X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=a5448133ca9a0a24eb1b7c84c4e240d45f1755f2;hb=4660fcf0745dbc1f6f6e7241b398301f93edb548;hp=9c1db3d39cd21fe5dc38e98bf9059b46afd85516;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 9c1db3d..a544813 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 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,15 +20,6 @@ */ package jalview.gui; -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; @@ -47,8 +38,9 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.geom.AffineTransform; import java.awt.image.BufferedImage; +import java.util.ArrayList; import java.util.Arrays; -import java.util.Vector; +import java.util.Collections; import java.util.regex.Pattern; import javax.swing.JCheckBoxMenuItem; @@ -58,6 +50,16 @@ import javax.swing.JPopupMenu; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; +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; + /** * DOCUMENT ME! * @@ -67,6 +69,8 @@ import javax.swing.ToolTipManager; public class AnnotationLabels extends JPanel implements MouseListener, MouseMotionListener, ActionListener { + 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"); @@ -99,7 +103,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, int selectedRow; - int scrollOffset = 0; + private int scrollOffset = 0; Font font = new Font("Arial", Font.PLAIN, 11); @@ -143,7 +147,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, addMouseListener(this); addMouseMotionListener(this); - addMouseWheelListener(ap.annotationPanel); + addMouseWheelListener(ap.getAnnotationPanel()); } public AnnotationLabels(AlignViewport av) @@ -249,7 +253,7 @@ 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)) { @@ -325,7 +329,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, */ public void mousePressed(MouseEvent evt) { - getSelectedRow(evt.getY() - scrollOffset); + getSelectedRow(evt.getY() - getScrollOffset()); oldY = evt.getY(); } @@ -338,7 +342,7 @@ 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) @@ -360,7 +364,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, resizePanel = false; dragEvent = null; repaint(); - ap.annotationPanel.repaint(); + ap.getAnnotationPanel().repaint(); } /** @@ -408,8 +412,8 @@ 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) { @@ -439,7 +443,7 @@ 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) @@ -460,7 +464,7 @@ 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, ""); } @@ -533,7 +537,7 @@ 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); @@ -542,7 +546,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, } else { - ap.seqPanel.ap.idPanel + ap.getSeqPanel().ap.getIdPanel() .highlightSearchResults(aa[selectedRow].groupRef .getSequences(null)); } @@ -552,13 +556,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, { if (evt.getClickCount() == 1) { - ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays + 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) { @@ -621,11 +625,11 @@ 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; hideType.setText(text); @@ -634,15 +638,18 @@ public class AnnotationLabels extends JPanel implements MouseListener, @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(); } }); @@ -665,6 +672,7 @@ 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) @@ -683,10 +691,10 @@ public class AnnotationLabels extends JPanel implements MouseListener, pop.addSeparator(); // av and sequencegroup need to implement same interface for final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem( - MessageManager.getString("label.ignore_gaps_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() { @@ -696,7 +704,7 @@ 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 { @@ -709,7 +717,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, if (aaa.groupRef != null) { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_histogram"), + MessageManager.getString("label.show_group_histogram"), aa[selectedRow].groupRef.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { @@ -728,7 +736,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem( - MessageManager.getString("label.show_group_logo"), + MessageManager.getString("label.show_group_logo"), aa[selectedRow].groupRef.isShowSequenceLogo()); cprofl.addActionListener(new ActionListener() { @@ -747,7 +755,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprofl); final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_group_logo"), + MessageManager.getString("label.normalise_group_logo"), aa[selectedRow].groupRef.isNormaliseSequenceLogo()); cproflnorm.addActionListener(new ActionListener() { @@ -772,7 +780,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, else { final JCheckBoxMenuItem chist = new JCheckBoxMenuItem( - MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); + MessageManager.getString("label.show_histogram"), av.isShowConsensusHistogram()); chist.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -791,7 +799,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(chist); final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem( - MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); + MessageManager.getString("label.show_logo"), av.isShowSequenceLogo()); cprof.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -810,7 +818,7 @@ public class AnnotationLabels extends JPanel implements MouseListener, }); pop.add(cprof); final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem( - MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); + MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo()); cprofnorm.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) @@ -872,16 +880,13 @@ public class AnnotationLabels extends JPanel implements MouseListener, 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[] + hiddenColumns.add(new int[] { region[0], region[1] }); } } @@ -962,7 +967,7 @@ 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(); @@ -976,7 +981,7 @@ 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 + int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap.getAnnotationPanel() .getVisibleVRange() : null; if (clip && visr != null) { @@ -1116,20 +1121,25 @@ 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; + } }