUrl = Cache.getDefault("DEFAULT_URL", + UrlConstants.DEFAULT_LABEL); + + // if both links lists are empty, add the DEFAULT_URL link + // otherwise we assume the default link is in one of the lists + if (inMenuString.isEmpty() && notInMenuString.isEmpty()) { - 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("$" + DB_ACCESSION + "$"); - if (rxstart == -1) - { - 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"); - } - { - // upgrade old SRS link - int srsPos = sequenceURLLinks.indexOf(SRS_STRING); - if (srsPos > -1) - { - sequenceURLLinks.setElementAt(EMBLEBI_STRING, srsPos); - } + inMenuString = UrlConstants.DEFAULT_STRING; } + UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl, + inMenuString, notInMenuString); + sequenceUrlLinks = factory.createUrlProvider(); + dataModel = new UrlLinkTableModel(sequenceUrlLinks); /** * TODO: reformulate groupURL encoding so two or more can be stored in the @@ -158,8 +154,6 @@ public class Preferences extends GPreferences groupURLLinks = new ArrayList(); } - Vector nameLinks, urlLinks; - JInternalFrame frame; DasSourceBrowser dasSource; @@ -343,18 +337,128 @@ public class Preferences extends GPreferences /* * Set Connections tab defaults */ - nameLinks = new Vector(); - urlLinks = new Vector(); - for (int i = 0; i < sequenceURLLinks.size(); i++) + + // set up sorting + linkUrlTable.setModel(dataModel); + final TableRowSorter sorter = new TableRowSorter<>( + linkUrlTable.getModel()); + linkUrlTable.setRowSorter(sorter); + List sortKeys = new ArrayList<>(); + + UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel(); + sortKeys.add(new RowSorter.SortKey(m.getDefaultColumn(), + SortOrder.DESCENDING)); + sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(), + SortOrder.DESCENDING)); + sortKeys.add(new RowSorter.SortKey(m.getNameColumn(), + SortOrder.ASCENDING)); + + sorter.setSortKeys(sortKeys); + sorter.sort(); + + // set up filtering + ActionListener onReset; + onReset = new ActionListener() { - String link = sequenceURLLinks.elementAt(i).toString(); - nameLinks.addElement(link.substring(0, link.indexOf("|"))); - urlLinks.addElement(link.substring(link.indexOf("|") + 1)); - } + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(RowFilter.regexFilter("")); + } + + }; + doReset.addActionListener(onReset); + + // filter to display only custom urls + final RowFilter customUrlFilter = new RowFilter() + { + @Override + public boolean include( + Entry entry) + { + return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry); + } + }; + + final TableRowSorter customSorter = new TableRowSorter<>( + linkUrlTable.getModel()); + customSorter.setRowFilter(customUrlFilter); + + ActionListener onCustomOnly; + onCustomOnly = new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + filterTB.setText(""); + sorter.setRowFilter(customUrlFilter); + } + }; + userOnly.addActionListener(onCustomOnly); + + filterTB.getDocument().addDocumentListener(new DocumentListener() + { + String caseInsensitiveFlag = "(?i)"; - updateLinkData(); + @Override + public void changedUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag + + filterTB.getText())); + } + + @Override + public void removeUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag + + filterTB.getText())); + } + + @Override + public void insertUpdate(DocumentEvent e) + { + sorter.setRowFilter(RowFilter.regexFilter(caseInsensitiveFlag + + filterTB.getText())); + } + }); + + // set up list selection functionality + linkUrlTable.getSelectionModel().addListSelectionListener( + new UrlListSelectionHandler()); + + // set up radio buttons + int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel()) + .getDefaultColumn(); + String onClickName = linkUrlTable.getColumnName(onClickCol); + linkUrlTable.getColumn(onClickName).setCellRenderer( + new RadioButtonRenderer()); + linkUrlTable.getColumn(onClickName) + .setCellEditor(new RadioButtonEditor()); + + // get boolean columns and resize those to min possible + for (int column = 0; column < linkUrlTable.getColumnCount(); column++) + { + if (linkUrlTable.getModel().getColumnClass(column) + .equals(Boolean.class)) + { + TableColumn tableColumn = linkUrlTable.getColumnModel().getColumn( + column); + int preferredWidth = tableColumn.getMinWidth(); + + TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0, + column); + Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column); + int cwidth = c.getPreferredSize().width + + linkUrlTable.getIntercellSpacing().width; + preferredWidth = Math.max(preferredWidth, cwidth); + + tableColumn.setPreferredWidth(preferredWidth); + } + } useProxy.setSelected(Cache.getDefault("USE_PROXY", false)); + useProxy_actionPerformed(); // make