X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1f437dde913c162bdcc66755f938da6f0b1b8a7c;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=07a9b034c905cabb8fda05a6ee56b75072199473;hpb=6b544d4a85673db44b7f75f40c22d9b7425d444e;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 07a9b03..1f437dd 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,27 +1,30 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.util.*; +import java.util.regex.Pattern; import java.awt.*; import java.awt.datatransfer.*; import java.awt.event.*; +import java.awt.geom.AffineTransform; import java.awt.image.*; import javax.swing.*; @@ -104,8 +107,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, { } - BufferedImage bi = new BufferedImage(temp.getHeight(this), temp - .getWidth(this), BufferedImage.TYPE_INT_RGB); + BufferedImage bi = new BufferedImage(temp.getHeight(this), + temp.getWidth(this), BufferedImage.TYPE_INT_RGB); Graphics2D g = (Graphics2D) bi.getGraphics(); g.rotate(Math.toRadians(90)); g.drawImage(temp, 0, -bi.getWidth(this), this); @@ -113,6 +116,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); + addMouseWheelListener(ap.annotationPanel); } public AnnotationLabels(AlignViewport av) @@ -142,7 +146,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, void getSelectedRow(int y) { int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); selectedRow = -2; if (aa != null) { @@ -174,20 +179,21 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void actionPerformed(ActionEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (evt.getActionCommand().equals(ADDNEW)) { AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null, - null, new Annotation[ap.av.alignment.getWidth()]); + null, new Annotation[ap.av.getAlignment().getWidth()]); if (!editLabelDescription(newAnnotation)) { return; } - ap.av.alignment.addAnnotation(newAnnotation); - ap.av.alignment.setAnnotationIndex(newAnnotation, 0); + ap.av.getAlignment().addAnnotation(newAnnotation); + ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); } else if (evt.getActionCommand().equals(EDITNAME)) { @@ -197,15 +203,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (evt.getActionCommand().equals(HIDE)) { aa[selectedRow].visible = false; - - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.quality = null; - } } else if (evt.getActionCommand().equals(DELETE)) { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); } else if (evt.getActionCommand().equals(SHOWALL)) { @@ -245,9 +246,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } - ap.annotationPanel.adjustPanelHeight(); - ap.annotationScroller.validate(); - ap.paintAlignment(true); + ap.validateAnnotationDimensions(false); + ap.addNotify(); + ap.repaint(); + // validate(); + // ap.paintAlignment(true); } /** @@ -307,16 +310,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (start != end) { // Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment + AlignmentAnnotation startAA = ap.av.getAlignment() .getAlignmentAnnotation()[start]; if (end == -1) { - end = ap.av.alignment.getAlignmentAnnotation().length - 1; + end = ap.av.getAlignment().getAlignmentAnnotation().length - 1; } - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end]; + AlignmentAnnotation endAA = ap.av.getAlignment() + .getAlignmentAnnotation()[end]; - ap.av.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } resizePanel = false; @@ -404,25 +408,57 @@ public class AnnotationLabels extends JPanel implements MouseListener, getSelectedRow(evt.getY() - scrollOffset); if (selectedRow > -1 - && ap.av.alignment.getAlignmentAnnotation().length > selectedRow) + && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) { - AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow]; - - StringBuffer desc = new StringBuffer(""); + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; + StringBuffer desc = new StringBuffer(); if (aa.description != null && !aa.description.equals("New description")) { - desc.append(aa.getDescription(true)); - if (aa.hasScore) - desc.append("
"); + // 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()) { - desc.append("Score: " + aa.score); + // 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) + if (desc.length() > 6) { desc.append(""); this.setToolTipText(desc.toString()); @@ -441,7 +477,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); if (SwingUtilities.isLeftMouseButton(evt)) { if (selectedRow > -1 && selectedRow < aa.length) @@ -450,13 +487,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() >= 2) { - // todo: make the ap scroll to the selection + // todo: make the ap scroll to the selection - not necessary, first + // click highlights/scrolls, second selects ap.seqPanel.ap.idPanel.highlightSearchResults(null); ap.av.setSelectionGroup(// new SequenceGroup( - aa[selectedRow].groupRef); // ); - ap.av.sendSelection(); + aa[selectedRow].groupRef); // ); ap.paintAlignment(false); PaintRefresher.Refresh(ap, ap.av.getSequenceSetId()); + ap.av.sendSelection(); } else { @@ -550,8 +588,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( "Ignore Gaps In Consensus", (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef - .getIgnoreGapsConsensus() - : ap.av.getIgnoreGapsConsensus()); + .getIgnoreGapsConsensus() : ap.av + .getIgnoreGapsConsensus()); final AlignmentAnnotation aaa = aa[selectedRow]; cbmi.addActionListener(new ActionListener() { @@ -574,8 +612,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - "Show Group Histogram", aa[selectedRow].groupRef - .isShowConsensusHistogram()); + "Show Group Histogram", + aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -593,8 +631,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - "Show Group Logo", aa[selectedRow].groupRef - .isShowSequenceLogo()); + "Show Group