X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=e16867a4c0d9389ee6614cc6ec625068a1a235dd;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=97499c970421b0fa0373abbbfc4abccd286e199c;hpb=8d6b113f475c6b5916f7685cfd289e054d95a9ee;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 97499c9..e16867a 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * 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. * @@ -20,12 +20,14 @@ */ package jalview.gui; +import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.util.MessageManager; @@ -47,8 +49,9 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; import java.awt.image.BufferedImage; +import java.util.ArrayList; import java.util.Arrays; -import java.util.Vector; +import java.util.Collections; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -67,11 +70,16 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column"); + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern + .compile("<"); + + String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); String ADDNEW = MessageManager.getString("label.add_new_row"); - String EDITNAME = MessageManager.getString("label.edit_label_description"); + String EDITNAME = MessageManager + .getString("label.edit_label_description"); String HIDE = MessageManager.getString("label.hide_row"); @@ -81,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); - String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence"); + String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); boolean resizePanel = false; @@ -204,11 +213,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void actionPerformed(ActionEvent evt) { AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); + boolean fullRepaint = false; if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, @@ -221,11 +232,16 @@ public class AnnotationLabels extends JPanel implements MouseListener, ap.av.getAlignment().addAnnotation(newAnnotation); ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); + fullRepaint = true; } else if (evt.getActionCommand().equals(EDITNAME)) { + String name = aa[selectedRow].label; editLabelDescription(aa[selectedRow]); - repaint(); + if (!name.equalsIgnoreCase(aa[selectedRow].label)) + { + fullRepaint = true; + } } else if (evt.getActionCommand().equals(HIDE)) { @@ -234,6 +250,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (evt.getActionCommand().equals(DELETE)) { ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); + ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); + fullRepaint = true; } else if (evt.getActionCommand().equals(SHOWALL)) { @@ -244,12 +262,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[i].visible = true; } } + fullRepaint = true; } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { new AnnotationExporter().exportAnnotations(ap, - new AlignmentAnnotation[] - { aa[selectedRow] }); + new AlignmentAnnotation[] { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -273,21 +291,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - refresh(); + ap.refresh(fullRepaint); } /** - * Redraw sensibly. - */ - protected void refresh() - { - ap.validateAnnotationDimensions(false); - ap.addNotify(); - ap.repaint(); - } - - /** * DOCUMENT ME! * * @param e @@ -295,6 +303,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ boolean editLabelDescription(AlignmentAnnotation annotation) { + // TODO i18n EditNameDialog dialog = new EditNameDialog(annotation.label, annotation.description, " Annotation Name ", "Annotation Description ", "Edit Annotation Name/Description", @@ -317,16 +326,283 @@ public class AnnotationLabels extends JPanel implements MouseListener, return true; } + @Override + public void mousePressed(MouseEvent evt) + { + getSelectedRow(evt.getY() - getScrollOffset()); + oldY = evt.getY(); + if (evt.isPopupTrigger()) + { + showPopupMenu(evt); + } + } + /** - * DOCUMENT ME! + * Build and show the Pop-up menu at the right-click mouse position * * @param evt - * DOCUMENT ME! */ - public void mousePressed(MouseEvent evt) + void showPopupMenu(MouseEvent evt) { - getSelectedRow(evt.getY() - getScrollOffset()); - oldY = evt.getY(); + evt.consume(); + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); + JMenuItem item = new JMenuItem(ADDNEW); + item.addActionListener(this); + pop.add(item); + if (selectedRow < 0) + { + if (hasHiddenRows) + { // let the user make everything visible again + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } + pop.show(this, evt.getX(), evt.getY()); + return; + } + item = new JMenuItem(EDITNAME); + item.addActionListener(this); + pop.add(item); + item = new JMenuItem(HIDE); + item.addActionListener(this); + pop.add(item); + // JAL-1264 hide all sequence-specific annotations of this type + if (selectedRow < aa.length) + { + if (aa[selectedRow].sequenceRef != null) + { + final String label = aa[selectedRow].label; + JMenuItem hideType = new JMenuItem(); + String text = MessageManager.getString("label.hide_all") + " " + + label; + hideType.setText(text); + hideType.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + AlignmentUtils.showOrHideSequenceAnnotations( + ap.av.getAlignment(), Collections.singleton(label), + null, false, false); + // for (AlignmentAnnotation ann : ap.av.getAlignment() + // .getAlignmentAnnotation()) + // { + // if (ann.sequenceRef != null && ann.label != null + // && ann.label.equals(label)) + // { + // ann.visible = false; + // } + // } + ap.refresh(true); + } + }); + pop.add(hideType); + } + } + item = new JMenuItem(DELETE); + item.addActionListener(this); + pop.add(item); + if (hasHiddenRows) + { + item = new JMenuItem(SHOWALL); + item.addActionListener(this); + pop.add(item); + } + item = new JMenuItem(OUTPUT_TEXT); + item.addActionListener(this); + pop.add(item); + // TODO: annotation object should be typed for autocalculated/derived + // property methods + if (selectedRow < aa.length) + { + final String label = aa[selectedRow].label; + if (!aa[selectedRow].autoCalculated) + { + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) + { + // display formatting settings for this row. + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, + aa[selectedRow].scaleColLabel); + item.addActionListener(this); + pop.add(item); + } + } + else if (label.indexOf("Consensus") > -1) + { + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString("label.ignore_gaps_consensus"), + (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef + .getIgnoreGapsConsensus() : ap.av + .isIgnoreGapsConsensus()); + final AlignmentAnnotation aaa = aa[selectedRow]; + cbmi.