sure useProxy is correctly initialised proxyServerTB.setEnabled(useProxy.isSelected()); proxyPortTB.setEnabled(useProxy.isSelected()); proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", "")); @@ -548,28 +652,32 @@ public class Preferences extends GPreferences jalview.util.BrowserLauncher.resetBrowser(); - if (nameLinks.size() > 0) + // save user-defined and selected links + String menuLinks = sequenceUrlLinks.writeUrlsAsString(true); + if (menuLinks.isEmpty()) + { + Cache.applicationProperties.remove("SEQUENCE_LINKS"); + } + else { - 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()); + menuLinks.toString()); + } + + String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false); + if (nonMenuLinks.isEmpty()) + { + Cache.applicationProperties.remove("STORED_LINKS"); } else { - Cache.applicationProperties.remove("SEQUENCE_LINKS"); - sequenceURLLinks.clear(); + Cache.applicationProperties.setProperty("STORED_LINKS", + nonMenuLinks.toString()); } + Cache.applicationProperties.setProperty("DEFAULT_URL", + sequenceUrlLinks.getDefaultUrlId()); + Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected())); @@ -750,7 +858,6 @@ public class Preferences extends GPreferences @Override public void newLink_actionPerformed(ActionEvent e) { - GSequenceLink link = new GSequenceLink(); boolean valid = false; while (!valid) @@ -761,10 +868,18 @@ public class Preferences extends GPreferences { if (link.checkValid()) { - nameLinks.addElement(link.getName()); - urlLinks.addElement(link.getURL()); - updateLinkData(); - valid = true; + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName())) + { + ((UrlLinkTableModel) linkUrlTable.getModel()).insertRow( + link.getName(), link.getURL()); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } else @@ -779,36 +894,40 @@ public class Preferences extends GPreferences { GSequenceLink link = new GSequenceLink(); - int index = linkNameList.getSelectedIndex(); + int index = linkUrlTable.getSelectedRow(); if (index == -1) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.no_link_selected"), - MessageManager.getString("label.no_link_selected"), - JvOptionPane.WARNING_MESSAGE); + // button no longer enabled if row is not selected + Cache.log.debug("Edit with no row selected in linkUrlTable"); return; } - link.setName(nameLinks.elementAt(index).toString()); - link.setURL(urlLinks.elementAt(index).toString()); + link.setName(linkUrlTable.getValueAt(index, 0).toString()); + link.setURL(linkUrlTable.getValueAt(index, 1).toString()); boolean valid = false; while (!valid) { - if (JvOptionPane.showInternalConfirmDialog(Desktop.desktop, link, - MessageManager.getString("label.new_sequence_url_link"), + MessageManager.getString("label.edit_sequence_url_link"), JvOptionPane.OK_CANCEL_OPTION, -1, null) == JvOptionPane.OK_OPTION) { if (link.checkValid()) { - nameLinks.setElementAt(link.getName(), index); - urlLinks.setElementAt(link.getURL(), index); - updateLinkData(); - valid = true; + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isUniqueName(link.getName())) + { + linkUrlTable.setValueAt(link.getName(), index, 0); + linkUrlTable.setValueAt(link.getURL(), index, 1); + valid = true; + } + else + { + link.notifyDuplicate(); + continue; + } } } - else { break; @@ -819,26 +938,24 @@ public class Preferences extends GPreferences @Override public void deleteLink_actionPerformed(ActionEvent e) { - int index = linkNameList.getSelectedIndex(); + int index = linkUrlTable.getSelectedRow(); + int modelIndex = -1; if (index == -1) { - JvOptionPane.showInternalMessageDialog(Desktop.desktop, - MessageManager.getString("label.no_link_selected"), - MessageManager.getString("label.no_link_selected"), - JvOptionPane.WARNING_MESSAGE); + // button no longer enabled if row is not selected + Cache.log.debug("Delete with no row selected in linkUrlTable"); return; } - nameLinks.removeElementAt(index); - urlLinks.removeElementAt(index); - updateLinkData(); - } + else + { + modelIndex = linkUrlTable.convertRowIndexToModel(index); + } - void updateLinkData() - { - linkNameList.setListData(nameLinks); - linkURLList.setListData(urlLinks); + // make sure we use the model index to delete, and not the table index + ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex); } + @Override public void defaultBrowser_mouseClicked(MouseEvent e) { @@ -1055,4 +1172,45 @@ public class Preferences extends GPreferences return name.hashCode() + code.hashCode(); } } + + private class UrlListSelectionHandler implements ListSelectionListener + { + + @Override + public void valueChanged(ListSelectionEvent e) + { + ListSelectionModel lsm = (ListSelectionModel) e.getSource(); + + int index = lsm.getMinSelectionIndex(); + if (index == -1) + { + // no selection, so disable delete/edit buttons + editLink.setEnabled(false); + deleteLink.setEnabled(false); + return; + } + int modelIndex = linkUrlTable.convertRowIndexToModel(index); + + // enable/disable edit and delete link buttons + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowDeletable(modelIndex)) + { + deleteLink.setEnabled(true); + } + else + { + deleteLink.setEnabled(false); + } + + if (((UrlLinkTableModel) linkUrlTable.getModel()) + .isRowEditable(modelIndex)) + { + editLink.setEnabled(true); + } + else + { + editLink.setEnabled(false); + } + } +} } diff --git a/src/jalview/gui/WsPreferences.java b/src/jalview/gui/WsPreferences.java index 165e8f2..32671d5 100644 --- a/src/jalview/gui/WsPreferences.java +++ b/src/jalview/gui/WsPreferences.java @@ -454,7 +454,7 @@ public class WsPreferences extends GWsPreferences JTextField urltf = new JTextField(url, 40); JPanel panel = new JPanel(new BorderLayout()); JPanel pane12 = new JPanel(new BorderLayout()); - pane12.add(new JLabel(MessageManager.getString("label.url")), + pane12.add(new JLabel(MessageManager.getString("label.url:")), BorderLayout.CENTER); pane12.add(urltf, BorderLayout.EAST); panel.add(pane12, BorderLayout.NORTH); @@ -574,6 +574,7 @@ public class WsPreferences extends GWsPreferences new Thread(new Runnable() { + @Override public void run() { // force a refresh. @@ -599,6 +600,7 @@ public class WsPreferences extends GWsPreferences new Thread(new Runnable() { + @Override public void run() { progressBar.setVisible(true); @@ -624,6 +626,7 @@ public class WsPreferences extends GWsPreferences new Thread(new Runnable() { + @Override public void run() { long ct = System.currentTimeMillis(); @@ -681,6 +684,7 @@ public class WsPreferences extends GWsPreferences new Thread(new Runnable() { + @Override public void run() { updateWsMenuConfig(false); diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index 90053f5..c1737a1 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -45,6 +45,7 @@ import java.awt.event.KeyEvent; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; +import javax.swing.AbstractCellEditor; import javax.swing.BorderFactory; import javax.swing.ButtonGroup; import javax.swing.DefaultListCellRenderer; @@ -53,11 +54,11 @@ import javax.swing.JCheckBox; import javax.swing.JComboBox; import javax.swing.JFileChooser; import javax.swing.JLabel; -import javax.swing.JList; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JScrollPane; import javax.swing.JTabbedPane; +import javax.swing.JTable; import javax.swing.JTextField; import javax.swing.ListSelectionModel; import javax.swing.SwingConstants; @@ -67,8 +68,8 @@ import javax.swing.border.EtchedBorder; import javax.swing.border.TitledBorder; import javax.swing.event.ChangeEvent; import javax.swing.event.ChangeListener; -import javax.swing.event.ListSelectionEvent; -import javax.swing.event.ListSelectionListener; +import javax.swing.table.TableCellEditor; +import javax.swing.table.TableCellRenderer; /** * Base class for the Preferences panel. @@ -180,7 +181,21 @@ public class GPreferences extends JPanel /* * Connections tab components */ - protected JList linkURLList = new JList(); + protected JTable linkUrlTable = new JTable(); + + protected JButton editLink = new JButton(); + + protected JButton deleteLink = new JButton(); + + protected JTextField filterTB = new JTextField(); + + protected JButton doReset = new JButton(); + + protected JButton userOnly = new JButton(); + + protected JLabel portLabel = new JLabel(); + + protected JLabel serverLabel = new JLabel(); protected JTextField proxyServerTB = new JTextField(); @@ -188,8 +203,6 @@ public class GPreferences extends JPanel protected JTextField defaultBrowser = new JTextField(); - protected JList linkNameList = new JList(); - protected JCheckBox useProxy = new JCheckBox(); protected JCheckBox usagestats = new JCheckBox(); @@ -483,38 +496,261 @@ public class GPreferences extends JPanel { JPanel connectTab = new JPanel(); connectTab.setLayout(new GridBagLayout()); - JLabel serverLabel = new JLabel(); + + // Label for browser text box + JLabel browserLabel = new JLabel(); + browserLabel.setFont(LABEL_FONT); + browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); + browserLabel.setText(MessageManager + .getString("label.default_browser_unix")); + defaultBrowser.setFont(LABEL_FONT); + defaultBrowser.setText(""); + + defaultBrowser.addMouseListener(new MouseAdapter() + { + @Override + public void mouseClicked(MouseEvent e) + { + if (e.getClickCount() > 1) + { + defaultBrowser_mouseClicked(e); + } + } + }); + + JPanel proxyPanel = initConnTabProxyPanel(); + JPanel linkPanel = initConnTabUrlLinks(); + initConnTabCheckboxes(); + + // Add URL link panel + connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 2.0, 2.0, + GridBagConstraints.WEST, GridBagConstraints.BOTH, new Insets( + 16, 0, 0, 12), 359, 32)); + + // Add default Browser text box + connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, + new Insets(10, 0, 0, 0), 5, 1)); + + connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(10, 0, 0, 10), 307, 1)); + + // Add proxy server panel + connectTab.add(proxyPanel, new GridBagConstraints(0, 2, 2, 1, 1.0, 0.0, + GridBagConstraints.CENTER, GridBagConstraints.HORIZONTAL, + new Insets(10, 0, 0, 12), 4, 10)); + + // Add usage stats, version check and questionnaire checkboxes + connectTab.add(usagestats, new GridBagConstraints(0, 3, 1, 1, 1.0, 0.0, + GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 2, 4, 2), 70, 1)); + connectTab.add(questionnaire, new GridBagConstraints(1, 3, 1, 1, 1.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 2, 4, 10), 70, 1)); + connectTab.add(versioncheck, new GridBagConstraints(0, 4, 1, 1, 1.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 2, 4, 2), 70, 1)); + return connectTab; + } + + /** + * Initialises the proxy server panel in the Connections tab + * + * @return the proxy server panel + */ + private JPanel initConnTabProxyPanel() + { + // Label for server text box serverLabel.setText(MessageManager.getString("label.address")); serverLabel.setHorizontalAlignment(SwingConstants.RIGHT); serverLabel.setFont(LABEL_FONT); + + // Proxy server and port text boxes proxyServerTB.setFont(LABEL_FONT); proxyPortTB.setFont(LABEL_FONT); - JLabel portLabel = new JLabel(); + + // Label for Port text box portLabel.setFont(LABEL_FONT); portLabel.setHorizontalAlignment(SwingConstants.RIGHT); portLabel.setText(MessageManager.getString("label.port")); - JLabel browserLabel = new JLabel(); - browserLabel.setFont(new java.awt.Font("SansSerif", 0, 11)); - browserLabel.setHorizontalAlignment(SwingConstants.TRAILING); - browserLabel.setText(MessageManager - .getString("label.default_browser_unix")); - defaultBrowser.setFont(LABEL_FONT); - defaultBrowser.setText(""); + + // Use proxy server checkbox + useProxy.setFont(LABEL_FONT); + useProxy.setHorizontalAlignment(SwingConstants.RIGHT); + useProxy.setHorizontalTextPosition(SwingConstants.LEADING); + useProxy.setText(MessageManager.getString("label.use_proxy_server")); + useProxy.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + useProxy_actionPerformed(); + } + }); + + // Make proxy server panel + JPanel proxyPanel = new JPanel(); + TitledBorder titledBorder1 = new TitledBorder( + MessageManager.getString("label.proxy_server")); + proxyPanel.setBorder(titledBorder1); + proxyPanel.setLayout(new GridBagLayout()); + proxyPanel.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, + new Insets(0, 2, 2, 0), 5, 0)); + proxyPanel.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0, + GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, + 0, 2, 0), 11, 0)); + proxyPanel.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0, + GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, + 2, 5, 185), 2, -4)); + proxyPanel.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 2, 2, 2), 54, 1)); + proxyPanel.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, + 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, + new Insets(0, 2, 2, 0), 263, 1)); + + return proxyPanel; + } + + /** + * Initialises the checkboxes in the Connections tab + */ + private void initConnTabCheckboxes() + { + // Usage stats checkbox label usagestats.setText(MessageManager .getString("label.send_usage_statistics")); usagestats.setFont(LABEL_FONT); usagestats.setHorizontalAlignment(SwingConstants.RIGHT); usagestats.setHorizontalTextPosition(SwingConstants.LEADING); + + // Questionnaire checkbox label questionnaire.setText(MessageManager .getString("label.check_for_questionnaires")); questionnaire.setFont(LABEL_FONT); questionnaire.setHorizontalAlignment(SwingConstants.RIGHT); questionnaire.setHorizontalTextPosition(SwingConstants.LEADING); + + // Check for latest version checkbox label versioncheck.setText(MessageManager .getString("label.check_for_latest_version")); versioncheck.setFont(LABEL_FONT); versioncheck.setHorizontalAlignment(SwingConstants.RIGHT); versioncheck.setHorizontalTextPosition(SwingConstants.LEADING); + } + + /** + * Initialises the URL links panel in the Connection tab + * + * @return the URL links panel + */ + private JPanel initConnTabUrlLinks() + { + // Set up table for Url links + linkUrlTable.setFillsViewportHeight(true); + linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS); + linkUrlTable.setAutoCreateRowSorter(true); + linkUrlTable.