X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationLabels.java;h=c049326f1837e00582471efcfd0336318fbef587;hb=9214cffc006412ed194565b82c8663df2ea641c6;hp=e066d0aaca573e95fd4856faf520927dc0156989;hpb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;p=jalview.git diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java index e066d0a..c049326 100755 --- a/src/jalview/appletgui/AnnotationLabels.java +++ b/src/jalview/appletgui/AnnotationLabels.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1) - * Copyright (C) 2015 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. * @@ -31,6 +31,7 @@ import jalview.util.ParseHtmlBodyAndLinks; import java.awt.Checkbox; import java.awt.CheckboxMenuItem; import java.awt.Color; +import java.awt.Cursor; import java.awt.Dimension; import java.awt.FlowLayout; import java.awt.FontMetrics; @@ -52,8 +53,8 @@ import java.util.Arrays; import java.util.Collections; import java.util.Vector; -public class AnnotationLabels extends Panel implements ActionListener, - MouseListener, MouseMotionListener +public class AnnotationLabels extends Panel + implements ActionListener, MouseListener, MouseMotionListener { Image image; @@ -162,6 +163,7 @@ public class AnnotationLabels extends Panel implements ActionListener, return row; } + @Override public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -200,8 +202,9 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.alignFrame); Frame frame = new Frame(); frame.add(cap); - jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle() - + " - " + aa[selectedRow].label, 500, 100); + jalview.bin.JalviewLite.addFrame(frame, + ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500, + 100); cap.setText(aa[selectedRow].toString()); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) @@ -224,13 +227,15 @@ public class AnnotationLabels extends Panel implements ActionListener, ap.annotationPanel.adjustPanelHeight(); setSize(getSize().width, ap.annotationPanel.getSize().height); ap.validate(); - ap.paintAlignment(true); + // TODO: only paint if we needed to + ap.paintAlignment(true, true); } boolean editLabelDescription(AlignmentAnnotation annotation) { - Checkbox padGaps = new Checkbox("Fill Empty Gaps With \"" - + ap.av.getGapCharacter() + "\"", annotation.padGaps); + Checkbox padGaps = new Checkbox( + "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"", + annotation.padGaps); EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Label", @@ -261,9 +266,12 @@ public class AnnotationLabels extends Panel implements ActionListener, boolean resizePanel = false; + @Override public void mouseMoved(MouseEvent evt) { resizePanel = evt.getY() < 10 && evt.getX() < 14; + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); int row = getSelectedRow(evt.getY() + scrollOffset); if (row > -1) @@ -306,6 +314,7 @@ public class AnnotationLabels extends Panel implements ActionListener, dragCancelled = true; } + @Override public void mouseDragged(MouseEvent evt) { if (dragCancelled) @@ -317,8 +326,9 @@ public class AnnotationLabels extends Panel implements ActionListener, if (resizePanel) { - Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder - .getSize(), f = ap.seqPanelHolder.getSize(); + Dimension d = ap.annotationPanelHolder.getSize(), + e = ap.annotationSpaceFillerHolder.getSize(), + f = ap.seqPanelHolder.getSize(); int dif = evt.getY() - oldY; dif /= ap.av.getCharHeight(); @@ -328,15 +338,16 @@ public class AnnotationLabels extends Panel implements ActionListener, { ap.annotationPanel.setSize(d.width, d.height - dif); setSize(new Dimension(e.width, d.height - dif)); - ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width, - d.height - dif)); - ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height - - dif)); + ap.annotationSpaceFillerHolder + .setSize(new Dimension(e.width, d.height - dif)); + ap.annotationPanelHolder + .setSize(new Dimension(d.width, d.height - dif)); ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0, av.calcPanelHeight()); f.height += dif; ap.seqPanelHolder.setPreferredSize(f); - ap.setScrollValues(av.getStartRes(), av.getStartSeq()); + ap.setScrollValues(av.getRanges().getStartRes(), + av.getRanges().getStartSeq()); ap.validate(); // ap.paintAlignment(true); ap.addNotify(); @@ -365,10 +376,12 @@ public class AnnotationLabels extends Panel implements ActionListener, } } + @Override public void mouseClicked(MouseEvent evt) { } + @Override public void mouseReleased(MouseEvent evt) { if (!resizePanel && !dragCancelled) @@ -396,10 +409,12 @@ public class AnnotationLabels extends Panel implements ActionListener, resizePanel = false; dragEvent = null; dragCancelled = false; + setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR)); repaint(); ap.annotationPanel.repaint(); } + @Override public void mouseEntered(MouseEvent evt) { if (evt.getY() < 10 && evt.getX() < 14) @@ -407,8 +422,11 @@ public class AnnotationLabels extends Panel implements ActionListener, resizePanel = true; repaint(); } + setCursor(Cursor.getPredefinedCursor( + resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR)); } + @Override public void mouseExited(MouseEvent evt) { dragCancelled = false; @@ -427,6 +445,7 @@ public class AnnotationLabels extends Panel implements ActionListener, repaint(); } + @Override public void mousePressed(MouseEvent evt) { oldY = evt.getY(); @@ -442,7 +461,8 @@ public class AnnotationLabels extends Panel implements ActionListener, .getAlignmentAnnotation(); // DETECT RIGHT MOUSE BUTTON IN AWT - if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) + if ((evt.getModifiers() + & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { PopupMenu popup = new PopupMenu( @@ -516,12 +536,14 @@ public class AnnotationLabels extends Panel implements ActionListener, popup.addSeparator(); final CheckboxMenuItem cbmi = new CheckboxMenuItem( MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .isIgnoreGapsConsensus()); + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef + .getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { if (aaa.groupRef != null) @@ -533,7 +555,7 @@ public class AnnotationLabels extends Panel implements ActionListener, { ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } - ap.paintAlignment(true); + ap.paintAlignment(true, true); } }); popup.add(cbmi); @@ -545,6 +567,7 @@ public class AnnotationLabels extends Panel implements ActionListener, aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -564,6 +587,7 @@ public class AnnotationLabels extends Panel implements ActionListener, aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -585,6 +609,7 @@ public class AnnotationLabels extends Panel implements ActionListener, aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -608,6 +633,7 @@ public class AnnotationLabels extends Panel implements ActionListener, av.isShowConsensusHistogram()); chist.