X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1f437dde913c162bdcc66755f938da6f0b1b8a7c;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=0ea7730e46e279b7410fa2f392c4df536e8ae05b;hpb=2eae25971bb6fc582e1f5ad831b1ca228da2a495;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 0ea7730..1f437dd 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,28 +1,30 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.*; @@ -31,36 +33,56 @@ import jalview.io.*; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ -public class AnnotationLabels - extends JPanel implements MouseListener, - MouseMotionListener, ActionListener +public class AnnotationLabels extends JPanel implements MouseListener, + MouseMotionListener, ActionListener { + static String TOGGLE_LABELSCALE = "Scale Label to Column"; + static String ADDNEW = "Add New Row"; + static String EDITNAME = "Edit Label/Description"; + static String HIDE = "Hide This Row"; + static String DELETE = "Delete This Row"; + static String SHOWALL = "Show All Hidden Rows"; + static String OUTPUT_TEXT = "Export Annotation"; + static String COPYCONS_SEQ = "Copy Consensus Sequence"; + boolean resizePanel = false; + Image image; + AlignmentPanel ap; + AlignViewport av; + boolean resizing = false; + MouseEvent dragEvent; + int oldY; + int selectedRow; + int scrollOffset = 0; + Font font = new Font("Arial", Font.PLAIN, 11); + private boolean hasHiddenRows; + /** * Creates a new AnnotationLabels object. - * - * @param ap DOCUMENT ME! + * + * @param ap + * DOCUMENT ME! */ public AnnotationLabels(AlignmentPanel ap) { @@ -81,14 +103,12 @@ public class AnnotationLabels MediaTracker mt = new MediaTracker(this); mt.addImage(temp, 0); mt.waitForID(0); - } - catch (Exception ex) + } catch (Exception ex) { } BufferedImage bi = new BufferedImage(temp.getHeight(this), - temp.getWidth(this), - BufferedImage.TYPE_INT_RGB); + 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); @@ -96,6 +116,7 @@ public class AnnotationLabels addMouseListener(this); addMouseMotionListener(this); + addMouseWheelListener(ap.annotationPanel); } public AnnotationLabels(AlignViewport av) @@ -105,8 +126,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param y DOCUMENT ME! + * + * @param y + * DOCUMENT ME! */ public void setScrollOffset(int y) { @@ -114,15 +136,24 @@ public class AnnotationLabels repaint(); } + /** + * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at + * y + * + * @param y + * coordinate position to search for a row + */ void getSelectedRow(int y) { int height = 0; - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); - + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + selectedRow = -2; if (aa != null) { for (int i = 0; i < aa.length; i++) { + selectedRow = -1; if (!aa[i].visible) { continue; @@ -142,31 +173,27 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void actionPerformed(ActionEvent evt) { - int dif = 0; - 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); - if (aa != null) - { - dif = aa[aa.length - 1].height; - } + ap.av.getAlignment().addAnnotation(newAnnotation); + ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0); } else if (evt.getActionCommand().equals(EDITNAME)) { @@ -176,66 +203,68 @@ public class AnnotationLabels else if (evt.getActionCommand().equals(HIDE)) { aa[selectedRow].visible = false; - - if (aa[selectedRow].label.equals("Quality")) - { - ap.av.quality = null; - } - - dif = aa[selectedRow].height * -1; } else if (evt.getActionCommand().equals(DELETE)) { - ap.av.alignment.deleteAnnotation(aa[selectedRow]); - dif = aa[selectedRow].height * -1; + ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); } else if (evt.getActionCommand().equals(SHOWALL)) { for (int i = 0; i < aa.length; i++) { - if (!aa[i].visible && aa[i].annotations!=null) + if (!aa[i].visible && aa[i].annotations != null) { - dif += aa[i].height; aa[i].visible = true; } } } else if (evt.getActionCommand().equals(OUTPUT_TEXT)) { - new AnnotationExporter().exportAnnotations( - ap, - new AlignmentAnnotation[] - {aa[selectedRow]}, - null, null - ); + new AnnotationExporter().exportAnnotations(ap, + new AlignmentAnnotation[] + { aa[selectedRow] }, null, null); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { - SequenceI cons = av.getConsensusSeq(); + SequenceI cons = null; + if (aa[selectedRow].groupRef != null) + { + cons = aa[selectedRow].groupRef.getConsensusSeq(); + } + else + { + cons = av.getConsensusSeq(); + } if (cons != null) { copy_annotseqtoclipboard(cons); } } + else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE)) + { + 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); } /** * DOCUMENT ME! - * - * @param e DOCUMENT ME! + * + * @param e + * DOCUMENT ME! */ boolean editLabelDescription(AlignmentAnnotation annotation) { EditNameDialog dialog = new EditNameDialog(annotation.label, - annotation.description, - " Annotation Name ", - "Annotation Description ", - "Edit Annotation Name/Description"); + annotation.description, " Annotation Name ", + "Annotation Description ", "Edit Annotation Name/Description", + ap.alignFrame); if (!dialog.accept) { @@ -245,7 +274,7 @@ public class AnnotationLabels annotation.label = dialog.getName(); String text = dialog.getDescription(); - if (text!=null && text.length() == 0) + if (text != null && text.length() == 0) { text = null; } @@ -256,8 +285,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mousePressed(MouseEvent evt) { @@ -267,8 +297,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseReleased(MouseEvent evt) { @@ -278,13 +309,18 @@ public class AnnotationLabels if (start != end) { - //Swap these annotations - AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[ - start]; - AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[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.alignment.getAlignmentAnnotation()[end] = startAA; - ap.av.alignment.getAlignmentAnnotation()[start] = endAA; + ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA; + ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA; } resizePanel = false; @@ -295,8 +331,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseEntered(MouseEvent evt) { @@ -309,8 +346,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseExited(MouseEvent evt) { @@ -323,8 +361,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseDragged(MouseEvent evt) { @@ -338,13 +377,13 @@ public class AnnotationLabels dif /= ap.av.charHeight; dif *= ap.av.charHeight; - if ( (d.height - dif) > 20) + if ((d.height - dif) > 20) { ap.annotationScroller.setPreferredSize(new Dimension(d.width, - d.height - dif)); + d.height - dif)); d = ap.annotationSpaceFillerHolder.getPreferredSize(); ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension( - d.width, d.height - dif)); + d.width, d.height - dif)); ap.paintAlignment(true); } @@ -358,8 +397,9 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseMoved(MouseEvent evt) { @@ -367,25 +407,58 @@ public class AnnotationLabels 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]; + AlignmentAnnotation aa = ap.av.getAlignment() + .getAlignmentAnnotation()[selectedRow]; - StringBuffer desc = new StringBuffer(""); + 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.description != null && !aa.description.equals("New description")) + } + else { - desc.append(aa.description+"
"); + // begin the tooltip's html fragment + desc.append(""); } - if(!Float.isNaN(aa.score)) + 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()); @@ -398,26 +471,63 @@ public class AnnotationLabels /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void mouseClicked(MouseEvent evt) { - if (!SwingUtilities.isRightMouseButton(evt)) + AlignmentAnnotation[] aa = ap.av.getAlignment() + .getAlignmentAnnotation(); + if (SwingUtilities.isLeftMouseButton(evt)) { - return; - } - - AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation(); + 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 ( (aa == null) || (aa.length == 0)) + } + } + } + if (!SwingUtilities.isRightMouseButton(evt)) { - JPopupMenu pop = new JPopupMenu("Annotations"); - JMenuItem item = new JMenuItem(ADDNEW); - item.addActionListener(this); - pop.add(item); - pop.show(this, evt.getX(), evt.getY()); - return; } @@ -425,6 +535,17 @@ public class AnnotationLabels 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); @@ -434,100 +555,251 @@ public class AnnotationLabels item = new JMenuItem(DELETE); item.addActionListener(this); pop.add(item); - item = new JMenuItem(SHOWALL); - 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); - // annotation object should be typed - if (aa[selectedRow] == ap.av.consensus) - { - pop.addSeparator(); - final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - "Ignore Gaps In Consensus", - ap.av.getIgnoreGapsConsensus()); - cbmi.addActionListener(new ActionListener() + // TODO: annotation object should be typed for autocalculated/derived + // property methods + if (selectedRow < aa.length) + { + if (!aa[selectedRow].autoCalculated) { - public