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + + // adjust row height so radio buttons actually fit + // don't do this in the renderer, it causes the awt thread to activate + // constantly + JRadioButton temp = new JRadioButton(); + linkUrlTable.setRowHeight(temp.getMinimumSize().height); + + // Table in scrollpane so that the table is given a scrollbar + JScrollPane linkScrollPane = new JScrollPane(linkUrlTable); + linkScrollPane.setBorder(null); + + // Panel for links functionality + JPanel linkPanel = new JPanel(new GridBagLayout()); + linkPanel.setBorder(new TitledBorder(MessageManager + .getString("label.url_linkfrom_sequence_id"))); + + // Put the Url links panel together + + // Buttons go at top right, resizing only resizes the blank space vertically + JPanel buttonPanel = initConnTabUrlButtons(); + GridBagConstraints linkConstraints1 = new GridBagConstraints(); + linkConstraints1.gridx = 1; + linkConstraints1.gridy = 0; + linkConstraints1.fill = GridBagConstraints.VERTICAL; + linkPanel.add(buttonPanel, linkConstraints1); + + // Links table goes at top left, resizing resizes the table + GridBagConstraints linkConstraints2 = new GridBagConstraints(); + linkConstraints2.gridx = 0; + linkConstraints2.gridy = 0; + linkConstraints2.weightx = 1.0; + linkConstraints2.weighty = 1.0; + linkConstraints2.fill = GridBagConstraints.BOTH; + linkPanel.add(linkScrollPane, linkConstraints2); + + // Filter box and buttons goes at bottom left, resizing resizes the text box + JPanel filterPanel = initConnTabFilterPanel(); + GridBagConstraints linkConstraints3 = new GridBagConstraints(); + linkConstraints3.gridx = 0; + linkConstraints3.gridy = 1; + linkConstraints3.weightx = 1.0; + linkConstraints3.fill = GridBagConstraints.HORIZONTAL; + linkPanel.add(filterPanel, linkConstraints3); + + return linkPanel; + } + + private JPanel initConnTabFilterPanel() + { + // Filter textbox and reset button + JLabel filterLabel = new JLabel( + MessageManager.getString("label.filter")); + filterLabel.setFont(LABEL_FONT); + filterLabel.setHorizontalAlignment(SwingConstants.RIGHT); + filterLabel.setHorizontalTextPosition(SwingConstants.LEADING); + + filterTB.setFont(LABEL_FONT); + filterTB.setText(""); + + doReset.setText(MessageManager.getString("action.showall")); + userOnly.setText(MessageManager.getString("action.customfilter")); + + // Panel for filter functionality + JPanel filterPanel = new JPanel(new GridBagLayout()); + GridBagConstraints gbc = new GridBagConstraints(); + gbc.gridx = 0; + gbc.gridy = 0; + gbc.fill = GridBagConstraints.NONE; + gbc.anchor = GridBagConstraints.WEST; + + filterPanel.add(filterLabel, gbc); + + GridBagConstraints gbc1 = new GridBagConstraints(); + gbc1.gridx = 0; + gbc1.gridx = 1; + gbc1.fill = GridBagConstraints.HORIZONTAL; + gbc1.anchor = GridBagConstraints.WEST; + gbc1.weightx = 1.0; + filterPanel.add(filterTB, gbc1); + + GridBagConstraints gbc2 = new GridBagConstraints(); + gbc2.gridx = 2; + gbc2.fill = GridBagConstraints.NONE; + gbc2.anchor = GridBagConstraints.WEST; + filterPanel.add(doReset, gbc2); + + GridBagConstraints gbc3 = new GridBagConstraints(); + gbc3.gridx = 3; + gbc3.fill = GridBagConstraints.NONE; + gbc3.anchor = GridBagConstraints.WEST; + filterPanel.add(userOnly, gbc3); + + return filterPanel; + } + + private JPanel initConnTabUrlButtons() + { + // Buttons for new / edit / delete Url links JButton newLink = new JButton(); newLink.setText(MessageManager.getString("action.new")); newLink.addActionListener(new java.awt.event.ActionListener() @@ -525,7 +761,7 @@ public class GPreferences extends JPanel newLink_actionPerformed(e); } }); - JButton editLink = new JButton(); + editLink.setText(MessageManager.getString("action.edit")); editLink.addActionListener(new java.awt.event.ActionListener() { @@ -535,7 +771,7 @@ public class GPreferences extends JPanel editLink_actionPerformed(e); } }); - JButton deleteLink = new JButton(); + deleteLink.setText(MessageManager.getString("action.delete")); deleteLink.addActionListener(new java.awt.event.ActionListener() { @@ -546,117 +782,21 @@ public class GPreferences extends JPanel } }); - linkURLList.addListSelectionListener(new ListSelectionListener() - { - @Override - public void valueChanged(ListSelectionEvent e) - { - int index = linkURLList.getSelectedIndex(); - linkNameList.setSelectedIndex(index); - } - }); + // no current selection, so initially disable delete/edit buttons + editLink.setEnabled(false); + deleteLink.setEnabled(false); - linkNameList.addListSelectionListener(new ListSelectionListener() - { - @Override - public void valueChanged(ListSelectionEvent e) - { - int