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -617,10 +643,10 @@ public class AnnotationLabels extends Panel implements ActionListener, // can be // updated. av.setShowConsensusHistogram(chist.getState()); - ap.alignFrame.showConsensusHistogram.setState(chist - .getState()); // TODO: implement - // ap.updateGUI()/alignFrame.updateGUI - // for applet + ap.alignFrame.showConsensusHistogram + .setState(chist.getState()); // TODO: implement + // ap.updateGUI()/alignFrame.updateGUI + // for applet ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -631,6 +657,7 @@ public class AnnotationLabels extends Panel implements ActionListener, av.isShowSequenceLogo()); cprof.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -655,6 +682,7 @@ public class AnnotationLabels extends Panel implements ActionListener, av.isNormaliseSequenceLogo()); cprofn.addItemListener(new ItemListener() { + @Override public void itemStateChanged(ItemEvent e) { // TODO: pass on reference @@ -664,11 +692,12 @@ public class AnnotationLabels extends Panel implements ActionListener, // can be // updated. av.setShowSequenceLogo(true); - ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO: - // implement - // ap.updateGUI()/alignFrame.updateGUI - // for - // applet + ap.alignFrame.normSequenceLogo + .setState(cprofn.getState()); // TODO: + // implement + // ap.updateGUI()/alignFrame.updateGUI + // for + // applet av.setNormaliseSequenceLogo(cprofn.getState()); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); @@ -697,17 +726,51 @@ public class AnnotationLabels extends Panel implements ActionListener, // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects ap.seqPanel.ap.idPanel.highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); - ap.av.sendSelection(); - ap.paintAlignment(false); + // process modifiers + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null || sg == aa[selectedRow].groupRef + || !(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) + { + if (jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown()) + { + // clone a new selection group from the associated group + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); + } + else + { + // set selection to the associated group so it can be edited + ap.av.setSelectionGroup(aa[selectedRow].groupRef); + } + } + else + { + // modify current selection with associated group + int remainToAdd = aa[selectedRow].groupRef.getSize(); + for (SequenceI sgs : aa[selectedRow].groupRef.getSequences()) + { + if (jalview.util.Platform.isControlDown(evt)) + { + sg.addOrRemove(sgs, --remainToAdd == 0); + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? + sg.addSequence(sgs, --remainToAdd == 0); + } + } + } + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } else { - ap.seqPanel.ap.idPanel - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.seqPanel.ap.idPanel.highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); } return; } @@ -716,8 +779,8 @@ public class AnnotationLabels extends Panel implements ActionListener, if (evt.getClickCount() == 1) { ap.seqPanel.ap.idPanel - .highlightSearchResults(Arrays - .asList(new SequenceI[] { aa[selectedRow].sequenceRef })); + .highlightSearchResults(Arrays.asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { @@ -728,7 +791,8 @@ public class AnnotationLabels extends Panel implements ActionListener, // we make a copy rather than edit the current selection if no // modifiers pressed // see Enhancement JAL-1557 - if (!(evt.isControlDown() || evt.isShiftDown())) + if (!(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -736,7 +800,7 @@ public class AnnotationLabels extends Panel implements ActionListener, } else { - if (evt.isControlDown()) + if (jalview.util.Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); } @@ -756,7 +820,7 @@ public class AnnotationLabels extends Panel implements ActionListener, sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.paintAlignment(false); + ap.paintAlignment(false, false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } @@ -780,25 +844,23 @@ public class AnnotationLabels extends Panel implements ActionListener, return; } jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer(); - jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" - + sq.getStart() + "\t" + sq.getEnd() + "\t" - + sq.getSequenceAsString() + "\n"); + jalview.appletgui.AlignFrame.copiedSequences + .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd() + + "\t" + sq.getSequenceAsString() + "\n"); if (av.hasHiddenColumns()) { - jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector(); - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - jalview.appletgui.AlignFrame.copiedHiddenColumns - .addElement(new int[] { region[0], region[1] }); - } + jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>( + av.getAlignment().getHiddenColumns().getHiddenColumnsCopy()); } } + @Override public void update(Graphics g) { paint(g); } + @Override public void paint(Graphics g) { int w = getSize().width; @@ -849,10 +911,10 @@ public class AnnotationLabels extends Panel implements ActionListener, g.translate(0, +scrollOffset); if (resizePanel) { - g.setColor(Color.red); - g.setPaintMode(); - g.drawLine(2, 8, 5, 2); - g.drawLine(5, 2, 8, 8); + // g.setColor(Color.red); + // g.setPaintMode(); + // g.drawLine(2, 8, 5, 2); + // g.drawLine(5, 2, 8, 8); } else if (!dragCancelled && dragEvent != null && aa != null) {