X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1a9541c3794b0a2b44d34ca02bea69145b767270;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=0a3423e92b4f2c345f9fa0ffe2e2c448bff11993;hpb=ffa00ba3e195e98fb547ba6dff8028042e9a592b;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 0a3423e..1a9541c 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. * @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; @@ -47,8 +48,10 @@ 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.List; 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; @@ -99,7 +108,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, int selectedRow; - int scrollOffset = 0; + private int scrollOffset = 0; Font font = new Font("Arial", Font.PLAIN, 11); @@ -143,7 +152,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); - addMouseWheelListener(ap.annotationPanel); + addMouseWheelListener(ap.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -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] }, null, null); + new AlignmentAnnotation[] { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -273,18 +291,30 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - refresh(); + refresh(fullRepaint); } /** * Redraw sensibly. + * + * @adjustHeight if true, try to recalculate panel height for visible + * annotations */ - protected void refresh() + protected void refresh(boolean adjustHeight) { - ap.validateAnnotationDimensions(false); + ap.validateAnnotationDimensions(adjustHeight); ap.addNotify(); - ap.repaint(); + if (adjustHeight) + { + // sort, repaint, update overview + ap.paintAlignment(true); + } + else + { + // lightweight repaint + ap.repaint(); + } } /** @@ -295,6 +325,7 @@ 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", @@ -317,287 +348,27 @@ public class AnnotationLabels extends JPanel implements MouseListener, return true; } - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ + @Override public void mousePressed(MouseEvent evt) { - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); oldY = evt.getY(); - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseReleased(MouseEvent evt) - { - int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); - int end = selectedRow; - - if (start != end) - { - // Swap these annotations - AlignmentAnnotation startAA = ap.av.getAlignment() - .getAlignmentAnnotation()[start]; - if (end == -1) - { - end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; - } - AlignmentAnnotation endAA = ap.av.getAlignment() - .getAlignmentAnnotation()[end]; - - ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; - ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; - } - - resizePanel = false; - dragEvent = null; - repaint(); - ap.annotationPanel.repaint(); - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseEntered(MouseEvent evt) - { - if (evt.getY() < 10) - { - resizePanel = true; - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseExited(MouseEvent evt) - { - if (dragEvent == null) - { - resizePanel = false; - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseDragged(MouseEvent evt) - { - dragEvent = evt; - - if (resizePanel) - { - Dimension d = ap.annotationScroller.getPreferredSize(); - int dif = evt.getY() - oldY; - - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; - - if ((d.height - dif) > 20) - { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); - d = ap.annotationSpaceFillerHolder.getPreferredSize(); - ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); - ap.paintAlignment(true); - } - - ap.addNotify(); - } - else - { - repaint(); - } - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseMoved(MouseEvent evt) - { - resizePanel = evt.getY() < 10; - - getSelectedRow(evt.getY() - scrollOffset); - - if (selectedRow > -1 - && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + if (evt.isPopupTrigger()) { - AlignmentAnnotation aa = ap.av.getAlignment() - .getAlignmentAnnotation()[selectedRow]; - - StringBuffer desc = new StringBuffer(); - if (aa.description != null - && !aa.description.equals("New description")) - { - // TODO: we could refactor and merge this code with the code in - // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature - // tooltips - desc.append(aa.getDescription(true).trim()); - // check to see if the description is an html fragment. - if (desc.length() < 6 - || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) - { - // clean the description ready for embedding in html - desc = new StringBuffer(Pattern.compile("<").matcher(desc) - .replaceAll("<")); - desc.insert(0, ""); - } - else - { - // remove terminating html if any - int i = desc.substring(desc.length() - 7).toLowerCase() - .lastIndexOf(""); - if (i > -1) - { - desc.setLength(desc.length() - 7 + i); - } - } - if (aa.hasScore()) - { - desc.append("
"); - } - // if (aa.hasProperties()) - // { - // desc.append(""); - // for (String prop : aa.getProperties()) - // { - // desc.append(""); - // } - // desc.append("
" + prop + "" - // + aa.getProperty(prop) + "