index = linkNameList.getSelectedIndex(); - linkURLList.setSelectedIndex(index); - } - }); + // Panels for new/edit/delete link buttons + // buttonContent prevents the buttons from being resized when the window is + JPanel buttonContent = new JPanel(new GridLayout(0, 1, 0, 0)); + JPanel buttonPanel = new JPanel(new BorderLayout()); - JScrollPane linkScrollPane = new JScrollPane(); - linkScrollPane.setBorder(null); - JPanel linkPanel = new JPanel(); - linkPanel.setBorder(new TitledBorder(MessageManager - .getString("label.url_linkfrom_sequence_id"))); - linkPanel.setLayout(new BorderLayout()); - GridLayout gridLayout1 = new GridLayout(); - JPanel editLinkButtons = new JPanel(); - editLinkButtons.setLayout(gridLayout1); - gridLayout1.setRows(3); - linkNameList.setFont(LABEL_FONT); - linkNameList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); - BorderLayout borderLayout3 = new BorderLayout(); - JPanel linkPanel2 = new JPanel(); - linkPanel2.setLayout(borderLayout3); - linkURLList.setFont(LABEL_FONT); - linkURLList.setSelectionMode(ListSelectionModel.SINGLE_SELECTION); + buttonContent.add(newLink, null); + buttonContent.add(editLink, null); + buttonContent.add(deleteLink, null); + buttonPanel.add(buttonContent, BorderLayout.NORTH); - defaultBrowser.addMouseListener(new MouseAdapter() - { - @Override - public void mouseClicked(MouseEvent e) - { - if (e.getClickCount() > 1) - { - defaultBrowser_mouseClicked(e); - } - } - }); - useProxy.setFont(LABEL_FONT); - useProxy.setHorizontalAlignment(SwingConstants.RIGHT); - useProxy.setHorizontalTextPosition(SwingConstants.LEADING); - useProxy.setText(MessageManager.getString("label.use_proxy_server")); - useProxy.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - useProxy_actionPerformed(); - } - }); - linkPanel.add(editLinkButtons, BorderLayout.EAST); - editLinkButtons.add(newLink, null); - editLinkButtons.add(editLink, null); - editLinkButtons.add(deleteLink, null); - linkPanel.add(linkScrollPane, BorderLayout.CENTER); - linkScrollPane.getViewport().add(linkPanel2, null); - linkPanel2.add(linkURLList, BorderLayout.CENTER); - linkPanel2.add(linkNameList, BorderLayout.WEST); - JPanel jPanel1 = new JPanel(); - TitledBorder titledBorder1 = new TitledBorder( - MessageManager.getString("label.proxy_server")); - jPanel1.setBorder(titledBorder1); - jPanel1.setLayout(new GridBagLayout()); - jPanel1.add(serverLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, - 2, 4, 0), 5, 0)); - jPanel1.add(portLabel, new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, - 0, 4, 0), 11, 6)); - connectTab.add(linkPanel, new GridBagConstraints(0, 0, 2, 1, 1.0, 1.0, - GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets( - 16, 0, 0, 12), 359, -17)); - connectTab.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0, - GridBagConstraints.CENTER, GridBagConstraints.BOTH, new Insets( - 21, 0, 35, 12), 4, 6)); - connectTab.add(browserLabel, new GridBagConstraints(0, 1, 1, 1, 0.0, - 0.0, GridBagConstraints.WEST, GridBagConstraints.NONE, - new Insets(16, 0, 0, 0), 5, 1)); - jPanel1.add(useProxy, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.NONE, new Insets(0, - 2, 5, 185), 2, -4)); - jPanel1.add(proxyPortTB, new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 2, 4, 2), 54, 1)); - jPanel1.add(proxyServerTB, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 2, 4, 0), 263, 1)); - connectTab.add(defaultBrowser, new GridBagConstraints(1, 1, 1, 1, 1.0, - 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(15, 0, 0, 15), 307, 1)); - connectTab.add(usagestats, new GridBagConstraints(0, 4, 1, 1, 1.0, 0.0, - GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 2, 4, 2), 70, 1)); - connectTab.add(questionnaire, new GridBagConstraints(1, 4, 1, 1, 1.0, - 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 2, 4, 2), 70, 1)); - connectTab.add(versioncheck, new GridBagConstraints(0, 5, 1, 1, 1.0, - 0.0, GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL, - new Insets(0, 2, 4, 2), 70, 1)); - return connectTab; + return buttonPanel; } /** @@ -1357,8 +1497,82 @@ public class GPreferences extends JPanel public void useProxy_actionPerformed() { - proxyServerTB.setEnabled(useProxy.isSelected()); - proxyPortTB.setEnabled(useProxy.isSelected()); + boolean enabled = useProxy.isSelected(); + portLabel.setEnabled(enabled); + serverLabel.setEnabled(enabled); + proxyServerTB.setEnabled(enabled); + proxyPortTB.setEnabled(enabled); } + /** + * Customer renderer for JTable: supports column of radio buttons + */ + public class RadioButtonRenderer extends JRadioButton implements + TableCellRenderer + { + public