Logo", + aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -611,6 +649,28 @@ public class AnnotationLabels extends JPanel implements MouseListener, } }); pop.add(cprofl); + final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( + "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 { @@ -627,6 +687,7 @@ 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()); } @@ -645,11 +706,32 @@ 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()); } }); pop.add(cprof); + final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( + "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); @@ -681,7 +763,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs); @@ -690,11 +772,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, String output = new FormatAdapter().formatSequences("Fasta", seqs, omitHidden); - Toolkit.getDefaultToolkit().getSystemClipboard().setContents( - new StringSelection(output), Desktop.instance); + Toolkit.getDefaultToolkit().getSystemClipboard() + .setContents(new StringSelection(output), Desktop.instance); Vector hiddenColumns = null; - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { hiddenColumns = new Vector(); for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++) @@ -735,18 +817,32 @@ public class AnnotationLabels extends JPanel implements MouseListener, RenderingHints.VALUE_ANTIALIAS_ON); } - drawComponent(g2, width); + drawComponent(g2, true, width); } /** - * DOCUMENT ME! + * Draw the full set of annotation Labels for the alignment at the given cursor * - * @param g - * DOCUMENT ME! + * @param g Graphics2D instance (needed for font scaling) + * @param width Width for scaling labels + * */ public void drawComponent(Graphics g, int width) { + drawComponent(g, false, width); + } + + private final boolean debugRedraw = false; + /** + * Draw the full set of annotation Labels for the alignment at the given cursor + * + * @param g Graphics2D instance (needed for font scaling) + * @param clip - true indicates that only current visible area needs to be rendered + * @param width Width for scaling labels + */ + public void drawComponent(Graphics g, boolean clip, int width) + { if (av.getFont().getSize() < 10) { g.setFont(font); @@ -762,28 +858,64 @@ public class AnnotationLabels extends JPanel implements MouseListener, g.translate(0, scrollOffset); g.setColor(Color.black); - - AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation(); + + AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation(); int fontHeight = g.getFont().getSize(); int y = 0; int x = 0; int graphExtras = 0; int offset = 0; - + Font baseFont = g.getFont(); + FontMetrics baseMetrics = fm; + int ofontH = fontHeight; + int sOffset=0; + int visHeight = 0; + int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null; + if (clip && visr!=null){ + sOffset = visr[0]; + visHeight = visr[1]; + } + boolean visible = true,before=false,after=false; if (aa != null) { hasHiddenRows = false; + int olY=0; for (int i = 0; i < aa.length; i++) { - g.setColor(Color.black); - + visible = true; if (!aa[i].visible) { hasHiddenRows = true; continue; } - + olY=y; y += aa[i].height; + if (clip) {if (yvisHeight) + { + + if (!after) + { + if (debugRedraw) { + System.out.println("Scroll offset: "+sOffset+" after vis: "+i); + } + after=true; + } + // don't draw what isn't visible + continue; + }} + g.setColor(Color.black); offset = -aa[i].height / 2; @@ -800,6 +932,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aa[i].graphGroup > -1) { int groupSize = 0; + // TODO: JAL-1291 revise rendering model so the graphGroup map is computed efficiently for all visible labels for (int gg = 0; gg < aa.length; gg++) { if (aa[gg].graphGroup == aa[i].graphGroup) @@ -807,30 +940,55 @@ public class AnnotationLabels extends JPanel implements MouseListener, groupSize++; } } - if (groupSize * (fontHeight + 8) < aa[i].height) { graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; } - - for (int gg = 0; gg < aa.length; gg++) + else { - if (aa[gg].graphGroup == aa[i].graphGroup) + // scale font to fit + float h = aa[i].height / (float) groupSize, s; + if (h < 9) + { + visible = false; + } + else { - x = width - fm.stringWidth(aa[gg].label) - 3; - g.drawString(aa[gg].label, x, y - graphExtras); - if (aa[gg].annotations[0] != null) + fontHeight = -8 + (int) h; + s = ((float) fontHeight) / (float) ofontH; + Font f = baseFont.deriveFont(AffineTransform + .getScaleInstance(s, s)); + g.setFont(f); + fm = g.getFontMetrics(); + graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2; + } + } + if (visible) + { + for (int gg = 0; gg < aa.length; gg++) + { + if (aa[gg].graphGroup == aa[i].graphGroup) { - g.setColor(aa[gg].annotations[0].colour); - } + x = width - fm.stringWidth(aa[gg].label) - 3; + g.drawString(aa[gg].label, x, y - graphExtras); - g.drawLine(x, y - graphExtras - 3, x - + fm.stringWidth(aa[gg].label), y - graphExtras - 3); + if (aa[gg]._linecolour != null) + { - g.setColor(Color.black); - graphExtras += fontHeight + 8; + g.setColor(aa[gg]._linecolour); + g.drawLine(x, y - graphExtras + 3, + x + fm.stringWidth(aa[gg].label), y - graphExtras + + 3); + } + + g.setColor(Color.black); + graphExtras += fontHeight + 8; + } } } + g.setFont(baseFont); + fm = baseMetrics; + fontHeight = ofontH; } else { @@ -846,12 +1004,11 @@ public class AnnotationLabels extends JPanel implements MouseListener, else if (dragEvent != null && aa != null) { g.setColor(Color.lightGray); - g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent - .getY() - - scrollOffset); + g.drawString(aa[selectedRow].label, dragEvent.getX(), + dragEvent.getY() - scrollOffset); } - if ((aa == null) || (aa.length < 1)) + if (!av.wrapAlignment && ((aa == null) || (aa.length < 1))) { g.drawString("Right click", 2, 8); g.drawString("to add annotation", 2, 18);