X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=eb8dd292dc93d4ddb336837b3aed33fdfcb67770;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=2178e37ef8abb920386662214a112048dc40761c;hpb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 2178e37..eb8dd29 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,36 +1,65 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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 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.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.List; +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! @@ -41,21 +70,27 @@ import jalview.util.MessageManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - static String TOGGLE_LABELSCALE = "Scale Label to Column"; + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern + .compile("<"); + + 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; @@ -73,7 +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); @@ -113,11 +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) @@ -222,8 +257,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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)) { @@ -247,11 +281,18 @@ 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); } /** @@ -292,7 +333,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mousePressed(MouseEvent evt) { - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); oldY = evt.getY(); } @@ -305,7 +346,7 @@ 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) @@ -327,7 +368,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, resizePanel = false; dragEvent = null; repaint(); - ap.annotationPanel.repaint(); + ap.getAnnotationPanel().repaint(); } /** @@ -375,8 +416,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, Dimension d = ap.annotationScroller.getPreferredSize(); int dif = evt.getY() - oldY; - dif /= ap.av.charHeight; - dif *= ap.av.charHeight; + dif /= ap.av.getCharHeight(); + dif *= ap.av.getCharHeight(); if ((d.height - dif) > 20) { @@ -406,7 +447,7 @@ 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) @@ -427,7 +468,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, || (desc.substring(0, 6).toLowerCase().indexOf("") < 0)) { // clean the description ready for embedding in html - desc = new StringBuffer(Pattern.compile("<").matcher(desc) + desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc) .replaceAll("<")); desc.insert(0, ""); } @@ -445,29 +486,39 @@ 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); + } } - } /** @@ -478,7 +529,7 @@ 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)) { @@ -490,7 +541,7 @@ 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); @@ -499,25 +550,56 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - ap.seqPanel.ap.idPanel - .highlightSearchResults(aa[selectedRow].groupRef - .getSequences(null)); + ap.getSeqPanel().ap.getIdPanel().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); + 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); @@ -532,7 +614,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, return; } - JPopupMenu pop = new JPopupMenu(MessageManager.getString("label.annotations")); + JPopupMenu pop = new JPopupMenu( + MessageManager.getString("label.annotations")); JMenuItem item = new JMenuItem(ADDNEW); item.addActionListener(this); pop.add(item); @@ -553,6 +636,39 @@ 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; + // } + // } + refresh(); + } + }); + pop.add(hideType); + } + } item = new JMenuItem(DELETE); item.addActionListener(this); pop.add(item); @@ -569,6 +685,7 @@ 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) @@ -582,15 +699,15 @@ 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() { @@ -600,7 +717,8 @@ 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.annotationPanel.paint(ap.annotationPanel.getGraphics()); + ap.getAnnotationPanel().paint( + ap.getAnnotationPanel().getGraphics()); } else { @@ -613,7 +731,7 @@ 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() { @@ -632,7 +750,7 @@ 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() { @@ -651,7 +769,7 @@ 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() { @@ -676,7 +794,8 @@ 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) @@ -695,7 +814,8 @@ 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) @@ -714,7 +834,8 @@ 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) @@ -750,11 +871,9 @@ 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); @@ -770,28 +889,33 @@ public class AnnotationLabels extends JPanel implements MouseListener, sq.getLength(), seqs); } + int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 }; + List hiddenCols = av.getColumnSelection().getHiddenColumns(); + if (hiddenCols != null) + { + alignmentStartEnd = AlignFrame.getStartEnd(alignmentStartEnd, + hiddenCols); + } String output = new FormatAdapter().formatSequences("Fasta", seqs, - omitHidden); + 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++) + hiddenColumns = new ArrayList(); + for (int[] region : av.getColumnSelection().getHiddenColumns()) { - int[] region = (int[]) av.getColumnSelection().getHiddenColumns() - .elementAt(i); - - hiddenColumns.addElement(new int[] - { region[0], region[1] }); + hiddenColumns.add(new int[] { region[0], region[1] }); } } - 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 }; } @@ -823,11 +947,14 @@ public class AnnotationLabels extends JPanel implements MouseListener, } /** - * Draw the full set of annotation Labels for the alignment at the given cursor + * 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 * - * @param g Graphics2D instance (needed for font scaling) - * @param width Width for scaling labels - * */ public void drawComponent(Graphics g, int width) { @@ -835,12 +962,18 @@ public class AnnotationLabels extends JPanel implements MouseListener, } private final boolean debugRedraw = false; + /** - * Draw the full set of annotation Labels for the alignment at the given cursor + * 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 + * @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) { @@ -857,9 +990,9 @@ 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(); int fontHeight = g.getFont().getSize(); int y = 0; @@ -869,18 +1002,20 @@ public class AnnotationLabels extends JPanel implements MouseListener, Font baseFont = g.getFont(); FontMetrics baseMetrics = fm; int ofontH = fontHeight; - int sOffset=0; + int sOffset = 0; int visHeight = 0; - int[] visr = (ap!=null && ap.annotationPanel!=null) ? ap.annotationPanel.getVisibleVRange() : null; - if (clip && visr!=null){ - sOffset = visr[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; + boolean visible = true, before = false, after = false; if (aa != null) { hasHiddenRows = false; - int olY=0; + int olY = 0; for (int i = 0; i < aa.length; i++) { visible = true; @@ -889,33 +1024,39 @@ public class AnnotationLabels extends JPanel implements MouseListener, hasHiddenRows = true; continue; } - olY=y; + olY = y; y += aa[i].height; - if (clip) {if (yvisHeight) - { - - if (!after) + if (olY > visHeight) { - if (debugRedraw) { - System.out.println("Scroll offset: "+sOffset+" after vis: "+i); + + if (!after) + { + if (debugRedraw) + { + System.out.println("Scroll offset: " + sOffset + + " after vis: " + i); + } + after = true; } - after=true; + // don't draw what isn't visible + continue; } - // don't draw what isn't visible - continue; - }} + } g.setColor(Color.black); offset = -aa[i].height / 2; @@ -926,14 +1067,17 @@ 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 + // 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) @@ -1000,19 +1144,25 @@ 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); + g.drawString(MessageManager.getString("label.to_add_annotation"), 2, + 18); } } + + public int getScrollOffset() + { + return scrollOffset; + } }