RadioButtonRenderer() + { + setHorizontalAlignment(CENTER); + setToolTipText(MessageManager.getString("label.urltooltip")); + } + + @Override + public Component getTableCellRendererComponent(JTable table, + Object value, boolean isSelected, boolean hasFocus, int row, + int column) + { + setSelected((boolean) value); + + // set colours to match rest of table + if (isSelected) + { + setBackground(table.getSelectionBackground()); + setForeground(table.getSelectionForeground()); + } + else + { + setBackground(table.getBackground()); + setForeground(table.getForeground()); + } + return this; + } + } + + /** + * Customer cell editor for JTable: supports column of radio buttons in + * conjunction with renderer + */ + public class RadioButtonEditor extends AbstractCellEditor implements + TableCellEditor + { + private JRadioButton button = new JRadioButton(); + + public RadioButtonEditor() + { + button.setHorizontalAlignment(SwingConstants.CENTER); + this.button.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + fireEditingStopped(); + } + }); + } + + @Override + public Component getTableCellEditorComponent(JTable table, + Object value, boolean isSelected, int row, int column) + { + button.setSelected((boolean) value); + return button; + } + + @Override + public Object getCellEditorValue() + { + return button.isSelected(); + } + + } } diff --git a/src/jalview/jbgui/GSequenceLink.java b/src/jalview/jbgui/GSequenceLink.java index dbce5f3..ab3ea2c 100755 --- a/src/jalview/jbgui/GSequenceLink.java +++ b/src/jalview/jbgui/GSequenceLink.java @@ -29,19 +29,48 @@ import java.awt.Font; import java.awt.GridBagConstraints; import java.awt.GridBagLayout; import java.awt.Insets; -import java.awt.Panel; import java.awt.Rectangle; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.awt.event.KeyAdapter; import java.awt.event.KeyEvent; import javax.swing.BorderFactory; +import javax.swing.JButton; import javax.swing.JLabel; import javax.swing.JPanel; import javax.swing.JTextField; import javax.swing.SwingConstants; -public class GSequenceLink extends Panel +public class GSequenceLink extends JPanel { + + JTextField nameTB = new JTextField(); + + JTextField urlTB = new JTextField(); + + JButton insertSeq = new JButton(); + + JButton insertDBAcc = new JButton(); + + JLabel insert = new JLabel(); + + JLabel jLabel1 = new JLabel(); + + JLabel jLabel2 = new JLabel(); + + JLabel jLabel3 = new JLabel(); + + JLabel jLabel4 = new JLabel(); + + JLabel jLabel5 = new JLabel(); + + JLabel jLabel6 = new JLabel(); + + JPanel jPanel1 = new JPanel(); + + GridBagLayout gridBagLayout1 = new GridBagLayout(); + public GSequenceLink() { try @@ -77,23 +106,53 @@ public class GSequenceLink extends Panel urlTB_keyTyped(e); } }); + + insertSeq.setLocation(77, 75); + insertSeq.setSize(141, 24); + insertSeq.setText(MessageManager.getString("action.seq_id")); + insertSeq.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + insertSeq_action(e); + } + }); + + insertDBAcc.setLocation(210, 75); + insertDBAcc.setSize(141, 24); + insertDBAcc.setText(MessageManager.getString("action.db_acc")); + insertDBAcc.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + insertDBAcc_action(e); + } + }); + + insert.setText(MessageManager.getString("label.insert")); + insert.setFont(JvSwingUtils.getLabelFont()); + insert.setHorizontalAlignment(SwingConstants.RIGHT); + insert.setBounds(17, 78, 58, 16); + jLabel1.setFont(JvSwingUtils.getLabelFont()); jLabel1.setHorizontalAlignment(SwingConstants.TRAILING); jLabel1.setText(MessageManager.getString("label.link_name")); jLabel1.setBounds(new Rectangle(4, 10, 71, 24)); jLabel2.setFont(JvSwingUtils.getLabelFont()); jLabel2.setHorizontalAlignment(SwingConstants.TRAILING); - jLabel2.setText(MessageManager.getString("label.url")); + jLabel2.setText(MessageManager.getString("label.url:")); jLabel2.setBounds(new Rectangle(17, 37, 54, 27)); jLabel3.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); jLabel3.setText(MessageManager.getString("label.use_sequence_id_1")); - jLabel3.setBounds(new Rectangle(21, 72, 351, 15)); + jLabel3.setBounds(new Rectangle(21, 102, 351, 15)); jLabel4.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); jLabel4.setText(MessageManager.getString("label.use_sequence_id_2")); - jLabel4.setBounds(new Rectangle(21, 88, 351, 15)); + jLabel4.setBounds(new Rectangle(21, 118, 351, 15)); jLabel5.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); jLabel5.setText(MessageManager.getString("label.use_sequence_id_3")); - jLabel5.setBounds(new Rectangle(21, 106, 351, 15)); + jLabel5.setBounds(new Rectangle(21, 136, 351, 15)); String lastLabel = MessageManager.getString("label.use_sequence_id_4"); if (lastLabel.length() > 0) @@ -101,7 +160,7 @@ public class GSequenceLink extends Panel // e.g. Spanish version has longer text jLabel6.