X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=97499c970421b0fa0373abbbfc4abccd286e199c;hb=8d6b113f475c6b5916f7685cfd289e054d95a9ee;hp=319dcf48016060ca170b041f7b92bef3d92ae215;hpb=3beb22d0e20da65b123d44039a9f1e8bc8690f5e;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 319dcf4..97499c9 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,34 +1,62 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) + * 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. - * + * 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 . + * 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 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.FormatAdapter; +import jalview.util.MessageManager; + +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.Arrays; +import java.util.Vector; +import java.util.regex.Pattern; -import jalview.datamodel.*; -import jalview.io.*; +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! @@ -39,21 +67,21 @@ import jalview.io.*; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - static String TOGGLE_LABELSCALE = "Scale Label to Column"; + String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column"); - static String ADDNEW = "Add New Row"; + String ADDNEW = MessageManager.getString("label.add_new_row"); - static String EDITNAME = "Edit Label/Description"; + String EDITNAME = MessageManager.getString("label.edit_label_description"); - static String HIDE = "Hide This Row"; + String HIDE = MessageManager.getString("label.hide_row"); - static String DELETE = "Delete This Row"; + String DELETE = MessageManager.getString("label.delete_row"); - static String SHOWALL = "Show All Hidden Rows"; + String SHOWALL = MessageManager.getString("label.show_all_hidden_rows"); - static String OUTPUT_TEXT = "Export Annotation"; + String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); - static String COPYCONS_SEQ = "Copy Consensus Sequence"; + String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence"); boolean resizePanel = false; @@ -71,7 +99,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, int selectedRow; - int scrollOffset = 0; + private int scrollOffset = 0; Font font = new Font("Arial", Font.PLAIN, 11); @@ -111,10 +139,11 @@ 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.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -220,7 +249,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { new AnnotationExporter().exportAnnotations(ap, new AlignmentAnnotation[] - { aa[selectedRow] }, null, null); + { aa[selectedRow] }); } else if (evt.getActionCommand().equals(COPYCONS_SEQ)) { @@ -244,11 +273,18 @@ public class AnnotationLabels extends JPanel implements MouseListener, aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel; } + refresh(); + + } + + /** + * Redraw sensibly. + */ + protected void refresh() + { ap.validateAnnotationDimensions(false); ap.addNotify(); ap.repaint(); - // validate(); - // ap.paintAlignment(true); } /** @@ -289,7 +325,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mousePressed(MouseEvent evt) { - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); oldY = evt.getY(); } @@ -302,7 +338,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, public void mouseReleased(MouseEvent evt) { int start = selectedRow; - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); int end = selectedRow; if (start != end) @@ -324,7 +360,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, resizePanel = false; dragEvent = null; repaint(); - ap.annotationPanel.repaint(); + ap.getAnnotationPanel().repaint(); } /** @@ -403,7 +439,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { resizePanel = evt.getY() < 10; - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); if (selectedRow > -1 && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow) @@ -442,29 +478,39 @@ public class AnnotationLabels extends JPanel implements MouseListener, { 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 (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); + } } - } /** @@ -475,7 +521,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mouseClicked(MouseEvent evt) { - AlignmentAnnotation[] aa = ap.av.getAlignment() + final AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); if (SwingUtilities.isLeftMouseButton(evt)) { @@ -487,7 +533,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { // todo: make the ap scroll to the selection - not necessary, first // click highlights/scrolls, second selects - ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); ap.av.setSelectionGroup(// new SequenceGroup( aa[selectedRow].groupRef); // ); ap.paintAlignment(false); @@ -496,7 +542,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - ap.seqPanel.ap.idPanel + ap.getSeqPanel().ap.getIdPanel() .highlightSearchResults(aa[selectedRow].groupRef .getSequences(null)); } @@ -504,17 +550,40 @@ public class AnnotationLabels extends JPanel implements MouseListener, } 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); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(Arrays + .asList(new SequenceI[] + { aa[selectedRow].sequenceRef })); } else if (evt.getClickCount() >= 2) { - ap.seqPanel.ap.idPanel.highlightSearchResults(null); - SequenceGroup sg = new SequenceGroup(); - sg.addSequence(aa[selectedRow].sequenceRef, false); + 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 (!(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); @@ -529,7 +598,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, return; } - JPopupMenu pop = new JPopupMenu("Annotations"); + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); JMenuItem item = new JMenuItem(ADDNEW); item.addActionListener(this); pop.add(item); @@ -550,6 +620,35 @@ 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 + final String label = aa[selectedRow].label; + if (selectedRow < aa.length) + { + if (aa[selectedRow].sequenceRef != null) + { + 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) + { + for (AlignmentAnnotation ann : ap.av.getAlignment() + .getAlignmentAnnotation()) + { + if (ann.sequenceRef != null && ann.label != null + && ann.label.equals(label)) + { + ann.visible = false; + } + } + refresh(); + } + }); + pop.add(hideType); + } + } item = new JMenuItem(DELETE); item.addActionListener(this); pop.add(item); @@ -579,12 +678,12 @@ 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()); @@ -597,7 +696,7 @@ 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.annotationPanel.paint(ap.annotationPanel.getGraphics()); + ap.getAnnotationPanel().paint(ap.getAnnotationPanel().getGraphics()); } else { @@ -610,7 +709,7 @@ 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() { @@ -629,7 +728,7 @@ 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() { @@ -648,7 +747,7 @@ 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() { @@ -673,7 +772,7 @@ 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() { public void actionPerformed(ActionEvent e) @@ -692,7 +791,7 @@ 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() { public void actionPerformed(ActionEvent e) @@ -711,7 +810,7 @@ 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() { public void actionPerformed(ActionEvent e) @@ -815,18 +914,41 @@ 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! + * 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); @@ -840,7 +962,7 @@ 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(); @@ -852,22 +974,62 @@ public class AnnotationLabels extends JPanel implements MouseListener, Font baseFont = g.getFont(); FontMetrics baseMetrics = fm; int ofontH = fontHeight; - boolean visible = true; + int sOffset = 0; + int visHeight = 0; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel() + .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++) { visible = true; - g.setColor(Color.black); - if (!aa[i].visible) { hasHiddenRows = true; continue; } - + olY = y; y += aa[i].height; + if (clip) + { + if (y < sOffset) + { + if (!before) + { + if (debugRedraw) + { + System.out.println("before vis: " + i); + } + before = true; + } + // don't draw what isn't visible + continue; + } + if (olY > visHeight) + { + + 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; @@ -877,13 +1039,17 @@ public class AnnotationLabels extends JPanel implements MouseListener, offset -= fm.getDescent(); } else + { offset += fm.getDescent(); + } x = width - fm.stringWidth(aa[i].label) - 3; 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) @@ -922,7 +1088,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, { x = width - fm.stringWidth(aa[gg].label) - 3; g.drawString(aa[gg].label, x, y - graphExtras); - + if (aa[gg]._linecolour != null) { @@ -950,19 +1116,25 @@ 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 ((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); + g.drawString(MessageManager.getString("label.right_click"), 2, 8); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); } } + + public int getScrollOffset() + { + return scrollOffset; + } }