"); - // } - } - else - { - // begin the tooltip's html fragment - desc.append(""); - } - if (aa.hasScore()) - { - // TODO: limit precision of score to avoid noise from imprecise doubles - // (64.7 becomes 64.7+/some tiny value). - desc.append(" Score: " + aa.score); - } - - if (desc.length() > 6) - { - desc.append(""); - this.setToolTipText(desc.toString()); - } - else - { - this.setToolTipText(null); - } + showPopupMenu(evt); } - } /** - * DOCUMENT ME! + * Build and show the Pop-up menu at the right-click mouse position * * @param evt - * DOCUMENT ME! */ - public void mouseClicked(MouseEvent evt) + void showPopupMenu(MouseEvent evt) { + evt.consume(); final AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - if (SwingUtilities.isLeftMouseButton(evt)) - { - if (selectedRow > -1 && selectedRow < aa.length) - { - if (aa[selectedRow].groupRef != null) - { - if (evt.getClickCount() >= 2) - { - // 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.paintAlignment(false); - PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); - ap.av.sendSelection(); - } - else - { - ap.seqPanel.ap.idPanel - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); - } - return; - } - else if (aa[selectedRow].sequenceRef != null) - { - if (evt.getClickCount() == 1) - { - 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 = 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.av.sendSelection(); - ap.paintAlignment(false); - PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); - } - - } - } - } - if (!SwingUtilities.isRightMouseButton(evt)) - { - return; - } JPopupMenu pop = new JPopupMenu( MessageManager.getString("label.annotations")); @@ -622,29 +393,33 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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) { + final String label = aa[selectedRow].label; JMenuItem hideType = new JMenuItem(); - String text = MessageManager.getString("label.hide_all") + " " + label; + 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(); + 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; + // } + // } + refresh(true); } }); pop.add(hideType); @@ -666,6 +441,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // property methods if (selectedRow < aa.length) { + final String label = aa[selectedRow].label; if (!aa[selectedRow].autoCalculated) { if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) @@ -684,25 +460,28 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.addSeparator(); // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - MessageManager.getString("label.ignore_gaps_consensus"), + MessageManager.getString("label.ignore_gaps_consensus"), (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef .getIgnoreGapsConsensus() : ap.av - .getIgnoreGapsConsensus()); + .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.annotationPanel.paint(ap.annotationPanel.getGraphics()); + ap.getAnnotationPanel().paint( + ap.getAnnotationPanel().getGraphics()); } else { ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); } + ap.alignmentChanged(); } }); pop.add(cbmi); @@ -710,10 +489,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_histogram"), + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -729,10 +509,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_logo"), + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -748,10 +529,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprofl); final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_group_logo"), + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cproflnorm.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -773,9 +555,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, else { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), + av.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -792,9 +576,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), + av.isShowSequenceLogo()); cprof.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -811,9 +597,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), + av.isNormaliseSequenceLogo()); cprofnorm.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { // TODO: pass on reference @@ -840,18 +628,335 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * do a single sequence copy to jalview and the system clipboard + * DOCUMENT ME! * - * @param sq - * sequence to be copied to clipboard + * @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; + + if (start != end) + { + // Swap these annotations + AlignmentAnnotation startAA = ap.av.getAlignment() + .getAlignmentAnnotation()[start]; + if (end == -1) + { + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; + } + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; + + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; + } + + resizePanel = false; + dragEvent = null; + repaint(); + ap.getAnnotationPanel().repaint(); + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseEntered(MouseEvent evt) + { + if (evt.getY() < 10) + { + resizePanel = true; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseExited(MouseEvent evt) + { + if (dragEvent == null) + { + resizePanel = false; + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseDragged(MouseEvent evt) + { + dragEvent = evt; + + if (resizePanel) + { + Dimension d = ap.annotationScroller.getPreferredSize(); + int dif = evt.getY() - oldY; + + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); + + if ((d.height - dif) > 20) + { + ap.annotationScroller.setPreferredSize(new Dimension(d.width, + d.height - dif)); + d = ap.annotationSpaceFillerHolder.getPreferredSize(); + ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( + d.width, d.height - dif)); + ap.paintAlignment(true); + } + + ap.addNotify(); + } + else + { + repaint(); + } + } + + /** + * DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! + */ + @Override + public void mouseMoved(MouseEvent evt) + { + resizePanel = evt.getY() < 10; + + getSelectedRow(evt.getY() - getScrollOffset()); + + if (selectedRow > -1 + && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + { + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; + + StringBuffer desc = new StringBuffer(); + if (aa.description != null + && !aa.description.equals("New description")) + { + // TODO: we could refactor and merge this code with the code in + // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature + // tooltips + desc.append(aa.getDescription(true).trim()); + // check to see if the description is an html fragment. + if (desc.length() < 6 + || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) + { + // clean the description ready for embedding in html + desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) + .replaceAll("<")); + desc.insert(0, ""); + } + else + { + // remove terminating html if any + int i = desc.substring(desc.length() - 7).toLowerCase() + .lastIndexOf(""); + if (i > -1) + { + desc.setLength(desc.length() - 7 + i); + } + } + if (aa.hasScore()) + { + desc.append("
"); + } + // if (aa.hasProperties()) + // { + // desc.append(""); + // for (String prop : aa.getProperties()) + // { + // desc.append(""); + // } + // desc.append("
" + prop + "" + // + aa.getProperty(prop) + "
"); + // } + } + else + { + // begin the tooltip's html fragment + desc.append(""); + if (aa.hasScore()) + { + // TODO: limit precision of score to avoid noise from imprecise + // doubles + // (64.7 becomes 64.7+/some tiny value). + desc.append(" Score: " + aa.score); + } + } + if (desc.length() > 6) + { + desc.append(""); + this.setToolTipText(desc.toString()); + } + else + { + this.setToolTipText(null); + } + } + } + + @Override + public void mouseClicked(MouseEvent evt) + { + final AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (!evt.isPopupTrigger() && SwingUtilities.isLeftMouseButton(evt)) + { + if (selectedRow > -1 && selectedRow < aa.length) + { + if (aa[selectedRow].groupRef != null) + { + if (evt.getClickCount() >= 2) + { + // todo: make the ap scroll to the selection - not necessary, first + // click highlights/scrolls, second selects + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); + // 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)); + } + return; + } + else if (aa[selectedRow].sequenceRef != null) + { + if (evt.getClickCount() == 1) + { + 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) + { + // we make a copy rather than edit the current selection if no + // modifiers pressed + // see Enhancement JAL-1557 + if (!(jalview.util.Platform.isControlDown(evt) || evt + .isShiftDown())) + { + sg = new SequenceGroup(sg); + sg.clear(); + sg.addSequence(aa[selectedRow].sequenceRef, false); + } + 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 ? + 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()); + ap.av.sendSelection(); + } + + } + } + return; + } + } + + /** + * do a single sequence copy to jalview and the system clipboard + * + * @param sq + * sequence to be copied to clipboard */ 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); @@ -867,28 +972,33 @@ public class AnnotationLabels extends JPanel implements MouseListener, sq.getLength(), seqs); } + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; + List hiddenCols = av.getColumnSelection().getHiddenColumns(); + if (hiddenCols != null) + { + alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex( + hiddenCols); + } String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + 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++) + hiddenColumns = new ArrayList(); + for (int[] region : av.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(i); - - hiddenColumns.addElement(new int[] - { region[0], region[1] }); + hiddenColumns.add(new int[] { region[0], region[1] }); } } - 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 }; } @@ -899,6 +1009,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param g1 * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { @@ -963,7 +1074,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - g.translate(0, scrollOffset); + g.translate(0, getScrollOffset()); g.setColor(Color.black); AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); @@ -977,8 +1088,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel - .getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap + .getAnnotationPanel().getVisibleVRange() : null; if (clip && visr != null) { sOffset = visr[0]; @@ -1117,20 +1228,25 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (resizePanel) { - g.drawImage(image, 2, 0 - scrollOffset, this); + g.drawImage(image, 2, 0 - getScrollOffset(), this); } else if (dragEvent != null && aa != null) { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - scrollOffset); + 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, 18); } } + + public int getScrollOffset() + { + return scrollOffset; + } }