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11)); jLabel6.setText(lastLabel); - jLabel6.setBounds(new Rectangle(21, 122, 351, 15)); + jLabel6.setBounds(new Rectangle(21, 152, 351, 15)); } jPanel1.setBorder(BorderFactory.createEtchedBorder()); @@ -109,16 +168,19 @@ public class GSequenceLink extends Panel jPanel1.add(jLabel1); jPanel1.add(nameTB); jPanel1.add(urlTB); + jPanel1.add(insertSeq); + jPanel1.add(insertDBAcc); + jPanel1.add(insert); jPanel1.add(jLabel2); jPanel1.add(jLabel3); jPanel1.add(jLabel4); jPanel1.add(jLabel5); - int height = 130; + int height = 160; if (lastLabel.length() > 0) { jPanel1.add(jLabel6); - height = 146; + height = 176; } this.add(jPanel1, new GridBagConstraints(0, 0, 1, 1, 1.0, 1.0, @@ -163,25 +225,13 @@ public class GSequenceLink extends Panel return false; } - JTextField nameTB = new JTextField(); - - JTextField urlTB = new JTextField(); - - JLabel jLabel1 = new JLabel(); - - JLabel jLabel2 = new JLabel(); - - JLabel jLabel3 = new JLabel(); - - JLabel jLabel4 = new JLabel(); - - JLabel jLabel5 = new JLabel(); - - JLabel jLabel6 = new JLabel(); - - JPanel jPanel1 = new JPanel(); - - GridBagLayout gridBagLayout1 = new GridBagLayout(); + public void notifyDuplicate() + { + JvOptionPane.showInternalMessageDialog(jalview.gui.Desktop.desktop, + MessageManager.getString("warn.name_cannot_be_duplicate"), + MessageManager.getString("label.invalid_name"), + JvOptionPane.WARNING_MESSAGE); + } public void nameTB_keyTyped(KeyEvent e) { @@ -200,4 +250,23 @@ public class GSequenceLink extends Panel // } } + + public void insertSeq_action(ActionEvent e) + { + insertIntoUrl(insertSeq.getText()); + } + + public void insertDBAcc_action(ActionEvent e) + { + insertIntoUrl(insertDBAcc.getText()); + } + + private void insertIntoUrl(String insertion) + { + int pos = urlTB.getCaretPosition(); + String text = urlTB.getText(); + String newText = text.substring(0, pos) + insertion + + text.substring(pos); + urlTB.setText(newText); + } } diff --git a/src/jalview/urls/CustomUrlProvider.java b/src/jalview/urls/CustomUrlProvider.java new file mode 100644 index 0000000..dae9ccd --- /dev/null +++ b/src/jalview/urls/CustomUrlProvider.java @@ -0,0 +1,337 @@ +/* + * 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ + +package jalview.urls; + +import static jalview.util.UrlConstants.DB_ACCESSION; +import static jalview.util.UrlConstants.DELIM; +import static jalview.util.UrlConstants.SEP; +import static jalview.util.UrlConstants.SEQUENCE_ID; + +import jalview.util.MessageManager; +import jalview.util.UrlConstants; +import jalview.util.UrlLink; + +import java.util.ArrayList; +import java.util.HashMap; +import java.util.Iterator; +import java.util.List; +import java.util.Map; +import java.util.Map.Entry; +import java.util.StringTokenizer; +import java.util.Vector; + +/** + * + * Implements the UrlProviderI interface for a UrlProvider object which serves + * custom URLs defined by the user + * + * @author $author$ + * @version $Revision$ + */ +public class CustomUrlProvider extends UrlProviderImpl +{ + // Default sequence URL link label for SRS + private static final String SRS_LABEL = "SRS"; + + // map of string ids to urlLinks (selected) + private HashMap selectedUrls; + + // map of string ids to urlLinks (not selected) + private HashMap nonselectedUrls; + + /** + * Construct UrlProvider for custom (user-entered) URLs + * + * @param inMenuUrlList + * list of URLs set to be displayed in menu, in form stored in Cache. + * i.e. SEP delimited string + * @param storedUrlList + * list of custom URLs entered by user but not currently displayed in + * menu, in form stored in Cache + */ + public CustomUrlProvider(String inMenuUrlList, String storedUrlList) + { + try + { + selectedUrls = parseUrlStrings(inMenuUrlList); + nonselectedUrls = parseUrlStrings(storedUrlList); + } catch (Exception ex) + { + System.out + .println(ex.getMessage() + "\nError parsing sequence links"); + } + } + + /** + * Construct UrlProvider for custom (user-entered) URLs + * + * @param urlList + * list of URLs to be displayed in menu, as (label,url) pairs + * @param storedUrlList + * list of custom URLs entered by user but not currently displayed in + * menu, as (label,url) pairs + */ + public CustomUrlProvider(Map inMenuUrlList, + Map storedUrlList) + { + try + { + selectedUrls = parseUrlList(inMenuUrlList); + nonselectedUrls = parseUrlList(storedUrlList); + } catch (Exception ex) + { + System.out + .println(ex.getMessage() + "\nError parsing sequence links"); + } + } + + private HashMap parseUrlStrings(String urlStrings) + { + // cachedUrlList is in form