X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=e16867a4c0d9389ee6614cc6ec625068a1a235dd;hb=163ed5b997bbda48e4cdd950e87a8fe01baae7fb;hp=ec7b46e65af683908772ce4df6100f79d78f44ad;hpb=58afea88095280d807e5c2ac8b9155de5ba3503c;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index ec7b46e..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. * @@ -20,19 +20,46 @@ */ package jalview.gui; -import java.util.*; -import java.util.regex.Pattern; +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; -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.event.*; +import java.awt.Color; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.Image; +import java.awt.MediaTracker; +import java.awt.RenderingHints; +import java.awt.Toolkit; +import java.awt.datatransfer.StringSelection; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.MouseEvent; +import java.awt.event.MouseListener; +import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; -import java.awt.image.*; -import javax.swing.*; +import java.awt.image.BufferedImage; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.regex.Pattern; -import jalview.datamodel.*; -import jalview.io.*; -import jalview.util.MessageManager; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.SwingUtilities; +import javax.swing.ToolTipManager; /** * DOCUMENT ME! @@ -43,11 +70,16 @@ import jalview.util.MessageManager; 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"); @@ -57,7 +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; @@ -75,7 +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); @@ -115,11 +148,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, Graphics2D g = (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); g.drawImage(temp, 0, -bi.getWidth(this), this); - image = (Image) bi; + image = bi; addMouseListener(this); addMouseMotionListener(this); - addMouseWheelListener(ap.annotationPanel); + addMouseWheelListener(ap.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -180,11 +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, @@ -197,11 +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)) { @@ -210,6 +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)) { @@ -220,12 +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)) { @@ -249,11 +291,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.validateAnnotationDimensions(false); - ap.addNotify(); - ap.repaint(); - // validate(); - // ap.paintAlignment(true); + ap.refresh(fullRepaint); + } /** @@ -264,6 +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", @@ -286,253 +326,27 @@ 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) + if (evt.isPopupTrigger()) { - 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(); + showPopupMenu(evt); } } /** - * DOCUMENT ME! + * Build and show the Pop-up menu at the right-click mouse position * * @param evt - * DOCUMENT ME! */ - public void mouseMoved(MouseEvent evt) + void showPopupMenu(MouseEvent evt) { - resizePanel = evt.getY() < 10; - - getSelectedRow(evt.getY() - scrollOffset); - - 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(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("
"); - } - - } - 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); - } - - } - - /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! - */ - public void mouseClicked(MouseEvent evt) - { - AlignmentAnnotation[] aa = ap.av.getAlignment() + 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) - { - Vector sr = new Vector(); - sr.addElement(aa[selectedRow].sequenceRef); - if (evt.getClickCount() == 1) - { - ap.seqPanel.ap.idPanel.highlightSearchResults(sr); - } - else if (evt.getClickCount() >= 2) - { - ap.seqPanel.ap.idPanel.highlightSearchResults(null); - SequenceGroup sg = new SequenceGroup(); - 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")); @@ -556,6 +370,39 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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); @@ -572,6 +419,7 @@ 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) @@ -585,30 +433,33 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.add(item); } } - else if (aa[selectedRow].label.indexOf("Consensus") > -1) + else if (label.indexOf("Consensus") > -1) { pop.addSeparator(); // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In 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); @@ -616,10 +467,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "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 @@ -635,10 +487,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - "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 @@ -654,10 +507,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprofl); final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - "Normalise Group Logo", + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cproflnorm.addActionListener(new ActionListener() { + @Override public void actionPerformed(ActionEvent e) { @@ -679,9 +533,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, else { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "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 @@ -698,9 +554,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - "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 @@ -717,9 +575,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - "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 @@ -746,6 +606,325 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** + * DOCUMENT ME! + * + * @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 @@ -753,11 +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); @@ -769,32 +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 }; } @@ -805,6 +986,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, * @param g1 * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { @@ -869,7 +1051,7 @@ 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(); @@ -883,8 +1065,8 @@ 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]; @@ -946,7 +1128,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, offset -= fm.getDescent(); } else + { offset += fm.getDescent(); + } x = width - fm.stringWidth(aa[i].label) - 3; @@ -1021,20 +1205,25 @@ 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; + } }