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (aaa.groupRef != null) + { + // TODO: pass on reference to ap so the view can be updated. + aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); + ap.getAnnotationPanel().paint( + ap.getAnnotationPanel().getGraphics()); + } + else + { + ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + } + ap.alignmentChanged(); + } + }); + pop.add(cbmi); + // av and sequencegroup need to implement same interface for + if (aaa.groupRef != null) + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + aa[selectedRow].groupRef.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setShowConsensusHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_logo"), + aa[selectedRow].groupRef.isShowSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setshowSequenceLogo(cprofl.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_group_logo"), + aa[selectedRow].groupRef.isNormaliseSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowSequenceLogo(true); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cproflnorm); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + av.isShowConsensusHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowConsensusHistogram(chist.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + av.isShowSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(cprof.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + av.isNormaliseSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowSequenceLogo(true); + av.setNormaliseSequenceLogo(cprofnorm.getState()); + ap.alignFrame.setMenusForViewport(); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofnorm); + } + final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); + consclipbrd.addActionListener(this); + pop.add(consclipbrd); + } + } + pop.show(this, evt.getX(), evt.getY()); } /** @@ -335,8 +611,15 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent evt) { + if (evt.isPopupTrigger()) + { + showPopupMenu(evt); + return; + } + int start = selectedRow; getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; @@ -369,6 +652,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent evt) { if (evt.getY() < 10) @@ -384,6 +668,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent evt) { if (dragEvent == null) @@ -399,6 +684,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent evt) { dragEvent = evt; @@ -408,8 +694,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, Dimension d = ap.annotationScroller.getPreferredSize(); int dif = evt.getY() - oldY; - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); if ((d.height - dif) > 20) { @@ -435,6 +721,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param evt * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent evt) { resizePanel = evt.getY() < 10; @@ -460,7 +747,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) { // clean the description ready for embedding in html - desc = new StringBuffer(Pattern.compile("<").matcher(desc) + desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) .replaceAll("<")); desc.insert(0, ""); } @@ -513,17 +800,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, } } - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ + @Override public void mouseClicked(MouseEvent evt) { final AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - if (SwingUtilities.isLeftMouseButton(evt)) + if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) { if (selectedRow > -1 && selectedRow < aa.length) { @@ -534,17 +816,53 @@ public class AnnotationLabels extends JPanel implements MouseListener, // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); - ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); + // 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); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); ap.av.sendSelection(); } else { - ap.getSeqPanel().ap.getIdPanel() - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults( + aa[selectedRow].groupRef.getSequences(null)); } return; } @@ -552,290 +870,58 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays - .asList(new SequenceI[] - { aa[selectedRow].sequenceRef })); + ap.getSeqPanel().ap + .getIdPanel() + .highlightSearchResults( + Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg!=null) + if (sg != null) { - // we make a copy rather than edit the current selection if no modifiers pressed + // 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(); sg.addSequence(aa[selectedRow].sequenceRef, false); - } else { - if (evt.isControlDown()) + } + else + { + if (jalview.util.Platform.isControlDown(evt)) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); - } else { - // notionally, we should also add intermediate sequences from last added sequence ? + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? sg.addSequence(aa[selectedRow].sequenceRef, true); } } - } else { + } + else + { sg = new SequenceGroup(); sg.setStartRes(0); - sg.setEndRes(ap.av.getAlignment().getWidth()-1); + sg.setEndRes(ap.av.getAlignment().getWidth() - 1); sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); - ap.av.sendSelection(); ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } } } - } - if (!SwingUtilities.isRightMouseButton(evt)) - { - return; - } - - JPopupMenu pop = new JPopupMenu( - MessageManager.getString("label.annotations")); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - if (selectedRow < 0) - { - if (hasHiddenRows) - { // let the user make everything visible again - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); - } - pop.show(this, evt.getX(), evt.getY()); return; } - item = new JMenuItem(EDITNAME); - item.addActionListener(this); - pop.add(item); - item = new JMenuItem(HIDE); - item.addActionListener(this); - pop.add(item); - // JAL-1264 hide all sequence-specific annotations of this type - final String label = aa[selectedRow].label; - if (selectedRow < aa.length) - { - if (aa[selectedRow].sequenceRef != null) - { - JMenuItem hideType = new JMenuItem(); - String text = MessageManager.getString("label.hide_all") + " " + label; - hideType.setText(text); - hideType.