X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=f7b48fac54ee75309e1d7e857175cf558e13bbf3;hb=36e82a30ba2cd0c1331d8735214ebbe2139790ce;hp=4b774d60cbab3252eaa0868b182136f0545f6bda;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 4b774d6..f7b48fa 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -52,7 +52,6 @@ import java.awt.image.BufferedImage; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.List; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -68,12 +67,13 @@ import javax.swing.ToolTipManager; * @author $author$ * @version $Revision$ */ -public class AnnotationLabels extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel + implements MouseListener, MouseMotionListener, ActionListener { private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern .compile("<"); + String TOGGLE_LABELSCALE = MessageManager .getString("label.scale_label_to_column"); @@ -268,7 +268,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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)) { @@ -292,30 +293,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - refresh(fullRepaint); - - } + ap.refresh(fullRepaint); - /** - * Redraw sensibly. - * - * @adjustHeight if true, try to recalculate panel height for visible - * annotations - */ - protected void refresh(boolean adjustHeight) - { - ap.validateAnnotationDimensions(adjustHeight); - ap.addNotify(); - if (adjustHeight) - { - // sort, repaint, update overview - ap.paintAlignment(true); - } - else - { - // lightweight repaint - ap.repaint(); - } } /** @@ -420,7 +399,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, // ann.visible = false; // } // } - refresh(true); + ap.refresh(true); } }); pop.add(hideType); @@ -443,7 +422,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (selectedRow < aa.length) { final String label = aa[selectedRow].label; - if (!aa[selectedRow].autoCalculated) + if (!(aa[selectedRow].autoCalculated) + && !("HMM".equals(aa[selectedRow].getCalcId()))) { if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) { @@ -458,13 +438,16 @@ public class AnnotationLabels extends JPanel implements MouseListener, } 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()); + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef.getIgnoreGapsConsensus() + : ap.av.isIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addActionListener(new ActionListener() { @@ -475,8 +458,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { // TODO: pass on reference to ap so the view can be updated. aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState()); - ap.getAnnotationPanel().paint( - ap.getAnnotationPanel().getGraphics()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); } else { @@ -570,7 +553,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, // can be // updated. av.setShowConsensusHistogram(chist.getState()); - ap.alignFrame.setMenusForViewport(); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -591,7 +573,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, // can be // updated. av.setShowSequenceLogo(cprof.getState()); - ap.alignFrame.setMenusForViewport(); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -613,7 +594,6 @@ public class AnnotationLabels extends JPanel implements MouseListener, // updated. av.setShowSequenceLogo(true); av.setNormaliseSequenceLogo(cprofnorm.getState()); - ap.alignFrame.setMenusForViewport(); ap.repaint(); // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); } @@ -624,6 +604,212 @@ public class AnnotationLabels extends JPanel implements MouseListener, consclipbrd.addActionListener(this); pop.add(consclipbrd); } + else if ("HMM".equals(aa[selectedRow].getCalcId())) // TODO create labels + // in message resource + // for these + { + pop.addSeparator(); + final AlignmentAnnotation aaa = aa[selectedRow]; + + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + MessageManager.getString( + "label.ignore_below_background_frequency"), + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef + .getIgnoreBelowBackground() + : ap.av.isIgnoreBelowBackground()); + + 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. + if (aaa.groupRef.getInfoLetterHeight() == false) + { + aaa.groupRef.setIgnoreBelowBackground(cbmi.getState()); + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); + } + } + else if (ap.av.isInfoLetterHeight() == false) + { + ap.av.setIgnoreBelowBackground(cbmi.getState(), ap); + } + ap.alignmentChanged(); + } + }); + pop.add(cbmi); + final JCheckBoxMenuItem letteHeight = new JCheckBoxMenuItem( + MessageManager.getString("label.use_info_for_height"), + (aa[selectedRow].groupRef != null) + ? aa[selectedRow].groupRef.getInfoLetterHeight() + : ap.av.isInfoLetterHeight()); + + letteHeight.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.setInfoLetterHeight((letteHeight.getState())); + if (aaa.groupRef.getIgnoreBelowBackground() == false) + { + aaa.groupRef.setIgnoreBelowBackground(true); + } + ap.getAnnotationPanel() + .paint(ap.getAnnotationPanel().getGraphics()); + } + else + { + ap.av.setInfoLetterHeight(letteHeight.getState(), ap); + if (ap.av.isIgnoreBelowBackground() == false) + { + ap.av.setIgnoreBelowBackground(true, ap); + } + } + ap.alignmentChanged(); + } + }); + pop.add(letteHeight); + if (aaa.groupRef != null) + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_group_histogram"), + aa[selectedRow].groupRef.isShowInformationHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setShowInformationHistogram(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.isShowHMMSequenceLogo()); + cprofl.