X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=60324e506fdc0482907a8e00c8a5f87bba44b9f9;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=0c29840034c1629a0d54a385d1699d47b5c9af0c;hpb=32973e4c3a37dd4485c4190f45bbf43017af40df;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 0c29840..60324e5 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.analysis.AlignmentUtils; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; @@ -47,7 +48,10 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; import java.awt.image.BufferedImage; -import java.util.Vector; +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; @@ -66,11 +70,16 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { - String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column"); + private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern + .compile("<"); + + String TOGGLE_LABELSCALE = MessageManager + .getString("label.scale_label_to_column"); String ADDNEW = MessageManager.getString("label.add_new_row"); - String EDITNAME = MessageManager.getString("label.edit_label_description"); + String EDITNAME = MessageManager + .getString("label.edit_label_description"); String HIDE = MessageManager.getString("label.hide_row"); @@ -80,7 +89,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, String OUTPUT_TEXT = MessageManager.getString("label.export_annotation"); - String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence"); + String COPYCONS_SEQ = MessageManager + .getString("label.copy_consensus_sequence"); boolean resizePanel = false; @@ -98,7 +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); @@ -142,7 +152,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); - addMouseWheelListener(ap.annotationPanel); + addMouseWheelListener(ap.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -247,8 +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)) { @@ -324,7 +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(); } @@ -337,7 +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) @@ -359,7 +368,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, resizePanel = false; dragEvent = null; repaint(); - ap.annotationPanel.repaint(); + ap.getAnnotationPanel().repaint(); } /** @@ -407,8 +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) { @@ -438,7 +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) @@ -459,7 +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, ""); } @@ -477,29 +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); + } } - } /** @@ -522,7 +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); @@ -531,9 +550,8 @@ 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; } @@ -541,36 +559,45 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.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) { - ap.seqPanel.ap.idPanel.highlightSearchResults(null); + ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null); SequenceGroup sg = ap.av.getSelectionGroup(); - if (sg!=null) + if (sg != null) { - // we make a copy rather than edit the current selection if no modifiers pressed + // 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 { + } + else + { if (evt.isControlDown()) { sg.addOrRemove(aa[selectedRow].sequenceRef, true); - } else { - // notionally, we should also add intermediate sequences from last added sequence ? + } + else + { + // notionally, we should also add intermediate sequences from + // last added sequence ? sg.addSequence(aa[selectedRow].sequenceRef, true); } } - } else { + } + else + { sg = new SequenceGroup(); sg.setStartRes(0); - sg.setEndRes(ap.av.getAlignment().getWidth()-1); + sg.setEndRes(ap.av.getAlignment().getWidth() - 1); sg.addSequence(aa[selectedRow].sequenceRef, false); } ap.av.setSelectionGroup(sg); @@ -610,28 +637,32 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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) { + final String label = aa[selectedRow].label; JMenuItem hideType = new JMenuItem(); - String text = MessageManager.getString("label.hide_all") + " " + label; + 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; - } - } + 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(); } }); @@ -654,6 +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) @@ -672,10 +704,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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() { @@ -685,7 +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 { @@ -698,7 +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() { @@ -717,7 +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() { @@ -736,7 +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() { @@ -761,7 +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) @@ -780,7 +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) @@ -799,7 +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) @@ -835,11 +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); @@ -855,28 +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 }; } @@ -951,7 +990,7 @@ 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(); @@ -965,8 +1004,8 @@ public class AnnotationLabels extends JPanel implements MouseListener, int ofontH = fontHeight; int sOffset = 0; int visHeight = 0; - int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel - .getVisibleVRange() : null; + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap + .getAnnotationPanel().getVisibleVRange() : null; if (clip && visr != null) { sOffset = visr[0]; @@ -1028,7 +1067,9 @@ public class AnnotationLabels extends JPanel implements MouseListener, offset -= fm.getDescent(); } else + { offset += fm.getDescent(); + } x = width - fm.stringWidth(aa[i].label) - 3; @@ -1103,20 +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); } } + + public int getScrollOffset() + { + return scrollOffset; + } }