X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=aa3cad49ba9e45d6976f869e4e11d6d399854603;hb=bb90751010ab798f54dabddb8cfb6f51e847072c;hp=497f3ba7b53a1dbe7bafe7c03b67337a28e69803;hpb=048a384fa19ac37fbe2b63bbba139d5fa17107c5;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 497f3ba..aa3cad4 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -49,13 +49,11 @@ import jalview.schemes.HydrophobicColourScheme; import jalview.schemes.NucleotideColourScheme; import jalview.schemes.PIDColourScheme; import jalview.schemes.PurinePyrimidineColourScheme; -import jalview.schemes.ResidueProperties; import jalview.schemes.StrandColourScheme; import jalview.schemes.TaylorColourScheme; import jalview.schemes.TurnColourScheme; import jalview.schemes.UserColourScheme; import jalview.schemes.ZappoColourScheme; -import jalview.util.DBRefUtils; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; @@ -64,8 +62,8 @@ import jalview.util.UrlLink; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; -import java.util.ArrayList; import java.util.Arrays; +import java.util.Collection; import java.util.Collections; import java.util.Hashtable; import java.util.LinkedHashMap; @@ -91,8 +89,6 @@ import javax.swing.JRadioButtonMenuItem; */ public class PopupMenu extends JPopupMenu { - private static final String ALL_ANNOTATIONS = "All"; - JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -478,8 +474,6 @@ public class PopupMenu extends JPopupMenu if (sg != null && sg.getSize() > 0) { - groupName.setText(MessageManager.formatMessage("label.name_param", - new Object[] { sg.getName() })); groupName.setText(MessageManager .getString("label.edit_name_and_description_current_group")); @@ -622,7 +616,8 @@ public class PopupMenu extends JPopupMenu void addFeatureLinks(final SequenceI seq, List links) { JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - List linkset = new ArrayList(); + Map linkset = new LinkedHashMap(); + for (String link : links) { UrlLink urlLink = null; @@ -634,97 +629,18 @@ public class PopupMenu extends JPopupMenu Cache.log.error("Exception for URLLink '" + link + "'", foo); continue; } - ; + if (!urlLink.isValid()) { Cache.log.error(urlLink.getInvalidMessage()); continue; } - final String label = urlLink.getLabel(); - if (seq != null && urlLink.isDynamic()) - { - // collect matching db-refs - DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(), - new String[] { urlLink.getTarget() }); - // collect id string too - String id = seq.getName(); - String descr = seq.getDescription(); - if (descr != null && descr.length() < 1) - { - descr = null; - } - - if (dbr != null) - { - for (int r = 0; r < dbr.length; r++) - { - if (id != null && dbr[r].getAccessionId().equals(id)) - { - // suppress duplicate link creation for the bare sequence ID - // string with this link - id = null; - } - // create Bare ID link for this URL - String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); - } - } - } - } - } - if (id != null) - { - // create Bare ID link for this URL - String[] urls = urlLink.makeUrls(id, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - // Create urls from description but only for URL links which are regex - // links - if (descr != null && urlLink.getRegexReplace() != null) - { - // create link for this URL from description where regex matches - String[] urls = urlLink.makeUrls(descr, true); - if (urls != null) - { - for (int u = 0; u < urls.length; u += 2) - { - if (!linkset.contains(urls[u] + "|" + urls[u + 1])) - { - linkset.add(urls[u] + "|" + urls[u + 1]); - addshowLink(linkMenu, label, urls[u + 1]); - } - } - } - } - } - else - { - if (!linkset.contains(label + "|" + urlLink.getUrl_prefix())) - { - linkset.add(label + "|" + urlLink.getUrl_prefix()); - // Add a non-dynamic link - addshowLink(linkMenu, label, urlLink.getUrl_prefix()); - } - } + urlLink.createLinksFromSeq(seq, linkset); } + + addshowLinks(linkMenu, linkset.values()); + if (sequence != null) { sequenceMenu.add(linkMenu); @@ -735,6 +651,8 @@ public class PopupMenu extends JPopupMenu } } + + /** * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus. * "All" is added first, followed by a separator. Then add any annotation @@ -756,7 +674,8 @@ public class PopupMenu extends JPopupMenu showMenu.removeAll(); hideMenu.removeAll(); - final List all = Arrays.asList(ALL_ANNOTATIONS); + final List all = Arrays.asList(new String[] { MessageManager + .getString("label.all") }); addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, false); @@ -932,8 +851,7 @@ public class PopupMenu extends JPopupMenu urlLink = new GroupUrlLink(link); } catch (Exception foo) { - Cache.log.error("Exception for GroupURLLink '" + link - + "'", foo); + Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); continue; } ; @@ -1009,6 +927,15 @@ public class PopupMenu extends JPopupMenu } } + private void addshowLinks(JMenu linkMenu, Collection linkset) + { + for (String[] linkstrset : linkset) + { + // split linkstr into label and url + addshowLink(linkMenu, linkstrset[1], linkstrset[3]); + } + } + /** * add a show URL menu item to the given linkMenu * @@ -1098,7 +1025,6 @@ public class PopupMenu extends JPopupMenu */ private void jbInit() throws Exception { - groupMenu.setText(MessageManager.getString("label.group")); groupMenu.setText(MessageManager.getString("label.selection")); groupName.setText(MessageManager.getString("label.name")); groupName.addActionListener(new java.awt.event.ActionListener() @@ -2043,9 +1969,8 @@ public class PopupMenu extends JPopupMenu if (conservationMenuItem.isSelected()) { // JBPNote: Conservation name shouldn't be i18n translated - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.getSequences(ap.av - .getHiddenRepSequences()), sg.getStartRes(), + Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av + .getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1); c.calculate();