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef.setshowHMMSequenceLogo(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.isNormaliseHMMSequenceLogo()); + cproflnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + aaa.groupRef + .setNormaliseHMMSequenceLogo(cproflnorm.getState()); + // automatically enable logo display if we're clicked + aaa.groupRef.setshowHMMSequenceLogo(true); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cproflnorm); + } + else + { + final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( + MessageManager.getString("label.show_histogram"), + av.isShowInformationHistogram()); + chist.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowInformationHistogram(chist.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(chist); + final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( + MessageManager.getString("label.show_logo"), + av.isShowHMMSequenceLogo()); + cprof.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.updateInformation(ap); + av.setShowHMMSequenceLogo(cprof.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + MessageManager.getString("label.normalise_logo"), + av.isNormaliseHMMSequenceLogo()); + cprofnorm.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + // TODO: pass on reference + // to ap + // so the + // view + // can be + // updated. + av.setShowHMMSequenceLogo(true); + av.setNormaliseHMMSequenceLogo(cprofnorm.getState()); + ap.repaint(); + // ap.annotationPanel.paint(ap.annotationPanel.getGraphics()); + } + }); + pop.add(cprofnorm); + } + } } pop.show(this, evt.getX(), evt.getY()); } @@ -722,11 +908,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, if ((d.height - dif) > 20) { - ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + 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.annotationSpaceFillerHolder + .setPreferredSize(new Dimension(d.width, d.height - dif)); ap.paintAlignment(true); } @@ -751,8 +937,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - getScrollOffset()); - if (selectedRow > -1 - && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) + if (selectedRow > -1 && ap.av.getAlignment() + .getAlignmentAnnotation().length > selectedRow) { AlignmentAnnotation aa = ap.av.getAlignment() .getAlignmentAnnotation()[selectedRow]; @@ -766,8 +952,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, // 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)) + 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) @@ -841,17 +1027,16 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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 (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)); + ap.av.setSelectionGroup( + new SequenceGroup(aa[selectedRow].groupRef)); } else { @@ -893,10 +1078,9 @@ 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) { @@ -907,8 +1091,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, // 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())) + if (!(jalview.util.Platform.isControlDown(evt) + || evt.isShiftDown())) { sg = new SequenceGroup(sg); sg.clear(); @@ -969,17 +1153,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, Alignment ds = new Alignment(dseqs); if (av.hasHiddenColumns()) { - omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + omitHidden = av.getAlignment().getHiddenColumns() + .getVisibleSequenceStrings(0, sq.getLength(), seqs); } int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; - List hiddenCols = av.getColumnSelection().getHiddenColumns(); - if (hiddenCols != null) + if (av.hasHiddenColumns()) { - alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex( - hiddenCols); + alignmentStartEnd = av.getAlignment().getHiddenColumns() + .getVisibleStartAndEndIndex(av.getAlignment().getWidth()); } + String output = new FormatAdapter().formatSequences(FileFormat.Fasta, seqs, omitHidden, alignmentStartEnd); @@ -987,13 +1171,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, .setContents(new StringSelection(output), Desktop.instance); ArrayList hiddenColumns = null; + if (av.hasHiddenColumns()) { - hiddenColumns = new ArrayList(); - for (int[] region : av.getColumnSelection().getHiddenColumns()) - { - hiddenColumns.add(new int[] { region[0], region[1] }); - } + + hiddenColumns = av.getAlignment().getHiddenColumns() + .getHiddenColumnsCopy(); + } Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset @@ -1089,8 +1273,9 @@ 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]; @@ -1133,8 +1318,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (debugRedraw) { - System.out.println("Scroll offset: " + sOffset - + " after vis: " + i); + System.out.println( + "Scroll offset: " + sOffset + " after vis: " + i); } after = true; } @@ -1172,7 +1357,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, } if (groupSize * (fontHeight + 8) < aa[i].height) { - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } else { @@ -1186,11 +1372,12 @@ public class AnnotationLabels extends JPanel implements MouseListener, { fontHeight = -8 + (int) h; s = ((float) fontHeight) / (float) ofontH; - Font f = baseFont.deriveFont(AffineTransform - .getScaleInstance(s, s)); + Font f = baseFont + .deriveFont(AffineTransform.getScaleInstance(s, s)); g.setFont(f); fm = g.getFontMetrics(); - graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) + / 2; } } if (visible) @@ -1207,8 +1394,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.setColor(aa[gg]._linecolour); g.drawLine(x, y - graphExtras + 3, - x + fm.stringWidth(aa[gg].label), y - graphExtras - + 3); + x + fm.stringWidth(aa[gg].label), + y - graphExtras + 3); } g.setColor(Color.black);