void actionPerformed(ActionEvent e) + if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH) { - ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap); + // 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); } - }); - pop.add(cbmi); - final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ); - consclipbrd.addActionListener(this); - pop.add(consclipbrd); - } + } + else if (aa[selectedRow].label.indexOf("Consensus") > -1) + { + pop.addSeparator(); + // av and sequencegroup need to implement same interface for + final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( + "Ignore Gaps In 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.annotationPanel.paint(ap.annotationPanel.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( + "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( + "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( + "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( + "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( + "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( + "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()); } /** * do a single sequence copy to jalview and the system clipboard - * - * @param sq sequence to be copied to clipboard + * + * @param sq + * sequence to be copied to clipboard */ protected void copy_annotseqtoclipboard(SequenceI sq) { SequenceI[] seqs = new SequenceI[] - { - sq}; + { sq }; String[] omitHidden = null; SequenceI[] dseqs = new SequenceI[] - { - sq.getDatasetSequence()}; + { sq.getDatasetSequence() }; if (dseqs[0] == null) { dseqs[0] = new Sequence(sq); - dseqs[0].setSequence( - jalview.analysis.AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, - sq.getSequenceAsString())); + dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, sq.getSequenceAsString())); sq.setDatasetSequence(dseqs[0]); } Alignment ds = new Alignment(dseqs); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, - sq.getLength(), seqs); + sq.getLength(), seqs); } - String output = new FormatAdapter().formatSequences( - "Fasta", - seqs, - omitHidden); + String output = new FormatAdapter().formatSequences("Fasta", seqs, + omitHidden); Toolkit.getDefaultToolkit().getSystemClipboard() - .setContents(new StringSelection(output), Desktop.instance); + .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++) { - int[] region = (int[]) - av.getColumnSelection().getHiddenColumns().elementAt(i); + int[] region = (int[]) av.getColumnSelection().getHiddenColumns() + .elementAt(i); hiddenColumns.addElement(new int[] - {region[0], - region[1]}); + { region[0], region[1] }); } } Desktop.jalviewClipboard = new Object[] - { - seqs, - ds, // what is the dataset of a consensus sequence ? need to flag sequence as special. - hiddenColumns}; + { seqs, ds, // what is the dataset of a consensus sequence ? need to flag + // sequence as special. + hiddenColumns }; } /** * DOCUMENT ME! - * - * @param g1 DOCUMENT ME! + * + * @param g1 + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -542,20 +814,35 @@ public class AnnotationLabels if (av.antiAlias) { g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, - RenderingHints.VALUE_ANTIALIAS_ON); + RenderingHints.VALUE_ANTIALIAS_ON); } - drawComponent(g2, width); + drawComponent(g2, true, width); } /** - * DOCUMENT ME! - * - * @param g DOCUMENT ME! + * Draw the full set of annotation Labels for the alignment at the given cursor + * + * @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); @@ -571,33 +858,70 @@ public class AnnotationLabels 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; - + 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) + { - offset = -aa[i].height/2; + 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; - if(aa[i].hasText) + if (aa[i].hasText) { - offset += fm.getHeight()/2; + offset += fm.getHeight() / 2; offset -= fm.getDescent(); } else @@ -608,6 +932,7 @@ public class AnnotationLabels 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) @@ -615,41 +940,59 @@ public class AnnotationLabels 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 { - if(aa[i].belowAlignment) - g.setColor(Color.ORANGE); - else - g.setColor(Color.red); - - g.drawString(aa[i].label, x, y +offset); - + g.drawString(aa[i].label, x, y + offset); } } } @@ -662,10 +1005,10 @@ public class AnnotationLabels { g.setColor(Color.lightGray); g.drawString(aa[selectedRow].label, dragEvent.getX(), - dragEvent.getY() - scrollOffset); + 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);