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - for (AlignmentAnnotation ann : ap.av.getAlignment() - .getAlignmentAnnotation()) - { - if (ann.sequenceRef != null && ann.label != null - && ann.label.equals(label)) - { - ann.visible = false; - } - } - refresh(); - } - }); - pop.add(hideType); - } - } - item = new JMenuItem(DELETE); - item.addActionListener(this); - pop.add(item); - if (hasHiddenRows) - { - item = new JMenuItem(SHOWALL); - item.addActionListener(this); - pop.add(item); - } - item = new JMenuItem(OUTPUT_TEXT); - item.addActionListener(this); - pop.add(item); - // TODO: annotation object should be typed for autocalculated/derived - // property methods - if (selectedRow < aa.length) - { - if (!aa[selectedRow].autoCalculated) - { - if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) - { - // display formatting settings for this row. - pop.addSeparator(); - // av and sequencegroup need to implement same interface for - item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE, - aa[selectedRow].scaleColLabel); - item.addActionListener(this); - pop.add(item); - } - } - else if (label.indexOf("Consensus") > -1) - { - pop.addSeparator(); - // av and sequencegroup need to implement same interface for - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - MessageManager.getString("label.ignore_gaps_consensus"), - (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() : ap.av - .getIgnoreGapsConsensus()); - final AlignmentAnnotation aaa = aa[selectedRow]; - cbmi.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - if (aaa.groupRef != null) - { - // TODO: pass on reference to ap so the view can be updated. - aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics()); - } - else - { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); - } - } - }); - pop.add(cbmi); - // av and sequencegroup need to implement same interface for - if (aaa.groupRef != null) - { - final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_histogram"), - aa[selectedRow].groupRef.isShowConsensusHistogram()); - chist.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setShowConsensusHistogram(chist.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(chist); - final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_logo"), - aa[selectedRow].groupRef.isShowSequenceLogo()); - cprofl.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setshowSequenceLogo(cprofl.getState()); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cprofl); - final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_group_logo"), - aa[selectedRow].groupRef.isNormaliseSequenceLogo()); - cproflnorm.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState()); - // automatically enable logo display if we're clicked - aaa.groupRef.setshowSequenceLogo(true); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cproflnorm); - } - else - { - final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); - chist.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowConsensusHistogram(chist.getState()); - ap.alignFrame.setMenusForViewport(); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(chist); - final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); - cprof.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowSequenceLogo(cprof.getState()); - ap.alignFrame.setMenusForViewport(); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cprof); - final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); - cprofnorm.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - // TODO: pass on reference - // to ap - // so the - // view - // can be - // updated. - av.setShowSequenceLogo(true); - av.setNormaliseSequenceLogo(cprofnorm.getState()); - ap.alignFrame.setMenusForViewport(); - ap.repaint(); - // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); - } - }); - pop.add(cprofnorm); - } - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); - } - } - pop.show(this, evt.getX(), evt.getY()); } /** @@ -846,11 +932,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ protected void copy_annotseqtoclipboard(SequenceI sq) { - SequenceI[] seqs = new SequenceI[] - { sq }; + SequenceI[] seqs = new SequenceI[] { sq }; String[] omitHidden = null; - SequenceI[] dseqs = new SequenceI[] - { sq.getDatasetSequence() }; + SequenceI[] dseqs = new SequenceI[] { sq.getDatasetSequence() }; if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); @@ -862,32 +946,36 @@ public class AnnotationLabels extends JPanel implements MouseListener, Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, + omitHidden = av.getAlignment().getHiddenColumns() + .getVisibleSequenceStrings(0, sq.getLength(), seqs); } - String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; + if (av.hasHiddenColumns()) + { + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); + } + + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, + seqs, omitHidden, alignmentStartEnd); Toolkit.getDefaultToolkit().getSystemClipboard() .setContents(new StringSelection(output), Desktop.instance); - Vector hiddenColumns = null; + ArrayList hiddenColumns = null; + if (av.hasHiddenColumns()) { - hiddenColumns = new Vector(); - for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) - { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(i); - - hiddenColumns.addElement(new int[] - { region[0], region[1] }); - } + hiddenColumns = av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy(); } - Desktop.jalviewClipboard = new Object[] - { seqs, ds, // what is the dataset of a consensus sequence ? need to flag + Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset + // of a consensus + // sequence ? need to + // flag // sequence as special. hiddenColumns }; } @@ -898,6 +986,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param g1 * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { @@ -976,8 +1065,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel() - .getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap + .getAnnotationPanel().getVisibleVRange() : null; if (clip && visr != null) { sOffset = visr[0]; @@ -1125,7 +1214,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, dragEvent.getY() - getScrollOffset()); } - if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) + if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1))) { g.drawString(MessageManager.getString("label.right_click"), 2, 8); g.drawString(MessageManager.getString("label.to_add_annotation"), 2,