X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=f2881889cf600ac72b569a81473d2197d30db63d;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=858c055dc3deba637837bfe48dbcca9b99a916e8;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index 858c055..f288188 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,32 +1,55 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 The Jalview Authors + * 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. + * 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 . + * 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.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.datamodel.*; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.Annotation; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; import jalview.util.MessageManager; import jalview.util.ParseHtmlBodyAndLinks; +import java.awt.Checkbox; +import java.awt.CheckboxMenuItem; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.FlowLayout; +import java.awt.FontMetrics; +import java.awt.Frame; +import java.awt.Graphics; +import java.awt.Image; +import java.awt.MenuItem; +import java.awt.Panel; +import java.awt.PopupMenu; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.InputEvent; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; +import java.util.Arrays; +import java.util.Vector; + public class AnnotationLabels extends Panel implements ActionListener, MouseListener, MouseMotionListener { @@ -93,10 +116,13 @@ public class AnnotationLabels extends Panel implements ActionListener, this.av = av; } - public void setScrollOffset(int y) + public void setScrollOffset(int y, boolean repaint) { scrollOffset = y; - repaint(); + if (repaint) + { + repaint(); + } } /** @@ -217,7 +243,9 @@ public class AnnotationLabels extends Panel implements ActionListener, return true; } else + { return false; + } } @@ -407,7 +435,8 @@ public class AnnotationLabels extends Panel implements ActionListener, if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - PopupMenu popup = new PopupMenu(MessageManager.getString("label.annotations")); + PopupMenu popup = new PopupMenu( + MessageManager.getString("label.annotations")); MenuItem item = new MenuItem(ADDNEW); item.addActionListener(this); @@ -450,7 +479,7 @@ public class AnnotationLabels extends Panel implements ActionListener, { popup.addSeparator(); final CheckboxMenuItem cbmi = new CheckboxMenuItem( - "Ignore Gaps In Consensus", + MessageManager.getString("label.ignore_gaps_consensus"), (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef .getIgnoreGapsConsensus() : ap.av .getIgnoreGapsConsensus()); @@ -475,7 +504,7 @@ public class AnnotationLabels extends Panel implements ActionListener, if (aaa.groupRef != null) { final CheckboxMenuItem chist = new CheckboxMenuItem( - "Show Group Histogram", + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { @@ -494,7 +523,7 @@ public class AnnotationLabels extends Panel implements ActionListener, }); popup.add(chist); final CheckboxMenuItem cprofl = new CheckboxMenuItem( - "Show Group Logo", + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addItemListener(new ItemListener() { @@ -514,7 +543,7 @@ public class AnnotationLabels extends Panel implements ActionListener, popup.add(cprofl); final CheckboxMenuItem cprofn = new CheckboxMenuItem( - "Normalise Group Logo", + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { @@ -537,7 +566,7 @@ public class AnnotationLabels extends Panel implements ActionListener, else { final CheckboxMenuItem chist = new CheckboxMenuItem( - "Show Histogram", av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) @@ -559,7 +588,7 @@ public class AnnotationLabels extends Panel implements ActionListener, }); popup.add(chist); final CheckboxMenuItem cprof = new CheckboxMenuItem( - "Show Logo", av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); cprof.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) @@ -582,7 +611,7 @@ public class AnnotationLabels extends Panel implements ActionListener, }); popup.add(cprof); final CheckboxMenuItem cprofn = new CheckboxMenuItem( - "Normalise Logo", av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { public void itemStateChanged(ItemEvent e) @@ -643,17 +672,40 @@ public class AnnotationLabels extends Panel implements ActionListener, } else if (aa[selectedRow].sequenceRef != null) { - Vector sr = new Vector(); - sr.addElement(aa[selectedRow].sequenceRef); if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.highlightSearchResults(sr); + ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays + .asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { ap.seqPanel.ap.idPanel.highlightSearchResults(null); - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(aa[selectedRow].sequenceRef, false); + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg!=null) + { + // we make a copy rather than edit the current selection if no modifiers pressed + // see Enhancement JAL-1557 + if (!(evt.isControlDown() || evt.isShiftDown())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } else { + if (evt.isControlDown()) + { + sg.addOrRemove(aa[selectedRow].sequenceRef, true); + } else { + // notionally, we should also add intermediate sequences from last added sequence ? + sg.addSequence(aa[selectedRow].sequenceRef, true); + } + } + } else { + sg = new SequenceGroup(); + sg.setStartRes(0); + sg.setEndRes(ap.av.getAlignment().getWidth()-1); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } ap.av.setSelectionGroup(sg); ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); @@ -685,11 +737,8 @@ public class AnnotationLabels extends Panel implements ActionListener, if (av.hasHiddenColumns()) { jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector(); - for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) + for (int[] region : av.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(i); - jalview.appletgui.AlignFrame.copiedHiddenColumns .addElement(new int[] { region[0], region[1] }); @@ -768,7 +817,8 @@ public class AnnotationLabels extends Panel implements ActionListener, { g.setColor(Color.black); g.drawString(MessageManager.getString("label.right_click"), 2, 8); - g.drawString(MessageManager.getString("label.to_add_annotation"), 2, 18); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); } } }