X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=f4b3903ca4125e2fcba4d5a92b4e75c91379c79f;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=f7ecfda72c98b7430ccc041856f3be4b7953220b;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index f7ecfda..f4b3903 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle * - * This program 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 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program 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. + * 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. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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 . */ package jalview.appletgui; @@ -79,6 +78,8 @@ public class APopupMenu extends java.awt.PopupMenu implements CheckboxMenuItem showColourText = new CheckboxMenuItem(); + CheckboxMenuItem displayNonconserved = new CheckboxMenuItem(); + Menu editMenu = new Menu("Edit"); MenuItem copy = new MenuItem("Copy (Jalview Only)"); @@ -150,6 +151,7 @@ public class APopupMenu extends java.awt.PopupMenu implements showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); + displayNonconserved.setState(sg.getShowNonconserved()); if (!ap.av.alignment.getGroups().contains(sg)) { groupMenu.remove(unGroupMenuItem); @@ -176,7 +178,7 @@ public class APopupMenu extends java.awt.PopupMenu implements continue; } final String target = urlLink.getTarget(); // link.substring(0, - // link.indexOf("|")); + // link.indexOf("|")); final String label = urlLink.getLabel(); if (urlLink.isDynamic()) { @@ -187,6 +189,11 @@ public class APopupMenu extends java.awt.PopupMenu implements { target }); // 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++) @@ -222,6 +229,20 @@ public class APopupMenu extends java.awt.PopupMenu implements } // addshowLink(linkMenu, target, url_pref + id + url_suff); } + // Now construct URLs from description but only try to do it for regex + // URL links + if (descr != null && urlLink.getRegexReplace() != null) + { + // create link for this URL from description only if regex matches + String[] urls = urlLink.makeUrls(descr, true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + addshowLink(linkMenu, label, urls[u + 1]); + } + } + } } else { @@ -231,11 +252,12 @@ public class APopupMenu extends java.awt.PopupMenu implements * final String url; * * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID - * string and any matching database reference accessions String url_pref = - * link.substring(link.indexOf("|") + 1, link.indexOf("$SEQUENCE_ID$")); + * string and any matching database reference accessions String url_pref + * = link.substring(link.indexOf("|") + 1, + * link.indexOf("$SEQUENCE_ID$")); * * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13); - * // collect matching db-refs DBRefEntry[] dbr = + * // collect matching db-refs DBRefEntry[] dbr = * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new * String[]{target}); // collect id string too String id = * seq.getName(); if (id.indexOf("|") > -1) { id = @@ -250,16 +272,19 @@ public class APopupMenu extends java.awt.PopupMenu implements * link.substring(link.lastIndexOf("|")+1)); } */ } - - if (seq != null) + if (linkMenu.getItemCount() > 0) { - seqMenu.add(linkMenu); - } - else - { - add(linkMenu); + if (seq != null) + { + seqMenu.add(linkMenu); + } + else + { + add(linkMenu); + } } } + // TODO: add group link menu entry here if (seq != null) { seqMenu.setLabel(seq.getName()); @@ -280,10 +305,10 @@ public class APopupMenu extends java.awt.PopupMenu implements * add a show URL menu item to the given linkMenu * * @param linkMenu - * @param target - - * menu label string - * @param url - - * url to open + * @param target + * - menu label string + * @param url + * - url to open */ private void addshowLink(Menu linkMenu, final String target, final String url) @@ -295,12 +320,12 @@ public class APopupMenu extends java.awt.PopupMenu implements * add a show URL menu item to the given linkMenu * * @param linkMenu - * @param target - - * URL target window - * @param label - - * menu label string - * @param url - - * url to open + * @param target + * - URL target window + * @param label + * - menu label string + * @param url + * - url to open */ private void addshowLink(Menu linkMenu, final String target, final String label, final String url) @@ -334,6 +359,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { showBoxes_itemStateChanged(); } + else if (evt.getSource() == displayNonconserved) + { + this.showNonconserved_itemStateChanged(); + } } public void actionPerformed(ActionEvent evt) @@ -557,18 +586,28 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - int gSize = sg.getSize(); - SequenceI[] seqs = new SequenceI[gSize]; - SequenceFeature[] features = new SequenceFeature[gSize]; + int rsize = 0, gSize = sg.getSize(); + SequenceI[] rseqs, seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; for (int i = 0; i < gSize; i++) { - seqs[i] = sg.getSequenceAt(i); int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - features[i] = new SequenceFeature(null, null, null, start, end, - "Jalview"); + if (start <= end) + { + seqs[rsize] = sg.getSequenceAt(i); + features[rsize] = new SequenceFeature(null, null, null, start, + end, "Jalview"); + rsize++; + } } + rseqs = new SequenceI[rsize]; + tfeatures = new SequenceFeature[rsize]; + System.arraycopy(seqs, 0, rseqs, 0, rsize); + System.arraycopy(features, 0, tfeatures, 0, rsize); + features = tfeatures; + seqs = rseqs; if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) @@ -659,7 +698,9 @@ public class APopupMenu extends java.awt.PopupMenu implements showBoxes.setState(true); showBoxes.addItemListener(this); sequenceName.addActionListener(this); - + displayNonconserved.setLabel("Show Nonconserved"); + displayNonconserved.setState(false); + displayNonconserved.addItemListener(this); showText.setLabel("Text"); showText.addItemListener(this); showColourText.setLabel("Colour Text"); @@ -748,6 +789,7 @@ public class APopupMenu extends java.awt.PopupMenu implements menu1.add(showBoxes); menu1.add(showText); menu1.add(showColourText); + menu1.add(displayNonconserved); toggleCase.addActionListener(this); pdb.addActionListener(this); hideSeqs.addActionListener(this); @@ -948,6 +990,12 @@ public class APopupMenu extends java.awt.PopupMenu implements refresh(); } + public void showNonconserved_itemStateChanged() + { + getGroup().setShowNonconserved(this.displayNonconserved.getState()); + refresh(); + } + public void showBoxes_itemStateChanged() { getGroup().setDisplayBoxes(showBoxes.getState());