X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=0727b0cfe2c070638fb9e76f299032c493293f0c;hb=fd026dead85b733e64fdc7c2e6c88d1adc10626a;hp=1fa9f7cf37cbaaa5ad10a27af1fa0e3a77506426;hpb=61f35f2177eb22c3d42cafda13db82d4e904b9f0;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 1fa9f7c..0727b0c 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 2.7) + * Copyright (C) 2011 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)"); @@ -111,6 +112,11 @@ public class APopupMenu extends java.awt.PopupMenu implements MenuItem revealAll = new MenuItem(); + MenuItem revealSeq = new MenuItem(); + /** + * index of sequence to be revealed + */ + int revealSeq_index=-1; Menu menu1 = new Menu(); public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) @@ -146,10 +152,11 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null && sg.getSize() > 0) { - editGroupName.setLabel(sg.getName()); + editGroupName.setLabel("Name: "+sg.getName()); 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); @@ -176,19 +183,19 @@ 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()) + if (seq!=null && urlLink.isDynamic()) { // collect matching db-refs - DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq - .getDBRef(), new String[] - { target }); + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( + seq.getDBRef(), new String[] + { target }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); - if (descr!=null && descr.length()<1) + if (descr != null && descr.length() < 1) { descr = null; } @@ -227,21 +234,20 @@ public class APopupMenu extends java.awt.PopupMenu implements } // addshowLink(linkMenu, target, url_pref + id + url_suff); } - // TODO: introduce applet parameter option to dis/en/able URl generation from description - // hard-disable the construction of URLs from regexes that match the description -// if (descr != null) -// { -// // create link for this URL from description where regex matches -// String[] urls = urlLink.makeUrls(descr, false); -// if (urls != null) -// { -// for (int u = 0; u < urls.length; u += 2) -// { -// addshowLink(linkMenu, label, urls[u + 1]); -// } -// } -// // 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 { @@ -251,11 +257,12 @@ 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 = @@ -270,16 +277,19 @@ 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()); @@ -293,6 +303,17 @@ public class APopupMenu extends java.awt.PopupMenu implements if (!ap.av.hasHiddenRows) { remove(revealAll); + remove(revealSeq); + } else { + final int index = ap.av.alignment.findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) + - ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + revealSeq_index=index; + } else { + remove(revealSeq); + } } } @@ -300,10 +321,10 @@ 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) @@ -315,12 +336,12 @@ 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) @@ -354,6 +375,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { showBoxes_itemStateChanged(); } + else if (evt.getSource() == displayNonconserved) + { + this.showNonconserved_itemStateChanged(); + } } public void actionPerformed(ActionEvent evt) @@ -437,6 +462,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { hideSequences(true); } + else if (source == revealSeq) + { + ap.av.showSequence(revealSeq_index); + } else if (source == revealAll) { ap.av.showAllHiddenSeqs(); @@ -483,8 +512,8 @@ public class APopupMenu extends java.awt.PopupMenu implements { EditCommand editCommand = new EditCommand("Edit Sequences", EditCommand.REPLACE, dialog.getName().replace(' ', - ap.av.getGapCharacter()), sg - .getSequencesAsArray(ap.av.hiddenRepSequences), + ap.av.getGapCharacter()), + sg.getSequencesAsArray(ap.av.hiddenRepSequences), sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment); ap.alignFrame.addHistoryItem(editCommand); @@ -577,18 +606,28 @@ 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)) @@ -611,19 +650,20 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Selection output - " - + e.getActionCommand(), 600, 500); + jalview.bin.JalviewLite.addFrame(frame, + "Selection output - " + e.getActionCommand(), 600, 500); - cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e - .getActionCommand(), new Alignment(ap.av - .getSelectionAsNewSequence()), ap.av.showJVSuffix)); + cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( + e.getActionCommand(), + new Alignment(ap.av.getSelectionAsNewSequence()), + ap.av.showJVSuffix)); } void editName() { - EditNameDialog dialog = new EditNameDialog(seq.getName(), seq - .getDescription(), " Sequence Name", + EditNameDialog dialog = new EditNameDialog(seq.getName(), + seq.getDescription(), " Sequence Name", "Sequence Description", ap.alignFrame, "Edit Sequence Name / Description", 500, 100, true); @@ -656,7 +696,7 @@ public class APopupMenu extends java.awt.PopupMenu implements cap.setPDBImport(seq); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300); + jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file for sequence "+seq.getName(), 400, 300); } } @@ -679,7 +719,9 @@ 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"); @@ -690,10 +732,12 @@ public class APopupMenu extends java.awt.PopupMenu implements hideSeqs.setLabel("Hide Sequences"); repGroup.setLabel("Represent Group with"); revealAll.setLabel("Reveal All"); + revealSeq.setLabel("Reveal Sequences"); menu1.setLabel("Group"); add(groupMenu); this.add(seqMenu); this.add(hideSeqs); + this.add(revealSeq); this.add(revealAll); groupMenu.add(editGroupName); groupMenu.add(editMenu); @@ -761,18 +805,23 @@ public class APopupMenu extends java.awt.PopupMenu implements toLower.addActionListener(this); editMenu.add(toggleCase); seqMenu.add(sequenceName); - seqMenu.add(pdb); + if (!ap.av.applet.useXtrnalSviewer) + { + seqMenu.add(pdb); + } seqMenu.add(repGroup); menu1.add(unGroupMenuItem); menu1.add(colourMenu); menu1.add(showBoxes); menu1.add(showText); menu1.add(showColourText); + menu1.add(displayNonconserved); toggleCase.addActionListener(this); pdb.addActionListener(this); hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); + revealSeq.addActionListener(this); } void refresh() @@ -783,9 +832,9 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void clustalColour_actionPerformed() { SequenceGroup sg = getGroup(); - sg.cs = new ClustalxColourScheme(sg - .getSequences(ap.av.hiddenRepSequences), ap.av.alignment - .getWidth()); + sg.cs = new ClustalxColourScheme( + sg.getSequences(ap.av.hiddenRepSequences), + ap.av.alignment.getWidth()); refresh(); } @@ -847,9 +896,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (abovePIDColour.getState()) { - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment - .getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), 0, + ap.av.alignment.getWidth())); int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); @@ -877,9 +926,9 @@ public class APopupMenu extends java.awt.PopupMenu implements { SequenceGroup sg = getGroup(); sg.cs = new PIDColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment - .getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), 0, + ap.av.alignment.getWidth())); refresh(); } @@ -889,9 +938,9 @@ public class APopupMenu extends java.awt.PopupMenu implements sg.cs = new Blosum62ColourScheme(); - sg.cs.setConsensus(AAFrequency.calculate(sg - .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment - .getWidth())); + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.hiddenRepSequences), 0, + ap.av.alignment.getWidth())); refresh(); } @@ -914,8 +963,8 @@ public class APopupMenu extends java.awt.PopupMenu implements { Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg - .getSequences(ap.av.hiddenRepSequences), 0, + ResidueProperties.propHash, 3, + sg.getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment.getWidth()); c.calculate(); @@ -968,6 +1017,12 @@ 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()); @@ -1005,6 +1060,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } ap.av.hideSequence(hseqs); + ap.av.sendSelection(); } }