X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=a56f76dcb2e437a13a9d459cc0bb2a0db2b01ea7;hb=4fcca76a6c1460d492469ace09a728925b733bfe;hp=56a3794e41346a750178a1460ddeb8fbef0b44f7;hpb=1a506ea005a3c4aba6108199ee6d2122e7528ea9;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 56a3794..a56f76d 100755 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 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; @@ -113,6 +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) @@ -152,7 +156,7 @@ public class APopupMenu extends java.awt.PopupMenu implements showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); - displayNonconserved.setState(sg.getShowunconserved()); + displayNonconserved.setState(sg.getShowNonconserved()); if (!ap.av.alignment.getGroups().contains(sg)) { groupMenu.remove(unGroupMenuItem); @@ -185,9 +189,9 @@ public class APopupMenu extends java.awt.PopupMenu implements { // 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(); @@ -285,6 +289,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } } } + // TODO: add group link menu entry here if (seq != null) { seqMenu.setLabel(seq.getName()); @@ -298,6 +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); + } } } @@ -446,6 +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(); @@ -492,8 +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); @@ -586,26 +606,25 @@ public class APopupMenu extends java.awt.PopupMenu implements return; } - - int rsize=0,gSize = sg.getSize(); - SequenceI[] rseqs,seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures,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++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); - if (start<=end) + if (start <= end) { seqs[rsize] = sg.getSequenceAt(i); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); + 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(seqs, 0, rseqs, 0, rsize); System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; @@ -631,19 +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); @@ -712,10 +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); @@ -796,6 +818,7 @@ public class APopupMenu extends java.awt.PopupMenu implements hideSeqs.addActionListener(this); repGroup.addActionListener(this); revealAll.addActionListener(this); + revealSeq.addActionListener(this); } void refresh() @@ -806,9 +829,9 @@ 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(); } @@ -870,9 +893,9 @@ 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()); @@ -900,9 +923,9 @@ 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(); } @@ -912,9 +935,9 @@ 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(); } @@ -937,8 +960,8 @@ 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(); @@ -993,7 +1016,7 @@ public class APopupMenu extends java.awt.PopupMenu implements public void showNonconserved_itemStateChanged() { - getGroup().setShowunconserved(this.displayNonconserved.getState()); + getGroup().setShowNonconserved(this.displayNonconserved.getState()); refresh(); } @@ -1034,6 +1057,7 @@ public class APopupMenu extends java.awt.PopupMenu implements } ap.av.hideSequence(hseqs); + ap.av.sendSelection(); } }